Initial port to python3

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
index 875d3bdd9d8205df2eaff65b2b48b5462366645a..0f474d7434fd10f5f2762eeb46619e7d90e1dcd8 100644 (file)
--- a/encode_submission/encode3.py
+++ b/encode_submission/encode3.py
@@ -2,7 +2,7 @@
 """
 
 #!/usr/bin/env python
 """
 
 #!/usr/bin/env python

-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser

 import fnmatch
 from glob import glob
 import json
 import fnmatch
 from glob import glob
 import json


@@ -12,14 +12,14 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
 import os
 from pprint import pprint, pformat
 import shlex

-from StringIO import StringIO
+from io import StringIO

 import stat
 import sys
 import time
 import types
 import stat
 import sys
 import time
 import types

-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse

 from zipfile import ZipFile
 
 import RDF
 from zipfile import ZipFile
 
 import RDF


@@ -130,7 +130,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
 
     if opts.print_rdf:
         writer = get_serializer()

-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))

 
 
 def make_manifest(mapper, results, filename=None):
 
 
 def make_manifest(mapper, results, filename=None):

diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py
index 7589f5487aef5ef85a6c4ec65072aa3d025ef5bc..6c8b94223ef2fdd1a80194d43422917f558b63a7 100644 (file)
--- a/encode_submission/encode_find.py
+++ b/encode_submission/encode_find.py
@@ -17,8 +17,8 @@ import re
 # redland rdf lib
 import RDF
 import sys
 # redland rdf lib
 import RDF
 import sys

-import urllib
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.parse

 
 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
 
 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'


@@ -130,7 +130,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         serializer = get_serializer(name=opts.rdf_parser_name)
 
     if opts.print_rdf:
         serializer = get_serializer(name=opts.rdf_parser_name)

-        print serializer.serialize_model_to_string(model)
+        print(serializer.serialize_model_to_string(model))

 
 
 def make_parser():
 
 
 def make_parser():


@@ -261,11 +261,11 @@ def report_submissions_with_no_library(model):
     for row in results:
         subid = row['subid']
         name = row['name']
     for row in results:
         subid = row['subid']
         name = row['name']

-        print "# {0}".format(name)
-        print "<{0}>".format(subid.uri)
-        print "  encodeSubmit:library_urn "\
-              "<http://jumpgate.caltech.edu/library/> ."
-        print ""
+        print("# {0}".format(name))
+        print("<{0}>".format(subid.uri))
+        print("  encodeSubmit:library_urn "\
+              "<http://jumpgate.caltech.edu/library/> .")
+        print("")

 
 def find_submissions_with_no_library(model):
     missing_lib_query_text = """
 
 def find_submissions_with_no_library(model):
     missing_lib_query_text = """


@@ -482,7 +482,7 @@ def reload_libraries(model, library_list):
         load_library_detail(model, library_urn)
 
 def user_library_id_to_library_urn(library_id):
         load_library_detail(model, library_urn)
 
 def user_library_id_to_library_urn(library_id):

-    split_url = urlparse.urlsplit(library_id)
+    split_url = urllib.parse.urlsplit(library_id)

     if len(split_url.scheme) == 0:
         return LIBRARY_NS[library_id]
     else:
     if len(split_url.scheme) == 0:
         return LIBRARY_NS[library_id]
     else:


@@ -536,11 +536,11 @@ def load_encodedcc_files(model, genome, composite):
 
     lib_term = submissionOntology['library_urn']
     sub_term = submissionOntology['submission_urn']
 
     lib_term = submissionOntology['library_urn']
     sub_term = submissionOntology['submission_urn']

-    for filename, attributes in file_index.items():
+    for filename, attributes in list(file_index.items()):

         s = RDF.Node(RDF.Uri(filename))
         model.add_statement(
             RDF.Statement(s, TYPE_N, submissionOntology['ucsc_track']))
         s = RDF.Node(RDF.Uri(filename))
         model.add_statement(
             RDF.Statement(s, TYPE_N, submissionOntology['ucsc_track']))

-        for name, value in attributes.items():
+        for name, value in list(attributes.items()):

             p = RDF.Node(DCC_NS[name])
             o = RDF.Node(value)
             model.add_statement(RDF.Statement(s,p,o))
             p = RDF.Node(DCC_NS[name])
             o = RDF.Node(value)
             model.add_statement(RDF.Statement(s,p,o))


@@ -566,7 +566,7 @@ def load_library_detail(model, libraryUrn):
         try:
             body = get_url_as_text(str(libraryUrn.uri), 'GET')
             rdfaParser.parse_string_into_model(model, body, libraryUrn.uri)
         try:
             body = get_url_as_text(str(libraryUrn.uri), 'GET')
             rdfaParser.parse_string_into_model(model, body, libraryUrn.uri)

-        except httplib2.HttpLib2ErrorWithResponse, e:
+        except httplib2.HttpLib2ErrorWithResponse as e:

             LOGGER.error(str(e))
     elif len(results) == 1:
         pass  # Assuming that a loaded dataset has one record
             LOGGER.error(str(e))
     elif len(results) == 1:
         pass  # Assuming that a loaded dataset has one record


@@ -644,7 +644,7 @@ def login(cookie=None):
     response, content = http.request(LOGIN_URL,
                                      'POST',
                                      headers=headers,
     response, content = http.request(LOGIN_URL,
                                      'POST',
                                      headers=headers,

-                                     body=urllib.urlencode(credentials))
+                                     body=urllib.parse.urlencode(credentials))

     LOGGER.debug("Login to {0}, status {1}".format(LOGIN_URL,
                                                     response['status']))
 
     LOGGER.debug("Login to {0}, status {1}".format(LOGIN_URL,
                                                     response['status']))
 


@@ -709,7 +709,7 @@ def select_by_library_id(submission_list):
     for lib_id, subobj in subl:
         libraries.setdefault(lib_id, []).append(subobj)
 
     for lib_id, subobj in subl:
         libraries.setdefault(lib_id, []).append(subobj)
 

-    for submission in libraries.values():
+    for submission in list(libraries.values()):

         submission.sort(key=attrgetter('date'), reverse=True)
 
     return libraries
         submission.sort(key=attrgetter('date'), reverse=True)
 
     return libraries

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index 751264cc4276a658491c387852a180fff94929a0..20910f603d287d16fdc583905fecaa388e512aee 100644 (file)
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
 #!/usr/bin/env python

-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser

 import fnmatch
 from glob import glob
 import json
 import fnmatch
 from glob import glob
 import json


@@ -9,14 +9,14 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
 import os
 from pprint import pprint, pformat
 import shlex

-from StringIO import StringIO
+from io import StringIO

 import stat
 import sys
 import time
 import types
 import stat
 import sys
 import time
 import types

-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse

 from zipfile import ZipFile
 
 import RDF
 from zipfile import ZipFile
 
 import RDF


@@ -98,7 +98,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
 
     if opts.print_rdf:
         writer = get_serializer()

-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))

 
 
 def make_parser():
 
 
 def make_parser():

diff --git a/encode_submission/scan_extension.py b/encode_submission/scan_extension.py
index 39f19c6461c87e86d24f040a81d37f23dbaffd97..8e2e5ae070d6dca45920b77816d90d32adfcdb62 100644 (file)
--- a/encode_submission/scan_extension.py
+++ b/encode_submission/scan_extension.py
@@ -13,7 +13,7 @@ def main(cmdline=None):
     if opts.rdf:
         print_rdf(common_extensions)
     else:
     if opts.rdf:
         print_rdf(common_extensions)
     else:

-        print common_extensions
+        print(common_extensions)

         
 def make_parser():
     parser = OptionParser("%prog: directory [directory...]")
         
 def make_parser():
     parser = OptionParser("%prog: directory [directory...]")


@@ -39,7 +39,7 @@ def find_common_suffix(index, tail=[]):
         return "".join(tail[::-1])
 
     results = []
         return "".join(tail[::-1])
 
     results = []

-    for key, choice in index.items():
+    for key, choice in list(index.items()):

         r = find_common_suffix(choice, tail+[key])
         if r is not None:
             results.append (r)
         r = find_common_suffix(choice, tail+[key])
         if r is not None:
             results.append (r)


@@ -70,7 +70,7 @@ def print_rdf(common_extensions):
         
     writer = rdfhelp.get_serializer()
     writer.set_namespace('thisSubmissionView', subView._prefix)
         
     writer = rdfhelp.get_serializer()
     writer.set_namespace('thisSubmissionView', subView._prefix)

-    print writer.serialize_model_to_string(model)
+    print(writer.serialize_model_to_string(model))

 
 if __name__ == "__main__":
     main()
 
 if __name__ == "__main__":
     main()

diff --git a/encode_submission/submission_report.py b/encode_submission/submission_report.py
index d8ace391888686c0d0650fb0b080b0e79399aa67..fe424192e19d88ed1a592558c93fbdfc9b8a285d 100644 (file)
--- a/encode_submission/submission_report.py
+++ b/encode_submission/submission_report.py
@@ -13,7 +13,7 @@ from htsworkflow.util.rdfns import *
 TYPE_N = rdfNS['type']
 CREATION_DATE = libraryOntology['date']
 
 TYPE_N = rdfNS['type']
 CREATION_DATE = libraryOntology['date']
 

-from encode_find import DBDIR
+from .encode_find import DBDIR

 
 DEFAULT_GENOME='hg19'
 DEFAULT_OUTPUT='/tmp/submission_report.html'
 
 DEFAULT_GENOME='hg19'
 DEFAULT_OUTPUT='/tmp/submission_report.html'

diff --git a/encode_submission/test_encode_find.py b/encode_submission/test_encode_find.py
index 77c758547f8c89ea33838936b9e6ec47b34f7ff5..87778d794b2a3181571ca3092655cea86dcf285b 100644 (file)
--- a/encode_submission/test_encode_find.py
+++ b/encode_submission/test_encode_find.py
@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 from datetime import datetime
 import os
 #!/usr/bin/env python
 from datetime import datetime
 import os

-from unittest2 import TestCase
+from unittest import TestCase

 
 import RDF
 
 
 import RDF
 

-import encode_find
+from . import encode_find

 from htsworkflow.submission.ucsc import submission_view_url
 from htsworkflow.util.rdfhelp import add_default_schemas, \
      dump_model, get_model, fromTypedNode
 from htsworkflow.submission.ucsc import submission_view_url
 from htsworkflow.util.rdfhelp import add_default_schemas, \
      dump_model, get_model, fromTypedNode


@@ -162,12 +162,12 @@ _:bnode120970
                              '12097')
 
 def suite():
                              '12097')
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main()
     main()

diff --git a/encode_submission/test_ucsc_gather.py b/encode_submission/test_ucsc_gather.py
index 6063951db788a2e9f9562f9a113fae5e335cec7b..3a91465c2efb1ad9b4425468b459cc91a9b4f9e4 100644 (file)
--- a/encode_submission/test_ucsc_gather.py
+++ b/encode_submission/test_ucsc_gather.py
@@ -1,6 +1,6 @@
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader

 
 

-import ucsc_gather
+from . import ucsc_gather

 
 class testUCSCGather(TestCase):
     pass
 
 class testUCSCGather(TestCase):
     pass


@@ -11,5 +11,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index a9fa72a83ddc1c4263e509070f50053d238fa405..695541aeb713252cd37345e5475739516a0f4dac 100644 (file)
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
 #!/usr/bin/env python

-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser

 import fnmatch
 from glob import glob
 import json
 import fnmatch
 from glob import glob
 import json


@@ -9,14 +9,14 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
 import os
 from pprint import pprint, pformat
 import shlex

-from StringIO import StringIO
+from io import StringIO

 import stat
 import sys
 import time
 import types
 import stat
 import sys
 import time
 import types

-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse

 from zipfile import ZipFile
 
 import RDF
 from zipfile import ZipFile
 
 import RDF


@@ -119,7 +119,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
 
     if opts.print_rdf:
         writer = get_serializer()

-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))

 
 
 def make_parser():
 
 
 def make_parser():


@@ -177,7 +177,7 @@ def make_parser():
 
 def make_all_ddfs(view_map, library_result_map, daf_name, make_condor=True, force=False):
     dag_fragment = []
 
 def make_all_ddfs(view_map, library_result_map, daf_name, make_condor=True, force=False):
     dag_fragment = []

-    for lib_id, result_dir in library_result_map.items():
+    for lib_id, result_dir in list(library_result_map.items()):

         submissionNode = view_map.get_submission_node(result_dir)
         dag_fragment.extend(
             make_ddf(view_map, submissionNode, daf_name, make_condor, result_dir)
         submissionNode = view_map.get_submission_node(result_dir)
         dag_fragment.extend(
             make_ddf(view_map, submissionNode, daf_name, make_condor, result_dir)


@@ -268,7 +268,7 @@ ORDER BY  ?submitView"""
             else:
                 current[variable_name] = value
 
             else:
                 current[variable_name] = value
 

-    for view in all_views.keys():
+    for view in list(all_views.keys()):

         line = []
         for variable_name in variables:
             if variable_name in ('files', 'md5sum'):
         line = []
         for variable_name in variables:
             if variable_name in ('files', 'md5sum'):

diff --git a/htsworkflow/automation/copier.py b/htsworkflow/automation/copier.py
index 1dc719d96b0c0bdfc851e0ef3e56e162b00e77bc..25fc6ee5afdab7da089409fb8280739b2cc6e048 100644 (file)
--- a/htsworkflow/automation/copier.py
+++ b/htsworkflow/automation/copier.py
@@ -1,4 +1,4 @@
-import ConfigParser
+import configparser

 import copy
 import logging
 import logging.handlers
 import copy
 import logging
 import logging.handlers


@@ -9,7 +9,7 @@ import subprocess
 import sys
 import time
 import traceback
 import sys
 import time
 import traceback

-import urlparse
+import urllib.parse

 
 from benderjab import rpc
 
 
 from benderjab import rpc
 


@@ -45,7 +45,7 @@ class rsync(object):
         # We made sure source ends in a / earlier
         cur_list = [ source+subdir for subdir in self.list_filter(stdout)]
         entries.extend(cur_list)
         # We made sure source ends in a / earlier
         cur_list = [ source+subdir for subdir in self.list_filter(stdout)]
         entries.extend(cur_list)

-    LOGGER.debug(u"Found the following: %s" % (unicode(entries)))
+    LOGGER.debug("Found the following: %s" % (str(entries)))

     return entries
 
   def list_filter(self, lines):
     return entries
 
   def list_filter(self, lines):


@@ -54,7 +54,7 @@ class rsync(object):
     """
     dirs_to_copy = []
     direntries = [ x[0:42].split() + [x[43:-1]] for x in lines ]
     """
     dirs_to_copy = []
     direntries = [ x[0:42].split() + [x[43:-1]] for x in lines ]

-    LOGGER.debug(u'direntries: %s' % (unicode(direntries),))
+    LOGGER.debug('direntries: %s' % (str(direntries),))

     for permissions, size, filedate, filetime, filename in direntries:
       if permissions[0] == 'd':
         # hey its a directory, the first step to being something we want to
     for permissions, size, filedate, filetime, filename in direntries:
       if permissions[0] == 'd':
         # hey its a directory, the first step to being something we want to


@@ -122,7 +122,7 @@ class rsync(object):
 
       return path roots that have finished.
       """
 
       return path roots that have finished.
       """

-      for dir_key, proc_value in self.processes.items():
+      for dir_key, proc_value in list(self.processes.items()):

           retcode = proc_value.poll()
           if retcode is None:
               # process hasn't finished yet
           retcode = proc_value.poll()
           if retcode is None:
               # process hasn't finished yet


@@ -145,7 +145,7 @@ class rsync(object):
       """
       Return list of current run folder names
       """
       """
       Return list of current run folder names
       """

-      return self.processes.keys()
+      return list(self.processes.keys())

 
 class CopierBot(rpc.XmlRpcBot):
     def __init__(self, section=None, configfile=None):
 
 class CopierBot(rpc.XmlRpcBot):
     def __init__(self, section=None, configfile=None):


@@ -200,7 +200,7 @@ class CopierBot(rpc.XmlRpcBot):
                                    require_resource=True)
         except bot.JIDMissingResource:
             msg = 'need a full jabber ID + resource for xml-rpc destinations'
                                    require_resource=True)
         except bot.JIDMissingResource:
             msg = 'need a full jabber ID + resource for xml-rpc destinations'

-            print >>sys.stderr, msg
+            print(msg, file=sys.stderr)

             raise bot.JIDMissingResource(msg)
 
     def run(self):
             raise bot.JIDMissingResource(msg)
 
     def run(self):


@@ -215,7 +215,7 @@ class CopierBot(rpc.XmlRpcBot):
         start our copy
         """
         # Note, args comes in over the network, so don't trust it.
         start our copy
         """
         # Note, args comes in over the network, so don't trust it.

-        LOGGER.debug("Arguments to startCopy %s" % (unicode(args),))
+        LOGGER.debug("Arguments to startCopy %s" % (str(args),))

         copy_urls = []
         for a in args:
             clean_url = self.validate_url(a)
         copy_urls = []
         for a in args:
             clean_url = self.validate_url(a)


@@ -265,7 +265,7 @@ class CopierBot(rpc.XmlRpcBot):
         """
         self.rsync.poll()
         for p in self.pending:
         """
         self.rsync.poll()
         for p in self.pending:

-            if p not in self.rsync.keys():
+            if p not in list(self.rsync.keys()):

                 self.reportSequencingFinished(p)
                 self.pending.remove(p)
 
                 self.reportSequencingFinished(p)
                 self.pending.remove(p)
 


@@ -273,29 +273,29 @@ class CopierBot(rpc.XmlRpcBot):
         """
         Parse xmpp chat messages
         """
         """
         Parse xmpp chat messages
         """

-        help = u"I can [copy], or report current [status]"
-        if re.match(u"help", msg):
+        help = "I can [copy], or report current [status]"
+        if re.match("help", msg):

             reply = help
         elif re.match("copy", msg):
             started = self.startCopy()
             reply = help
         elif re.match("copy", msg):
             started = self.startCopy()

-            reply = u"started copying " + ", ".join(started)
-        elif re.match(u"status", msg):
-            msg = [u"Currently %d rsync processes are running." % (len(self.rsync))]
-            for d in self.rsync.keys():
-              msg.append(u"  " + d)
+            reply = "started copying " + ", ".join(started)
+        elif re.match("status", msg):
+            msg = ["Currently %d rsync processes are running." % (len(self.rsync))]
+            for d in list(self.rsync.keys()):
+              msg.append("  " + d)

             reply = os.linesep.join(msg)
         else:
             reply = os.linesep.join(msg)
         else:

-            reply = u"I didn't understand '%s'" % (unicode(msg))
+            reply = "I didn't understand '%s'" % (str(msg))

         return reply
 
     def validate_url(self, url):
         return reply
 
     def validate_url(self, url):

-        user_url = urlparse.urlsplit(url)
+        user_url = urllib.parse.urlsplit(url)

         user_scheme = user_url[0]
         user_netloc = user_url[1]
         user_path = user_url[2]
 
         for source in self.sources:
         user_scheme = user_url[0]
         user_netloc = user_url[1]
         user_path = user_url[2]
 
         for source in self.sources:

-            source_url = urlparse.urlsplit(source)
+            source_url = urllib.parse.urlsplit(source)

             source_scheme = source_url[0]
             source_netloc = source_url[1]
             source_path = source_url[2]
             source_scheme = source_url[0]
             source_netloc = source_url[1]
             source_path = source_url[2]

diff --git a/htsworkflow/automation/runner.py b/htsworkflow/automation/runner.py
index 7b0c4c9d7ca6b47e59254b27e2171876525e6715..154c79e824d74bd07fdb05c7e4b011fede45d648 100644 (file)
--- a/htsworkflow/automation/runner.py
+++ b/htsworkflow/automation/runner.py
@@ -68,27 +68,27 @@ class Runner(rpc.XmlRpcBot):
         """
         Parse xmpp chat messages
         """
         """
         Parse xmpp chat messages
         """

-        help = u"I can send [start] a run, or report [status]"
-        if re.match(u"help", msg):
+        help = "I can send [start] a run, or report [status]"
+        if re.match("help", msg):

             reply = help
         elif re.match("status", msg):
             words = msg.split()
             if len(words) == 2:
                 reply = self.getStatusReport(words[1])
             else:
             reply = help
         elif re.match("status", msg):
             words = msg.split()
             if len(words) == 2:
                 reply = self.getStatusReport(words[1])
             else:

-                reply = u"Status available for: %s" \
-                        % (', '.join([k for k in self.conf_info_dict.keys()]))
-        elif re.match(u"start", msg):
+                reply = "Status available for: %s" \
+                        % (', '.join([k for k in list(self.conf_info_dict.keys())]))
+        elif re.match("start", msg):

             words = msg.split()
             if len(words) == 2:
                 self.sequencingFinished(words[1])
             words = msg.split()
             if len(words) == 2:
                 self.sequencingFinished(words[1])

-                reply = u"starting run for %s" % (words[1])
+                reply = "starting run for %s" % (words[1])

             else:
             else:

-                reply = u"need runfolder name"
-        elif re.match(u"path", msg):
-           reply = u"My path is: " + unicode(os.environ['PATH'])
+                reply = "need runfolder name"
+        elif re.match("path", msg):
+           reply = "My path is: " + str(os.environ['PATH'])

         else:
         else:

-            reply = u"I didn't understand '%s'" %(msg)
+            reply = "I didn't understand '%s'" %(msg)

 
         LOGGER.debug("reply: " + str(reply))
         return reply
 
         LOGGER.debug("reply: " + str(reply))
         return reply


@@ -196,7 +196,7 @@ class Runner(rpc.XmlRpcBot):
                 #startCmdLineStatusMonitor(ci)
 
                 # running step
                 #startCmdLineStatusMonitor(ci)
 
                 # running step

-                print 'Running pipeline now!'
+                print('Running pipeline now!')

                 run_status = run_pipeline(conf_info)
                 if run_status is True:
                     LOGGER.info('Runner: Pipeline: success')
                 run_status = run_pipeline(conf_info)
                 if run_status is True:
                     LOGGER.info('Runner: Pipeline: success')

diff --git a/htsworkflow/automation/spoolwatcher.py b/htsworkflow/automation/spoolwatcher.py
index e226234d6d392f67cd774cb436dc9660ad22e71b..ce08be7eddd0ae55328ab32abddb51bf203f07d2 100644 (file)
--- a/htsworkflow/automation/spoolwatcher.py
+++ b/htsworkflow/automation/spoolwatcher.py
@@ -35,7 +35,7 @@ class WatcherEvent(object):
            complete = "(completed)"
         else:
            complete = ""
            complete = "(completed)"
         else:
            complete = ""

-        return u"<WatchEvent: %s %s %s>" % (time.ctime(self.time), self.event_root, complete)
+        return "<WatchEvent: %s %s %s>" % (time.ctime(self.time), self.event_root, complete)

 
 class Handler(pyinotify.ProcessEvent):
     def __init__(self, watchmanager, bot, completion_files=None):
 
 class Handler(pyinotify.ProcessEvent):
     def __init__(self, watchmanager, bot, completion_files=None):


@@ -72,7 +72,7 @@ class Handler(pyinotify.ProcessEvent):
 
                     # if we've already seen an event in this directory (AKA runfolder)
                     # keep track if its already hit the "completed" flag
 
                     # if we've already seen an event in this directory (AKA runfolder)
                     # keep track if its already hit the "completed" flag

-                    if watch_path_events.has_key(target):
+                    if target in watch_path_events:

                        run_already_complete = watch_path_events[target].complete
 
                     watch_path_events[target] = WatcherEvent(target)
                        run_already_complete = watch_path_events[target].complete
 
                     watch_path_events[target] = WatcherEvent(target)


@@ -205,7 +205,7 @@ class SpoolWatcher(rpc.XmlRpcBot):
                 mounts.append(w)
                 self.mounts_to_watches[mount_location] = mounts
 
                 mounts.append(w)
                 self.mounts_to_watches[mount_location] = mounts
 

-            self.log.info(u"Watching:"+unicode(w))
+            self.log.info("Watching:"+str(w))

             self.wdds.append(self.wm.add_watch(w, mask, rec=True, auto_add=True))
 
     def unmount_watch(self, event_path):
             self.wdds.append(self.wm.add_watch(w, mask, rec=True, auto_add=True))
 
     def unmount_watch(self, event_path):


@@ -213,8 +213,8 @@ class SpoolWatcher(rpc.XmlRpcBot):
         # the list getting shorter
         for i in range(len(self.wdds),0, -1):
             wdd = self.wdds[i]
         # the list getting shorter
         for i in range(len(self.wdds),0, -1):
             wdd = self.wdds[i]

-            self.log.info(u'unmounting: '+unicode(wdd.items()))
-            self.wm.rm_watch(wdd.values())
+            self.log.info('unmounting: '+str(list(wdd.items())))
+            self.wm.rm_watch(list(wdd.values()))

             del self.wdds[i]
         self.mounted = False
 
             del self.wdds[i]
         self.mounted = False
 


@@ -238,11 +238,11 @@ class SpoolWatcher(rpc.XmlRpcBot):
             self.notifier.read_events()
             # should we do something?
         # has something happened?
             self.notifier.read_events()
             # should we do something?
         # has something happened?

-        for watchdir, last_events in self.handler.last_event.items():
-            for last_event_dir, last_event_detail in last_events.items():
+        for watchdir, last_events in list(self.handler.last_event.items()):
+            for last_event_dir, last_event_detail in list(last_events.items()):

                 time_delta = time.time() - last_event_detail.time
                 if time_delta > self.write_timeout:
                 time_delta = time.time() - last_event_detail.time
                 if time_delta > self.write_timeout:

-                    LOGGER.info("timeout: %s" % (unicode(last_event_detail),))
+                    LOGGER.info("timeout: %s" % (str(last_event_detail),))

                     copy_url = self.make_copy_url(watchdir, last_event_dir)
                     self.startCopy(copy_url)
                     if last_event_detail.complete:
                     copy_url = self.make_copy_url(watchdir, last_event_dir)
                     self.startCopy(copy_url)
                     if last_event_detail.complete:


@@ -250,7 +250,7 @@ class SpoolWatcher(rpc.XmlRpcBot):
 
                     self.handler.last_event[watchdir] = {}
         # handle unmounted filesystems
 
                     self.handler.last_event[watchdir] = {}
         # handle unmounted filesystems

-        for mount_point, was_mounted in self.mounted_points.items():
+        for mount_point, was_mounted in list(self.mounted_points.items()):

             if not was_mounted and mount.is_mounted(mount_point):
                 # we've been remounted. Huzzah!
                 # restart the watch
             if not was_mounted and mount.is_mounted(mount_point):
                 # we've been remounted. Huzzah!
                 # restart the watch


@@ -266,21 +266,21 @@ class SpoolWatcher(rpc.XmlRpcBot):
         """
         Parse xmpp chat messages
         """
         """
         Parse xmpp chat messages
         """

-        help = u"I can send [copy] message, or squencer [finished]"
-        if re.match(u"help", msg):
+        help = "I can send [copy] message, or squencer [finished]"
+        if re.match("help", msg):

             reply = help
         elif re.match("copy", msg):
             self.startCopy(msg)
             reply = help
         elif re.match("copy", msg):
             self.startCopy(msg)

-            reply = u"sent copy message"
-        elif re.match(u"finished", msg):
+            reply = "sent copy message"
+        elif re.match("finished", msg):

             words = msg.split()
             if len(words) == 2:
                 self.sequencingFinished(words[1])
             words = msg.split()
             if len(words) == 2:
                 self.sequencingFinished(words[1])

-                reply = u"sending sequencing finished for %s" % (words[1])
+                reply = "sending sequencing finished for %s" % (words[1])

             else:
             else:

-                reply = u"need runfolder name"
+                reply = "need runfolder name"

         else:
         else:

-            reply = u"I didn't understand '%s'" %(msg)
+            reply = "I didn't understand '%s'" %(msg)

         return reply
 
     def run(self):
         return reply
 
     def run(self):

diff --git a/htsworkflow/automation/test/test_runner.py b/htsworkflow/automation/test/test_runner.py
index a60c458401b2f0e8129c72d1a5864b0c11f045a5..22c5b19a68cfe04cdf7d667c9bc854601613de36 100644 (file)
--- a/htsworkflow/automation/test/test_runner.py
+++ b/htsworkflow/automation/test/test_runner.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 import os
 from htsworkflow.automation.solexa import is_runfolder
 
 import os
 from htsworkflow.automation.solexa import is_runfolder


@@ -41,12 +41,12 @@ class testRunner(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testRunner))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/automation/test/test_solexa_utils.py b/htsworkflow/automation/test/test_solexa_utils.py
index 210906ecaf7b1cdf7aa3aeaeea008414dd0b4e14..2111406b474620a0457ccb86b6a18004e8ab131a 100644 (file)
--- a/htsworkflow/automation/test/test_solexa_utils.py
+++ b/htsworkflow/automation/test/test_solexa_utils.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.automation import solexa
 
 
 from htsworkflow.automation import solexa
 


@@ -24,12 +24,12 @@ class testSolexaRunfolderUtils(TestCase):
             
 
 def suite():
             
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSolexaRunfolderUtils))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/frontend/analysis/main.py b/htsworkflow/frontend/analysis/main.py
index ba2a739d5be0b461aaf02264a40dda6ed90e6863..71d711d72dca7e9dac47806e9b3e4635d842d123 100644 (file)
--- a/htsworkflow/frontend/analysis/main.py
+++ b/htsworkflow/frontend/analysis/main.py
@@ -14,20 +14,20 @@ def updStatus(request):
     ClIP = request.META['REMOTE_ADDR']
     #Check client access permission                                                                                                                                       
     granted = False
     ClIP = request.META['REMOTE_ADDR']
     #Check client access permission                                                                                                                                       
     granted = False

-    if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)):  granted = True
+    if (ClIP in settings.ALLOWED_ANALYS_IPS):  granted = True

     if not granted: return HttpResponse("access denied.")
 
     output=''
     taskid=-1;
     # Check required param
     if not granted: return HttpResponse("access denied.")
 
     output=''
     taskid=-1;
     # Check required param

-    if request.has_key('taskid'): taskid = request['taskid']
+    if 'taskid' in request: taskid = request['taskid']

     else:  return HttpResponse('missing param task id')
 
     try:
       rec = Task.objects.get(id=taskid)
       mytimestamp = datetime.now().__str__()
       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
     else:  return HttpResponse('missing param task id')
 
     try:
       rec = Task.objects.get(id=taskid)
       mytimestamp = datetime.now().__str__()
       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)

-      if request.has_key('msg'):
+      if 'msg' in request:

         rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
       else :
         rec.task_status = "Registered ("+mytimestamp+")"
         rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
       else :
         rec.task_status = "Registered ("+mytimestamp+")"


@@ -43,13 +43,13 @@ def getProjects(request):
     ClIP = request.META['REMOTE_ADDR']
     #Check client access permission 
     granted = False
     ClIP = request.META['REMOTE_ADDR']
     #Check client access permission 
     granted = False

-    if (settings.ALLOWED_ANALYS_IPS.has_key(ClIP)):  granted = True
+    if (ClIP in settings.ALLOWED_ANALYS_IPS):  granted = True

     if not granted: return HttpResponse("access denied.")
 
     outputfile = ''
     
     All=False
     if not granted: return HttpResponse("access denied.")
 
     outputfile = ''
     
     All=False

-    if (request.has_key('mode')):
+    if ('mode' in request):

       if request['mode']=='all':
         All=True
 
       if request['mode']=='all':
         All=True
 

diff --git a/htsworkflow/frontend/auth.py b/htsworkflow/frontend/auth.py
index 31650a6bb56d6189503a8e6a04d6240c8330459f..bd1771b58f1144bbded017d74d4c94c7a5d7f7be 100644 (file)
--- a/htsworkflow/frontend/auth.py
+++ b/htsworkflow/frontend/auth.py
@@ -4,11 +4,11 @@ Define some alternate authentication methods
 from django.core.exceptions import PermissionDenied
 from django.conf import settings
 
 from django.core.exceptions import PermissionDenied
 from django.conf import settings
 

-apidata = {'apiid': u'0', 'apikey': settings.DEFAULT_API_KEY}
+apidata = {'apiid': '0', 'apikey': settings.DEFAULT_API_KEY}

 
 def require_api_key(request):
     # make sure we have the api component
 
 def require_api_key(request):
     # make sure we have the api component

-    if not (request.REQUEST.has_key('apiid') or request.REQUEST.has_key('apikey')):
+    if not ('apiid' in request.REQUEST or 'apikey' in request.REQUEST):

         raise PermissionDenied
 
     # make sure the id and key are right
         raise PermissionDenied
 
     # make sure the id and key are right

diff --git a/htsworkflow/frontend/bcmagic/models.py b/htsworkflow/frontend/bcmagic/models.py
index 4db58a3ddd8e5b27bfcc539cae7fd12fa92a4f74..3d9b6075b92ae00383be8358d5f73ec7c5aa7ac7 100644 (file)
--- a/htsworkflow/frontend/bcmagic/models.py
+++ b/htsworkflow/frontend/bcmagic/models.py
@@ -28,4 +28,4 @@ class Printer(models.Model):
     notes = models.TextField()
 
     def __unicode__(self):
     notes = models.TextField()
 
     def __unicode__(self):

-        return u'%s, %s, %s, %s, %sx%s' % (self.name, self.model, self.ip_address, self.label_shape, self.label_width, self.label_width)
\ No newline at end of file
+        return '%s, %s, %s, %s, %sx%s' % (self.name, self.model, self.ip_address, self.label_shape, self.label_width, self.label_width)
\ No newline at end of file

diff --git a/htsworkflow/frontend/bcmagic/plugin.py b/htsworkflow/frontend/bcmagic/plugin.py
index d701cf383d3bd91b12d5ade1db3e8beb55629015..22cd1ed70b9e8834ce9a64347459311d0112c197 100644 (file)
--- a/htsworkflow/frontend/bcmagic/plugin.py
+++ b/htsworkflow/frontend/bcmagic/plugin.py
@@ -28,7 +28,7 @@ def register_search_plugin(label, search_function):
     
     if label in _SEARCH_FUNCTIONS:
         msg = "search function for label (%s) already registered." % (label)
     
     if label in _SEARCH_FUNCTIONS:
         msg = "search function for label (%s) already registered." % (label)

-        raise ValueError, msg
+        raise ValueError(msg)

     
     _SEARCH_FUNCTIONS[label] = search_function
     
\ No newline at end of file
     
     _SEARCH_FUNCTIONS[label] = search_function
     
\ No newline at end of file

diff --git a/htsworkflow/frontend/bcmagic/utils.py b/htsworkflow/frontend/bcmagic/utils.py
index 5acc6ddefd6045473ad498c000ec60ae48f8b49c..0317ca7fa3370fa3ee9830ee3adc5a4649594ac5 100644 (file)
--- a/htsworkflow/frontend/bcmagic/utils.py
+++ b/htsworkflow/frontend/bcmagic/utils.py
@@ -2,7 +2,7 @@ from django.conf import settings
 
 import ftplib
 import socket
 
 import ftplib
 import socket

-import StringIO
+import io

 
 
 def print_zpl(zpl_text, host=settings.BCPRINTER_PRINTER1_HOST):
 
 
 def print_zpl(zpl_text, host=settings.BCPRINTER_PRINTER1_HOST):


@@ -11,7 +11,7 @@ def print_zpl(zpl_text, host=settings.BCPRINTER_PRINTER1_HOST):
     """
     ftp = ftplib.FTP(host=host, user='blank', passwd='')
     ftp.login()
     """
     ftp = ftplib.FTP(host=host, user='blank', passwd='')
     ftp.login()

-    ftp.storlines("STOR printme.txt", StringIO.StringIO(zpl_text))
+    ftp.storlines("STOR printme.txt", io.StringIO(zpl_text))

     ftp.quit()
 
 
     ftp.quit()
 
 

diff --git a/htsworkflow/frontend/bcmagic/views.py b/htsworkflow/frontend/bcmagic/views.py
index f9fb7933cdecbe70230cc57f04d50c2ec7569e4f..43b32b5668277eb47b160fac71f5df814a5939b2 100644 (file)
--- a/htsworkflow/frontend/bcmagic/views.py
+++ b/htsworkflow/frontend/bcmagic/views.py
@@ -11,7 +11,7 @@ from htsworkflow.frontend.bcmagic import plugin
 
 try:
     import json
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 import re
     import simplejson as json
 
 import re


@@ -34,7 +34,7 @@ def __plugin_search(text):
     """
     
     hits = []
     """
     
     hits = []

-    for label, search_func in plugin._SEARCH_FUNCTIONS.items():
+    for label, search_func in list(plugin._SEARCH_FUNCTIONS.items()):

         result = search_func(text)
         if result is not None:
             hits.extend(result)
         result = search_func(text)
         if result is not None:
             hits.extend(result)


@@ -72,7 +72,7 @@ def __magic_process(text):
     # Attempt to find a KeywordMap based on keyword
     try:
         keymap = models.KeywordMap.objects.get(keyword=keyword)
     # Attempt to find a KeywordMap based on keyword
     try:
         keymap = models.KeywordMap.objects.get(keyword=keyword)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         return report_error('Keyword (%s) is not defined' % (keyword))
     
     # Remove keyword and only scan the content
         return report_error('Keyword (%s) is not defined' % (keyword))
     
     # Remove keyword and only scan the content

diff --git a/htsworkflow/frontend/eland_config/forms.py b/htsworkflow/frontend/eland_config/forms.py
index a2245f9f35548fe8f231f30cfd7505e18230ea9f..31e73cab50ab41bc84c979c9a54dcd553377fb85 100644 (file)
--- a/htsworkflow/frontend/eland_config/forms.py
+++ b/htsworkflow/frontend/eland_config/forms.py
@@ -14,8 +14,8 @@ class DivErrorList(ErrorList):
     return self.as_divs()
   
   def as_divs(self):
     return self.as_divs()
   
   def as_divs(self):

-    if not self: return u''
-    return u'<div class="errorlist">%s</div>' % (''.join([u'<div class="error">%s</div>' % e for e in self]))
+    if not self: return ''
+    return '<div class="errorlist">%s</div>' % (''.join(['<div class="error">%s</div>' % e for e in self]))

 
 
 
 
 
 

diff --git a/htsworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py
index d21f86bb9d9995a9bb3dd1e69c08fe3ddc8a44d3..f63caf4e5b74e570b7425e27ec470b195388904d 100644 (file)
--- a/htsworkflow/frontend/eland_config/views.py
+++ b/htsworkflow/frontend/eland_config/views.py
@@ -273,7 +273,7 @@ def getElandConfig(flowcell, regenerate=False):
   #Convert all newline conventions to unix style
   for lane in fcObj.lane_set.all():
     data.append("# Lane%d: %s | %s" % \
   #Convert all newline conventions to unix style
   for lane in fcObj.lane_set.all():
     data.append("# Lane%d: %s | %s" % \

-      (lane.lane_number, unicode(lane.library.id),  lane.library.library_name.replace('%', '%%')))
+      (lane.lane_number, str(lane.library.id),  lane.library.library_name.replace('%', '%%')))

   
   #data.append("GENOME_DIR %s" % (BASE_DIR))
   #data.append("CONTAM_DIR %s" % (BASE_DIR))
   
   #data.append("GENOME_DIR %s" % (BASE_DIR))
   #data.append("CONTAM_DIR %s" % (BASE_DIR))


@@ -288,9 +288,9 @@ def getElandConfig(flowcell, regenerate=False):
   #l1s = form['lane1_species']
   for lane in fcObj.lane_set.all():
     species = lane.library.library_species.scientific_name
   #l1s = form['lane1_species']
   for lane in fcObj.lane_set.all():
     species = lane.library.library_species.scientific_name

-    genome_dict.setdefault(species, []).append(unicode(lane.lane_number))
+    genome_dict.setdefault(species, []).append(str(lane.lane_number))

   
   

-  genome_list = genome_dict.keys()
+  genome_list = list(genome_dict.keys())

   genome_list.sort()
   
   #Loop through and create entries for each species.
   genome_list.sort()
   
   #Loop through and create entries for each species.

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index 23c8098400643c402d302f1a4c3668f2988529d2..0882fc45d835a8d27763a6c89f0048d8a293172d 100644 (file)
--- a/htsworkflow/frontend/experiments/admin.py
+++ b/htsworkflow/frontend/experiments/admin.py
@@ -151,13 +151,13 @@ class SequencerSelect(Select):
         output = []
         for option_value, option_label in chain(self.choices, choices):
             if isinstance(option_label, (list, tuple)):
         output = []
         for option_value, option_label in chain(self.choices, choices):
             if isinstance(option_label, (list, tuple)):

-                output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
+                output.append('<optgroup label="%s">' % escape(force_unicode(option_value)))

                 for option in option_label:
                     output.append(self.render_option(selected_choices, *option))
                 for option in option_label:
                     output.append(self.render_option(selected_choices, *option))

-                output.append(u'</optgroup>')
+                output.append('</optgroup>')

             else:
                 output.append(self.render_option(selected_choices, option_value, option_label))
             else:
                 output.append(self.render_option(selected_choices, option_value, option_label))

-        return u'\n'.join(output)
+        return '\n'.join(output)

 
     # render_options blatently grabbed from 1.3.1 as the 1.2 version
     # has render_option, which is what I needed to overload as a
 
     # render_options blatently grabbed from 1.3.1 as the 1.2 version
     # has render_option, which is what I needed to overload as a


@@ -168,21 +168,21 @@ class SequencerSelect(Select):
         output = []
         for option_value, option_label in chain(self.choices, choices):
             if isinstance(option_label, (list, tuple)):
         output = []
         for option_value, option_label in chain(self.choices, choices):
             if isinstance(option_label, (list, tuple)):

-                output.append(u'<optgroup label="%s">' % escape(force_unicode(option_value)))
+                output.append('<optgroup label="%s">' % escape(force_unicode(option_value)))

                 for option in option_label:
                     output.append(self.render_option(selected_choices, *option))
                 for option in option_label:
                     output.append(self.render_option(selected_choices, *option))

-                output.append(u'</optgroup>')
+                output.append('</optgroup>')

             else:
                 output.append(self.render_option(selected_choices, option_value, option_label))
             else:
                 output.append(self.render_option(selected_choices, option_value, option_label))

-        return u'\n'.join(output)
+        return '\n'.join(output)

 
 
     def render_option(self, selected_choices, option_value, option_label):
 
 
     def render_option(self, selected_choices, option_value, option_label):

-        disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
-        option_value = unicode(option_value)
-        selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
+        disabled_sequencers = [ str(s.id) for s in self.queryset.filter(active=False) ]
+        option_value = str(option_value)
+        selected_html = (option_value in selected_choices) and ' selected="selected"' or ''

         cssclass = "strikeout" if option_value in disabled_sequencers else ''
         cssclass = "strikeout" if option_value in disabled_sequencers else ''

-        return u'<option class="%s" value="%s"%s>%s</option>' % (
+        return '<option class="%s" value="%s"%s>%s</option>' % (

             cssclass, escape(option_value), selected_html,
             conditional_escape(force_unicode(option_label)))
 
             cssclass, escape(option_value), selected_html,
             conditional_escape(force_unicode(option_label)))
 

diff --git a/htsworkflow/frontend/experiments/experiments.py b/htsworkflow/frontend/experiments/experiments.py
index f24d13d5b8dc3e830b2b3c1548251886ec7f1299..b9d19668cc2bed78bbe329ac258d0c52567c45c6 100644 (file)
--- a/htsworkflow/frontend/experiments/experiments.py
+++ b/htsworkflow/frontend/experiments/experiments.py
@@ -2,7 +2,7 @@
 from datetime import datetime, timedelta
 try:
     import json
 from datetime import datetime, timedelta
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 import os
     import simplejson as json
 
 import os


@@ -29,7 +29,7 @@ def flowcell_information(flowcell_id):
     """
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell_id)
     """
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell_id)

-    except FlowCell.DoesNotExist, e:
+    except FlowCell.DoesNotExist as e:

         return None
 
     lane_set = {}
         return None
 
     lane_set = {}


@@ -44,7 +44,7 @@ def flowcell_information(flowcell_id):
             'library_name': lane.library.library_name,
             'library_id': lane.library.id,
             'library_species': lane.library.library_species.scientific_name,
             'library_name': lane.library.library_name,
             'library_id': lane.library.id,
             'library_species': lane.library.library_species.scientific_name,

-            'pM': unicode(lane.pM),
+            'pM': str(lane.pM),

             'read_length': lane.flowcell.read_length,
             'status_code': lane.status,
             'status': LANE_STATUS_MAP[lane.status]
             'read_length': lane.flowcell.read_length,
             'status_code': lane.status,
             'status': LANE_STATUS_MAP[lane.status]


@@ -128,7 +128,7 @@ def lanes_for_json(request, username):
 
     try:
         result = lanes_for(username)
 
     try:
         result = lanes_for(username)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         raise Http404
 
     #convert query set to python structure
         raise Http404
 
     #convert query set to python structure


@@ -150,22 +150,22 @@ def updStatus(request):
       user = request.user
 
     #Check access permission
       user = request.user
 
     #Check access permission

-    if not (user.is_superuser and settings.ALLOWED_IPS.has_key(ClIP)):
+    if not (user.is_superuser and ClIP in settings.ALLOWED_IPS):

         return HttpResponse("%s access denied from %s." % (user, ClIP))
 
     # ~~~~~~Parameters for the job ~~~~
         return HttpResponse("%s access denied from %s." % (user, ClIP))
 
     # ~~~~~~Parameters for the job ~~~~

-    if request.REQUEST.has_key('fcid'):
+    if 'fcid' in request.REQUEST:

       fcid = request.REQUEST['fcid']
     else:
       return HttpResponse('missing fcid')
 
       fcid = request.REQUEST['fcid']
     else:
       return HttpResponse('missing fcid')
 

-    if request.REQUEST.has_key('runf'):
+    if 'runf' in request.REQUEST:

       runfolder = request.REQUEST['runf']
     else:
       return HttpResponse('missing runf')
 
 
       runfolder = request.REQUEST['runf']
     else:
       return HttpResponse('missing runf')
 
 

-    if request.REQUEST.has_key('updst'):
+    if 'updst' in request.REQUEST:

       UpdatedStatus = request.REQUEST['updst']
     else:
       return HttpResponse('missing status')
       UpdatedStatus = request.REQUEST['updst']
     else:
       return HttpResponse('missing status')


@@ -181,7 +181,7 @@ def updStatus(request):
       #if there's a message update that too
       mytimestamp = datetime.now().__str__()
       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
       #if there's a message update that too
       mytimestamp = datetime.now().__str__()
       mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)

-      if request.REQUEST.has_key('msg'):
+      if 'msg' in request.REQUEST:

         rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
       else :
         if UpdatedStatus == '1':
         rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
       else :
         if UpdatedStatus == '1':


@@ -230,7 +230,7 @@ def generateConfile(request,fcid):
 def getConfile(req):
     granted = False
     ClIP = req.META['REMOTE_ADDR']
 def getConfile(req):
     granted = False
     ClIP = req.META['REMOTE_ADDR']

-    if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
+    if (ClIP in settings.ALLOWED_IPS):  granted = True

 
     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 
 
     if not granted: return HttpResponse("access denied. IP: "+ClIP)
 


@@ -238,9 +238,9 @@ def getConfile(req):
     cnfgfile = 'Nothing found'
     runfolder = 'unknown'
     request = req.REQUEST
     cnfgfile = 'Nothing found'
     runfolder = 'unknown'
     request = req.REQUEST

-    if request.has_key('fcid'):
+    if 'fcid' in request:

       fcid = request['fcid']
       fcid = request['fcid']

-      if request.has_key('runf'):
+      if 'runf' in request:

         runfolder = request['runf']
         try:
           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
         runfolder = request['runf']
         try:
           rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)


@@ -264,14 +264,14 @@ def getConfile(req):
 def getLaneLibs(req):
     granted = False
     ClIP = req.META['REMOTE_ADDR']
 def getLaneLibs(req):
     granted = False
     ClIP = req.META['REMOTE_ADDR']

-    if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
+    if (ClIP in settings.ALLOWED_IPS):  granted = True

 
     if not granted: return HttpResponse("access denied.")
 
     request = req.REQUEST
     fcid = 'none'
     outputfile = ''
 
     if not granted: return HttpResponse("access denied.")
 
     request = req.REQUEST
     fcid = 'none'
     outputfile = ''

-    if request.has_key('fcid'):
+    if 'fcid' in request:

       fcid = request['fcid']
       try:
         rec = FlowCell.objects.get(flowcell_id=fcid)
       fcid = request['fcid']
       try:
         rec = FlowCell.objects.get(flowcell_id=fcid)

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 7a41d3d5902aebe32a56595db04dd859aa6e016d..c29026883f3bf8c59512e42d0c54fd24f0945ec4 100644 (file)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -20,7 +20,7 @@ LOGGER = logging.getLogger(__name__)
 default_pM = 5
 try:
     default_pM = int(settings.DEFAULT_PM)
 default_pM = 5
 try:
     default_pM = int(settings.DEFAULT_PM)

-except ValueError, e:
+except ValueError as e:

     LOGGER.error("invalid value for frontend.default_pm")
 
 # how many days to wait before trying to re-import a runfolder
     LOGGER.error("invalid value for frontend.default_pm")
 
 # how many days to wait before trying to re-import a runfolder


@@ -54,7 +54,7 @@ class ClusterStation(models.Model):
         ordering = ["-isdefault", "name"]
 
     def __unicode__(self):
         ordering = ["-isdefault", "name"]
 
     def __unicode__(self):

-        return unicode(self.name)
+        return str(self.name)

 
     @classmethod
     def default(cls):
 
     @classmethod
     def default(cls):


@@ -93,9 +93,9 @@ class Sequencer(models.Model):
         ordering = ["-isdefault", "-active", "name"]
 
     def __unicode__(self):
         ordering = ["-isdefault", "-active", "name"]
 
     def __unicode__(self):

-        name = [unicode(self.name)]
+        name = [str(self.name)]

         if self.instrument_name is not None:
         if self.instrument_name is not None:

-            name.append("(%s)" % (unicode(self.instrument_name),))
+            name.append("(%s)" % (str(self.instrument_name),))

         return " ".join(name)
 
     @models.permalink
         return " ".join(name)
 
     @models.permalink


@@ -150,7 +150,7 @@ class FlowCell(models.Model):
     notes = models.TextField(blank=True)
 
     def __unicode__(self):
     notes = models.TextField(blank=True)
 
     def __unicode__(self):

-        return unicode(self.flowcell_id)
+        return str(self.flowcell_id)

 
     def Lanes(self):
         html = ['<table>']
 
     def Lanes(self):
         html = ['<table>']


@@ -184,9 +184,9 @@ class FlowCell(models.Model):
         """Convert our boolean 'is paired' flag to a name
         """
         if self.paired_end:
         """Convert our boolean 'is paired' flag to a name
         """
         if self.paired_end:

-            return u"Paired"
+            return "Paired"

         else:
         else:

-            return u"Single"
+            return "Single"

 
     @models.permalink
     def get_absolute_url(self):
 
     @models.permalink
     def get_absolute_url(self):


@@ -304,7 +304,7 @@ class Lane(models.Model):
                 [str(self.id)])
 
     def __unicode__(self):
                 [str(self.id)])
 
     def __unicode__(self):

-        return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
+        return self.flowcell.flowcell_id + ':' + str(self.lane_number)

 
 
 class DataRun(models.Model):
 
 
 class DataRun(models.Model):

diff --git a/htsworkflow/frontend/experiments/test_experiments.py b/htsworkflow/frontend/experiments/test_experiments.py
index 5878d726d7ee1d268382230a56a235aef7ca29e6..cd212332c1f06b3e0846a88406f8ae5c23ffb8f4 100644 (file)
--- a/htsworkflow/frontend/experiments/test_experiments.py
+++ b/htsworkflow/frontend/experiments/test_experiments.py
@@ -2,13 +2,13 @@ import re
 from lxml.html import fromstring
 try:
     import json
 from lxml.html import fromstring
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 import os
 import shutil
 import sys
 import tempfile
     import simplejson as json
 import os
 import shutil
 import sys
 import tempfile

-from urlparse import urljoin
+from urllib.parse import urljoin

 
 from django.conf import settings
 from django.core import mail
 
 from django.conf import settings
 from django.core import mail


@@ -24,7 +24,7 @@ from htsworkflow.util.ethelp import validate_xhtml
 
 from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 
 
 from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 

-LANE_SET = range(1,9)
+LANE_SET = list(range(1,9))

 
 NSMAP = {'libns':'http://jumpgate.caltech.edu/wiki/LibraryOntology#'}
 
 
 NSMAP = {'libns':'http://jumpgate.caltech.edu/wiki/LibraryOntology#'}
 


@@ -177,7 +177,7 @@ class ExperimentsTestCases(TestCase):
         """
         Check the code that packs the django objects into simple types.
         """
         """
         Check the code that packs the django objects into simple types.
         """

-        for fc_id in [u'FC12150', u"42JTNAAXX", "42JU1AAXX"]:
+        for fc_id in ['FC12150', "42JTNAAXX", "42JU1AAXX"]:

             fc_dict = experiments.flowcell_information(fc_id)
             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
             self.assertEqual(fc_dict['flowcell_id'], fc_id)
             fc_dict = experiments.flowcell_information(fc_id)
             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
             self.assertEqual(fc_dict['flowcell_id'], fc_id)


@@ -211,7 +211,7 @@ class ExperimentsTestCases(TestCase):
 
 
             for lane in fc_django.lane_set.all():
 
 
             for lane in fc_django.lane_set.all():

-                lane_contents = fc_json['lane_set'][unicode(lane.lane_number)]
+                lane_contents = fc_json['lane_set'][str(lane.lane_number)]

                 lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
 
                 self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
                 lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
 
                 self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)


@@ -235,7 +235,7 @@ class ExperimentsTestCases(TestCase):
         """
         Require logging in to retrieve meta data
         """
         """
         Require logging in to retrieve meta data
         """

-        response = self.client.get(u'/experiments/config/FC12150/json')
+        response = self.client.get('/experiments/config/FC12150/json')

         self.assertEqual(response.status_code, 403)
 
     def test_library_id(self):
         self.assertEqual(response.status_code, 403)
 
     def test_library_id(self):


@@ -268,8 +268,8 @@ class ExperimentsTestCases(TestCase):
         This tests to make sure that the value entered in the raw library id field matches
         the library id looked up.
         """
         This tests to make sure that the value entered in the raw library id field matches
         the library id looked up.
         """

-        expected_ids = [u'10981',u'11016',u'SL039',u'11060',
-                        u'11061',u'11062',u'11063',u'11064']
+        expected_ids = ['10981','11016','SL039','11060',
+                        '11061','11062','11063','11064']

         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
         response = self.client.get('/admin/experiments/flowcell/153/')
 
         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
         response = self.client.get('/admin/experiments/flowcell/153/')
 


@@ -322,11 +322,11 @@ class ExperimentsTestCases(TestCase):
         lane_dict = multi_lane_to_dict(lane_contents)
 
         self.assertEqual(lane_dict['12044']['index_sequence'],
         lane_dict = multi_lane_to_dict(lane_contents)
 
         self.assertEqual(lane_dict['12044']['index_sequence'],

-                         {u'1': u'ATCACG',
-                          u'2': u'CGATGT',
-                          u'3': u'TTAGGC'})
+                         {'1': 'ATCACG',
+                          '2': 'CGATGT',
+                          '3': 'TTAGGC'})

         self.assertEqual(lane_dict['11045']['index_sequence'],
         self.assertEqual(lane_dict['11045']['index_sequence'],

-                         {u'1': u'ATCACG'})
+                         {'1': 'ATCACG'})

 
 
 
 
 
 


@@ -482,7 +482,7 @@ class ExperimentsTestCases(TestCase):
         count = 0
         for r in query.execute(model):
             count += 1
         count = 0
         for r in query.execute(model):
             count += 1

-            self.assertEqual(fromTypedNode(r['flowcell_id']), u'42JU1AAXX')
+            self.assertEqual(fromTypedNode(r['flowcell_id']), '42JU1AAXX')

             lane_id = fromTypedNode(r['lane_id'])
             library_id = fromTypedNode(r['library_id'])
             self.assertTrue(library_id in expected[lane_id])
             lane_id = fromTypedNode(r['lane_id'])
             library_id = fromTypedNode(r['library_id'])
             self.assertTrue(library_id in expected[lane_id])


@@ -494,8 +494,8 @@ class TestFileType(TestCase):
         file_type_objects = models.FileType.objects
         name = 'QSEQ tarfile'
         file_type_object = file_type_objects.get(name=name)
         file_type_objects = models.FileType.objects
         name = 'QSEQ tarfile'
         file_type_object = file_type_objects.get(name=name)

-        self.assertEqual(u"QSEQ tarfile",
-                             unicode(file_type_object))
+        self.assertEqual("QSEQ tarfile",
+                             str(file_type_object))

 
     def test_find_file_type(self):
         file_type_objects = models.FileType.objects
 
     def test_find_file_type(self):
         file_type_objects = models.FileType.objects


@@ -607,7 +607,7 @@ class TestSequencer(TestCase):
         seq.instrument_name = "HWI-SEQ1"
         seq.model = "Imaginary 5000"
 
         seq.instrument_name = "HWI-SEQ1"
         seq.model = "Imaginary 5000"
 

-        self.assertEqual(unicode(seq), "Seq1 (HWI-SEQ1)")
+        self.assertEqual(str(seq), "Seq1 (HWI-SEQ1)")

 
     def test_lookup(self):
         fc = models.FlowCell.objects.get(pk=153)
 
     def test_lookup(self):
         fc = models.FlowCell.objects.get(pk=153)


@@ -698,7 +698,7 @@ def tearDownModule():
     teardown_test_environment()
 
 def suite():
     teardown_test_environment()
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     for testcase in [ClusterStationTestCases,
                      SequencerTestCases,
     suite = TestSuite()
     for testcase in [ClusterStationTestCases,
                      SequencerTestCases,


@@ -710,5 +710,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
index 28a355f97271f65ba80d0e18502a03f55b93f652..8171e981e58a36edfe7fe431c6d50c14b036b25a 100644 (file)
--- a/htsworkflow/frontend/experiments/views.py
+++ b/htsworkflow/frontend/experiments/views.py
@@ -85,16 +85,16 @@ def startedEmail(request, pk):
             warnings.append((user.admin_url(), user.username))
     user=None
 
             warnings.append((user.admin_url(), user.username))
     user=None
 

-    for user_email in email_lane.keys():
+    for user_email in list(email_lane.keys()):

         sending = ""
         # build body
         context = RequestContext(request,
         sending = ""
         # build body
         context = RequestContext(request,

-                                 {u'flowcell': fc,
-                                  u'lanes': email_lane[user_email],
-                                  u'runfolder': 'blank',
-                                  u'finish_low': estimate_low,
-                                  u'finish_high': estimate_high,
-                                  u'now': datetime.now(),
+                                 {'flowcell': fc,
+                                  'lanes': email_lane[user_email],
+                                  'runfolder': 'blank',
+                                  'finish_low': estimate_low,
+                                  'finish_high': estimate_high,
+                                  'now': datetime.now(),

                                   })
 
         # build view
                                   })
 
         # build view

diff --git a/htsworkflow/frontend/inventory/models.py b/htsworkflow/frontend/inventory/models.py
index 46b37ec615a93647cd40a0de76d65e0efec72afe..34938919cf790a6fbe519229c140e117c755c5d5 100644 (file)
--- a/htsworkflow/frontend/inventory/models.py
+++ b/htsworkflow/frontend/inventory/models.py
@@ -11,7 +11,7 @@ LOGGER = logging.getLogger(__name__)
 
 try:
     import uuid
 
 try:
     import uuid

-except ImportError, e:
+except ImportError as e:

     # Some systems are using python 2.4, which doesn't have uuid
     # this is a stub
     LOGGER.warning('Real uuid is not available, initializing fake uuid module')
     # Some systems are using python 2.4, which doesn't have uuid
     # this is a stub
     LOGGER.warning('Real uuid is not available, initializing fake uuid module')


@@ -45,7 +45,7 @@ class Vendor(models.Model):
     url = models.URLField(blank=True, null=True)
 
     def __unicode__(self):
     url = models.URLField(blank=True, null=True)
 
     def __unicode__(self):

-        return u"%s" % (self.name)
+        return "%s" % (self.name)

 
 
 class Location(models.Model):
 
 
 class Location(models.Model):


@@ -59,9 +59,9 @@ class Location(models.Model):
 
     def __unicode__(self):
         if len(self.location_description) > 16:
 
     def __unicode__(self):
         if len(self.location_description) > 16:

-            return u"%s: %s" % (self.name, self.location_description[0:16]+u"...")
+            return "%s: %s" % (self.name, self.location_description[0:16]+"...")

         else:
         else:

-            return u"%s: %s" % (self.name, self.location_description)
+            return "%s: %s" % (self.name, self.location_description)

 
 pre_save.connect(_assign_uuid, sender=Location)
 
 
 pre_save.connect(_assign_uuid, sender=Location)
 


@@ -82,15 +82,15 @@ class ItemInfo(models.Model):
     notes = models.TextField(blank=True, null=True)
 
     def __unicode__(self):
     notes = models.TextField(blank=True, null=True)
 
     def __unicode__(self):

-        name = u''
+        name = ''

         if self.model_id:
         if self.model_id:

-            name += u"model:%s " % (self.model_id)
+            name += "model:%s " % (self.model_id)

         if self.part_number:
         if self.part_number:

-            name += u"part:%s " % (self.part_number)
+            name += "part:%s " % (self.part_number)

         if self.lot_number:
         if self.lot_number:

-            name += u"lot:%s " % (self.lot_number)
+            name += "lot:%s " % (self.lot_number)

 
 

-        return u"%s: %s" % (name, self.purchase_date)
+        return "%s: %s" % (name, self.purchase_date)

 
     class Meta:
         verbose_name_plural = "Item Info"
 
     class Meta:
         verbose_name_plural = "Item Info"


@@ -102,7 +102,7 @@ class ItemType(models.Model):
     description = models.TextField(blank=True, null=True)
 
     def __unicode__(self):
     description = models.TextField(blank=True, null=True)
 
     def __unicode__(self):

-        return u"%s" % (self.name)
+        return "%s" % (self.name)

 
 class ItemStatus(models.Model):
     name = models.CharField(max_length=64, unique=True)
 
 class ItemStatus(models.Model):
     name = models.CharField(max_length=64, unique=True)


@@ -140,9 +140,9 @@ class Item(models.Model):
 
     def __unicode__(self):
         if self.barcode_id is None or len(self.barcode_id) == 0:
 
     def __unicode__(self):
         if self.barcode_id is None or len(self.barcode_id) == 0:

-            return u"invu|%s" % (self.uuid)
+            return "invu|%s" % (self.uuid)

         else:
         else:

-            return u"invb|%s" % (self.barcode_id)
+            return "invb|%s" % (self.barcode_id)

 
     def get_absolute_url(self):
         return '/inventory/%s/' % (self.uuid)
 
     def get_absolute_url(self):
         return '/inventory/%s/' % (self.uuid)


@@ -163,9 +163,9 @@ class PrinterTemplate(models.Model):
 
     def __unicode__(self):
         if self.default:
 
     def __unicode__(self):
         if self.default:

-            return u'%s %s' % (self.item_type.name, self.printer.name)
+            return '%s %s' % (self.item_type.name, self.printer.name)

         else:
         else:

-            return u'%s %s (default)' % (self.item_type.name, self.printer.name)
+            return '%s %s (default)' % (self.item_type.name, self.printer.name)

 
 pre_save.connect(_switch_default, sender=PrinterTemplate)
 
 
 pre_save.connect(_switch_default, sender=PrinterTemplate)
 


@@ -181,7 +181,7 @@ class LongTermStorage(models.Model):
     modified_date = models.DateTimeField(auto_now=True)
 
     def __unicode__(self):
     modified_date = models.DateTimeField(auto_now=True)
 
     def __unicode__(self):

-        return u"%s: %s" % (str(self.flowcell), ', '.join([ str(s) for s in self.storage_devices.iterator() ]))
+        return "%s: %s" % (str(self.flowcell), ', '.join([ str(s) for s in self.storage_devices.iterator() ]))

 
     class Meta:
         verbose_name_plural = "Long Term Storage"
 
     class Meta:
         verbose_name_plural = "Long Term Storage"


@@ -206,7 +206,7 @@ class ReagentFlowcell(ReagentBase):
     flowcell = models.ForeignKey(FlowCell)
 
     def __unicode__(self):
     flowcell = models.ForeignKey(FlowCell)
 
     def __unicode__(self):

-        return u"%s: %s" % (str(self.flowcell), ', '.join([ str(s) for s in self.reagent.iterator() ]))
+        return "%s: %s" % (str(self.flowcell), ', '.join([ str(s) for s in self.reagent.iterator() ]))

 
 
 class ReagentLibrary(ReagentBase):
 
 
 class ReagentLibrary(ReagentBase):


@@ -216,4 +216,4 @@ class ReagentLibrary(ReagentBase):
     library = models.ForeignKey(Library)
 
     def __unicode__(self):
     library = models.ForeignKey(Library)
 
     def __unicode__(self):

-        return u"%s: %s" % (str(self.library), ', '.join([ str(s) for s in self.reagent.iterator() ]))
+        return "%s: %s" % (str(self.library), ', '.join([ str(s) for s in self.reagent.iterator() ]))

diff --git a/htsworkflow/frontend/inventory/test_inventory.py b/htsworkflow/frontend/inventory/test_inventory.py
index 86d37b7cbe7e740468f04df9380ae8fa82c98b35..a66ebce77cf0354f6571a304aa30f3d4db39db53 100644 (file)
--- a/htsworkflow/frontend/inventory/test_inventory.py
+++ b/htsworkflow/frontend/inventory/test_inventory.py
@@ -38,7 +38,7 @@ class InventoryTestCase(TestCase):
 
         itemNode = RDF.Node(RDF.Uri(url))
         item_type = fromTypedNode(model.get_target(itemNode, inventoryOntology['item_type']))
 
         itemNode = RDF.Node(RDF.Uri(url))
         item_type = fromTypedNode(model.get_target(itemNode, inventoryOntology['item_type']))

-        self.failUnlessEqual(item_type, u'Hard Drive')
+        self.failUnlessEqual(item_type, 'Hard Drive')

 
     def test_itemindex(self):
         url = '/inventory/it/Hard Drive/'
 
     def test_itemindex(self):
         url = '/inventory/it/Hard Drive/'


@@ -123,11 +123,11 @@ def tearDownModule():
     teardown_test_environment()
 
 def suite():
     teardown_test_environment()
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(InventoryTestCase))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(InventoryTestCase))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/frontend/inventory/views.py b/htsworkflow/frontend/inventory/views.py
index 265e1bc74f43d74d53957401a20d018c043ac170..226ef8a36674a2f65e12f1c05067fa1261811804 100644 (file)
--- a/htsworkflow/frontend/inventory/views.py
+++ b/htsworkflow/frontend/inventory/views.py
@@ -19,7 +19,7 @@ register_search_plugin('Inventory Item', item_search)
 
 try:
     import json
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 INVENTORY_CONTEXT_DEFAULTS = {
     import simplejson as json
 
 INVENTORY_CONTEXT_DEFAULTS = {


@@ -88,7 +88,7 @@ def getPrinterTemplateByType(item_type):
             printer_template = PrinterTemplate.objects.get(default=True)
         except ObjectDoesNotExist:
             msg = "No template for item type (%s) and no default template found" % (item_type.name)
             printer_template = PrinterTemplate.objects.get(default=True)
         except ObjectDoesNotExist:
             msg = "No template for item type (%s) and no default template found" % (item_type.name)

-            raise ValueError, msg
+            raise ValueError(msg)

 
         return printer_template
 
 
         return printer_template
 


@@ -214,7 +214,7 @@ def item_summary_by_barcode(request, barcode_id, msg=''):
     """
     try:
         item = Item.objects.get(barcode_id=barcode_id)
     """
     try:
         item = Item.objects.get(barcode_id=barcode_id)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         item = None
 
     return item_summary_by_uuid(request, None, msg, item)
         item = None
 
     return item_summary_by_uuid(request, None, msg, item)


@@ -229,7 +229,7 @@ def item_summary_by_uuid(request, uuid, msg='', item=None):
     if item is None:
         try:
             item = Item.objects.get(uuid=uuid)
     if item is None:
         try:
             item = Item.objects.get(uuid=uuid)

-        except ObjectDoesNotExist, e:
+        except ObjectDoesNotExist as e:

             item = None
 
     context_dict = {
             item = None
 
     context_dict = {


@@ -289,7 +289,7 @@ def item_print(request, uuid):
     """
     try:
         item = Item.objects.get(uuid=uuid)
     """
     try:
         item = Item.objects.get(uuid=uuid)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         item = None
         msg = "Item with UUID %s does not exist" % (uuid)
 
         item = None
         msg = "Item with UUID %s does not exist" % (uuid)
 


@@ -314,7 +314,7 @@ def link_flowcell_and_device(request, flowcell, serial):
     # Retrieve Storage Device
     try:
         sd = Item.objects.get(barcode_id=serial)
     # Retrieve Storage Device
     try:
         sd = Item.objects.get(barcode_id=serial)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         msg = "Item with barcode_id of %s not found." % (serial)
         raise ObjectDoesNotExist(msg)
 
         msg = "Item with barcode_id of %s not found." % (serial)
         raise ObjectDoesNotExist(msg)
 


@@ -322,7 +322,7 @@ def link_flowcell_and_device(request, flowcell, serial):
     # Retrieve FlowCell
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell)
     # Retrieve FlowCell
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell)

-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:

         msg = "FlowCell with flowcell_id of %s not found." % (flowcell)
         raise ObjectDoesNotExist(msg)
 
         msg = "FlowCell with flowcell_id of %s not found." % (flowcell)
         raise ObjectDoesNotExist(msg)
 


@@ -332,7 +332,7 @@ def link_flowcell_and_device(request, flowcell, serial):
     lts = None
     if count > 1:
         msg = "There really should only be one longtermstorage object per flowcell"
     lts = None
     if count > 1:
         msg = "There really should only be one longtermstorage object per flowcell"

-        raise ValueError, msg
+        raise ValueError(msg)

     elif count == 1:
         # lts already attached to flowcell
         lts = fc.longtermstorage_set.all()[0]
     elif count == 1:
         # lts already attached to flowcell
         lts = fc.longtermstorage_set.all()[0]

diff --git a/htsworkflow/frontend/labels/models.py b/htsworkflow/frontend/labels/models.py
index 8794492d0e5dab2b85f92ea58d656d65474f32e7..bdbdc856eaa79d0e5345f9b2f3e5bd702e092564 100644 (file)
--- a/htsworkflow/frontend/labels/models.py
+++ b/htsworkflow/frontend/labels/models.py
@@ -11,7 +11,7 @@ class LabelPrinter(models.Model):
     notes = models.TextField(null=True, blank=True)
 
     def __unicode__(self):
     notes = models.TextField(null=True, blank=True)
 
     def __unicode__(self):

-        return u'%s: %s' % (self.name, self.labels)
+        return '%s: %s' % (self.name, self.labels)

 
 class LabelTemplate(models.Model):
     """
 
 class LabelTemplate(models.Model):
     """

diff --git a/htsworkflow/frontend/labels/test_labels.py b/htsworkflow/frontend/labels/test_labels.py
index 29354b2b60ff3e14a9191d03f1909dd717e43e8e..ca3633bb6d2c73635640d8dca26ef16f3fc9999b 100644 (file)
--- a/htsworkflow/frontend/labels/test_labels.py
+++ b/htsworkflow/frontend/labels/test_labels.py
@@ -22,11 +22,11 @@ True
 """}
 
 def suite():
 """}
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SimpleTest))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SimpleTest))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/frontend/reports/libinfopar.py b/htsworkflow/frontend/reports/libinfopar.py
index 73072af68c8967f8f77a8dce6eac096ef264b4f4..7d6f458a31b752c50e4451551f19cb6b9c8a20e0 100644 (file)
--- a/htsworkflow/frontend/reports/libinfopar.py
+++ b/htsworkflow/frontend/reports/libinfopar.py
@@ -5,8 +5,8 @@ from string import *
 import re
 from xml.sax import make_parser
 from xml.sax.handler import ContentHandler
 import re
 from xml.sax import make_parser
 from xml.sax.handler import ContentHandler

-import urllib
-import urllib2
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse

 import os
 
 '''
 import os
 
 '''


@@ -63,9 +63,9 @@ def getLibReads(libid):
   return arRes
 
 def getWebPage(url,params):
   return arRes
 
 def getWebPage(url,params):

-  pdata = urllib.urlencode(params)
-  req = urllib2.Request(url,pdata)
-  wpage = urllib2.urlopen(req)
+  pdata = urllib.parse.urlencode(params)
+  req = urllib.request.Request(url,pdata)
+  wpage = urllib.request.urlopen(req)

   restext = wpage.read()
   wpage.close()
   return restext
   restext = wpage.read()
   wpage.close()
   return restext

diff --git a/htsworkflow/frontend/reports/models.py b/htsworkflow/frontend/reports/models.py
index b898537ae10b5ac42ee707b90a739370c2d19310..9bcb3e589409b7cfb5558f3aeaaa31bfe07ffa43 100644 (file)
--- a/htsworkflow/frontend/reports/models.py
+++ b/htsworkflow/frontend/reports/models.py
@@ -9,7 +9,7 @@ from string import *
 from htsworkflow.frontend.reports.utils import *
 import re
 ##from p1 import LibInfo
 from htsworkflow.frontend.reports.utils import *
 import re
 ##from p1 import LibInfo

-from libinfopar import *
+from .libinfopar import *

 
 ## This is a table based REPORT generator. The goal is to display a Progress Report for all the ENCODE projects, based on Study Name (e.g. NRSF, FOXP2, Methy-Seq on .. etc).
   
 
 ## This is a table based REPORT generator. The goal is to display a Progress Report for all the ENCODE projects, based on Study Name (e.g. NRSF, FOXP2, Methy-Seq on .. etc).
   

diff --git a/htsworkflow/frontend/reports/reports.py b/htsworkflow/frontend/reports/reports.py
index 18cd3285c5bb90b4fdeaea37292f02fdb9ade45a..e2ff54f817850babf06791e97ea26d0502af703d 100644 (file)
--- a/htsworkflow/frontend/reports/reports.py
+++ b/htsworkflow/frontend/reports/reports.py
@@ -27,7 +27,7 @@ def getBgColor(reads_cnt,exp_type):
 def report1(request):
   EXP = 'ChIP-seq'
 
 def report1(request):
   EXP = 'ChIP-seq'
 

-  if request.GET.has_key('aflid'):
+  if 'aflid' in request.GET:

     AFL_Id = request.GET['aflid']
     try:
       AFL = Affiliation.objects.get(id=AFL_Id).name
     AFL_Id = request.GET['aflid']
     try:
       AFL = Affiliation.objects.get(id=AFL_Id).name


@@ -170,10 +170,10 @@ def report1(request):
 def report_RM(request): #for RNA-Seq and Methyl-Seq
   EXP = 'RNA-seq'  
 
 def report_RM(request): #for RNA-Seq and Methyl-Seq
   EXP = 'RNA-seq'  
 

-  if request.GET.has_key('exp'):
+  if 'exp' in request.GET:

     EXP = request.GET['exp'] # Methyl-seq
 
     EXP = request.GET['exp'] # Methyl-seq
 

-  if request.GET.has_key('aflid'):
+  if 'aflid' in request.GET:

     AFL_Id = request.GET['aflid']
     try:
       AFL = Affiliation.objects.get(id=AFL_Id).name
     AFL_Id = request.GET['aflid']
     try:
       AFL = Affiliation.objects.get(id=AFL_Id).name

diff --git a/htsworkflow/frontend/reports/utils.py b/htsworkflow/frontend/reports/utils.py
index 7b2d1b8e00057994d1f9b0d8112ad0e87b2bc9e8..e42c26c921846ab13cb1002788358d7144f22502 100644 (file)
--- a/htsworkflow/frontend/reports/utils.py
+++ b/htsworkflow/frontend/reports/utils.py
@@ -30,7 +30,7 @@ def unique(s):
   except TypeError:
       del u  # move on to the next method                                                                                                                                                                                                                    
   else:
   except TypeError:
       del u  # move on to the next method                                                                                                                                                                                                                    
   else:

-      return u.keys()
+      return list(u.keys())

   # We can't hash all the elements.  Second fastest is to sort,                                                                                                                                                                                              
   # which brings the equal elements together; then duplicates are                                                                                                                                                                                            
   # easy to weed out in a single pass.                                                                                                                                                                                                                       
   # We can't hash all the elements.  Second fastest is to sort,                                                                                                                                                                                              
   # which brings the equal elements together; then duplicates are                                                                                                                                                                                            
   # easy to weed out in a single pass.                                                                                                                                                                                                                       

diff --git a/htsworkflow/frontend/samples/auth_backend.py b/htsworkflow/frontend/samples/auth_backend.py
index e09d4048cdcf6a37dfaabf978773d28bdfa7d1cf..6908956432857d9db6133b170722237da6b42fbd 100644 (file)
--- a/htsworkflow/frontend/samples/auth_backend.py
+++ b/htsworkflow/frontend/samples/auth_backend.py
@@ -12,16 +12,16 @@ class HTSUserModelBackend(ModelBackend):
             if user.check_password(password):
                 return user
         #except self.user_class.DoesNotExist:
             if user.check_password(password):
                 return user
         #except self.user_class.DoesNotExist:

-        except Exception, e:
-            print >>sys.stderr, e
+        except Exception as e:
+            print(e, file=sys.stderr)

             return None
 
     def get_user(self, user_id):
         try:
             return self.user_class.objects.get(pk=user_id)
         #except self.user_class.DoesNotExist:
             return None
 
     def get_user(self, user_id):
         try:
             return self.user_class.objects.get(pk=user_id)
         #except self.user_class.DoesNotExist:

-        except Exception, e:
-            print >>sys.stderr, e
+        except Exception as e:
+            print(e, file=sys.stderr)

             return None
 
     @property
             return None
 
     @property

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 5126bb504eb21f723e5845489c8085fdfbbb35a0..b01b39312c13d543adbe431124a12b729306ec31 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -1,6 +1,6 @@
 import types
 import logging
 import types
 import logging

-import urlparse
+import urllib.parse

 from django.db import models
 from django.contrib.auth.models import User, UserManager
 from django.core import urlresolvers
 from django.db import models
 from django.contrib.auth.models import User, UserManager
 from django.core import urlresolvers


@@ -27,7 +27,7 @@ class Antibody(models.Model):
     biology = models.TextField(blank=True, null=True)
     notes = models.TextField(blank=True, null=True)
     def __unicode__(self):
     biology = models.TextField(blank=True, null=True)
     notes = models.TextField(blank=True, null=True)
     def __unicode__(self):

-        return u'%s - %s' % (self.antigene, self.antibodies)
+        return '%s - %s' % (self.antigene, self.antibodies)

     class Meta:
         verbose_name_plural = "antibodies"
         ordering = ["antigene"]
     class Meta:
         verbose_name_plural = "antibodies"
         ordering = ["antigene"]


@@ -41,7 +41,7 @@ class Cellline(models.Model):
 
     notes = models.TextField(blank=True)
     def __unicode__(self):
 
     notes = models.TextField(blank=True)
     def __unicode__(self):

-        return unicode(self.cellline_name)
+        return str(self.cellline_name)

 
     class Meta:
         ordering = ["cellline_name"]
 
     class Meta:
         ordering = ["cellline_name"]


@@ -57,7 +57,7 @@ class Condition(models.Model):
     notes = models.TextField(blank=True)
 
     def __unicode__(self):
     notes = models.TextField(blank=True)
 
     def __unicode__(self):

-        return unicode(self.condition_name)
+        return str(self.condition_name)

 
     class Meta:
         ordering = ["condition_name"]
 
     class Meta:
         ordering = ["condition_name"]


@@ -67,7 +67,7 @@ class ExperimentType(models.Model):
   name = models.CharField(max_length=50, unique=True)
 
   def __unicode__(self):
   name = models.CharField(max_length=50, unique=True)
 
   def __unicode__(self):

-    return unicode(self.name)
+    return str(self.name)

 
 class Tag(models.Model):
   tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
 
 class Tag(models.Model):
   tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)


@@ -82,7 +82,7 @@ class Tag(models.Model):
       choices=TAG_CONTEXT, default='Library')
 
   def __unicode__(self):
       choices=TAG_CONTEXT, default='Library')
 
   def __unicode__(self):

-    return u'%s' % (self.tag_name)
+    return '%s' % (self.tag_name)

 
   class Meta:
     ordering = ["context","tag_name"]
 
   class Meta:
     ordering = ["context","tag_name"]


@@ -96,7 +96,7 @@ class Species(models.Model):
   #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
 
   def __unicode__(self):
   #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
 
   def __unicode__(self):

-    return u'%s (%s)' % (self.scientific_name, self.common_name)
+    return '%s (%s)' % (self.scientific_name, self.common_name)

 
   class Meta:
     verbose_name_plural = "species"
 
   class Meta:
     verbose_name_plural = "species"


@@ -114,14 +114,14 @@ class Affiliation(models.Model):
   users.admin_order_field = "username"
 
   def __unicode__(self):
   users.admin_order_field = "username"
 
   def __unicode__(self):

-    str = unicode(self.name)
+    str = str(self.name)

     if self.contact is not None and len(self.contact) > 0:
     if self.contact is not None and len(self.contact) > 0:

-      str += u' ('+self.contact+u')'
+      str += ' ('+self.contact+')'

     return str
 
   def Users(self):
       users = self.users.all().order_by('username')
     return str
 
   def Users(self):
       users = self.users.all().order_by('username')

-      return ", ".join([unicode(a) for a in users ])
+      return ", ".join([str(a) for a in users ])

 
   class Meta:
     ordering = ["name","contact"]
 
   class Meta:
     ordering = ["name","contact"]


@@ -136,7 +136,7 @@ class LibraryType(models.Model):
                     help_text="Does this adapter provide multiplexing?")
 
   def __unicode__(self):
                     help_text="Does this adapter provide multiplexing?")
 
   def __unicode__(self):

-      return unicode(self.name)
+      return str(self.name)

 
   class Meta:
       ordering = ["-id"]
 
   class Meta:
       ordering = ["-id"]


@@ -203,7 +203,7 @@ class Library(models.Model):
 
   undiluted_concentration = models.DecimalField("Concentration",
       max_digits=5, decimal_places=2, blank=True, null=True,
 
   undiluted_concentration = models.DecimalField("Concentration",
       max_digits=5, decimal_places=2, blank=True, null=True,

-      help_text=u"Undiluted concentration (ng/\u00b5l)")
+      help_text="Undiluted concentration (ng/\u00b5l)")

       # note \u00b5 is the micro symbol in unicode
   successful_pM = models.DecimalField(max_digits=9,
                                       decimal_places=1, blank=True, null=True)
       # note \u00b5 is the micro symbol in unicode
   successful_pM = models.DecimalField(max_digits=9,
                                       decimal_places=1, blank=True, null=True)


@@ -215,11 +215,11 @@ class Library(models.Model):
   bioanalyzer_summary = models.TextField(blank=True,default="")
   bioanalyzer_concentration = models.DecimalField(max_digits=5,
                                 decimal_places=2, blank=True, null=True,
   bioanalyzer_summary = models.TextField(blank=True,default="")
   bioanalyzer_concentration = models.DecimalField(max_digits=5,
                                 decimal_places=2, blank=True, null=True,

-                                help_text=u"(ng/\u00b5l)")
+                                help_text="(ng/\u00b5l)")

   bioanalyzer_image_url = models.URLField(blank=True,default="")
 
   def __unicode__(self):
   bioanalyzer_image_url = models.URLField(blank=True,default="")
 
   def __unicode__(self):

-    return u'#%s: %s' % (self.id, self.library_name)
+    return '#%s: %s' % (self.id, self.library_name)

 
   class Meta:
       verbose_name_plural = "libraries"
 
   class Meta:
       verbose_name_plural = "libraries"


@@ -273,7 +273,7 @@ class Library(models.Model):
               adapter_type = self.library_type.id,
               multiplex_id = multiplex_id)
           return multiplex.sequence
               adapter_type = self.library_type.id,
               multiplex_id = multiplex_id)
           return multiplex.sequence

-      except MultiplexIndex.DoesNotExist, e:
+      except MultiplexIndex.DoesNotExist as e:

           return None
 
   def index_sequence_text(self, seperator=' '):
           return None
 
   def index_sequence_text(self, seperator=' '):


@@ -281,9 +281,9 @@ class Library(models.Model):
       sequences = self.index_sequences()
       if sequences is None:
           return ""
       sequences = self.index_sequences()
       if sequences is None:
           return ""

-      if type(sequences) in types.StringTypes:
+      if type(sequences) in str:

           return sequences
           return sequences

-      multiplex_ids = sequences.keys()
+      multiplex_ids = list(sequences.keys())

       multiplex_ids.sort()
       return seperator.join(( "%s:%s" %(i,sequences[i]) for i in multiplex_ids))
   index_sequence_text.short_description = "Index"
       multiplex_ids.sort()
       return seperator.join(( "%s:%s" %(i,sequences[i]) for i in multiplex_ids))
   index_sequence_text.short_description = "Index"


@@ -320,7 +320,7 @@ class Library(models.Model):
     ar = []
     for t in affs:
       ar.append(t.__unicode__())
     ar = []
     for t in affs:
       ar.append(t.__unicode__())

-    return u'%s' % ( ", ".join(ar))
+    return '%s' % ( ", ".join(ar))

 
   def DataRun(self):
     str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
 
   def DataRun(self):
     str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'


@@ -335,7 +335,7 @@ class Library(models.Model):
 
     # Check data sanity
     if res[2] != "OK":
 
     # Check data sanity
     if res[2] != "OK":

-      return u'<div style="border:solid red 2px">'+res[2]+'</div>'
+      return '<div style="border:solid red 2px">'+res[2]+'</div>'

 
     rc = "%1.2f" % (res[1]/1000000.0)
     # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
 
     rc = "%1.2f" % (res[1]/1000000.0)
     # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled


@@ -388,7 +388,7 @@ class HTSUser(User):
 
     def __unicode__(self):
         #return unicode(self.username) + u" (" + unicode(self.get_full_name()) + u")"
 
     def __unicode__(self):
         #return unicode(self.username) + u" (" + unicode(self.get_full_name()) + u")"

-        return unicode(self.get_full_name()) + u' (' + unicode(self.username) + ')'
+        return str(self.get_full_name()) + ' (' + str(self.username) + ')'

 
 def HTSUserInsertID(sender, instance, **kwargs):
     """
 
 def HTSUserInsertID(sender, instance, **kwargs):
     """

diff --git a/htsworkflow/frontend/samples/test_samples.py b/htsworkflow/frontend/samples/test_samples.py
index f0844e55cce7fbf3b33fbdfbf03b9d9264b3e13a..12a4b5ba9e692366e585932ba7f7d93f8c118db7 100644 (file)
--- a/htsworkflow/frontend/samples/test_samples.py
+++ b/htsworkflow/frontend/samples/test_samples.py
@@ -2,7 +2,7 @@ import datetime
 
 try:
     import json
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 from django.test import TestCase
     import simplejson as json
 
 from django.test import TestCase


@@ -93,28 +93,28 @@ class SampleWebTestCase(TestCase):
                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
                     self.failUnlessEqual(d['undiluted_concentration'],
                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
                     self.failUnlessEqual(d['undiluted_concentration'],

-                                         unicode(lib.undiluted_concentration))
+                                         str(lib.undiluted_concentration))

                 # some specific tests
                 if lib.id == '10981':
                     # test a case where there is no known status
                 # some specific tests
                 if lib.id == '10981':
                     # test a case where there is no known status

-                    lane_set = {u'status': u'Unknown',
-                                u'paired_end': True,
-                                u'read_length': 75,
-                                u'lane_number': 1,
-                                u'lane_id': 1193,
-                                u'flowcell': u'303TUAAXX',
-                                u'status_code': None}
+                    lane_set = {'status': 'Unknown',
+                                'paired_end': True,
+                                'read_length': 75,
+                                'lane_number': 1,
+                                'lane_id': 1193,
+                                'flowcell': '303TUAAXX',
+                                'status_code': None}

                     self.failUnlessEqual(len(d['lane_set']), 1)
                     self.failUnlessEqual(d['lane_set'][0], lane_set)
                 elif lib.id == '11016':
                     # test a case where there is a status
                     self.failUnlessEqual(len(d['lane_set']), 1)
                     self.failUnlessEqual(d['lane_set'][0], lane_set)
                 elif lib.id == '11016':
                     # test a case where there is a status

-                    lane_set = {u'status': 'Good',
-                                u'paired_end': True,
-                                u'read_length': 75,
-                                u'lane_number': 5,
-                                u'lane_id': 1197,
-                                u'flowcell': u'303TUAAXX',
-                                u'status_code': 2}
+                    lane_set = {'status': 'Good',
+                                'paired_end': True,
+                                'read_length': 75,
+                                'lane_number': 5,
+                                'lane_id': 1197,
+                                'flowcell': '303TUAAXX',
+                                'status_code': 2}

                     self.failUnlessEqual(len(d['lane_set']), 1)
                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 
                     self.failUnlessEqual(len(d['lane_set']), 1)
                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 


@@ -169,11 +169,11 @@ class SampleWebTestCase(TestCase):
         }"""
         query = RDF.SPARQLQuery(body)
         for r in query.execute(model):
         }"""
         query = RDF.SPARQLQuery(body)
         for r in query.execute(model):

-            self.assertEqual(fromTypedNode(r['library_id']), u'10981')
+            self.assertEqual(fromTypedNode(r['library_id']), '10981')

             self.assertEqual(fromTypedNode(r['name']),
             self.assertEqual(fromTypedNode(r['name']),

-                             u'Paired End Multiplexed Sp-BAC')
+                             'Paired End Multiplexed Sp-BAC')

             self.assertEqual(fromTypedNode(r['gel_cut']), 400)
             self.assertEqual(fromTypedNode(r['gel_cut']), 400)

-            self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
+            self.assertEqual(fromTypedNode(r['made_by']), 'Igor')

 
         state = validate_xhtml(content)
         if state is not None:
 
         state = validate_xhtml(content)
         if state is not None:


@@ -220,7 +220,7 @@ class SampleWebTestCase(TestCase):
         count = 0
         for r in query.execute(model):
             count += 1
         count = 0
         for r in query.execute(model):
             count += 1

-            for name, value in r.items():
+            for name, value in list(r.items()):

                 self.assertTrue(name in bindings)
                 self.assertTrue(value is not None)
 
                 self.assertTrue(name in bindings)
                 self.assertTrue(value is not None)
 


@@ -274,7 +274,7 @@ try:
     rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
     xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
     libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
     rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
     xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
     libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")

-except ImportError,e:
+except ImportError as e:

     HAVE_RDF = False
 
 
     HAVE_RDF = False
 
 


@@ -300,12 +300,12 @@ class TestRDFaLibrary(TestCase):
         self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
 
         self.check_uri_object(model,
         self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
 
         self.check_uri_object(model,

-                              [u'http://localhost/lane/1193'],
+                              ['http://localhost/lane/1193'],

                               p=libNS['has_lane'])
 
         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
         self.check_literal_object(model,
                               p=libNS['has_lane'])
 
         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
         self.check_literal_object(model,

-                                  [u"303TUAAXX"],
+                                  ["303TUAAXX"],

                                   s=fc_uri, p=libNS['flowcell_id'])
 
     def check_literal_object(self, model, values, s=None, p=None, o=None):
                                   s=fc_uri, p=libNS['flowcell_id'])
 
     def check_literal_object(self, model, values, s=None, p=None, o=None):


@@ -323,7 +323,7 @@ class TestRDFaLibrary(TestCase):
         self.failUnlessEqual(len(statements), len(values),
                         "Couln't find %s %s %s" % (s,p,o))
         for s in statements:
         self.failUnlessEqual(len(statements), len(values),
                         "Couln't find %s %s %s" % (s,p,o))
         for s in statements:

-            self.failUnless(unicode(s.object.uri) in values)
+            self.failUnless(str(s.object.uri) in values)

 
 
 
 
 
 


@@ -342,7 +342,7 @@ def tearDownModule():
     teardown_test_environment()
 
 def suite():
     teardown_test_environment()
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))


@@ -350,5 +350,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index 5ab54a9e4fafd49b9fdfc1df1131bf1120a42766..5ddad93c02fdb99c6366ee4bc21a73f95681d24e 100644 (file)
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -1,12 +1,12 @@
 # Create your views here.
 # Create your views here.

-import StringIO
+import io

 import logging
 import os
 import sys
 
 try:
     import json
 import logging
 import os
 import sys
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 from django.views.decorators.csrf import csrf_exempt
     import simplejson as json
 
 from django.views.decorators.csrf import csrf_exempt


@@ -84,14 +84,14 @@ def create_library_context(cl):
            summary['amplified_from'] = ''
        lanes_run = count_lanes(lib.lane_set)
        # suppress zeros
            summary['amplified_from'] = ''
        lanes_run = count_lanes(lib.lane_set)
        # suppress zeros

-       for row in xrange(len(lanes_run)):
-           for col in xrange(len(lanes_run[row])):
+       for row in range(len(lanes_run)):
+           for col in range(len(lanes_run[row])):

                if lanes_run[row][col] == 0:
                    lanes_run[row][col] = ''
        summary['lanes_run'] = lanes_run
        summary['is_archived'] = lib.is_archived()
        records.append(summary)
                if lanes_run[row][col] == 0:
                    lanes_run[row][col] = ''
        summary['lanes_run'] = lanes_run
        summary['is_archived'] = lib.is_archived()
        records.append(summary)

-    cl.result_count = unicode(cl.paginator._count)
+    cl.result_count = str(cl.paginator._count)

     return {'library_list': records }
 
 
     return {'library_list': records }
 
 


@@ -379,7 +379,7 @@ def _make_eland_results(flowcell_id, lane_number, interesting_flowcells):
         storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
 
     results = []
         storage_ids = ', '.join([ '<a href="/inventory/%s/">%s</a>' % (s,s) for s in storage_id_list ])
 
     results = []

-    for cycle in cur_fc.keys():
+    for cycle in list(cur_fc.keys()):

         result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
         result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
         results.append({'flowcell_id': fc_id,
         result_path = cur_fc[cycle]['eland_results'].get(lanes[0], None)
         result_link = make_result_link(fc_id, cycle, lanes[0], result_path)
         results.append({'flowcell_id': fc_id,


@@ -459,7 +459,7 @@ def library_dict(library_id):
     """
     try:
         lib = Library.objects.get(id = library_id)
     """
     try:
         lib = Library.objects.get(id = library_id)

-    except Library.DoesNotExist, e:
+    except Library.DoesNotExist as e:

         return None
 
     #lane_info = lane_information(lib.lane_set)
         return None
 
     #lane_info = lane_information(lib.lane_set)

diff --git a/htsworkflow/frontend/static/js/jquery.min.js b/htsworkflow/frontend/static/js/jquery.min.js
new file mode 120000 (symlink)
index 0000000..7fff887
--- /dev/null
+++ b/htsworkflow/frontend/static/js/jquery.min.js
@@ -0,0 +1 @@
+/usr/share/javascript/jquery/jquery.min.js
\ No newline at end of file

diff --git a/htsworkflow/pipelines/__init__.py b/htsworkflow/pipelines/__init__.py
index 8b4b191e65efc072db8b74e2c2786020b27cff7d..9297f3e64d01d3eb074a960ed54c28ff786f011f 100644 (file)
--- a/htsworkflow/pipelines/__init__.py
+++ b/htsworkflow/pipelines/__init__.py
@@ -11,5 +11,5 @@ EUROPEAN_DATE_RE = "([0-9]{1,2}-[0-9]{1,2}-[0-9]{4,4})"
 VERSION_RE = "([0-9\.]+)"
 USER_RE = "([a-zA-Z0-9]+)"
 LANES_PER_FLOWCELL = 8
 VERSION_RE = "([0-9\.]+)"
 USER_RE = "([a-zA-Z0-9]+)"
 LANES_PER_FLOWCELL = 8

-LANE_LIST = range(1, LANES_PER_FLOWCELL + 1)
+LANE_LIST = list(range(1, LANES_PER_FLOWCELL + 1))

 
 

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 99f231dd73e748a0c88b528f4489968ab20b8428..b53813028c6e492265ca10cdf399919d04e2fec1 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -23,7 +23,7 @@ LOGGER = logging.getLogger(__name__)
 # make epydoc happy
 __docformat__ = "restructuredtext en"
 
 # make epydoc happy
 __docformat__ = "restructuredtext en"
 

-LANE_LIST = range(1,9)
+LANE_LIST = list(range(1,9))

 
 class Phasing(object):
     PHASING = 'Phasing'
 
 class Phasing(object):
     PHASING = 'Phasing'


@@ -111,7 +111,7 @@ class CrosstalkMatrix(object):
         for b in base_order:
             for value in self.base[b]:
                 crosstalk_value = ElementTree.SubElement(root, CrosstalkMatrix.ELEMENT)
         for b in base_order:
             for value in self.base[b]:
                 crosstalk_value = ElementTree.SubElement(root, CrosstalkMatrix.ELEMENT)

-                crosstalk_value.text = unicode(value)
+                crosstalk_value.text = str(value)

                 crosstalk_value.tail = os.linesep
 
         return root
                 crosstalk_value.tail = os.linesep
 
         return root


@@ -307,7 +307,7 @@ class Bustard(object):
 
         # add phasing parameters
         for lane in LANE_LIST:
 
         # add phasing parameters
         for lane in LANE_LIST:

-            if self.phasing.has_key(lane):
+            if lane in self.phasing:

                 params.append(self.phasing[lane].get_elements())
 
         # add crosstalk matrix if it exists
                 params.append(self.phasing[lane].get_elements())
 
         # add crosstalk matrix if it exists


@@ -456,7 +456,7 @@ def main(cmdline):
     opts, args = parser.parse_args(cmdline)
 
     for bustard_dir in args:
     opts, args = parser.parse_args(cmdline)
 
     for bustard_dir in args:

-        print u'analyzing bustard directory: ' + unicode(bustard_dir)
+        print('analyzing bustard directory: ' + str(bustard_dir))

         bustard_object = bustard(bustard_dir)
         bustard_object.dump()
 
         bustard_object = bustard(bustard_dir)
         bustard_object.dump()
 


@@ -470,8 +470,8 @@ def main(cmdline):
         b2 = ElementTree.tostring(b2_tree).split(os.linesep)
         for line1, line2 in zip(b1, b2):
             if b1 != b2:
         b2 = ElementTree.tostring(b2_tree).split(os.linesep)
         for line1, line2 in zip(b1, b2):
             if b1 != b2:

-                print "b1: ", b1
-                print "b2: ", b2
+                print("b1: ", b1)
+                print("b2: ", b2)

 
 if __name__ == "__main__":
     main(sys.argv[1:])
 
 if __name__ == "__main__":
     main(sys.argv[1:])

diff --git a/htsworkflow/pipelines/configure_run.py b/htsworkflow/pipelines/configure_run.py
index 83c7569d2816b03e3a67a3fb4f376589ae472a5f..02d0adfc1619035a007849b0e7e4e24b81254e67 100644 (file)
--- a/htsworkflow/pipelines/configure_run.py
+++ b/htsworkflow/pipelines/configure_run.py
@@ -243,7 +243,7 @@ def config_stdout_handler(line, conf_info):
 
     #Standard output handling
     else:
 
     #Standard output handling
     else:

-      print 'Sequence line:', line
+      print('Sequence line:', line)

       mo = s_seq_folder.search(line)
       conf_info.bustard_path = line[mo.end():]
       conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
       mo = s_seq_folder.search(line)
       conf_info.bustard_path = line[mo.end():]
       conf_info.run_path, temp = os.path.split(conf_info.bustard_path)


@@ -377,16 +377,16 @@ def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
   try:
     saveConfigFile(flowcell, options.url, cfg_filepath)
     conf_info.config_filepath = cfg_filepath
   try:
     saveConfigFile(flowcell, options.url, cfg_filepath)
     conf_info.config_filepath = cfg_filepath

-  except FlowCellNotFound, e:
+  except FlowCellNotFound as e:

     LOGGER.error(e)
     return False
     LOGGER.error(e)
     return False

-  except WebError404, e:
+  except WebError404 as e:

     LOGGER.error(e)
     return False
     LOGGER.error(e)
     return False

-  except IOError, e:
+  except IOError as e:

     LOGGER.error(e)
     return False
     LOGGER.error(e)
     return False

-  except Exception, e:
+  except Exception as e:

     LOGGER.error(e)
     return False
 
     LOGGER.error(e)
     return False
 


@@ -458,7 +458,7 @@ def configure(conf_info):
                            stdout=fout,
                            stderr=ferr)
 
                            stdout=fout,
                            stderr=ferr)
 

-  print "Configuring pipeline: %s" % (time.ctime())
+  print("Configuring pipeline: %s" % (time.ctime()))

   error_code = pipe.wait()
 
   # Clean up
   error_code = pipe.wait()
 
   # Clean up


@@ -509,8 +509,8 @@ def configure(conf_info):
   # 1) The stdout completed without error
   # 2) The program exited with status 0
   # 3) No errors found in stdout
   # 1) The stdout completed without error
   # 2) The program exited with status 0
   # 3) No errors found in stdout

-  print '#Expect: True, False, True, True'
-  print complete, bool(error_code), abort != RUN_ABORT, stderr_success is True
+  print('#Expect: True, False, True, True')
+  print(complete, bool(error_code), abort != RUN_ABORT, stderr_success is True)

   status = complete is True and \
            bool(error_code) is False and \
            abort != RUN_ABORT and \
   status = complete is True and \
            bool(error_code) is False and \
            abort != RUN_ABORT and \


@@ -592,9 +592,9 @@ def run_pipeline(conf_info):
   ferr.close()
 
   # Finished file check!
   ferr.close()
 
   # Finished file check!

-  print 'RUN SUCCESS CHECK:'
-  for key, value in event.run_status_dict.items():
-    print '  %s: %s' % (key, value)
+  print('RUN SUCCESS CHECK:')
+  for key, value in list(event.run_status_dict.items()):
+    print('  %s: %s' % (key, value))

 
   dstatus = event.run_status_dict
 
 
   dstatus = event.run_status_dict
 

diff --git a/htsworkflow/pipelines/desplit_fastq.py b/htsworkflow/pipelines/desplit_fastq.py
index 2ad853c1fe2053f91ffaf19268264b159798e520..c2507b97bb359ed84f9e079df37dc34b2ffd9e66 100644 (file)
--- a/htsworkflow/pipelines/desplit_fastq.py
+++ b/htsworkflow/pipelines/desplit_fastq.py
@@ -25,7 +25,7 @@ def main(cmdline=None):
     opts, args = parser.parse_args(cmdline)
 
     if opts.version:
     opts, args = parser.parse_args(cmdline)
 
     if opts.version:

-        print (version())
+        print((version()))

         return 0
 
     if opts.output is not None:
         return 0
 
     if opts.output is not None:

diff --git a/htsworkflow/pipelines/eland.py b/htsworkflow/pipelines/eland.py
index a508a494c8c24900e8574c75f43c3616bf309814..feb7ff7c066ea070b836f47ce4d03536b8416095 100644 (file)
--- a/htsworkflow/pipelines/eland.py
+++ b/htsworkflow/pipelines/eland.py
@@ -376,7 +376,7 @@ class ElandLane(ResultLane):
     def get_elements(self):
         lane = ElementTree.Element(ElandLane.LANE,
                                    {'version':
     def get_elements(self):
         lane = ElementTree.Element(ElandLane.LANE,
                                    {'version':

-                                    unicode(ElandLane.XML_VERSION)})
+                                    str(ElandLane.XML_VERSION)})

         sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
         sample_tag.text = self.sample_name
         lane_tag = ElementTree.SubElement(lane, LANE_ID)
         sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
         sample_tag.text = self.sample_name
         lane_tag = ElementTree.SubElement(lane, LANE_ID)


@@ -385,22 +385,22 @@ class ElandLane(ResultLane):
             end_tag = ElementTree.SubElement(lane, END)
             end_tag.text = str(self.end)
         genome_map = ElementTree.SubElement(lane, GENOME_MAP)
             end_tag = ElementTree.SubElement(lane, END)
             end_tag.text = str(self.end)
         genome_map = ElementTree.SubElement(lane, GENOME_MAP)

-        for k, v in self.genome_map.items():
+        for k, v in list(self.genome_map.items()):

             item = ElementTree.SubElement(
                 genome_map, GENOME_ITEM,
             item = ElementTree.SubElement(
                 genome_map, GENOME_ITEM,

-                {'name':k, 'value':unicode(v)})
+                {'name':k, 'value':str(v)})

         mapped_reads = ElementTree.SubElement(lane, MAPPED_READS)
         mapped_reads = ElementTree.SubElement(lane, MAPPED_READS)

-        for k, v in self.mapped_reads.items():
+        for k, v in list(self.mapped_reads.items()):

             item = ElementTree.SubElement(
                 mapped_reads, MAPPED_ITEM,
             item = ElementTree.SubElement(
                 mapped_reads, MAPPED_ITEM,

-                {'name':k, 'value':unicode(v)})
+                {'name':k, 'value':str(v)})

         match_codes = ElementTree.SubElement(lane, MATCH_CODES)
         match_codes = ElementTree.SubElement(lane, MATCH_CODES)

-        for k, v in self.match_codes.items():
+        for k, v in list(self.match_codes.items()):

             item = ElementTree.SubElement(
                 match_codes, MATCH_ITEM,
             item = ElementTree.SubElement(
                 match_codes, MATCH_ITEM,

-                {'name':k, 'value':unicode(v)})
+                {'name':k, 'value':str(v)})

         reads = ElementTree.SubElement(lane, READS)
         reads = ElementTree.SubElement(lane, READS)

-        reads.text = unicode(self.reads)
+        reads.text = str(self.reads)

 
         return lane
 
 
         return lane
 


@@ -457,7 +457,7 @@ class MatchCodes(collections.MutableMapping):
             for key in initializer:
                 if key not in self.match_codes:
                     errmsg = "Initializer can only contain: %s"
             for key in initializer:
                 if key not in self.match_codes:
                     errmsg = "Initializer can only contain: %s"

-                    raise ValueError(errmsg % (",".join(self.match_codes.keys())))
+                    raise ValueError(errmsg % (",".join(list(self.match_codes.keys()))))

                 self.match_codes[key] += initializer[key]
 
     def __iter__(self):
                 self.match_codes[key] += initializer[key]
 
     def __iter__(self):


@@ -472,7 +472,7 @@ class MatchCodes(collections.MutableMapping):
     def __setitem__(self, key, value):
         if key not in self.match_codes:
             errmsg = "Unrecognized key, allowed values are: %s"
     def __setitem__(self, key, value):
         if key not in self.match_codes:
             errmsg = "Unrecognized key, allowed values are: %s"

-            raise ValueError(errmsg % (",".join(self.match_codes.keys())))
+            raise ValueError(errmsg % (",".join(list(self.match_codes.keys()))))

         self.match_codes[key] = value
 
     def __len__(self):
         self.match_codes[key] = value
 
     def __len__(self):


@@ -483,7 +483,7 @@ class MatchCodes(collections.MutableMapping):
             raise ValueError("Expected a MatchCodes, got %s", str(type(other)))
 
         newobj = MatchCodes(self)
             raise ValueError("Expected a MatchCodes, got %s", str(type(other)))
 
         newobj = MatchCodes(self)

-        for key, value in other.items():
+        for key, value in list(other.items()):

             newobj[key] = self.get(key, 0) + other[key]
 
         return newobj
             newobj[key] = self.get(key, 0) + other[key]
 
         return newobj


@@ -574,7 +574,7 @@ class SequenceLane(ResultLane):
         LOGGER.info("summarizing results for %s" % (pathname))
         lines = 0
         f = open(pathname)
         LOGGER.info("summarizing results for %s" % (pathname))
         lines = 0
         f = open(pathname)

-        for l in f.xreadlines():
+        for l in f:

             lines += 1
         f.close()
 
             lines += 1
         f.close()
 


@@ -589,7 +589,7 @@ class SequenceLane(ResultLane):
     def get_elements(self):
         lane = ElementTree.Element(SequenceLane.LANE,
                                    {'version':
     def get_elements(self):
         lane = ElementTree.Element(SequenceLane.LANE,
                                    {'version':

-                                    unicode(SequenceLane.XML_VERSION)})
+                                    str(SequenceLane.XML_VERSION)})

         sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
         sample_tag.text = self.sample_name
         lane_tag = ElementTree.SubElement(lane, LANE_ID)
         sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
         sample_tag.text = self.sample_name
         lane_tag = ElementTree.SubElement(lane, LANE_ID)


@@ -598,16 +598,16 @@ class SequenceLane(ResultLane):
             end_tag = ElementTree.SubElement(lane, END)
             end_tag.text = str(self.end)
         reads = ElementTree.SubElement(lane, READS)
             end_tag = ElementTree.SubElement(lane, END)
             end_tag.text = str(self.end)
         reads = ElementTree.SubElement(lane, READS)

-        reads.text = unicode(self.reads)
+        reads.text = str(self.reads)

         sequence_type = ElementTree.SubElement(lane, SequenceLane.SEQUENCE_TYPE)
         sequence_type = ElementTree.SubElement(lane, SequenceLane.SEQUENCE_TYPE)

-        sequence_type.text = unicode(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type])
+        sequence_type.text = str(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type])

 
         return lane
 
     def set_elements(self, tree):
         if tree.tag != SequenceLane.LANE:
             raise ValueError('Exptecting %s' % (SequenceLane.LANE,))
 
         return lane
 
     def set_elements(self, tree):
         if tree.tag != SequenceLane.LANE:
             raise ValueError('Exptecting %s' % (SequenceLane.LANE,))

-        lookup_sequence_type = dict([ (v,k) for k,v in SequenceLane.SEQUENCE_DESCRIPTION.items()])
+        lookup_sequence_type = dict([ (v,k) for k,v in list(SequenceLane.SEQUENCE_DESCRIPTION.items())])

 
         for element in tree:
             tag = element.tag.lower()
 
         for element in tree:
             tag = element.tag.lower()


@@ -657,7 +657,7 @@ class ELAND(collections.MutableMapping):
         del self.result[key]
 
     def __iter__(self):
         del self.result[key]
 
     def __iter__(self):

-        keys = self.results.iterkeys()
+        keys = iter(self.results.keys())

         for k in sorted(keys):
             yield k
 
         for k in sorted(keys):
             yield k
 


@@ -670,18 +670,18 @@ class ELAND(collections.MutableMapping):
             raise ValueError("Key must be a %s" % (str(type(SampleKey))))
         if not search.iswild:
             yield self[search]
             raise ValueError("Key must be a %s" % (str(type(SampleKey))))
         if not search.iswild:
             yield self[search]

-        for key in self.keys():
+        for key in list(self.keys()):

             if key.matches(search): yield key
 
     def get_elements(self):
         root = ElementTree.Element(ELAND.ELAND,
             if key.matches(search): yield key
 
     def get_elements(self):
         root = ElementTree.Element(ELAND.ELAND,

-                                   {'version': unicode(ELAND.XML_VERSION)})
+                                   {'version': str(ELAND.XML_VERSION)})

 
         for key in self:
             eland_lane = self[key].get_elements()
 
         for key in self:
             eland_lane = self[key].get_elements()

-            eland_lane.attrib[ELAND.END] = unicode(self[key].end-1)
-            eland_lane.attrib[ELAND.LANE_ID] = unicode(self[key].lane_id)
-            eland_lane.attrib[ELAND.SAMPLE] = unicode(self[key].sample_name)
+            eland_lane.attrib[ELAND.END] = str(self[key].end-1)
+            eland_lane.attrib[ELAND.LANE_ID] = str(self[key].lane_id)
+            eland_lane.attrib[ELAND.SAMPLE] = str(self[key].sample_name)

             root.append(eland_lane)
         return root
         return root
             root.append(eland_lane)
         return root
         return root


@@ -895,7 +895,7 @@ def main(cmdline=None):
     for a in args:
         LOGGER.info("Starting scan of %s" % (a,))
         e = eland(a)
     for a in args:
         LOGGER.info("Starting scan of %s" % (a,))
         e = eland(a)

-        print ElementTree.tostring(e.get_elements())
+        print(ElementTree.tostring(e.get_elements()))

     return
 
 
     return
 
 

diff --git a/htsworkflow/pipelines/firecrest.py b/htsworkflow/pipelines/firecrest.py
index 3519eb0123600ef99602cccb25210d119a62a073..d8fa8721a6aad2237e1578f019ae41fafcba7a08 100644 (file)
--- a/htsworkflow/pipelines/firecrest.py
+++ b/htsworkflow/pipelines/firecrest.py
@@ -66,11 +66,11 @@ class Firecrest(object):
     def dump(self):
         """Report debugginf information
         """
     def dump(self):
         """Report debugginf information
         """

-        print "Starting cycle:", self.start
-        print "Ending cycle:", self.stop
-        print "Firecrest version:", self.version
-        print "Run date:", self.date
-        print "user:", self.user
+        print("Starting cycle:", self.start)
+        print("Ending cycle:", self.stop)
+        print("Firecrest version:", self.version)
+        print("Run date:", self.date)
+        print("user:", self.user)

 
     def get_elements(self):
         """Return XML serialization structure.
 
     def get_elements(self):
         """Return XML serialization structure.

diff --git a/htsworkflow/pipelines/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py
index fb16d7ffc60ed70ce11c10b4a204316de9e3f37e..9162fdf26edda84fc0f520fb14d3bfa7f2c6f65f 100644 (file)
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -30,7 +30,7 @@ def getAvailableGenomes(genome_base_dir):
   # Need valid directory
   if not os.path.exists(genome_base_dir):
     msg = "Directory does not exist: %s" % (genome_base_dir)
   # Need valid directory
   if not os.path.exists(genome_base_dir):
     msg = "Directory does not exist: %s" % (genome_base_dir)

-    raise IOError, msg
+    raise IOError(msg)

 
   # Find all subdirectories
   filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))
 
   # Find all subdirectories
   filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))


@@ -60,7 +60,7 @@ def getAvailableGenomes(genome_base_dir):
     build_dict = d.setdefault(species, {})
     if build in build_dict:
       msg = "Duplicate genome for %s|%s" % (species, build)
     build_dict = d.setdefault(species, {})
     if build in build_dict:
       msg = "Duplicate genome for %s|%s" % (species, build)

-      raise DuplicateGenome, msg
+      raise DuplicateGenome(msg)

 
     build_dict[build] = genome_dir
 
 
     build_dict[build] = genome_dir
 


@@ -88,7 +88,7 @@ class constructMapperDict(object):
           builds = self.genome_dict[elements[0]]
 
           # sort build names the way humans would
           builds = self.genome_dict[elements[0]]
 
           # sort build names the way humans would

-          keys = builds.keys()
+          keys = list(builds.keys())

           keys.sort(cmp=alphanum)
 
           # return the path from the 'last' build name
           keys.sort(cmp=alphanum)
 
           # return the path from the 'last' build name


@@ -103,26 +103,26 @@ class constructMapperDict(object):
     def get(self, key, default=None):
       try:
         return self[key]
     def get(self, key, default=None):
       try:
         return self[key]

-      except KeyError, e:
+      except KeyError as e:

         return default
 
     def keys(self):
         keys = []
         return default
 
     def keys(self):
         keys = []

-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):

             for build in self.genome_dict[species]:
                 keys.append([species+'|'+build])
         return keys
 
     def values(self):
         values = []
             for build in self.genome_dict[species]:
                 keys.append([species+'|'+build])
         return keys
 
     def values(self):
         values = []

-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):

             for build in self.genome_dict[species]:
                 values.append(self.genome_dict[species][build])
         return values
 
     def items(self):
         items = []
             for build in self.genome_dict[species]:
                 values.append(self.genome_dict[species][build])
         return values
 
     def items(self):
         items = []

-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):

             for build in self.genome_dict[species]:
                 key = [species+'|'+build]
                 value = self.genome_dict[species][build]
             for build in self.genome_dict[species]:
                 key = [species+'|'+build]
                 value = self.genome_dict[species][build]


@@ -132,13 +132,13 @@ class constructMapperDict(object):
 if __name__ == '__main__':
 
   if len(sys.argv) != 2:
 if __name__ == '__main__':
 
   if len(sys.argv) != 2:

-    print 'useage: %s <base_genome_dir>' % (sys.argv[0])
+    print('useage: %s <base_genome_dir>' % (sys.argv[0]))

     sys.exit(1)
 
   d = getAvailableGenomes(sys.argv[1])
   d2 = constructMapperDict(d)
 
     sys.exit(1)
 
   d = getAvailableGenomes(sys.argv[1])
   d2 = constructMapperDict(d)
 

-  for k,v in d2.items():
-    print '%s: %s' % (k,v)
+  for k,v in list(d2.items()):
+    print('%s: %s' % (k,v))

 
 
 
 

diff --git a/htsworkflow/pipelines/genomemap.py b/htsworkflow/pipelines/genomemap.py
index 1dd95df86578bd83b75468779f1d08e1c4f3988e..87d65eba01ff3ba51e906398b26cc385a5985c81 100644 (file)
--- a/htsworkflow/pipelines/genomemap.py
+++ b/htsworkflow/pipelines/genomemap.py
@@ -17,7 +17,7 @@ class GenomeMap(collections.MutableMapping):
         return len(self._contigs)
 
     def __iter__(self):
         return len(self._contigs)
 
     def __iter__(self):

-        return self._contigs.iterkeys()
+        return iter(self._contigs.keys())

 
     def __getitem__(self, name):
         return self._contigs[name]
 
     def __getitem__(self, name):
         return self._contigs[name]


@@ -68,7 +68,7 @@ class GenomeMap(collections.MutableMapping):
 
         genome = guess_genome(sizes)
 
 
         genome = guess_genome(sizes)
 

-        for contig, basese in sizes.items():
+        for contig, basese in list(sizes.items()):

             name = filenames[contig]
             self._contigs[name] = genome + '/' + name
 
             name = filenames[contig]
             self._contigs[name] = genome + '/' + name
 


@@ -93,6 +93,6 @@ def guess_genome(contig_sizes):
             return genomes[key][size]
 
     if len(contig_sizes) == 1:
             return genomes[key][size]
 
     if len(contig_sizes) == 1:

-        return os.path.splitext(contig_sizes.keys()[0])[0]
+        return os.path.splitext(list(contig_sizes.keys())[0])[0]

 
     raise RuntimeError("Unrecognized genome type, update detection code.")
 
     raise RuntimeError("Unrecognized genome type, update detection code.")

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 2eaff677e6d90c75848a24a43f4b28fad8d2beff..2d5d3d51a05e7fddc222b54d1dd2e3384e7af984 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -59,10 +59,10 @@ class Alignment(object):
         """
         Debugging function, report current object
         """
         """
         Debugging function, report current object
         """

-        print 'Software:'. self.__class__.__name__
-        print 'Alignment version:', self.version
-        print 'Run date:', self.date
-        print 'config.xml:', self.tree
+        print('Software:'. self.__class__.__name__)
+        print('Alignment version:', self.version)
+        print('Run date:', self.date)
+        print('config.xml:', self.tree)

         self.summary.dump()
 
     def get_elements(self, root_tag):
         self.summary.dump()
 
     def get_elements(self, root_tag):


@@ -70,7 +70,7 @@ class Alignment(object):
             return None
 
         gerald = ElementTree.Element(root_tag,
             return None
 
         gerald = ElementTree.Element(root_tag,

-                                     {'version': unicode(Gerald.XML_VERSION)})
+                                     {'version': str(Gerald.XML_VERSION)})

         gerald.append(self.tree)
         gerald.append(self.summary.get_elements())
         if self.eland_results:
         gerald.append(self.tree)
         gerald.append(self.summary.get_elements())
         if self.eland_results:


@@ -283,7 +283,7 @@ class LaneParametersGA(LaneParameters):
         lanes = [x.tag.split('_')[1] for x in container.getchildren()]
         try:
             index = lanes.index(self._lane_id)
         lanes = [x.tag.split('_')[1] for x in container.getchildren()]
         try:
             index = lanes.index(self._lane_id)

-        except ValueError, e:
+        except ValueError as e:

             return None
         element = container[index]
         return element.text
             return None
         element = container[index]
         return element.text


@@ -397,7 +397,7 @@ class LaneSpecificRunParameters(collections.MutableMapping):
     def __iter__(self):
         if self._lanes is None:
             self._initialize_lanes()
     def __iter__(self):
         if self._lanes is None:
             self._initialize_lanes()

-        return self._lanes.iterkeys()
+        return iter(self._lanes.keys())

 
     def __getitem__(self, key):
         if self._lanes is None:
 
     def __getitem__(self, key):
         if self._lanes is None:


@@ -410,7 +410,7 @@ class LaneSpecificRunParameters(collections.MutableMapping):
             return self._lanes[real_key]
         raise KeyError("%s not found in %s" % (
             repr(key),
             return self._lanes[real_key]
         raise KeyError("%s not found in %s" % (
             repr(key),

-            ",".join((repr(k) for k in self._lanes.keys()))))
+            ",".join((repr(k) for k in list(self._lanes.keys())))))

 
     def __setitem__(self, key, value):
         if len(self._lanes) > 100:
 
     def __setitem__(self, key, value):
         if len(self._lanes) > 100:

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index f818b3495fbf2fd2d8f2fba13d698188e7680d3f..576bff85aedba54c2cd01b0e0c12d2c18aff5b06 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -52,11 +52,11 @@ class Tiles(object):
     return value_list
 
   def items(self):
     return value_list
 
   def items(self):

-    return zip(self.keys(), self.values())
+    return list(zip(list(self.keys()), list(self.values())))

 
   def __getitem__(self, key):
     # FIXME: this is inefficient. building the dictionary be rescanning the xml.
 
   def __getitem__(self, key):
     # FIXME: this is inefficient. building the dictionary be rescanning the xml.

-    v = dict(self.items())
+    v = dict(list(self.items()))

     return v[key]
 
 class IPAR(object):
     return v[key]
 
 class IPAR(object):


@@ -146,12 +146,12 @@ class IPAR(object):
         """
         suffix_node = self.tree.find('RunParameters/CompressionSuffix')
         if suffix_node is None:
         """
         suffix_node = self.tree.find('RunParameters/CompressionSuffix')
         if suffix_node is None:

-          print "find compression suffix failed"
+          print("find compression suffix failed")

           return None
         suffix = suffix_node.text
         files = []
         format = "%s_%s_%04d_%s.txt%s"
           return None
         suffix = suffix_node.text
         files = []
         format = "%s_%s_%04d_%s.txt%s"

-        for lane, attrib in self.tiles.items():
+        for lane, attrib in list(self.tiles.items()):

           for file_type in ["int","nse"]:
             start, stop = attrib['TileRange']
             for tile in range(start, stop+1):
           for file_type in ["int","nse"]:
             start, stop = attrib['TileRange']
             for tile in range(start, stop+1):


@@ -159,8 +159,8 @@ class IPAR(object):
         return files
 
     def dump(self):
         return files
 
     def dump(self):

-        print "Matrix:", self.matrix
-        print "Tree:", self.tree
+        print("Matrix:", self.matrix)
+        print("Tree:", self.tree)

 
     def get_elements(self):
         attribs = {'version': str(IPAR.XML_VERSION) }
 
     def get_elements(self):
         attribs = {'version': str(IPAR.XML_VERSION) }


@@ -195,7 +195,7 @@ def load_ipar_param_tree(paramfile):
 
     tree = ElementTree.parse(paramfile).getroot()
     run = tree.find('Run')
 
     tree = ElementTree.parse(paramfile).getroot()
     run = tree.find('Run')

-    if run.attrib.has_key('Name') and run.attrib['Name'] in SOFTWARE_NAMES:
+    if 'Name' in run.attrib and run.attrib['Name'] in SOFTWARE_NAMES:

         return run
     else:
         LOGGER.info("No run found")
         return run
     else:
         LOGGER.info("No run found")

diff --git a/htsworkflow/pipelines/qseq2fastq.py b/htsworkflow/pipelines/qseq2fastq.py
index c33d0143228568b36d216986bf0aad47f60d57b9..15f1536bbf13844b64b1affc0a763040becf2c97 100644 (file)
--- a/htsworkflow/pipelines/qseq2fastq.py
+++ b/htsworkflow/pipelines/qseq2fastq.py
@@ -19,7 +19,7 @@ def main(cmdline=None):
     opts, args = parser.parse_args(cmdline)
 
     if opts.version:
     opts, args = parser.parse_args(cmdline)
 
     if opts.version:

-        print version()
+        print(version())

         return 0
 
     if opts.infile is not None:
         return 0
 
     if opts.infile is not None:

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index a189f097e3017b8c8aac8b26b3d96ccbb0ec4460..43c0af6a625cb87d78931ea2916a4acb38f2c0a8 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -1,18 +1,19 @@
 #!/usr/bin/env python
 
 import csv
 #!/usr/bin/env python
 
 import csv

-from ConfigParser import RawConfigParser
+from configparser import RawConfigParser

 import logging
 from optparse import OptionParser, IndentedHelpFormatter
 import os
 import sys
 import types
 import logging
 from optparse import OptionParser, IndentedHelpFormatter
 import os
 import sys
 import types

-import urllib
-import urllib2
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import collections

 
 try:
     import json
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 from htsworkflow.frontend.auth import apidata
     import simplejson as json
 
 from htsworkflow.frontend.auth import apidata


@@ -47,9 +48,9 @@ def retrieve_flowcell_info(base_host_url, flowcell):
     url = api.flowcell_url(base_host_url, flowcell)
 
     try:
     url = api.flowcell_url(base_host_url, flowcell)
 
     try:

-        apipayload = urllib.urlencode(apidata)
-        web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
+        apipayload = urllib.parse.urlencode(apidata)
+        web = urllib.request.urlopen(url, apipayload)
+    except urllib.error.URLError as e:

         errmsg = 'URLError: %d %s' % (e.code, e.msg)
         LOGGER.error(errmsg)
         LOGGER.error('opened %s' % (url,))
         errmsg = 'URLError: %d %s' % (e.code, e.msg)
         LOGGER.error(errmsg)
         LOGGER.error('opened %s' % (url,))


@@ -90,7 +91,7 @@ def group_lane_parameters(flowcell_info):
     (The same species, read length, and eland vs sequencing)
     """
     lane_groups = {}
     (The same species, read length, and eland vs sequencing)
     """
     lane_groups = {}

-    for lane_number, lane_contents in flowcell_info['lane_set'].items():
+    for lane_number, lane_contents in list(flowcell_info['lane_set'].items()):

         for lane_info in lane_contents:
             index = (lane_info['read_length'],
                      lane_info['library_species'],
         for lane_info in lane_contents:
             index = (lane_info['read_length'],
                      lane_info['library_species'],


@@ -139,11 +140,11 @@ def format_gerald_config(options, flowcell_info, genome_map):
     analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
     sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
     lane_groups = group_lane_parameters(flowcell_info)
     analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
     sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
     lane_groups = group_lane_parameters(flowcell_info)

-    for lane_index, lane_numbers in lane_groups.items():
+    for lane_index, lane_numbers in list(lane_groups.items()):

         # lane_index is return value of group_lane_parameters
         read_length, species, is_sequencing = lane_index
         lane_numbers.sort()
         # lane_index is return value of group_lane_parameters
         read_length, species, is_sequencing = lane_index
         lane_numbers.sort()

-        lane_prefix = u"".join(lane_numbers)
+        lane_prefix = "".join(lane_numbers)

 
         species_path = genome_map.get(species, None)
         LOGGER.debug("Looked for genome '%s' got location '%s'" % (species, species_path))
 
         species_path = genome_map.get(species, None)
         LOGGER.debug("Looked for genome '%s' got location '%s'" % (species, species_path))


@@ -310,18 +311,18 @@ def saveConfigFile(options):
   (i.e. http://sub.domain.edu:port)
   """
   LOGGER.info('USING OPTIONS:')
   (i.e. http://sub.domain.edu:port)
   """
   LOGGER.info('USING OPTIONS:')

-  LOGGER.info(u'     URL: %s' % (options.url,))
-  LOGGER.info(u'     OUT: %s' % (options.output_filepath,))
-  LOGGER.info(u'      FC: %s' % (options.flowcell,))
+  LOGGER.info('     URL: %s' % (options.url,))
+  LOGGER.info('     OUT: %s' % (options.output_filepath,))
+  LOGGER.info('      FC: %s' % (options.flowcell,))

   #LOGGER.info(': %s' % (options.genome_dir,))
   #LOGGER.info(': %s' % (options.genome_dir,))

-  LOGGER.info(u'post_run: %s' % ( unicode(options.post_run),))
+  LOGGER.info('post_run: %s' % ( str(options.post_run),))

 
   flowcell_info = retrieve_flowcell_info(options.url, options.flowcell)
 
   LOGGER.debug('genome_dir: %s' % ( options.genome_dir, ))
   available_genomes = getAvailableGenomes(options.genome_dir)
   genome_map = constructMapperDict(available_genomes)
 
   flowcell_info = retrieve_flowcell_info(options.url, options.flowcell)
 
   LOGGER.debug('genome_dir: %s' % ( options.genome_dir, ))
   available_genomes = getAvailableGenomes(options.genome_dir)
   genome_map = constructMapperDict(available_genomes)

-  LOGGER.debug('available genomes: %s' % ( unicode( genome_map.keys() ),))
+  LOGGER.debug('available genomes: %s' % ( str( list(genome_map.keys()) ),))

 
   config = format_gerald_config(options, flowcell_info, genome_map)
 
 
   config = format_gerald_config(options, flowcell_info, genome_map)
 


@@ -367,7 +368,7 @@ def save_sample_sheet(outstream, options, flowcell_info):
                 htsw_field = illumina_to_htsw_map.get(illumina_name, None)
                 if htsw_field is None:
                     continue
                 htsw_field = illumina_to_htsw_map.get(illumina_name, None)
                 if htsw_field is None:
                     continue

-                if callable(htsw_field):
+                if isinstance(htsw_field, collections.Callable):

                     renamed[illumina_name] = htsw_field(options,
                                                         flowcell_info,
                                                         library)
                     renamed[illumina_name] = htsw_field(options,
                                                         flowcell_info,
                                                         library)


@@ -403,14 +404,14 @@ def format_pooled_libraries(shared, library):
     sequences = library.get('index_sequence', None)
     if sequences is None:
         return []
     sequences = library.get('index_sequence', None)
     if sequences is None:
         return []

-    elif (type(sequences) in types.StringTypes and
+    elif (type(sequences) in str and

           sequences.lower().startswith('err')):
         shared['Index'] = ''
         shared['SampleProject'] = library['library_id']
         return [shared]
           sequences.lower().startswith('err')):
         shared['Index'] = ''
         shared['SampleProject'] = library['library_id']
         return [shared]

-    elif (type(sequences) == types.DictType):
+    elif (type(sequences) == dict):

         pooled = []
         pooled = []

-        multiplex_ids = sequences.keys()
+        multiplex_ids = list(sequences.keys())

         multiplex_ids.sort(cmp=alphanum.alphanum)
         for multiplex_id in multiplex_ids:
             sample = {}
         multiplex_ids.sort(cmp=alphanum.alphanum)
         for multiplex_id in multiplex_ids:
             sample = {}

diff --git a/htsworkflow/pipelines/run_status.py b/htsworkflow/pipelines/run_status.py
index e6a3ed8e6b2f41793f1109dac1334900860e8eaf..0903e7018f7760aa43fafeb3289c7194ebd0d9d6 100644 (file)
--- a/htsworkflow/pipelines/run_status.py
+++ b/htsworkflow/pipelines/run_status.py
@@ -78,7 +78,7 @@ def _p2f(pattern, lane, tile=None, cycle=None):
   # lane, and cycle provided (INVALID)
   if tile is None and cycle is not None:
     msg = "Handling of cycle without tile is not currently implemented."
   # lane, and cycle provided (INVALID)
   if tile is None and cycle is not None:
     msg = "Handling of cycle without tile is not currently implemented."

-    raise ValueError, msg
+    raise ValueError(msg)

 
   # lane, tile, cycle provided
   elif cycle:
 
   # lane, tile, cycle provided
   elif cycle:


@@ -299,7 +299,7 @@ class GARunStatus(object):
     """
     firecrest = self.status['firecrest']
     total = len(firecrest)
     """
     firecrest = self.status['firecrest']
     total = len(firecrest)

-    completed = firecrest.values().count(True)
+    completed = list(firecrest.values()).count(True)

 
     return (completed, total)
 
 
     return (completed, total)
 


@@ -310,7 +310,7 @@ class GARunStatus(object):
     """
     bustard = self.status['bustard']
     total = len(bustard)
     """
     bustard = self.status['bustard']
     total = len(bustard)

-    completed = bustard.values().count(True)
+    completed = list(bustard.values()).count(True)

 
     return (completed, total)
 
 
     return (completed, total)
 


@@ -321,7 +321,7 @@ class GARunStatus(object):
     """
     gerald = self.status['gerald']
     total = len(gerald)
     """
     gerald = self.status['gerald']
     total = len(gerald)

-    completed = gerald.values().count(True)
+    completed = list(gerald.values()).count(True)

 
     return (completed, total)
 
 
     return (completed, total)
 


@@ -410,13 +410,13 @@ def _cmdLineStatusMonitorFunc(conf_info):
 
   while 1:
     if conf_info.status is None:
 
   while 1:
     if conf_info.status is None:

-      print "No status object yet."
+      print("No status object yet.")

       time.sleep(SLEEP_AMOUNT)
       continue
 
     report = conf_info.status.statusReport()
       time.sleep(SLEEP_AMOUNT)
       continue
 
     report = conf_info.status.statusReport()

-    print os.linesep.join(report)
-    print
+    print(os.linesep.join(report))
+    print()

 
     time.sleep(SLEEP_AMOUNT)
 
 
     time.sleep(SLEEP_AMOUNT)
 


@@ -446,7 +446,7 @@ def main(cmdline=None):
     parser.error("need name of configuration file")
     
   status = GARunStatus(args[0])
     parser.error("need name of configuration file")
     
   status = GARunStatus(args[0])

-  print os.linesep.join(status.statusReport())
+  print(os.linesep.join(status.statusReport()))

   return 0
 
 if __name__ == "__main__":
   return 0
 
 if __name__ == "__main__":

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e217de63d5733e524ae551f06eea40528e11..aea06a692d7d8fe12a4db43c568a44a4d8a59b3e 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -334,7 +334,7 @@ def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathna
             p.bustard = b
             p.gerald = g
             runs.append(p)
             p.bustard = b
             p.gerald = g
             runs.append(p)

-        except IOError, e:
+        except IOError as e:

             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 
             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 


@@ -365,7 +365,7 @@ def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
             if aligned:
                 p.gerald = gerald.gerald(aligned)
             runs.append(p)
             if aligned:
                 p.gerald = gerald.gerald(aligned)
             runs.append(p)

-        except IOError, e:
+        except IOError as e:

             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 
             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 


@@ -484,7 +484,7 @@ def summarize_mapped_reads(genome_map, mapped_reads):
     summarized_reads = {}
     genome_reads = 0
     genome = 'unknown'
     summarized_reads = {}
     genome_reads = 0
     genome = 'unknown'

-    for k, v in mapped_reads.items():
+    for k, v in list(mapped_reads.items()):

         path, k = os.path.split(k)
         if len(path) > 0 and path not in genome_map:
             genome = path
         path, k = os.path.split(k)
         if len(path) > 0 and path not in genome_map:
             genome = path


@@ -526,7 +526,7 @@ def summarize_lane(gerald, lane_id):
         report.append("Mapped Reads")
         mapped_reads = summarize_mapped_reads(eland_result.genome_map,
                                               eland_result.mapped_reads)
         report.append("Mapped Reads")
         mapped_reads = summarize_mapped_reads(eland_result.genome_map,
                                               eland_result.mapped_reads)

-        for name, counts in mapped_reads.items():
+        for name, counts in list(mapped_reads.items()):

             report.append("  %s: %d" % (name, counts))
 
         report.append('')
             report.append("  %s: %d" % (name, counts))
 
         report.append('')

diff --git a/htsworkflow/pipelines/sequences.py b/htsworkflow/pipelines/sequences.py
index 87212dddbb0acda92894cf49fec9937b7f2d9e21..0a3c2fd61e856f04c9872600bc8f4025cc4ba6f4 100644 (file)
--- a/htsworkflow/pipelines/sequences.py
+++ b/htsworkflow/pipelines/sequences.py
@@ -7,7 +7,7 @@ import os
 import types
 import re
 import sys
 import types
 import re
 import sys

-from urlparse import urljoin, urlparse
+from urllib.parse import urljoin, urlparse

 
 import RDF
 from htsworkflow.util.rdfhelp import libraryOntology as libNS
 
 import RDF
 from htsworkflow.util.rdfhelp import libraryOntology as libNS


@@ -84,7 +84,7 @@ class SequenceFile(object):
         return (self.flowcell, self.lane, self.read, self.project, self.split)
 
     def __unicode__(self):
         return (self.flowcell, self.lane, self.read, self.project, self.split)
 
     def __unicode__(self):

-        return unicode(self.path)
+        return str(self.path)

 
     def __eq__(self, other):
         """
 
     def __eq__(self, other):
         """


@@ -109,7 +109,7 @@ class SequenceFile(object):
         return not self == other
 
     def __repr__(self):
         return not self == other
 
     def __repr__(self):

-        return u"<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
+        return "<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)

 
     def make_target_name(self, root):
         """
 
     def make_target_name(self, root):
         """


@@ -206,8 +206,8 @@ class SequenceFile(object):
         def get_one(s, p):
             values = get(s, p)
             if len(values) > 1:
         def get_one(s, p):
             values = get(s, p)
             if len(values) > 1:

-                errmsg = u"To many values for %s %s"
-                raise ValueError(errmsg % (unicode(s), unicode(p)))
+                errmsg = "To many values for %s %s"
+                raise ValueError(errmsg % (str(s), str(p)))

             elif len(values) == 1:
                 return values[0]
             else:
             elif len(values) == 1:
                 return values[0]
             else:


@@ -219,7 +219,7 @@ class SequenceFile(object):
                                          rdfNS['type'],
                                          libNS['IlluminaResult'])
         if not model.contains_statement(result_statement):
                                          rdfNS['type'],
                                          libNS['IlluminaResult'])
         if not model.contains_statement(result_statement):

-            raise KeyError(u"%s not found" % (unicode(seq_id),))
+            raise KeyError("%s not found" % (str(seq_id),))

 
         seq_type_node = model.get_target(seq_id, libNS['file_type'])
         seq_type = stripNamespace(libNS, seq_type_node)
 
         seq_type_node = model.get_target(seq_id, libNS['file_type'])
         seq_type = stripNamespace(libNS, seq_type_node)


@@ -376,7 +376,7 @@ def scan_for_sequences(dirs):
     Scan through a list of directories for sequence like files
     """
     sequences = []
     Scan through a list of directories for sequence like files
     """
     sequences = []

-    if type(dirs) in types.StringTypes:
+    if type(dirs) in str:

         raise ValueError("You probably want a list or set, not a string")
 
     for d in dirs:
         raise ValueError("You probably want a list or set, not a string")
 
     for d in dirs:

diff --git a/htsworkflow/pipelines/srf.py b/htsworkflow/pipelines/srf.py
index 5a6c969bd768aa09fab68e005f9ef5caae7ffcea..94445b600f2232b60bf35d35224934e89b5db389 100644 (file)
--- a/htsworkflow/pipelines/srf.py
+++ b/htsworkflow/pipelines/srf.py
@@ -111,7 +111,7 @@ def create_qseq_patterns(bustard_dir):
       qseq_patterns = []
       # grab a lane from the dictionary
       # I don't think it matters which one.
       qseq_patterns = []
       # grab a lane from the dictionary
       # I don't think it matters which one.

-      k = lanes.keys()[0]
+      k = list(lanes.keys())[0]

       # build the list of patterns
       for read in lanes[k]:
         read = int(read)
       # build the list of patterns
       for read in lanes[k]:
         read = int(read)

diff --git a/htsworkflow/pipelines/srf2fastq.py b/htsworkflow/pipelines/srf2fastq.py
index 0d895d9e4b18c8fbb968da470639df8808424339..4000fa092277d644c83d7ab588eee58f61ae8b8b 100644 (file)
--- a/htsworkflow/pipelines/srf2fastq.py
+++ b/htsworkflow/pipelines/srf2fastq.py
@@ -27,7 +27,7 @@ def main(cmdline=None):
         logging.basicConfig(level=logging.WARN)
 
     if opts.version:
         logging.basicConfig(level=logging.WARN)
 
     if opts.version:

-        print version()
+        print(version())

         return 0
 
     if len(args) != 1:
         return 0
 
     if len(args) != 1:


@@ -241,7 +241,7 @@ def foo():
     target2_name = base + '_r2.fastq'
 
     for target_name in [target1_name, target2_name]:
     target2_name = base + '_r2.fastq'
 
     for target_name in [target1_name, target2_name]:

-        print 'target name', target_name
+        print('target name', target_name)

         if os.path.exists(target_name):
             raise RuntimeError("%s exists" % (target_name,))
 
         if os.path.exists(target_name):
             raise RuntimeError("%s exists" % (target_name,))
 

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 8f47670d99521f37fc8afe75ab8edf292b4c5396..c3c5919977d3f3847a981f0ed826ea6bb9d1f301 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -40,9 +40,9 @@ class Summary(object):
 
     def get_elements(self):
         summary = etree.Element(Summary.SUMMARY,
 
     def get_elements(self):
         summary = etree.Element(Summary.SUMMARY,

-                                      {'version': unicode(Summary.XML_VERSION)})
+                                      {'version': str(Summary.XML_VERSION)})

         for end in self.lane_results:
         for end in self.lane_results:

-            for lane in end.values():
+            for lane in list(end.values()):

                 summary.append(lane.get_elements())
         return summary
 
                 summary.append(lane.get_elements())
         return summary
 


@@ -67,7 +67,7 @@ class Summary(object):
         Debugging function, report current object
         """
         tree = self.get_elements()
         Debugging function, report current object
         """
         tree = self.get_elements()

-        print etree.tostring(tree)
+        print(etree.tostring(tree))

 
 class SummaryGA(Summary):
     def __init__(self, filename=None, xml=None):
 
 class SummaryGA(Summary):
     def __init__(self, filename=None, xml=None):


@@ -130,7 +130,7 @@ class SummaryGA(Summary):
                             ('Lane Results Summary : Read 1', 0),
                             ('Lane Results Summary : Read 2', 1),]
             for name, end in table_names:
                             ('Lane Results Summary : Read 1', 0),
                             ('Lane Results Summary : Read 2', 1),]
             for name, end in table_names:

-                if tables.has_key(name):
+                if name in tables:

                     self._extract_lane_results_for_end(tables, name, end)
 
         if len(self.lane_results[0])  == 0:
                     self._extract_lane_results_for_end(tables, name, end)
 
         if len(self.lane_results[0])  == 0:


@@ -280,13 +280,13 @@ class LaneResultSummary(object):
     def get_elements(self):
         lane_result = etree.Element(
                         LaneResultSummary.LANE_RESULT_SUMMARY,
     def get_elements(self):
         lane_result = etree.Element(
                         LaneResultSummary.LANE_RESULT_SUMMARY,

-                        {'lane': unicode(self.lane), 'end': unicode(self.end)})
-        for tag, variable_name in LaneResultSummary.TAGS.items():
+                        {'lane': str(self.lane), 'end': str(self.end)})
+        for tag, variable_name in list(LaneResultSummary.TAGS.items()):

             value = getattr(self, variable_name)
             if value is None:
                 continue
             # it looks like a sequence
             value = getattr(self, variable_name)
             if value is None:
                 continue
             # it looks like a sequence

-            elif type(value) in (types.TupleType, types.ListType):
+            elif type(value) in (tuple, list):

                 element = make_mean_range_element(
                   lane_result,
                   tag,
                 element = make_mean_range_element(
                   lane_result,
                   tag,


@@ -294,7 +294,7 @@ class LaneResultSummary(object):
                 )
             else:
                 element = etree.SubElement(lane_result, tag)
                 )
             else:
                 element = etree.SubElement(lane_result, tag)

-                element.text = unicode(value)
+                element.text = str(value)

         return lane_result
 
     def set_elements(self, tree):
         return lane_result
 
     def set_elements(self, tree):


@@ -311,7 +311,7 @@ class LaneResultSummary(object):
                 variable_name = tags[element.tag]
                 setattr(self, variable_name,
                         parse_summary_element(element))
                 variable_name = tags[element.tag]
                 setattr(self, variable_name,
                         parse_summary_element(element))

-            except KeyError, e:
+            except KeyError as e:

                 LOGGER.warn('Unrecognized tag %s' % (element.tag,))
 
 
                 LOGGER.warn('Unrecognized tag %s' % (element.tag,))
 
 


@@ -333,7 +333,7 @@ class LaneResultSummaryGA(LaneResultSummary):
         else:
             self.lane_yield = None
 
         else:
             self.lane_yield = None
 

-        for GeraldName, LRSName in LaneResultSummary.GERALD_TAGS.items():
+        for GeraldName, LRSName in list(LaneResultSummary.GERALD_TAGS.items()):

             node = element.find(GeraldName)
             if node is None:
                 LOGGER.info("Couldn't find %s" % (GeraldName))
             node = element.find(GeraldName)
             if node is None:
                 LOGGER.info("Couldn't find %s" % (GeraldName))


@@ -414,7 +414,7 @@ def tonumber(v):
     """
     try:
         v = int(v)
     """
     try:
         v = int(v)

-    except ValueError, e:
+    except ValueError as e:

         v = float(v)
     return v
 
         v = float(v)
     return v
 


@@ -442,8 +442,8 @@ def make_mean_range_element(parent, name, mean, deviation):
     Make an etree subelement <Name mean='mean', deviation='deviation'/>
     """
     element = etree.SubElement(parent, name,
     Make an etree subelement <Name mean='mean', deviation='deviation'/>
     """
     element = etree.SubElement(parent, name,

-                                     { 'mean': unicode(mean),
-                                       'deviation': unicode(deviation)})
+                                     { 'mean': str(mean),
+                                       'deviation': str(deviation)})

     return element
 
 def parse_mean_range_element(element):
     return element
 
 def parse_mean_range_element(element):

diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 759a13ee37f2f463771ac2429e64e9be49873031..b94b91d22b7216fc246d08e2d2717317593356ab 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -7,8 +7,8 @@ import shutil
 
 TEST_CODE_DIR = os.path.split(__file__)[0]
 TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
 
 TEST_CODE_DIR = os.path.split(__file__)[0]
 TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')

-LANE_LIST = range(1,9)
-TILE_LIST = range(1,101)
+LANE_LIST = list(range(1,9))
+TILE_LIST = list(range(1,101))

 HISEQ_TILE_LIST = [1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108,
                    1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208,
                    2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108,
 HISEQ_TILE_LIST = [1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108,
                    1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208,
                    2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108,


@@ -653,15 +653,15 @@ class DemultiplexedPaths(object):
         return pathname
 
     def dump(self):
         return pathname
 
     def dump(self):

-        print ('index seq: {0}'.format(self.index_seq))
+        print(('index seq: {0}'.format(self.index_seq)))

 
 

-        print ('project dir: {0}'.format(self.project_dir))
-        print ('sample dir: {0}'.format(self.sample_dir))
-        print ('rootname: {0}'.format(self.rootname))
-        print ('path: {0}'.format(
+        print(('project dir: {0}'.format(self.project_dir)))
+        print(('sample dir: {0}'.format(self.sample_dir)))
+        print(('rootname: {0}'.format(self.rootname)))
+        print(('path: {0}'.format(

             os.path.join(self.project_dir,
                          self.sample_dir,
             os.path.join(self.project_dir,
                          self.sample_dir,

-                         self.rootname+'R1_001.fastq.gz')))
+                         self.rootname+'R1_001.fastq.gz'))))

 
 
 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
 
 
 def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):


@@ -697,7 +697,7 @@ def print_ls_tree(root):
     """
     for dirpath, dirnames, filenames in os.walk(root):
         for filename in filenames:
     """
     for dirpath, dirnames, filenames in os.walk(root):
         for filename in filenames:

-            print os.path.join(dirpath, filename)
+            print(os.path.join(dirpath, filename))

 
 
 class BaseCallInfo(object):
 
 
 class BaseCallInfo(object):

diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py
index 57ad62cfc2cd309f05c14cc12e23b1ee12727ab5..b18a0f78aa3a9edaa6e366bf062c48ec1f151960 100644 (file)
--- a/htsworkflow/pipelines/test/test_eland.py
+++ b/htsworkflow/pipelines/test/test_eland.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """

-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase

 
 from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
      SampleKey, MatchCodes, MappedReads
 
 from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
      SampleKey, MatchCodes, MappedReads


@@ -19,9 +19,9 @@ class MatchCodeTests(TestCase):
                        'U0':0, 'U1':0, 'U2':0,
                        'R0':0, 'R1':0, 'R2':0,
                       }
                        'U0':0, 'U1':0, 'U2':0,
                        'R0':0, 'R1':0, 'R2':0,
                       }

-        self.assertEqual(mc.keys(), match_codes.keys())
-        self.assertEqual(mc.items(), match_codes.items())
-        self.assertEqual(mc.values(), match_codes.values())
+        self.assertEqual(list(mc.keys()), list(match_codes.keys()))
+        self.assertEqual(list(mc.items()), list(match_codes.items()))
+        self.assertEqual(list(mc.values()), list(match_codes.values()))

         self.assertRaises(KeyError, mc.__getitem__, 'foo')
 
     def test_addition(self):
         self.assertRaises(KeyError, mc.__getitem__, 'foo')
 
     def test_addition(self):


@@ -53,7 +53,7 @@ class TestMappedReads(TestCase):
         mr1['chr9'] = 7
         self.assertEqual(list(mr1.keys()), ['chr9'])
         self.assertEqual(mr1['chr9'], 7)
         mr1['chr9'] = 7
         self.assertEqual(list(mr1.keys()), ['chr9'])
         self.assertEqual(mr1['chr9'], 7)

-        self.assertEqual(mr1.items(), [('chr9', 7)])
+        self.assertEqual(list(mr1.items()), [('chr9', 7)])

         del mr1['chr9']
         self.assertEqual(len(mr1), 0)
 
         del mr1['chr9']
         self.assertEqual(len(mr1), 0)
 


@@ -77,7 +77,7 @@ class ElandTests(TestCase):
     """Test specific Eland modules
     """
     def compare_match_array(self, current, expected):
     """Test specific Eland modules
     """
     def compare_match_array(self, current, expected):

-        for key in expected.keys():
+        for key in list(expected.keys()):

             self.assertEqual(current[key], expected[key],
                  "Key %s: %s != %s" % (key,current[key],expected[key]))
 
             self.assertEqual(current[key], expected[key],
                  "Key %s: %s != %s" % (key,current[key],expected[key]))
 


@@ -238,7 +238,7 @@ class ElandTests(TestCase):
         e.results[sl3] = 'Lane3'
         e.results[sl1] = 'Lane1'
 
         e.results[sl3] = 'Lane3'
         e.results[sl1] = 'Lane1'
 

-        e_list = e.values()
+        e_list = list(e.values())

         self.assertEqual(e_list[0], 'Lane1')
         self.assertEqual(e_list[1], 'Lane3')
         self.assertEqual(e_list[2], 'Lane5')
         self.assertEqual(e_list[0], 'Lane1')
         self.assertEqual(e_list[1], 'Lane3')
         self.assertEqual(e_list[2], 'Lane5')


@@ -253,13 +253,13 @@ class TestElandMatches(TestCase):
         self.assertEqual(len(em[key]), 1)
         filename = iter(em[key]).next().filename
         self.assertEqual(filename, 's_1_sequence.txt')
         self.assertEqual(len(em[key]), 1)
         filename = iter(em[key]).next().filename
         self.assertEqual(filename, 's_1_sequence.txt')

-        self.assertEqual(em.keys(), [key])
+        self.assertEqual(list(em.keys()), [key])

         em.add('s_1_eland_result.txt')
         self.assertEqual(len(em), 1)
         self.assertEqual(len(em[key]), 1)
         filename = iter(em[key]).next().filename
         self.assertEqual(filename, 's_1_eland_result.txt')
         em.add('s_1_eland_result.txt')
         self.assertEqual(len(em), 1)
         self.assertEqual(len(em[key]), 1)
         filename = iter(em[key]).next().filename
         self.assertEqual(filename, 's_1_eland_result.txt')

-        self.assertEqual(em.keys(), [key])
+        self.assertEqual(list(em.keys()), [key])

 
     def test_parts(self):
         key11111 = SampleKey(1, 1, '11111')
 
     def test_parts(self):
         key11111 = SampleKey(1, 1, '11111')


@@ -276,7 +276,7 @@ class TestElandMatches(TestCase):
         self.assertEqual(len(em[key11112]), 2)
 
 def suite():
         self.assertEqual(len(em[key11112]), 2)
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))


@@ -286,5 +286,5 @@ def suite():
 
 
 if __name__ == "__main__":
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_extract_results.py b/htsworkflow/pipelines/test/test_extract_results.py
index 7381d8c38908a41753b79a202daecb9d56df847f..29ab3fddd71d7f7af123fc882adec7657f8d8e54 100644 (file)
--- a/htsworkflow/pipelines/test/test_extract_results.py
+++ b/htsworkflow/pipelines/test/test_extract_results.py
@@ -6,7 +6,7 @@ import os
 import tempfile
 import shutil
 import sys
 import tempfile
 import shutil
 import sys

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -81,13 +81,13 @@ class RunfolderExtractTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderExtractTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
 
     main(defaultTest="suite")
 

diff --git a/htsworkflow/pipelines/test/test_genome_mapper.py b/htsworkflow/pipelines/test/test_genome_mapper.py
index 1101305effd80ede9a09d4db99abe3566b31c8ca..e7561adf567b124ea6b06702934335d60337752f 100644 (file)
--- a/htsworkflow/pipelines/test/test_genome_mapper.py
+++ b/htsworkflow/pipelines/test/test_genome_mapper.py
@@ -1,6 +1,6 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 

-from StringIO import StringIO
+from io import StringIO

 from htsworkflow.pipelines import genome_mapper
 
 class testGenomeMapper(TestCase):
 from htsworkflow.pipelines import genome_mapper
 
 class testGenomeMapper(TestCase):


@@ -21,18 +21,18 @@ class testGenomeMapper(TestCase):
         self.failUnlessEqual("%(Mus musculus|mm8)s" % (genome_map), "/mm8")
         self.failUnlessEqual("%(Mus musculus|mm10)s" % (genome_map), "/mm10")
         
         self.failUnlessEqual("%(Mus musculus|mm8)s" % (genome_map), "/mm8")
         self.failUnlessEqual("%(Mus musculus|mm10)s" % (genome_map), "/mm10")
         

-        self.failUnlessEqual(len(genome_map.keys()), 6)
-        self.failUnlessEqual(len(genome_map.values()), 6)
-        self.failUnlessEqual(len(genome_map.items()), 6)
+        self.failUnlessEqual(len(list(genome_map.keys())), 6)
+        self.failUnlessEqual(len(list(genome_map.values())), 6)
+        self.failUnlessEqual(len(list(genome_map.items())), 6)

         
         
 def suite():
         
         
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testGenomeMapper))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py
index 7195d0f044a0e29529dc9e903e9598b12d4ad040..350f46d19f636f2497700d34b6510b4ec3269cef 100644 (file)
--- a/htsworkflow/pipelines/test/test_genomemap.py
+++ b/htsworkflow/pipelines/test/test_genomemap.py
@@ -2,10 +2,10 @@
 """More direct synthetic test cases for the eland output file processing
 """
 import os
 """More direct synthetic test cases for the eland output file processing
 """
 import os

-from StringIO import StringIO
+from io import StringIO

 import shutil
 import tempfile
 import shutil
 import tempfile

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import ElementTree
 from htsworkflow.pipelines import genomemap
 
 from htsworkflow.pipelines import ElementTree
 from htsworkflow.pipelines import genomemap


@@ -77,12 +77,12 @@ class TestGenomeMap(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestGenomeMap))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_retrive_config.py b/htsworkflow/pipelines/test/test_retrive_config.py
index 1d0404aa42ec16baff63780f9afa7298e7d04f9b..6e6155c915c814cabc3c05ab2bc5ea0bd188fc09 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrive_config.py
+++ b/htsworkflow/pipelines/test/test_retrive_config.py
@@ -1,11 +1,11 @@
 import csv
 import os
 import re
 import csv
 import os
 import re

-from StringIO import StringIO
+from io import StringIO

 
 try:
     import json
 
 try:
     import json

-except ImportError, e:
+except ImportError as e:

     import simplejson as json
 
 from django.test import TestCase
     import simplejson as json
 
 from django.test import TestCase


@@ -28,7 +28,7 @@ class RetrieveTestCases(TestCase):
         flowcell_info = json.loads(flowcell_request.content)
 
         options = getCombinedOptions(['-f','FC12150','-g',os.getcwd()])
         flowcell_info = json.loads(flowcell_request.content)
 
         options = getCombinedOptions(['-f','FC12150','-g',os.getcwd()])

-        genome_map = {u'Homo sapiens': '/tmp/hg18' }
+        genome_map = {'Homo sapiens': '/tmp/hg18' }

 
         config = format_gerald_config(options, flowcell_info, genome_map)
         config_lines = config.split('\n')
 
         config = format_gerald_config(options, flowcell_info, genome_map)
         config_lines = config.split('\n')


@@ -54,7 +54,7 @@ class RetrieveTestCases(TestCase):
 
         output = StringIO()
         save_sample_sheet(output, options, flowcell_info)
 
         output = StringIO()
         save_sample_sheet(output, options, flowcell_info)

-        print output.buf
+        print(output.buf)

 
         output.seek(0)
         sheet = list(csv.DictReader(output))
 
         output.seek(0)
         sheet = list(csv.DictReader(output))


@@ -81,6 +81,6 @@ class RetrieveTestCases(TestCase):
                     ]
         self.failUnlessEqual(len(sheet), len(expected))
         for s, e in zip(sheet, expected):
                     ]
         self.failUnlessEqual(len(sheet), len(expected))
         for s, e in zip(sheet, expected):

-            for key in e.keys():
+            for key in list(e.keys()):

                 self.failUnlessEqual(s[key], e[key],
                   "%s != %s for key %s" % (s[key],e[key], key))
                 self.failUnlessEqual(s[key], e[key],
                   "%s != %s for key %s" % (s[key],e[key], key))

diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py
index 8b28b9e9cc88eb34d687865fc6ad5b78a1a4a19c..d6530d9866f785a2ca33c083504f37d8a7f5051d 100644 (file)
--- a/htsworkflow/pipelines/test/test_run_xml.py
+++ b/htsworkflow/pipelines/test/test_run_xml.py
@@ -1,8 +1,8 @@
 import os
 import os

-from unittest2 import TestCase
-from StringIO import StringIO
+from unittest import TestCase
+from io import StringIO

 
 

-from simulate_runfolder import TESTDATA_DIR
+from .simulate_runfolder import TESTDATA_DIR

 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 
 from htsworkflow.pipelines.eland import SampleKey
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 
 from htsworkflow.pipelines.eland import SampleKey


@@ -24,8 +24,8 @@ class testLoadRunXML(TestCase):
         self.failUnlessEqual(run.runfolder_name, runfolder_name)
         self.failUnlessEqual(run.gerald.runfolder_name, runfolder_name)
 
         self.failUnlessEqual(run.runfolder_name, runfolder_name)
         self.failUnlessEqual(run.gerald.runfolder_name, runfolder_name)
 

-        for (end, lane), lane_results in results['lane_results'].items():
-            for name, test_value in lane_results.items():
+        for (end, lane), lane_results in list(results['lane_results'].items()):
+            for name, test_value in list(lane_results.items()):

                 xml_value = getattr(run.gerald.summary[end][lane], name)
 
                 self.failUnlessEqual(xml_value, test_value,
                 xml_value = getattr(run.gerald.summary[end][lane], name)
 
                 self.failUnlessEqual(xml_value, test_value,


@@ -97,12 +97,12 @@ class testLoadRunXML(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testLoadRunXML))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py
index de68a2505cbb2e1e6f83726e23780008d6e90b83..eb491d54a8ee3c6ce35f2963fe4c475a27acb0e3 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder026.py
+++ b/htsworkflow/pipelines/test/test_runfolder026.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -311,7 +311,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,     b2.date )
         self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,     b2.date )
         self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -326,8 +326,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -364,8 +364,8 @@ class RunfolderTests(TestCase):
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -393,13 +393,13 @@ class RunfolderTests(TestCase):
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))

-                for k in g_results.mapped_reads.keys():
+                for k in list(g_results.mapped_reads.keys()):

                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))
                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))

-                for k in g_results.match_codes.keys():
+                for k in list(g_results.match_codes.keys()):

                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 
                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 


@@ -436,13 +436,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 3)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 3)

-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):

                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):

                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 


@@ -471,12 +471,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py
index cd631bf6070a4f7c5bdd105ca56631462b364d70..edababb9ed4fb62e06a3e01d857d071fa5678d1f 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder030.py
+++ b/htsworkflow/pipelines/test/test_runfolder030.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -733,7 +733,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,     b2.date )
         self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,     b2.date )
         self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -748,8 +748,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -788,8 +788,8 @@ class RunfolderTests(TestCase):
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -817,13 +817,13 @@ class RunfolderTests(TestCase):
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))

-                for k in g_results.mapped_reads.keys():
+                for k in list(g_results.mapped_reads.keys()):

                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))
                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))

-                for k in g_results.match_codes.keys():
+                for k in list(g_results.match_codes.keys()):

                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 
                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 


@@ -860,13 +860,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 3)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 3)

-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):

                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):

                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 


@@ -895,11 +895,11 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder110.py b/htsworkflow/pipelines/test/test_runfolder110.py
index 27e66499684b0860b08925ff24558b7959aafeb5..99553fe6efd18ec42122b34a112cef875cf35e65 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder110.py
+++ b/htsworkflow/pipelines/test/test_runfolder110.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -112,7 +112,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -127,8 +127,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -154,7 +154,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -183,8 +183,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -212,13 +212,13 @@ class RunfolderTests(TestCase):
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))

-                for k in g_results.mapped_reads.keys():
+                for k in list(g_results.mapped_reads.keys()):

                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))
                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))

-                for k in g_results.match_codes.keys():
+                for k in list(g_results.match_codes.keys()):

                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 
                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 


@@ -263,13 +263,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)

-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):

                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):

                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 


@@ -300,12 +300,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index 96a5bcf1102a1a558c00ac93876cfb870cc50677..a511437bbe31736abdec96f58921817c4402c99a 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@ -5,7 +5,7 @@ import glob
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland


@@ -91,8 +91,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.7.0')
         self.failUnlessEqual(g.date, datetime(2011,5,2,19,19,49))
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.7.0')
         self.failUnlessEqual(g.date, datetime(2011,5,2,19,19,49))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -128,7 +128,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*100+'y'*100)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*100+'y'*100)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnless(l.analysis in ('sequence_pair', 'eland_pair'))
           self.failUnlessEqual(l.read_length, '100')
           self.failUnlessEqual(l.use_bases, 'Y'*100+'y'*100)
           self.failUnless(l.analysis in ('sequence_pair', 'eland_pair'))
           self.failUnlessEqual(l.read_length, '100')
           self.failUnlessEqual(l.use_bases, 'Y'*100+'y'*100)


@@ -155,8 +155,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -185,13 +185,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -250,13 +250,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 7)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 7)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -300,12 +300,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
index 34a9c8a04e8ce85dfd97f4b46d77b02ee9256fd9..07a074b6cc2ffca6c13d34b7e9cea81f993d7977 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import bustard


@@ -111,7 +111,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -126,8 +126,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -153,7 +153,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -180,8 +180,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -209,13 +209,13 @@ class RunfolderTests(TestCase):
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))

-                for k in g_results.mapped_reads.keys():
+                for k in list(g_results.mapped_reads.keys()):

                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))
                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))

-                for k in g_results.match_codes.keys():
+                for k in list(g_results.match_codes.keys()):

                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 
                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 


@@ -262,13 +262,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)

-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):

                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):

                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 


@@ -299,12 +299,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar130.py b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
index c23ed9730808416484500e37c866a29e984e9ce0..673407f75c96666449b4be82a883cc878017a574 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar130.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar130.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -122,7 +122,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.user,    'diane')
         self.failUnlessEqual(len(b.phasing), 8)
         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
         self.failUnlessEqual(b.user,    'diane')
         self.failUnlessEqual(len(b.phasing), 8)
         self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)

-        self.failUnlessEqual(b.crosstalk.base.keys(), ['A','C','T','G'])
+        self.failUnlessEqual(list(b.crosstalk.base.keys()), ['A','C','T','G'])

         check_crosstalk(b.crosstalk)
 
         xml = b.get_elements()
         check_crosstalk(b.crosstalk)
 
         xml = b.get_elements()


@@ -132,7 +132,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -148,8 +148,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -175,7 +175,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -202,8 +202,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -232,13 +232,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -298,13 +298,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -337,12 +337,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_pair.py b/htsworkflow/pipelines/test/test_runfolder_pair.py
index dce07884228bdb154058af15e838a5926bca63d7..0b9d070ba23065d903907d23ea1de2f0b6deeed9 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_pair.py
+++ b/htsworkflow/pipelines/test/test_runfolder_pair.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard


@@ -115,7 +115,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
         self.failUnlessEqual(b.date,    b2.date )
         self.failUnlessEqual(b.user,    b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))

-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):

             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,


@@ -130,8 +130,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -157,7 +157,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -189,8 +189,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -218,13 +218,13 @@ class RunfolderTests(TestCase):
                                          g2_results.reads)
                     self.failUnlessEqual(len(g_results.mapped_reads),
                                          len(g2_results.mapped_reads))
                                          g2_results.reads)
                     self.failUnlessEqual(len(g_results.mapped_reads),
                                          len(g2_results.mapped_reads))

-                    for k in g_results.mapped_reads.keys():
+                    for k in list(g_results.mapped_reads.keys()):

                         self.failUnlessEqual(g_results.mapped_reads[k],
                                              g2_results.mapped_reads[k])
 
                     self.failUnlessEqual(len(g_results.match_codes),
                                          len(g2_results.match_codes))
                         self.failUnlessEqual(g_results.mapped_reads[k],
                                              g2_results.mapped_reads[k])
 
                     self.failUnlessEqual(len(g_results.match_codes),
                                          len(g2_results.match_codes))

-                    for k in g_results.match_codes.keys():
+                    for k in list(g_results.match_codes.keys()):

                         self.failUnlessEqual(g_results.match_codes[k],
                                              g2_results.match_codes[k])
 
                         self.failUnlessEqual(g_results.match_codes[k],
                                              g2_results.match_codes[k])
 


@@ -287,13 +287,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 17)

-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):

                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):

                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 


@@ -325,12 +325,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta.py b/htsworkflow/pipelines/test/test_runfolder_rta.py
index 497fe7b33181cd6896fb0cac05c0ce19d79c0b24..b8c516de373b8f2659aeba605cdcaf5af963100e 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -109,8 +109,8 @@ class RunfolderTests(TestCase):
 
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
 
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -136,7 +136,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -162,8 +162,8 @@ class RunfolderTests(TestCase):
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -192,13 +192,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -260,13 +260,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -299,12 +299,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta160.py b/htsworkflow/pipelines/test/test_runfolder_rta160.py
index 8d8f2f104744672fc5ceba1ec3379f970dc093ac..93e10d102b47c885cbab8f56a00e0e5f5f818194 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta160.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta160.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -79,8 +79,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -106,7 +106,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -133,8 +133,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -163,13 +163,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -231,13 +231,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -276,12 +276,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py
index 63b4a8df0c7176b8ced6aa1a022a8b22f7c6a7bb..4d7d65d5da510fcee5b7afe098030c0ec1dd2ff9 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta180.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta180.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines import ipar


@@ -92,8 +92,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
 
         # list of genomes, matches what was defined up in
 
 
         # list of genomes, matches what was defined up in


@@ -119,7 +119,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator

-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):

           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)


@@ -146,8 +146,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):


@@ -176,13 +176,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -245,13 +245,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 7)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 7)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -284,12 +284,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
index 8396bd0351265fe940a4b75dff3c421345272f56..00a3de5734093278ff0ee0c839c0e24a151364ec 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
@@ -5,7 +5,7 @@ import logging
 import os
 import tempfile
 import shutil
 import os
 import tempfile
 import shutil

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines.samplekey import SampleKey
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines.samplekey import SampleKey


@@ -98,8 +98,8 @@ class RunfolderTests(TestCase):
 
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.8.1')
 
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.8.1')

-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))

 
         # list of genomes, matches what was defined up in
         # make_gerald_config.
 
         # list of genomes, matches what was defined up in
         # make_gerald_config.


@@ -141,11 +141,11 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
         self.failUnlessEqual(g.software, g2.software)
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)

-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))

 
         # test lane specific parameters from gerald config file
 
         # test lane specific parameters from gerald config file

-        for i in g.lanes.keys():
+        for i in list(g.lanes.keys()):

             g_lane = g.lanes[i]
             g2_lane = g2.lanes[i]
             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
             g_lane = g.lanes[i]
             g2_lane = g2.lanes[i]
             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)


@@ -171,13 +171,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))
                 if isinstance(g_results, eland.ElandLane):
                   self.failUnlessEqual(len(g_results.mapped_reads),
                                        len(g2_results.mapped_reads))

-                  for k in g_results.mapped_reads.keys():
+                  for k in list(g_results.mapped_reads.keys()):

                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))
                       self.failUnlessEqual(g_results.mapped_reads[k],
                                            g2_results.mapped_reads[k])
 
                   self.failUnlessEqual(len(g_results.match_codes),
                                        len(g2_results.match_codes))

-                  for k in g_results.match_codes.keys():
+                  for k in list(g_results.match_codes.keys()):

                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 
                       self.failUnlessEqual(g_results.match_codes[k],
                                            g2_results.match_codes[k])
 


@@ -197,7 +197,7 @@ class RunfolderTests(TestCase):
 
         eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 
 
         eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 

-        for lane in eland_container.values():
+        for lane in list(eland_container.values()):

             # I added sequence lanes to the last 2 lanes of this test case
             if lane.sample_name == '11113':
                 self.assertEqual(lane.reads, 24)
             # I added sequence lanes to the last 2 lanes of this test case
             if lane.sample_name == '11113':
                 self.assertEqual(lane.reads, 24)


@@ -237,13 +237,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 1)
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 1)

-              for k in l1.mapped_reads.keys():
+              for k in list(l1.mapped_reads.keys()):

                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
                   self.failUnlessEqual(l1.mapped_reads[k],
                                        l2.mapped_reads[k])
 
               self.failUnlessEqual(len(l1.match_codes), 9)
               self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))

-              for k in l1.match_codes.keys():
+              for k in list(l1.match_codes.keys()):

                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):
                   self.failUnlessEqual(l1.match_codes[k],
                                        l2.match_codes[k])
             elif isinstance(l1, eland.SequenceLane):


@@ -275,12 +275,12 @@ class RunfolderTests(TestCase):
         self.failIfEqual(r2.gerald, None)
 
 def suite():
         self.failIfEqual(r2.gerald, None)
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_runfolder_utils.py b/htsworkflow/pipelines/test/test_runfolder_utils.py
index e7c0c3807d950e18cdb854c86932c8247e4b45f1..5471c18f1b64b5ab45b5e7ddd37179a1970fd3b3 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_utils.py
+++ b/htsworkflow/pipelines/test/test_runfolder_utils.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader

 
 from htsworkflow.pipelines import runfolder
 class TestRunfolderUtilities(TestCase):
 
 from htsworkflow.pipelines import runfolder
 class TestRunfolderUtilities(TestCase):


@@ -32,5 +32,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_samplekey.py b/htsworkflow/pipelines/test/test_samplekey.py
index ecd273dedd1c3eab53fc0c6b94b720ecadb5145f..80fcddeb7e8961fc1a98115579527f721ec389fd 100644 (file)
--- a/htsworkflow/pipelines/test/test_samplekey.py
+++ b/htsworkflow/pipelines/test/test_samplekey.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """

-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase

 
 from htsworkflow.pipelines.samplekey import SampleKey
 
 
 from htsworkflow.pipelines.samplekey import SampleKey
 


@@ -44,12 +44,12 @@ class TestSampleKey(TestCase):
         self.assertTrue(k3.matches(q3))
 
 def suite():
         self.assertTrue(k3.matches(q3))
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestSampleKey))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestSampleKey))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_sequences.py b/htsworkflow/pipelines/test/test_sequences.py
index 522a9aafdf1ff7f3364a99f70cbb530a622eeae8..6502c64901471753735b777fa292fd33652a4346 100644 (file)
--- a/htsworkflow/pipelines/test/test_sequences.py
+++ b/htsworkflow/pipelines/test/test_sequences.py
@@ -2,7 +2,7 @@
 import os
 import shutil
 import tempfile
 import os
 import shutil
 import tempfile

-from unittest2 import TestCase
+from unittest import TestCase

 
 import RDF
 
 
 import RDF
 


@@ -71,7 +71,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'srf')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'srf')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<srf 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
         self.assertEqual(repr(f0), "<srf 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')


@@ -96,7 +96,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<qseq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
         self.assertEqual(repr(f0), "<qseq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')


@@ -119,7 +119,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<qseq ilmn200901 1 %s>" %(pathname,))
         self.assertEqual(f0.lane, '1')
         self.assertEqual(f0.read, 1)
         self.assertEqual(repr(f0), "<qseq ilmn200901 1 %s>" %(pathname,))
         self.assertEqual(f0.lane, '1')
         self.assertEqual(f0.read, 1)


@@ -142,7 +142,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')


@@ -164,7 +164,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')


@@ -188,7 +188,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')
         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')


@@ -212,7 +212,7 @@ class SequenceFileTests(TestCase):
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)

-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))

         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')
         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')


@@ -612,12 +612,12 @@ class SimulateSimpleTree(SimulateTree):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/pipelines/test/test_summary.py b/htsworkflow/pipelines/test/test_summary.py
index 1f7e46108856a737846c93996212a3d9cf80b69c..b5c52c63dbe01e2752518cd817d23a22f9bc80d2 100644 (file)
--- a/htsworkflow/pipelines/test/test_summary.py
+++ b/htsworkflow/pipelines/test/test_summary.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 import os
 #!/usr/bin/env python
 import os

-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase

 
 from htsworkflow.pipelines import summary
 
 from htsworkflow.pipelines import summary

-from simulate_runfolder import TESTDATA_DIR
+from .simulate_runfolder import TESTDATA_DIR

 
 class SummaryTests(TestCase):
     """Test elements of the summary file parser
 
 class SummaryTests(TestCase):
     """Test elements of the summary file parser


@@ -36,12 +36,12 @@ class SummaryTests(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SummaryTests))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/settings.py b/htsworkflow/settings.py
index a0652c2dbdf9611131385e0c389778782efff41d..048d35cc9391580b4fe0d9212a2dcadff3ff1bf5 100644 (file)
--- a/htsworkflow/settings.py
+++ b/htsworkflow/settings.py
@@ -27,7 +27,7 @@ The options understood by this module are (with their defaults):
   localhost=127.0.0.1
 
 """
   localhost=127.0.0.1
 
 """

-import ConfigParser
+import configparser

 import logging
 import os
 import shlex
 import logging
 import os
 import shlex


@@ -60,14 +60,14 @@ def options_to_dict(dest, section_name):
       dest[name] = options.get(section_name, name)
 
 # define your defaults here
       dest[name] = options.get(section_name, name)
 
 # define your defaults here

-options = ConfigParser.SafeConfigParser()
+options = configparser.SafeConfigParser()

 
 def save_options(filename, options):
     try:
         ini_stream = open(filename, 'w')
         options.write(ini_stream)
         ini_stream.close()
 
 def save_options(filename, options):
     try:
         ini_stream = open(filename, 'w')
         options.write(ini_stream)
         ini_stream.close()

-    except IOError, e:
+    except IOError as e:

         LOGGER.debug("Error saving setting: %s" % (str(e)))
 
 INI_FILE = options.read([os.path.expanduser("~/.htsworkflow.ini"),
         LOGGER.debug("Error saving setting: %s" % (str(e)))
 
 INI_FILE = options.read([os.path.expanduser("~/.htsworkflow.ini"),


@@ -118,13 +118,13 @@ NOTIFICATION_BCC = []
 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 
 if not options.has_option('frontend', 'database'):
 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 
 if not options.has_option('frontend', 'database'):

-  raise ConfigParser.NoSectionError(
+  raise configparser.NoSectionError(

     "Please define [frontend] database=<Section>")
 
 database_section = options.get('frontend', 'database')
 
 if not options.has_section(database_section):
     "Please define [frontend] database=<Section>")
 
 database_section = options.get('frontend', 'database')
 
 if not options.has_section(database_section):

-    raise ConfigParser.NoSectionError(
+    raise configparser.NoSectionError(

         "No database=<database_section_name> defined")
 
 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
         "No database=<database_section_name> defined")
 
 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 17e463351282b7b8091f922760e8b1fd69a2c934..65b6b69d9846786f4b53f8c74775c3a4c6b73432 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -5,7 +5,7 @@ import os
 from pprint import pformat,pprint
 import sys
 import types
 from pprint import pformat,pprint
 import sys
 import types

-from urlparse import urljoin, urlparse
+from urllib.parse import urljoin, urlparse

 
 from htsworkflow.pipelines.sequences import scan_for_sequences, \
      update_model_sequence_library
 
 from htsworkflow.pipelines.sequences import scan_for_sequences, \
      update_model_sequence_library


@@ -68,7 +68,7 @@ class CondorFastqExtract(object):
         if pythonpath is not None:
             env = "PYTHONPATH=%s" % (pythonpath,)
         condor_entries = self.build_condor_arguments(result_map)
         if pythonpath is not None:
             env = "PYTHONPATH=%s" % (pythonpath,)
         condor_entries = self.build_condor_arguments(result_map)

-        for script_type in template_map.keys():
+        for script_type in list(template_map.keys()):

             template = loader.get_template(template_map[script_type])
             variables = {'python': sys.executable,
                          'logdir': self.log_path,
             template = loader.get_template(template_map[script_type])
             variables = {'python': sys.executable,
                          'logdir': self.log_path,


@@ -93,10 +93,10 @@ class CondorFastqExtract(object):
         sequences = self.find_archive_sequence_files(result_map)
         needed_targets = self.update_fastq_targets(result_map, sequences)
 
         sequences = self.find_archive_sequence_files(result_map)
         needed_targets = self.update_fastq_targets(result_map, sequences)
 

-        for target_pathname, available_sources in needed_targets.items():
+        for target_pathname, available_sources in list(needed_targets.items()):

             LOGGER.debug(' target : %s' % (target_pathname,))
             LOGGER.debug(' candidate sources: %s' % (available_sources,))
             LOGGER.debug(' target : %s' % (target_pathname,))
             LOGGER.debug(' candidate sources: %s' % (available_sources,))

-            for condor_type in available_sources.keys():
+            for condor_type in list(available_sources.keys()):

                 conversion = conversion_funcs.get(condor_type, None)
                 if conversion is None:
                     errmsg = "Unrecognized type: {0} for {1}"
                 conversion = conversion_funcs.get(condor_type, None)
                 if conversion is None:
                     errmsg = "Unrecognized type: {0} for {1}"


@@ -161,7 +161,7 @@ class CondorFastqExtract(object):
         return results
 
     def import_libraries(self, result_map):
         return results
 
     def import_libraries(self, result_map):

-        for lib_id in result_map.keys():
+        for lib_id in list(result_map.keys()):

             lib_id_encoded = lib_id.encode('utf-8')
             liburl = urljoin(self.host, 'library/%s/' % (lib_id_encoded,))
             library = RDF.Node(RDF.Uri(liburl))
             lib_id_encoded = lib_id.encode('utf-8')
             liburl = urljoin(self.host, 'library/%s/' % (lib_id_encoded,))
             library = RDF.Node(RDF.Uri(liburl))


@@ -322,7 +322,7 @@ class SequenceResult(object):
         self.cycle = fromTypedNode(result['cycle'])
         self.lane_number = fromTypedNode(result['lane_number'])
         self.read = fromTypedNode(result['read'])
         self.cycle = fromTypedNode(result['cycle'])
         self.lane_number = fromTypedNode(result['lane_number'])
         self.read = fromTypedNode(result['read'])

-        if type(self.read) in types.StringTypes:
+        if type(self.read) in str:

             self.read = 1
         self.library = result['library']
         self.library_id = fromTypedNode(result['library_id'])
             self.read = 1
         self.library = result['library']
         self.library_id = fromTypedNode(result['library_id'])


@@ -355,8 +355,8 @@ class SequenceResult(object):
         if url.scheme == 'file':
             return url.path
         else:
         if url.scheme == 'file':
             return url.path
         else:

-            errmsg = u"Unsupported scheme {0} for {1}"
-            raise ValueError(errmsg.format(url.scheme, unicode(url)))
+            errmsg = "Unsupported scheme {0} for {1}"
+            raise ValueError(errmsg.format(url.scheme, str(url)))

     path = property(_get_path)
 
     def __repr__(self):
     path = property(_get_path)
 
     def __repr__(self):

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index f04ac8fe5328e738a012738a5d256b9307e11504..51595931ff2fa7699109d6644214ebdd89d531d3 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -5,9 +5,9 @@ import os
 from pprint import pformat
 import re
 import string
 from pprint import pformat
 import re
 import string

-from StringIO import StringIO
+from io import StringIO

 import types
 import types

-import urlparse
+import urllib.parse

 
 import RDF
 from htsworkflow.util.rdfhelp import \
 
 import RDF
 from htsworkflow.util.rdfhelp import \


@@ -139,7 +139,7 @@ def _consume_whitespace(line, start=0):
 
     returns length of string if it can't find anything
     """
 
     returns length of string if it can't find anything
     """

-    for i in xrange(start, len(line)):
+    for i in range(start, len(line)):

         if line[i] not in string.whitespace:
             return i
 
         if line[i] not in string.whitespace:
             return i
 


@@ -151,7 +151,7 @@ def _extract_name_index(line, start=0):
 
     returns length of string if nothing matches
     """
 
     returns length of string if nothing matches
     """

-    for i in xrange(start, len(line)):
+    for i in range(start, len(line)):

         if line[i] in string.whitespace:
             return i
 
         if line[i] in string.whitespace:
             return i
 


@@ -232,7 +232,7 @@ def submission_uri_to_string(submission_uri):
 
 def get_view_namespace(submission_uri):
     submission_uri = submission_uri_to_string(submission_uri)
 
 def get_view_namespace(submission_uri):
     submission_uri = submission_uri_to_string(submission_uri)

-    view_uri = urlparse.urljoin(submission_uri, 'view/')
+    view_uri = urllib.parse.urljoin(submission_uri, 'view/')

     viewNS = RDF.NS(view_uri)
     return viewNS
 
     viewNS = RDF.NS(view_uri)
     return viewNS
 


@@ -296,11 +296,11 @@ class UCSCSubmission(object):
     def scan_submission_dirs(self, result_map):
         """Examine files in our result directory
         """
     def scan_submission_dirs(self, result_map):
         """Examine files in our result directory
         """

-        for lib_id, result_dir in result_map.items():
+        for lib_id, result_dir in list(result_map.items()):

             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_submission_dir(result_dir, lib_id)
             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_submission_dir(result_dir, lib_id)

-            except MetadataLookupException, e:
+            except MetadataLookupException as e:

                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_submission_dir(self, submission_dir, library_id):
                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_submission_dir(self, submission_dir, library_id):


@@ -491,7 +491,7 @@ class UCSCSubmission(object):
             self.__view_map = self._get_filename_view_map()
 
         results = []
             self.__view_map = self._get_filename_view_map()
 
         results = []

-        for pattern, view in self.__view_map.items():
+        for pattern, view in list(self.__view_map.items()):

             if re.match(pattern, filename):
                 results.append(view)
 
             if re.match(pattern, filename):
                 results.append(view)
 


@@ -531,7 +531,7 @@ class UCSCSubmission(object):
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)

-            except re.error, e:
+            except re.error as e:

                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns
                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns


@@ -588,7 +588,7 @@ class UCSCSubmission(object):
 
         base_daf = self.daf_name
 
 
         base_daf = self.daf_name
 

-        for result_dir in result_map.values():
+        for result_dir in list(result_map.values()):

             if not os.path.exists(result_dir):
                 raise RuntimeError(
                     "Couldn't find target directory %s" %(result_dir,))
             if not os.path.exists(result_dir):
                 raise RuntimeError(
                     "Couldn't find target directory %s" %(result_dir,))

diff --git a/htsworkflow/submission/fastqname.py b/htsworkflow/submission/fastqname.py
index 9dd52a0319fb9e9efa230e68344ef53156645be7..21341d6f16e71d451d32acc948b8aa262df5d7c9 100644 (file)
--- a/htsworkflow/submission/fastqname.py
+++ b/htsworkflow/submission/fastqname.py
@@ -55,7 +55,7 @@ class FastqName(collections.Mapping):
         if self.is_paired and self['read'] is None:
             return False
 
         if self.is_paired and self['read'] is None:
             return False
 

-        for k in self.keys():
+        for k in list(self.keys()):

             if k == 'read':
                 continue
             if self[k] is None:
             if k == 'read':
                 continue
             if self[k] is None:

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
index ef8d9457218a76ce53f0872f44efafd6d478dea1..20a56a06ff7fad01a36cd9f9325ad342acf0ca4f 100644 (file)
--- a/htsworkflow/submission/geo.py
+++ b/htsworkflow/submission/geo.py
@@ -28,7 +28,7 @@ class GEOSubmission(Submission):
         series = self.get_series_metadata()
         series_attribs = dict(series)
         series_id = series_attribs['^series']
         series = self.get_series_metadata()
         series_attribs = dict(series)
         series_id = series_attribs['^series']

-        for lib_id, result_dir in result_map.items():
+        for lib_id, result_dir in list(result_map.items()):

             an_analysis = self.get_submission_node(result_dir)
             metadata = self.get_sample_metadata(an_analysis)
             if len(metadata) == 0:
             an_analysis = self.get_submission_node(result_dir)
             metadata = self.get_sample_metadata(an_analysis)
             if len(metadata) == 0:


@@ -52,7 +52,7 @@ class GEOSubmission(Submission):
             'platform_id': platform_id,
             'series_id': series_id,
         })
             'platform_id': platform_id,
             'series_id': series_id,
         })

-        print str(soft_template.render(context))
+        print(str(soft_template.render(context)))

 
     def check_for_name(self, analysis_node):
         name = fromTypedNode(
 
     def check_for_name(self, analysis_node):
         name = fromTypedNode(


@@ -129,12 +129,12 @@ class GEOSubmission(Submission):
         lanes = {}
         for row in self.execute_query(query_template, context):
             data = {}
         lanes = {}
         for row in self.execute_query(query_template, context):
             data = {}

-            for k, v in row.items():
+            for k, v in list(row.items()):

                 data[k] = v
             library = str(data['library'])
             lanes.setdefault(library, []).append(data)
         result = []
                 data[k] = v
             library = str(data['library'])
             lanes.setdefault(library, []).append(data)
         result = []

-        for library, files in lanes.items():
+        for library, files in list(lanes.items()):

             if len(files) > 2:
                 errmsg = "Don't know what to do with more than 2 raw files"
                 raise ValueError(errmsg)
             if len(files) > 2:
                 errmsg = "Don't know what to do with more than 2 raw files"
                 raise ValueError(errmsg)

diff --git a/htsworkflow/submission/ncbi.py b/htsworkflow/submission/ncbi.py
index 3cc87365ce0186fdeb2c6024bbba84fd04c6c4fa..89c0dc2f2e9d697ca66ded2fc911445de3152ec6 100644 (file)
--- a/htsworkflow/submission/ncbi.py
+++ b/htsworkflow/submission/ncbi.py
@@ -9,7 +9,7 @@ from lxml.etree import parse, XSLT, tostring, fromstring
 from optparse import OptionParser
 import os
 import RDF
 from optparse import OptionParser
 import os
 import RDF

-import urllib
+import urllib.request, urllib.parse, urllib.error

 
 from htsworkflow.util.rdfhelp import get_model, dump_model
 
 
 from htsworkflow.util.rdfhelp import get_model, dump_model
 


@@ -35,7 +35,7 @@ def search_ncbi_ids(database, term, return_max=200):
     search = {'db': database,
               'term': term,
               'retmax': return_max}
     search = {'db': database,
               'term': term,
               'retmax': return_max}

-    tree = parse(ESEARCH_URL + urllib.urlencode(search))
+    tree = parse(ESEARCH_URL + urllib.parse.urlencode(search))

     root = tree.getroot()
     count = get_node_scalar(root, '/eSearchResult/Count', int)
     retmax_node = get_node_scalar(root, '/eSearchResult/RetMax', int)
     root = tree.getroot()
     count = get_node_scalar(root, '/eSearchResult/Count', int)
     retmax_node = get_node_scalar(root, '/eSearchResult/RetMax', int)


@@ -56,7 +56,7 @@ def parse_sra_metadata_into_model(model, ncbi_id):
     """
     search = {'db':DB,
               'id': ncbi_id}
     """
     search = {'db':DB,
               'id': ncbi_id}

-    url = EFETCH_URL + urllib.urlencode(search)
+    url = EFETCH_URL + urllib.parse.urlencode(search)

     tree = parse(url)
 
     context = Context()
     tree = parse(url)
 
     context = Context()

diff --git a/htsworkflow/submission/submission.py b/htsworkflow/submission/submission.py
index 12a5154c33a01bf15d1349040e7bfd2f71f51df8..cd2a8df03629296cc2db17dd582a8f072121db04 100644 (file)
--- a/htsworkflow/submission/submission.py
+++ b/htsworkflow/submission/submission.py
@@ -37,11 +37,11 @@ class Submission(object):
     def scan_submission_dirs(self, result_map):
         """Examine files in our result directory
         """
     def scan_submission_dirs(self, result_map):
         """Examine files in our result directory
         """

-        for lib_id, result_dir in result_map.items():
+        for lib_id, result_dir in list(result_map.items()):

             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_analysis_dir(result_dir, lib_id)
             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_analysis_dir(result_dir, lib_id)

-            except MetadataLookupException, e:
+            except MetadataLookupException as e:

                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_analysis_dir(self, analysis_dir, library_id):
                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_analysis_dir(self, analysis_dir, library_id):


@@ -60,7 +60,7 @@ class Submission(object):
     def analysis_nodes(self, result_map):
         """Return an iterable of analysis nodes
         """
     def analysis_nodes(self, result_map):
         """Return an iterable of analysis nodes
         """

-        for result_dir in result_map.values():
+        for result_dir in list(result_map.values()):

             an_analysis = self.get_submission_node(result_dir)
             yield an_analysis
 
             an_analysis = self.get_submission_node(result_dir)
             yield an_analysis
 


@@ -224,7 +224,7 @@ class Submission(object):
             LOGGER.debug("Importing %s" % (lane.uri,))
             try:
                 parser.parse_into_model(self.model, lane.uri)
             LOGGER.debug("Importing %s" % (lane.uri,))
             try:
                 parser.parse_into_model(self.model, lane.uri)

-            except RDF.RedlandError, e:
+            except RDF.RedlandError as e:

                 LOGGER.error("Error accessing %s" % (lane.uri,))
                 raise e
 
                 LOGGER.error("Error accessing %s" % (lane.uri,))
                 raise e
 


@@ -236,7 +236,7 @@ class Submission(object):
             self.__view_map = self._get_filename_view_map()
 
         results = []
             self.__view_map = self._get_filename_view_map()
 
         results = []

-        for pattern, view in self.__view_map.items():
+        for pattern, view in list(self.__view_map.items()):

             if re.match(pattern, filename):
                 results.append(view)
 
             if re.match(pattern, filename):
                 results.append(view)
 


@@ -265,7 +265,7 @@ class Submission(object):
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)

-            except re.error, e:
+            except re.error as e:

                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns
                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns


@@ -349,7 +349,7 @@ class Submission(object):
         results = []
         for record in rdfstream:
             d = {}
         results = []
         for record in rdfstream:
             d = {}

-            for key, value in record.items():
+            for key, value in list(record.items()):

                 d[key] = fromTypedNode(value)
             results.append(d)
         return results
                 d[key] = fromTypedNode(value)
             results.append(d)
         return results

diff --git a/htsworkflow/submission/test/test_condorfastq.py b/htsworkflow/submission/test/test_condorfastq.py
index 09d68083c1ec50052c450a71e9d9e24356573cf7..dbeb71cd6baac0e2c23f80873b38dc16482a60db 100644 (file)
--- a/htsworkflow/submission/test/test_condorfastq.py
+++ b/htsworkflow/submission/test/test_condorfastq.py
@@ -436,7 +436,7 @@ class TestCondorFastq(TestCase):
                 stream.write('testfile')
 
         self.result_map = ResultMap()
                 stream.write('testfile')
 
         self.result_map = ResultMap()

-        for lib_id in [u'11154', u'12345']:
+        for lib_id in ['11154', '12345']:

             subname = 'sub-%s' % (lib_id,)
             sub_dir = os.path.join(self.tempdir, subname)
             os.mkdir(sub_dir)
             subname = 'sub-%s' % (lib_id,)
             sub_dir = os.path.join(self.tempdir, subname)
             os.mkdir(sub_dir)


@@ -469,21 +469,21 @@ class TestCondorFastq(TestCase):
         seqs = self.extract.find_archive_sequence_files(self.result_map)
 
         expected = set([
         seqs = self.extract.find_archive_sequence_files(self.result_map)
 
         expected = set([

-            (u'11154', u'42JUYAAXX', '5', 1, 76, True, 'qseq'),
-            (u'11154', u'42JUYAAXX', '5', 2, 76, True, 'qseq'),
-            (u'11154', u'61MJTAAXX', '6', 1, 76, False, 'qseq'),
-            (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
-            (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
-            (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
-            (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
-            (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
-            (u'11154', u'30221AAXX', '4', 1, 33, False, 'srf'),
-            (u'11154', u'30DY0AAXX', '8', 1, 151, True, 'srf')
+            ('11154', '42JUYAAXX', '5', 1, 76, True, 'qseq'),
+            ('11154', '42JUYAAXX', '5', 2, 76, True, 'qseq'),
+            ('11154', '61MJTAAXX', '6', 1, 76, False, 'qseq'),
+            ('11154', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
+            ('11154', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
+            ('11154', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
+            ('11154', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
+            ('12345', 'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
+            ('11154', '30221AAXX', '4', 1, 33, False, 'srf'),
+            ('11154', '30DY0AAXX', '8', 1, 151, True, 'srf')

         ])
         found = set([(l.library_id, l.flowcell_id, l.lane_number, l.read, l.cycle, l.ispaired, l.filetype) for l in seqs])
         self.assertEqual(expected, found)
         ])
         found = set([(l.library_id, l.flowcell_id, l.lane_number, l.read, l.cycle, l.ispaired, l.filetype) for l in seqs])
         self.assertEqual(expected, found)


@@ -495,17 +495,17 @@ class TestCondorFastq(TestCase):
                                                            lib_db)
         self.assertEqual(len(needed_targets), 9)
         srf_30221 = needed_targets[
                                                            lib_db)
         self.assertEqual(len(needed_targets), 9)
         srf_30221 = needed_targets[

-            self.result_map['11154'] + u'/11154_30221AAXX_c33_l4.fastq']
+            self.result_map['11154'] + '/11154_30221AAXX_c33_l4.fastq']

         qseq_42JUY_r1 = needed_targets[
         qseq_42JUY_r1 = needed_targets[

-            self.result_map['11154'] + u'/11154_42JUYAAXX_c76_l5_r1.fastq']
+            self.result_map['11154'] + '/11154_42JUYAAXX_c76_l5_r1.fastq']

         qseq_42JUY_r2 = needed_targets[
         qseq_42JUY_r2 = needed_targets[

-            self.result_map['11154'] + u'/11154_42JUYAAXX_c76_l5_r2.fastq']
+            self.result_map['11154'] + '/11154_42JUYAAXX_c76_l5_r2.fastq']

         qseq_61MJT = needed_targets[
         qseq_61MJT = needed_targets[

-            self.result_map['11154'] + u'/11154_61MJTAAXX_c76_l6.fastq']
+            self.result_map['11154'] + '/11154_61MJTAAXX_c76_l6.fastq']

         split_C02F9_r1 = needed_targets[
         split_C02F9_r1 = needed_targets[

-            self.result_map['11154'] + u'/11154_C02F9ACXX_c202_l3_r1.fastq']
+            self.result_map['11154'] + '/11154_C02F9ACXX_c202_l3_r1.fastq']

         split_C02F9_r2 = needed_targets[
         split_C02F9_r2 = needed_targets[

-            self.result_map['11154'] + u'/11154_C02F9ACXX_c202_l3_r2.fastq']
+            self.result_map['11154'] + '/11154_C02F9ACXX_c202_l3_r2.fastq']

 
         self.assertEqual(len(srf_30221['srf']), 1)
         self.assertEqual(len(qseq_42JUY_r1['qseq']), 1)
 
         self.assertEqual(len(srf_30221['srf']), 1)
         self.assertEqual(len(qseq_42JUY_r1['qseq']), 1)


@@ -530,24 +530,24 @@ class TestCondorFastq(TestCase):
                          '11154_30221AAXX_c33_l4.fastq'): {
                 'mid': None,
                 'ispaired': False,
                          '11154_30221AAXX_c33_l4.fastq'): {
                 'mid': None,
                 'ispaired': False,

-                'sources': [u'woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'],
-                'flowcell': u'30221AAXX',
+                'sources': ['woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'],
+                'flowcell': '30221AAXX',

                 'target': os.path.join(self.result_map['11154'],
                 'target': os.path.join(self.result_map['11154'],

-                                       u'11154_30221AAXX_c33_l4.fastq'),
+                                       '11154_30221AAXX_c33_l4.fastq'),

             },
             os.path.join(self.result_map['11154'],
                          '11154_30DY0AAXX_c151_l8_r1.fastq'): {
                 'mid': None,
                 'ispaired': True,
             },
             os.path.join(self.result_map['11154'],
                          '11154_30DY0AAXX_c151_l8_r1.fastq'): {
                 'mid': None,
                 'ispaired': True,

-                'flowcell': u'30DY0AAXX',
-                'sources': [u'woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'],
+                'flowcell': '30DY0AAXX',
+                'sources': ['woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'],

                 'mid': 76,
                 'target':
                     os.path.join(self.result_map['11154'],
                 'mid': 76,
                 'target':
                     os.path.join(self.result_map['11154'],

-                                 u'11154_30DY0AAXX_c151_l8_r1.fastq'),
+                                 '11154_30DY0AAXX_c151_l8_r1.fastq'),

                 'target_right':
                     os.path.join(self.result_map['11154'],
                 'target_right':
                     os.path.join(self.result_map['11154'],

-                                 u'11154_30DY0AAXX_c151_l8_r2.fastq'),
+                                 '11154_30DY0AAXX_c151_l8_r2.fastq'),

             }
         }
         for args in srf:
             }
         }
         for args in srf:


@@ -569,21 +569,21 @@ class TestCondorFastq(TestCase):
                 'istar': True,
                 'ispaired': True,
                 'sources': [
                 'istar': True,
                 'ispaired': True,
                 'sources': [

-                    u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2']
+                    'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2']

             },
             os.path.join(self.result_map['11154'],
                          '11154_42JUYAAXX_c76_l5_r2.fastq'): {
                 'istar': True,
                 'ispaired': True,
                 'sources': [
             },
             os.path.join(self.result_map['11154'],
                          '11154_42JUYAAXX_c76_l5_r2.fastq'): {
                 'istar': True,
                 'ispaired': True,
                 'sources': [

-                    u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2']
+                    'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2']

             },
             os.path.join(self.result_map['11154'],
                          '11154_61MJTAAXX_c76_l6.fastq'): {
                 'istar': True,
                 'ispaired': False,
                 'sources': [
             },
             os.path.join(self.result_map['11154'],
                          '11154_61MJTAAXX_c76_l6.fastq'): {
                 'istar': True,
                 'ispaired': False,
                 'sources': [

-                    u'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'],
+                    'woldlab_100826_HSI-123_0001_61MJTAAXX_l6_r1.tar.bz2'],

             },
         }
         for args in qseq:
             },
         }
         for args in qseq:


@@ -596,26 +596,26 @@ class TestCondorFastq(TestCase):
 
 
         split_test = dict((( x['target'], x) for x in
 
 
         split_test = dict((( x['target'], x) for x in

-            [{'sources': [u'11154_NoIndex_L003_R1_001.fastq.gz',
-                         u'11154_NoIndex_L003_R1_002.fastq.gz'],
+            [{'sources': ['11154_NoIndex_L003_R1_001.fastq.gz',
+                         '11154_NoIndex_L003_R1_002.fastq.gz'],

              'pyscript': 'desplit_fastq.pyc',
              'pyscript': 'desplit_fastq.pyc',

-             'target': u'11154_C02F9ACXX_c202_l3_r1.fastq'},
-            {'sources': [u'11154_NoIndex_L003_R2_001.fastq.gz',
-                         u'11154_NoIndex_L003_R2_002.fastq.gz'],
+             'target': '11154_C02F9ACXX_c202_l3_r1.fastq'},
+            {'sources': ['11154_NoIndex_L003_R2_001.fastq.gz',
+                         '11154_NoIndex_L003_R2_002.fastq.gz'],

              'pyscript': 'desplit_fastq.pyc',
              'pyscript': 'desplit_fastq.pyc',

-             'target': u'11154_C02F9ACXX_c202_l3_r2.fastq'},
-            {'sources': [u'12345_CGATGT_L003_R1_001.fastq.gz',
-                         u'12345_CGATGT_L003_R1_002.fastq.gz',
-                         u'12345_CGATGT_L003_R1_003.fastq.gz',
+             'target': '11154_C02F9ACXX_c202_l3_r2.fastq'},
+            {'sources': ['12345_CGATGT_L003_R1_001.fastq.gz',
+                         '12345_CGATGT_L003_R1_002.fastq.gz',
+                         '12345_CGATGT_L003_R1_003.fastq.gz',

                          ],
              'pyscript': 'desplit_fastq.pyc',
                          ],
              'pyscript': 'desplit_fastq.pyc',

-             'target': u'12345_C02F9ACXX_c202_l3_r1.fastq'},
-            {'sources': [u'12345_CGATGT_L003_R2_001.fastq.gz',
-                         u'12345_CGATGT_L003_R2_002.fastq.gz',
-                         u'12345_CGATGT_L003_R2_003.fastq.gz',
+             'target': '12345_C02F9ACXX_c202_l3_r1.fastq'},
+            {'sources': ['12345_CGATGT_L003_R2_001.fastq.gz',
+                         '12345_CGATGT_L003_R2_002.fastq.gz',
+                         '12345_CGATGT_L003_R2_003.fastq.gz',

                          ],
              'pyscript': 'desplit_fastq.pyc',
                          ],
              'pyscript': 'desplit_fastq.pyc',

-             'target': u'12345_C02F9ACXX_c202_l3_r2.fastq'}
+             'target': '12345_C02F9ACXX_c202_l3_r2.fastq'}

              ]
          ))
         for arg in split:
              ]
          ))
         for arg in split:


@@ -691,11 +691,11 @@ def tearDownModule():
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index 7959d1e13d9a323281885d63454790f34f85c48f..3e960265f93fac6872382dd06aff1f0117ed175b 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -1,9 +1,9 @@
 from contextlib import contextmanager
 import os
 from contextlib import contextmanager
 import os

-from StringIO import StringIO
+from io import StringIO

 import shutil
 import tempfile
 import shutil
 import tempfile

-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader

 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \
 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \


@@ -121,7 +121,7 @@ class TestDAF(TestCase):
                 signal_view_node, None, None)))
         self.failUnlessEqual(len(statements), 6)
         name = model.get_target(signal_view_node, dafTermOntology['name'])
                 signal_view_node, None, None)))
         self.failUnlessEqual(len(statements), 6)
         name = model.get_target(signal_view_node, dafTermOntology['name'])

-        self.failUnlessEqual(fromTypedNode(name), u'Signal')
+        self.failUnlessEqual(fromTypedNode(name), 'Signal')

 
     def test_get_view_namespace_from_string(self):
         url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
 
     def test_get_view_namespace_from_string(self):
         url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"


@@ -162,7 +162,7 @@ def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
 def dump_model(model):
     writer = get_serializer()
     turtle =  writer.serialize_model_to_string(model)
 def dump_model(model):
     writer = get_serializer()
     turtle =  writer.serialize_model_to_string(model)

-    print turtle
+    print(turtle)

 
 
 class TestUCSCSubmission(TestCase):
 
 
 class TestUCSCSubmission(TestCase):


@@ -335,5 +335,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_fastqname.py b/htsworkflow/submission/test/test_fastqname.py
index d51ad0e303e106126c62df30b00d4240374e68c9..beea3a8293f8fa769dd8f736cc864d511d36749f 100644 (file)
--- a/htsworkflow/submission/test/test_fastqname.py
+++ b/htsworkflow/submission/test/test_fastqname.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 from htsworkflow.submission.fastqname import FastqName
 
 class TestFastqName(TestCase):
 from htsworkflow.submission.fastqname import FastqName
 
 class TestFastqName(TestCase):


@@ -99,11 +99,11 @@ class TestFastqName(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_results.py b/htsworkflow/submission/test/test_results.py
index e4d28cfd20c1da4f5b5a642f4b02511c808a08b0..479ef0ffaf4ef9edd420d155284a9ef3a9dc37c6 100644 (file)
--- a/htsworkflow/submission/test/test_results.py
+++ b/htsworkflow/submission/test/test_results.py
@@ -3,10 +3,10 @@
 from pprint import pprint
 import shutil
 
 from pprint import pprint
 import shutil
 

-from unittest2 import TestCase, defaultTestLoader
+from unittest import TestCase, defaultTestLoader

 
 from htsworkflow.submission.results import ResultMap
 
 from htsworkflow.submission.results import ResultMap

-from submission_test_common import *
+from .submission_test_common import *

 
 def generate_sample_results_tree(obj):
     obj.tempdir = tempfile.mkdtemp(prefix="results_test")
 
 def generate_sample_results_tree(obj):
     obj.tempdir = tempfile.mkdtemp(prefix="results_test")


@@ -43,7 +43,7 @@ class TestResultMap(TestCase):
         results['2000'] = 'dir2000'
         results['1500'] = 'dir1500'
 
         results['2000'] = 'dir2000'
         results['1500'] = 'dir1500'
 

-        self.failUnlessEqual(results.keys(), ['1000', '2000', '1500'])
+        self.failUnlessEqual(list(results.keys()), ['1000', '2000', '1500'])

         self.failUnlessEqual(list(results.values()),
                              ['dir1000', 'dir2000', 'dir1500'])
         self.failUnlessEqual(list(results.items()),
         self.failUnlessEqual(list(results.values()),
                              ['dir1000', 'dir2000', 'dir1500'])
         self.failUnlessEqual(list(results.items()),


@@ -55,9 +55,9 @@ class TestResultMap(TestCase):
         self.failUnlessEqual(results['1500'], 'dir1500')
         self.failUnlessEqual(results['2000'], 'dir2000')
 
         self.failUnlessEqual(results['1500'], 'dir1500')
         self.failUnlessEqual(results['2000'], 'dir2000')
 

-        self.assertTrue(u'2000' in results)

         self.assertTrue('2000' in results)
         self.assertTrue('2000' in results)

-        self.assertFalse(u'77777' in results)
+        self.assertTrue('2000' in results)
+        self.assertFalse('77777' in results)

         self.assertFalse('77777' in results)
 
     def test_make_from_absolute(self):
         self.assertFalse('77777' in results)
 
     def test_make_from_absolute(self):


@@ -104,5 +104,5 @@ def suite():
 if __name__ == "__main__":
     import logging
     logging.basicConfig(level=logging.DEBUG)
 if __name__ == "__main__":
     import logging
     logging.basicConfig(level=logging.DEBUG)

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_submission.py b/htsworkflow/submission/test/test_submission.py
index 90852ceb766f56a871fc199d675982fc095b98c2..699254cdc0521d5f80ba65d283e23133a57f1c2c 100644 (file)
--- a/htsworkflow/submission/test/test_submission.py
+++ b/htsworkflow/submission/test/test_submission.py
@@ -1,8 +1,8 @@
 import os
 import os

-from StringIO import StringIO
+from io import StringIO

 import shutil
 import tempfile
 import shutil
 import tempfile

-from unittest2 import TestCase, TestSuite, defaultTestLoader
+from unittest import TestCase, TestSuite, defaultTestLoader

 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \
 
 from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \


@@ -18,7 +18,7 @@ from htsworkflow.util.rdfhelp import \
      get_serializer
 from htsworkflow.submission.submission import list_submissions, Submission
 from htsworkflow.submission.results import ResultMap
      get_serializer
 from htsworkflow.submission.submission import list_submissions, Submission
 from htsworkflow.submission.results import ResultMap

-from submission_test_common import *
+from .submission_test_common import *

 
 import RDF
 #import logging
 
 import RDF
 #import logging


@@ -122,8 +122,8 @@ thisView:alignments ucscDaf:filename_re ".*\\.bam$" ;
 
         """
         map = ResultMap()
 
         """
         map = ResultMap()

-        print self.tempdir
-        print os.listdir(self.tempdir)
+        print(self.tempdir)
+        print(os.listdir(self.tempdir))

         map['1000'] = os.path.join(self.tempdir, S1_NAME)
         map['2000'] = os.path.join(self.tempdir, S2_NAME)
 
         map['1000'] = os.path.join(self.tempdir, S1_NAME)
         map['2000'] = os.path.join(self.tempdir, S2_NAME)
 


@@ -189,5 +189,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/test/test_ucsc.py b/htsworkflow/submission/test/test_ucsc.py
index fad690e27f5ee638d315c593336dbd110a84fa96..2cc237c94b54cf0e918521946d4f9e15e7982c40 100644 (file)
--- a/htsworkflow/submission/test/test_ucsc.py
+++ b/htsworkflow/submission/test/test_ucsc.py
@@ -1,5 +1,5 @@
-from unittest2 import TestCase, TestSuite, defaultTestLoader
-from StringIO import StringIO
+from unittest import TestCase, TestSuite, defaultTestLoader
+from io import StringIO

 
 from htsworkflow.submission import ucsc
 
 
 from htsworkflow.submission import ucsc
 


@@ -15,7 +15,7 @@ class TestUCSCInfo(TestCase):
         file_index = ucsc.parse_ucsc_file_index(stream, 'http://example.com/files')
         self.assertEquals(len(file_index), 2)
 
         file_index = ucsc.parse_ucsc_file_index(stream, 'http://example.com/files')
         self.assertEquals(len(file_index), 2)
 

-        for attributes in file_index.values():
+        for attributes in list(file_index.values()):

             self.failUnless('subId' in attributes)
             self.failUnless('project' in attributes)
             self.assertEquals(attributes['project'], 'wgEncode')
             self.failUnless('subId' in attributes)
             self.failUnless('project' in attributes)
             self.assertEquals(attributes['project'], 'wgEncode')


@@ -26,5 +26,5 @@ def suite():
     return suite
 
 if __name__ == "__main__":
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest='suite')
     main(defaultTest='suite')

diff --git a/htsworkflow/submission/trackhub_submission.py b/htsworkflow/submission/trackhub_submission.py
index 5003fc0fa27772bb542f4d40e15e11a69a97c5db..0686da109a55ecbd40fd8972ab87380626936799 100644 (file)
--- a/htsworkflow/submission/trackhub_submission.py
+++ b/htsworkflow/submission/trackhub_submission.py
@@ -40,7 +40,7 @@ class TrackHubSubmission(Submission):
         self.baseurl = os.path.join(baseurl, self.name)
         if baseupload:
             sshurl = parse_ssh_url(baseupload)
         self.baseurl = os.path.join(baseurl, self.name)
         if baseupload:
             sshurl = parse_ssh_url(baseupload)

-            print sshurl
+            print(sshurl)

             self.user = sshurl.user
             self.host = sshurl.host
             self.uploadpath =  sshurl.path
             self.user = sshurl.user
             self.host = sshurl.host
             self.uploadpath =  sshurl.path


@@ -191,7 +191,7 @@ class TrackHubSubmission(Submission):
                 subgroups.append(definitions)
                 names.append(name)
                 sortorder.append("{}=+".format(name))
                 subgroups.append(definitions)
                 names.append(name)
                 sortorder.append("{}=+".format(name))

-                d = dimnames.next()
+                d = next(dimnames)

                 dimensions.append("{}={}".format(d, name))
                 filtercomposite.append("{}=multi".format(d))
 
                 dimensions.append("{}={}".format(d, name))
                 filtercomposite.append("{}=multi".format(d))
 

diff --git a/htsworkflow/submission/ucsc.py b/htsworkflow/submission/ucsc.py
index f7734adbd972b26db9150b155a7cdeb39818e0c1..3fd83484096858207be4a7e056a56632ae049bb7 100644 (file)
--- a/htsworkflow/submission/ucsc.py
+++ b/htsworkflow/submission/ucsc.py
@@ -1,8 +1,8 @@
 """Utilities for extracting information from the ENCODE DCC
 """
 import logging
 """Utilities for extracting information from the ENCODE DCC
 """
 import logging

-import urlparse
-import urllib2
+import urllib.parse
+import urllib.request, urllib.error, urllib.parse

 
 LOGGER = logging.getLogger(__name__)
 
 
 LOGGER = logging.getLogger(__name__)
 


@@ -21,7 +21,7 @@ def ddf_download_url(submission_id):
     'http://encodesubmit.ucsc.edu/pipeline/download_ddf/1234'
     """
     fragment = 'download_ddf/%s' % (submission_id,)
     'http://encodesubmit.ucsc.edu/pipeline/download_ddf/1234'
     """
     fragment = 'download_ddf/%s' % (submission_id,)

-    return urlparse.urljoin(UCSCEncodePipeline, fragment)
+    return urllib.parse.urljoin(UCSCEncodePipeline, fragment)

 
 
 def daf_download_url(submission_id):
 
 
 def daf_download_url(submission_id):


@@ -31,7 +31,7 @@ def daf_download_url(submission_id):
     'http://encodesubmit.ucsc.edu/pipeline/download_daf/1234'
     """
     fragment = 'download_daf/%s' % (submission_id,)
     'http://encodesubmit.ucsc.edu/pipeline/download_daf/1234'
     """
     fragment = 'download_daf/%s' % (submission_id,)

-    return urlparse.urljoin(UCSCEncodePipeline, fragment)
+    return urllib.parse.urljoin(UCSCEncodePipeline, fragment)

 
 
 def submission_view_url(submission_id):
 
 
 def submission_view_url(submission_id):


@@ -41,7 +41,7 @@ def submission_view_url(submission_id):
     'http://encodesubmit.ucsc.edu/pipeline/show/1234'
     """
     fragment = 'show/%s' % (submission_id,)
     'http://encodesubmit.ucsc.edu/pipeline/show/1234'
     """
     fragment = 'show/%s' % (submission_id,)

-    return urlparse.urljoin(UCSCEncodePipeline, fragment)
+    return urllib.parse.urljoin(UCSCEncodePipeline, fragment)

 
 
 def get_encodedcc_file_index(genome, composite):
 
 
 def get_encodedcc_file_index(genome, composite):


@@ -58,10 +58,10 @@ def get_encodedcc_file_index(genome, composite):
         request_url = base_url + 'files.txt'
 
         try:
         request_url = base_url + 'files.txt'
 
         try:

-            request = urllib2.urlopen(request_url)
+            request = urllib.request.urlopen(request_url)

             file_index = parse_ucsc_file_index(request, base_url)
             return file_index
             file_index = parse_ucsc_file_index(request, base_url)
             return file_index

-        except urllib2.HTTPError, e:
+        except urllib.error.HTTPError as e:

             err = e
             pass
 
             err = e
             pass
 

diff --git a/htsworkflow/util/alphanum.py b/htsworkflow/util/alphanum.py
index c9d66495e76fe672a5c41019ce378358c4ee736b..9413f492248cfc8d4f8e9b49f1b0206c9079bc12 100644 (file)
--- a/htsworkflow/util/alphanum.py
+++ b/htsworkflow/util/alphanum.py
@@ -35,12 +35,12 @@ def chunkify(str):
     return a list of numbers and non-numeric substrings of +str+
     the numeric substrings are converted to integer, non-numeric are left as is
     """
     return a list of numbers and non-numeric substrings of +str+
     the numeric substrings are converted to integer, non-numeric are left as is
     """

-    if type(str) in types.StringTypes:
+    if type(str) in str:

         chunks = re.findall("(\d+|\D+)",str)
         #convert numeric strings to numbers
         chunks = [re.match('\d',x) and int(x) or x for x in chunks]
         return chunks
         chunks = re.findall("(\d+|\D+)",str)
         #convert numeric strings to numbers
         chunks = [re.match('\d',x) and int(x) or x for x in chunks]
         return chunks

-    elif type(str) in [types.IntType, types.LongType, types.FloatType]:
+    elif type(str) in [int, int, float]:

         return [str]
     else:
         raise ValueError("Unsupported type %s for input %s" % (type(str), str))
         return [str]
     else:
         raise ValueError("Unsupported type %s for input %s" % (type(str), str))

diff --git a/htsworkflow/util/api.py b/htsworkflow/util/api.py
index 76ee84dc318005fea7281d6b838244fb869b811f..a90503e8d1e6e10d60da4b927adee95b640f0863 100644 (file)
--- a/htsworkflow/util/api.py
+++ b/htsworkflow/util/api.py
@@ -1,7 +1,7 @@
 """Common functions for accessing the HTS Workflow REST API
 """
 import base64
 """Common functions for accessing the HTS Workflow REST API
 """
 import base64

-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser

 import random
 import logging
 
 import random
 import logging
 


@@ -13,9 +13,9 @@ except ImportError:
 
 import os
 from optparse import OptionGroup
 
 import os
 from optparse import OptionGroup

-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse

 
 LOGGER = logging.getLogger(__name__)
 
 
 LOGGER = logging.getLogger(__name__)
 


@@ -79,7 +79,7 @@ def library_url(root_url, library_id):
 
     """
     url_fragment = '/samples/library/%s/json' % (library_id,)
 
     """
     url_fragment = '/samples/library/%s/json' % (library_id,)

-    url = urlparse.urljoin(root_url, url_fragment)
+    url = urllib.parse.urljoin(root_url, url_fragment)

 
     return url
 
 
     return url
 


@@ -99,7 +99,7 @@ def flowcell_url(root_url, flowcell_id):
     http://localhost/experiments/config/1234AAXX/json
     """
     url_fragment = '/experiments/config/%s/json' % (flowcell_id,)
     http://localhost/experiments/config/1234AAXX/json
     """
     url_fragment = '/experiments/config/%s/json' % (flowcell_id,)

-    url = urlparse.urljoin(root_url, url_fragment)
+    url = urllib.parse.urljoin(root_url, url_fragment)

 
     return url
 
 
     return url
 


@@ -120,7 +120,7 @@ def lanes_for_user_url(root_url, username):
 
     """
     url_fragment = '/lanes_for/%s/json' % (username,)
 
     """
     url_fragment = '/lanes_for/%s/json' % (username,)

-    url = urlparse.urljoin(root_url, url_fragment)
+    url = urllib.parse.urljoin(root_url, url_fragment)

 
     return url
 
 
     return url
 


@@ -129,9 +129,9 @@ def retrieve_info(url, apidata):
     Return a dictionary from the HTSworkflow API
     """
     try:
     Return a dictionary from the HTSworkflow API
     """
     try:

-        apipayload = urllib.urlencode(apidata)
-        web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
+        apipayload = urllib.parse.urlencode(apidata)
+        web = urllib.request.urlopen(url, apipayload)
+    except urllib.error.URLError as e:

         if hasattr(e, 'code') and e.code == 404:
             LOGGER.info("%s was not found" % (url,))
             return None
         if hasattr(e, 'code') and e.code == 404:
             LOGGER.info("%s was not found" % (url,))
             return None


@@ -168,7 +168,7 @@ def make_django_secret_key(size=216):
     """return key suitable for use as secret key"""
     try:
         source = random.SystemRandom()
     """return key suitable for use as secret key"""
     try:
         source = random.SystemRandom()

-    except AttributeError, e:
+    except AttributeError as e:

         source = random.random()
     bits = source.getrandbits(size)
     chars = []
         source = random.random()
     bits = source.getrandbits(size)
     chars = []

diff --git a/htsworkflow/util/conversion.py b/htsworkflow/util/conversion.py
index d3eb4f6cc5dad43f619ca8db662ed6abbcc402a2..bc9df065c806a0dc564a49689b287d0e98762d59 100644 (file)
--- a/htsworkflow/util/conversion.py
+++ b/htsworkflow/util/conversion.py
@@ -9,7 +9,7 @@ def unicode_or_none(value):
     if value is None:
         return None
     else:
     if value is None:
         return None
     else:

-        return unicode(value)
+        return str(value)

 
 def parse_flowcell_id(flowcell_id):
     """
 
 def parse_flowcell_id(flowcell_id):
     """

diff --git a/htsworkflow/util/fctracker.py b/htsworkflow/util/fctracker.py
index 5ba33892f741213bb1932292e5821551df379295..8ff8967fae872aae7d514ac9796f59d02e79868f 100644 (file)
--- a/htsworkflow/util/fctracker.py
+++ b/htsworkflow/util/fctracker.py
@@ -57,7 +57,7 @@ class fctracker:
         # extract just the field name
         description = [ f[0] for f in c.description]
         for row in c:
         # extract just the field name
         description = [ f[0] for f in c.description]
         for row in c:

-            row_dict = dict(zip(description, row))
+            row_dict = dict(list(zip(description, row)))

             table[row_dict[pkey_name]] = row_dict
         c.close()
         return table
             table[row_dict[pkey_name]] = row_dict
         c.close()
         return table


@@ -68,11 +68,11 @@ class fctracker:
         """
         library_id_re = re.compile('lane_\d_library_id')
 
         """
         library_id_re = re.compile('lane_\d_library_id')
 

-        for fc_id, fc in self.flowcells.items():
-            lane_library = [ (x[0][5], x[1]) for x in fc.items() 
+        for fc_id, fc in list(self.flowcells.items()):
+            lane_library = [ (x[0][5], x[1]) for x in list(fc.items()) 

                                              if library_id_re.match(x[0]) ]
             for lane, library_id in lane_library:
                                              if library_id_re.match(x[0]) ]
             for lane, library_id in lane_library:

-                if not self.library[library_id].has_key('lanes'):
+                if 'lanes' not in self.library[library_id]:

                     self.library[library_id]['lanes'] = []
                 self.library[library_id]['lanes'].append((fc_id, lane))
 
                     self.library[library_id]['lanes'] = []
                 self.library[library_id]['lanes'].append((fc_id, lane))
 


@@ -110,7 +110,7 @@ class fctracker:
         # extract just the field name
         description = [ f[0] for f in c.description ]
         for row in c:
         # extract just the field name
         description = [ f[0] for f in c.description ]
         for row in c:

-            row_dict = dict(zip(description, row))
+            row_dict = dict(list(zip(description, row)))

             fcid, status = self._parse_flowcell_id(row_dict)
             row_dict['flowcell_id'] = fcid
             row_dict['flowcell_status'] = status
             fcid, status = self._parse_flowcell_id(row_dict)
             row_dict['flowcell_id'] = fcid
             row_dict['flowcell_status'] = status


@@ -173,7 +173,7 @@ def recoverable_drive_report(flowcells):
 
     # sort flowcells by run date
     flowcell_list = []
 
     # sort flowcells by run date
     flowcell_list = []

-    for key, cell in flowcells.items():
+    for key, cell in list(flowcells.items()):

         flowcell_list.append( (cell['run_date'], key) )
     flowcell_list.sort()
 
         flowcell_list.append( (cell['run_date'], key) )
     flowcell_list.sort()
 

diff --git a/htsworkflow/util/hdquery.py b/htsworkflow/util/hdquery.py
index 57c05e6025bf847e31e32875f44b34ea49c6adc6..a4c6b71ba3ff7d2ab853efa85f0a260685f50649 100644 (file)
--- a/htsworkflow/util/hdquery.py
+++ b/htsworkflow/util/hdquery.py
@@ -23,8 +23,8 @@ try:
         #  the 2nd of which is the serial number
         return data.strip('\x00').split()[1]
     
         #  the 2nd of which is the serial number
         return data.strip('\x00').split()[1]
     

-except ImportError, e:
-    print >>sys.stderr, "hdquery requires py_sg"
+except ImportError as e:
+    print("hdquery requires py_sg", file=sys.stderr)

 
     def get_hd_serial_num(device):
         raise NotImplemented('get_hd_serial_num is not available for anything other than linux')
 
     def get_hd_serial_num(device):
         raise NotImplemented('get_hd_serial_num is not available for anything other than linux')

diff --git a/htsworkflow/util/opener.py b/htsworkflow/util/opener.py
index 035bb24dabc9cc43d2f9ae10a3fe8562243230fd..ab83146d39604b1588301b7e016166721d889692 100644 (file)
--- a/htsworkflow/util/opener.py
+++ b/htsworkflow/util/opener.py
@@ -5,7 +5,7 @@ import os
 import gzip
 import bz2
 import types
 import gzip
 import bz2
 import types

-import urllib2
+import urllib.request, urllib.error, urllib.parse

 
 def isfilelike(file_ref, mode):
     """Does file_ref have the core file operations?
 
 def isfilelike(file_ref, mode):
     """Does file_ref have the core file operations?


@@ -47,7 +47,7 @@ def autoopen(file_ref, mode='r'):
     elif isfilelike(file_ref, mode):
         return file_ref
     elif isurllike(file_ref, mode):
     elif isfilelike(file_ref, mode):
         return file_ref
     elif isurllike(file_ref, mode):

-        return urllib2.urlopen(file_ref)
+        return urllib.request.urlopen(file_ref)

     elif os.path.splitext(file_ref)[1] == ".gz":
         return gzip.open(file_ref, mode)
     elif os.path.splitext(file_ref)[1] == '.bz2':
     elif os.path.splitext(file_ref)[1] == ".gz":
         return gzip.open(file_ref, mode)
     elif os.path.splitext(file_ref)[1] == '.bz2':

diff --git a/htsworkflow/util/queuecommands.py b/htsworkflow/util/queuecommands.py
index 4396f0a5b7bcd76259248a84102e008f2d5ae594..4c5a9ee8860ed5769b47f509b2498509c2a90999 100644 (file)
--- a/htsworkflow/util/queuecommands.py
+++ b/htsworkflow/util/queuecommands.py
@@ -75,7 +75,7 @@ class QueueCommands(object):
 
             # build a list of file descriptors
             # fds=file desciptors
 
             # build a list of file descriptors
             # fds=file desciptors

-            fds = [ x.stdout for x in self.running.values()]
+            fds = [ x.stdout for x in list(self.running.values())]

 
             # wait for something to finish
             # wl= write list, xl=exception list (not used so get bad names)
 
             # wait for something to finish
             # wl= write list, xl=exception list (not used so get bad names)

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index cbe2a9188b091d0cb5f22fa99069345728204ee9..76cde06e97d10593e9eef6d166df59e0329270d6 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -3,8 +3,8 @@
 import collections
 from datetime import datetime
 from glob import glob
 import collections
 from datetime import datetime
 from glob import glob

-from urlparse import urlparse, urlunparse
-from urllib2 import urlopen
+from urllib.parse import urlparse, urlunparse
+from urllib.request import urlopen

 import logging
 import os
 import sys
 import logging
 import os
 import sys


@@ -42,9 +42,9 @@ def display_query_results(results):
     """A very simple display of sparql query results showing name value pairs
     """
     for row in results:
     """A very simple display of sparql query results showing name value pairs
     """
     for row in results:

-        for k, v in row.items()[::-1]:
-            print "{0}: {1}".format(k, v)
-        print
+        for k, v in list(row.items())[::-1]:
+            print("{0}: {1}".format(k, v))
+        print()

 
 def html_query_results(result_stream):
     from django.conf import settings
 
 def html_query_results(result_stream):
     from django.conf import settings


@@ -65,11 +65,11 @@ def html_query_results(result_stream):
     for row in result_stream:
         new_row = collections.OrderedDict()
         row_urls = []
     for row in result_stream:
         new_row = collections.OrderedDict()
         row_urls = []

-        for k,v in row.items():
+        for k,v in list(row.items()):

             new_row[k] = Simplified(v)
         results.append(new_row)
     context = Context({'results': results,})
             new_row[k] = Simplified(v)
         results.append(new_row)
     context = Context({'results': results,})

-    print template.render(context)
+    print(template.render(context))

 
 def blankOrUri(value=None):
     """Return a blank node for None or a resource node for strings.
 
 def blankOrUri(value=None):
     """Return a blank node for None or a resource node for strings.


@@ -77,7 +77,7 @@ def blankOrUri(value=None):
     node = None
     if value is None:
         node = RDF.Node()
     node = None
     if value is None:
         node = RDF.Node()

-    elif type(value) in types.StringTypes:
+    elif type(value) in str:

         node = RDF.Node(uri_string=value)
     elif isinstance(value, RDF.Node):
         node = value
         node = RDF.Node(uri_string=value)
     elif isinstance(value, RDF.Node):
         node = value


@@ -88,18 +88,18 @@ def blankOrUri(value=None):
 def toTypedNode(value, language="en"):
     """Convert a python variable to a RDF Node with its closest xsd type
     """
 def toTypedNode(value, language="en"):
     """Convert a python variable to a RDF Node with its closest xsd type
     """

-    if type(value) == types.BooleanType:
+    if type(value) == bool:

         value_type = xsdNS['boolean'].uri
         if value:
         value_type = xsdNS['boolean'].uri
         if value:

-            value = u'1'
+            value = '1'

         else:
         else:

-            value = u'0'
-    elif type(value) in (types.IntType, types.LongType):
+            value = '0'
+    elif type(value) in (int, int):

         value_type = xsdNS['decimal'].uri
         value_type = xsdNS['decimal'].uri

-        value = unicode(value)
-    elif type(value) == types.FloatType:
+        value = str(value)
+    elif type(value) == float:

         value_type = xsdNS['float'].uri
         value_type = xsdNS['float'].uri

-        value = unicode(value)
+        value = str(value)

     elif isinstance(value, datetime):
         value_type = xsdNS['dateTime'].uri
         if value.microsecond == 0:
     elif isinstance(value, datetime):
         value_type = xsdNS['dateTime'].uri
         if value.microsecond == 0:


@@ -108,12 +108,12 @@ def toTypedNode(value, language="en"):
             value = value.strftime(ISOFORMAT_MS)
     else:
         value_type = None
             value = value.strftime(ISOFORMAT_MS)
     else:
         value_type = None

-        value = unicode(value)
+        value = str(value)

 
     if value_type is not None:
         node = RDF.Node(literal=value, datatype=value_type)
     else:
 
     if value_type is not None:
         node = RDF.Node(literal=value, datatype=value_type)
     else:

-        node = RDF.Node(literal=unicode(value).encode('utf-8'), language=language)
+        node = RDF.Node(literal=str(value).encode('utf-8'), language=language)

     return node
 
 
     return node
 
 


@@ -147,7 +147,7 @@ def fromTypedNode(node):
     elif value_type in ('dateTime'):
         try:
             return datetime.strptime(literal, ISOFORMAT_MS)
     elif value_type in ('dateTime'):
         try:
             return datetime.strptime(literal, ISOFORMAT_MS)

-        except ValueError, _:
+        except ValueError as _:

             return datetime.strptime(literal, ISOFORMAT_SHORT)
     return literal
 
             return datetime.strptime(literal, ISOFORMAT_SHORT)
     return literal
 


@@ -249,7 +249,7 @@ def get_model(model_name=None, directory=None):
 
 
 def load_into_model(model, parser_name, path, ns=None):
 
 
 def load_into_model(model, parser_name, path, ns=None):

-    if type(ns) in types.StringTypes:
+    if type(ns) in str:

         ns = RDF.Uri(ns)
 
     if isinstance(path, RDF.Node):
         ns = RDF.Uri(ns)
 
     if isinstance(path, RDF.Node):


@@ -276,7 +276,7 @@ def load_into_model(model, parser_name, path, ns=None):
             retries -= 1
             statements = rdf_parser.parse_as_stream(url, ns)
             retries = 0
             retries -= 1
             statements = rdf_parser.parse_as_stream(url, ns)
             retries = 0

-        except RDF.RedlandError, e:
+        except RDF.RedlandError as e:

             errmsg = "RDF.RedlandError: {0} {1} tries remaining"
             logger.error(errmsg.format(str(e), retries))
 
             errmsg = "RDF.RedlandError: {0} {1} tries remaining"
             logger.error(errmsg.format(str(e), retries))
 


@@ -296,7 +296,7 @@ def load_string_into_model(model, parser_name, data, ns=None):
 def fixup_namespace(ns):
     if ns is None:
         ns = RDF.Uri("http://localhost/")
 def fixup_namespace(ns):
     if ns is None:
         ns = RDF.Uri("http://localhost/")

-    elif type(ns) in types.StringTypes:
+    elif type(ns) in str:

         ns = RDF.Uri(ns)
     elif not(isinstance(ns, RDF.Uri)):
         errmsg = "Namespace should be string or uri not {0}"
         ns = RDF.Uri(ns)
     elif not(isinstance(ns, RDF.Uri)):
         errmsg = "Namespace should be string or uri not {0}"


@@ -330,7 +330,7 @@ def add_default_schemas(model, schema_path=None):
         add_schema(model, schema, namespace)
 
     if schema_path:
         add_schema(model, schema, namespace)
 
     if schema_path:

-        if type(schema_path) in types.StringTypes:
+        if type(schema_path) in str:

             schema_path = [schema_path]
 
         for path in schema_path:
             schema_path = [schema_path]
 
         for path in schema_path:

diff --git a/htsworkflow/util/test/test_alphanum.py b/htsworkflow/util/test/test_alphanum.py
index 29a53859a6bcb70699f0e028039759c15882540d..e6ad5bd644784f87520d2c2b0d061146cb1e08df 100644 (file)
--- a/htsworkflow/util/test/test_alphanum.py
+++ b/htsworkflow/util/test/test_alphanum.py
@@ -1,6 +1,6 @@
 import copy
 import os
 import copy
 import os

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util.alphanum import alphanum
 
 
 from htsworkflow.util.alphanum import alphanum
 


@@ -11,9 +11,9 @@ class testAlphanum(TestCase):
       scratch = copy.copy(unsorted)
       scratch.sort(alphanum)
 
       scratch = copy.copy(unsorted)
       scratch.sort(alphanum)
 

-      for i in xrange(len(scratch)):
+      for i in range(len(scratch)):

         self.failIfEqual(scratch[i], unsorted[i])
         self.failIfEqual(scratch[i], unsorted[i])

-      for i in xrange(len(scratch)):
+      for i in range(len(scratch)):

         self.failUnlessEqual(scratch[i], sorted[i])
 
     def test_numbers(self):
         self.failUnlessEqual(scratch[i], sorted[i])
 
     def test_numbers(self):


@@ -22,9 +22,9 @@ class testAlphanum(TestCase):
       scratch = copy.copy(unsorted)
       scratch.sort(alphanum)
 
       scratch = copy.copy(unsorted)
       scratch.sort(alphanum)
 

-      for i in xrange(len(scratch)):
+      for i in range(len(scratch)):

         self.failIfEqual(scratch[i], unsorted[i])
         self.failIfEqual(scratch[i], unsorted[i])

-      for i in xrange(len(scratch)):
+      for i in range(len(scratch)):

         self.failUnlessEqual(scratch[i], sorted[i])
 
     def test_long_names(self):
         self.failUnlessEqual(scratch[i], sorted[i])
 
     def test_long_names(self):


@@ -42,12 +42,12 @@ class testAlphanum(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testAlphanum))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_api.py b/htsworkflow/util/test/test_api.py
index dadd6afd198fa841c19f81a56f3f6249becbdd47..4d5045738e4df5d131250df368e13e7f9ddb6667 100644 (file)
--- a/htsworkflow/util/test/test_api.py
+++ b/htsworkflow/util/test/test_api.py
@@ -1,6 +1,6 @@
 import copy
 import os
 import copy
 import os

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util import api
 
 
 from htsworkflow.util import api
 


@@ -14,12 +14,12 @@ class testApi(TestCase):
         self.failUnless(k1 != k2)
 
 def suite():
         self.failUnless(k1 != k2)
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestApi))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestApi))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_conversion.py b/htsworkflow/util/test/test_conversion.py
index 4919e56a4c4a6527e4af1c185403e0a6952946ca..6eb15896bc6ac42a1afdeda756995446d3d1c4e3 100644 (file)
--- a/htsworkflow/util/test/test_conversion.py
+++ b/htsworkflow/util/test/test_conversion.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
 #!/usr/bin/env python
 

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util import conversion
 
 
 from htsworkflow.util import conversion
 


@@ -15,12 +15,12 @@ class TestConversion(TestCase):
         self.failUnlessEqual(s.stop, 2)
 
 def suite():
         self.failUnlessEqual(s.stop, 2)
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestConversion))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestConversion))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_ethelp.py b/htsworkflow/util/test/test_ethelp.py
index 461a564ab8f8d325dbb41f0f908555bc0b5d036b..5d982e8a29c200fe49b8393900a13bd600862c9f 100644 (file)
--- a/htsworkflow/util/test/test_ethelp.py
+++ b/htsworkflow/util/test/test_ethelp.py
@@ -1,9 +1,9 @@
 import os
 import os

-from unittest2 import TestCase
+from unittest import TestCase

 
 try:
   from xml.etree import ElementTree
 
 try:
   from xml.etree import ElementTree

-except ImportError, e:
+except ImportError as e:

   from elementtree import ElementTree
 
 from htsworkflow.util.ethelp import indent, flatten
   from elementtree import ElementTree
 
 from htsworkflow.util.ethelp import indent, flatten


@@ -25,12 +25,12 @@ class testETHelper(TestCase):
         self.failUnless(flatten(self.foo_tree), 'asdf')
 
 def suite():
         self.failUnless(flatten(self.foo_tree), 'asdf')
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testETHelper))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testETHelper))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py
index af815b6644236a5df8b0c34d76e32b2342c714f8..2c9ea4f66bdff80ac9ca6c87d2271331acb3866a 100644 (file)
--- a/htsworkflow/util/test/test_makebed.py
+++ b/htsworkflow/util/test/test_makebed.py
@@ -1,6 +1,6 @@
 import os
 import os

-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase

 
 from htsworkflow.util import makebed
 
 
 from htsworkflow.util import makebed
 


@@ -47,12 +47,12 @@ class testMakeBed(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testMakeBed))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testMakeBed))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_queuecommands.py b/htsworkflow/util/test/test_queuecommands.py
index 5885f73515e4422f3acaa39723f57dc1564ab26a..e320819be3094a27e053a3a10e8e02bd4c533a77 100644 (file)
--- a/htsworkflow/util/test/test_queuecommands.py
+++ b/htsworkflow/util/test/test_queuecommands.py
@@ -1,7 +1,7 @@
 import os
 import logging
 import time
 import os
 import logging
 import time

-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util.queuecommands import QueueCommands
 
 
 from htsworkflow.util.queuecommands import QueueCommands
 


@@ -44,12 +44,12 @@ class testQueueCommands(TestCase):
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testQueueCommands))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testQueueCommands))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index 3f328d8d18b43b8ec5bd80fb5f2f4a70501b67a8..bbf380aaf11c8304e5c87007b1f8e837dccf585a 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -1,6 +1,6 @@
 import os
 import types
 import os
 import types

-from unittest2 import TestCase
+from unittest import TestCase

 
 from datetime import datetime
 
 
 from datetime import datetime
 


@@ -33,7 +33,7 @@ try:
 
         def test_typed_node_boolean(self):
             node = toTypedNode(True)
 
         def test_typed_node_boolean(self):
             node = toTypedNode(True)

-            self.assertIn(node.literal_value['string'], (u'1', u'true'))
+            self.assertIn(node.literal_value['string'], ('1', 'true'))

             self.assertEqual(str(node.literal_value['datatype']),
                                  'http://www.w3.org/2001/XMLSchema#boolean')
 
             self.assertEqual(str(node.literal_value['datatype']),
                                  'http://www.w3.org/2001/XMLSchema#boolean')
 


@@ -49,7 +49,7 @@ try:
 
         def test_typed_node_string(self):
             node = toTypedNode('hello')
 
         def test_typed_node_string(self):
             node = toTypedNode('hello')

-            self.assertEqual(node.literal_value['string'], u'hello')
+            self.assertEqual(node.literal_value['string'], 'hello')

             self.assertTrue(node.literal_value['datatype'] is None)
 
         def test_typed_real_like(self):
             self.assertTrue(node.literal_value['datatype'] is None)
 
         def test_typed_real_like(self):


@@ -67,7 +67,7 @@ try:
             s = "Argh matey"
             node = toTypedNode(s)
             self.assertEqual(fromTypedNode(node), s)
             s = "Argh matey"
             node = toTypedNode(s)
             self.assertEqual(fromTypedNode(node), s)

-            self.assertEqual(type(fromTypedNode(node)), types.UnicodeType)
+            self.assertEqual(type(fromTypedNode(node)), str)

 
         def test_blank_or_uri_blank(self):
             node = blankOrUri()
 
         def test_blank_or_uri_blank(self):
             node = blankOrUri()


@@ -86,10 +86,10 @@ try:
             self.assertEqual(node, s)
 
         def test_unicode_node_roundtrip(self):
             self.assertEqual(node, s)
 
         def test_unicode_node_roundtrip(self):

-            literal = u'\u5927'
+            literal = '\u5927'

             roundtrip = fromTypedNode(toTypedNode(literal))
             self.assertEqual(roundtrip, literal)
             roundtrip = fromTypedNode(toTypedNode(literal))
             self.assertEqual(roundtrip, literal)

-            self.assertEqual(type(roundtrip), types.UnicodeType)
+            self.assertEqual(type(roundtrip), str)

 
         def test_datetime_no_microsecond(self):
             dateTimeType = xsdNS['dateTime'].uri
 
         def test_datetime_no_microsecond(self):
             dateTimeType = xsdNS['dateTime'].uri


@@ -261,11 +261,11 @@ _:a owl:imports "{loc}extra.turtle" .
             self.assertTrue(model.contains_statement(s))
 
 
             self.assertTrue(model.contains_statement(s))
 
 

-except ImportError, e:
-    print "Unable to test rdfhelp"
+except ImportError as e:
+    print("Unable to test rdfhelp")

 
 def suite():
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFHelp))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFSchemas))
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFHelp))
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFSchemas))


@@ -273,5 +273,5 @@ def suite():
 
 
 if __name__ == "__main__":
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_rdfinfer.py b/htsworkflow/util/test/test_rdfinfer.py
index b40f46151f2d45c1243318fdd79d7720fcb3ee07..ce733b8ed2a1e9d73fd46a6511ccc16f7b64465d 100644 (file)
--- a/htsworkflow/util/test/test_rdfinfer.py
+++ b/htsworkflow/util/test/test_rdfinfer.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 import RDF
 
 
 import RDF
 


@@ -225,17 +225,17 @@ class TestInfer(TestCase):
         inference = Infer(self.model)
 
         errmsg = list(inference._validate_property_types())
         inference = Infer(self.model)
 
         errmsg = list(inference._validate_property_types())

-        print errmsg
+        print(errmsg)

         self.failUnlessEqual(len(errmsg), 0)
 
 
 def suite():
         self.failUnlessEqual(len(errmsg), 0)
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestInfer))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_url.py b/htsworkflow/util/test/test_url.py
index 979e1441a23a42cb471a8fff78b4c6c8830f99fa..0d2c3a07225dfa5d01e016087121c3fc8d7f6e0e 100644 (file)
--- a/htsworkflow/util/test/test_url.py
+++ b/htsworkflow/util/test/test_url.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util.url import normalize_url, parse_ssh_url
 
 
 from htsworkflow.util.url import normalize_url, parse_ssh_url
 


@@ -36,11 +36,11 @@ class TestURLUtilities(TestCase):
         self.assertRaises(ValueError, parse_ssh_url, 'hello')
         
 def suite():
         self.assertRaises(ValueError, parse_ssh_url, 'hello')
         
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestURLUtilities))
     return suite
 
 if __name__ == '__main__':
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestURLUtilities))
     return suite
 
 if __name__ == '__main__':

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_validate.py b/htsworkflow/util/test/test_validate.py
index cc05f3c56641e645ccbabb8c5006f83c3b7168da..80fed82554fa2fb2ffb1da367a1d6155b7641256 100644 (file)
--- a/htsworkflow/util/test/test_validate.py
+++ b/htsworkflow/util/test/test_validate.py
@@ -1,58 +1,58 @@
 import os
 import os

-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase

 
 from htsworkflow.util import validate
 
 class TestValidate(TestCase):
     def test_phred33_works(self):
 
 from htsworkflow.util import validate
 
 class TestValidate(TestCase):
     def test_phred33_works(self):

-        q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n")
+        q = StringIO("@ abc\nAGCT\n+\nBBBB\n")

         errors = validate.validate_fastq(q)
         self.failUnlessEqual(0, errors)
 
     def test_phred64_works(self):
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(0, errors)
 
     def test_phred64_works(self):

-        q = StringIO(u"@ abc\nAGCT\n+\nfgh]\n")
+        q = StringIO("@ abc\nAGCT\n+\nfgh]\n")

         errors = validate.validate_fastq(q, 'phred64')
         self.failUnlessEqual(0, errors)
 
     def test_fasta_fails(self):
         errors = validate.validate_fastq(q, 'phred64')
         self.failUnlessEqual(0, errors)
 
     def test_fasta_fails(self):

-        q = StringIO(u">abc\nAGCT\n>foo\nCGAT\n")
+        q = StringIO(">abc\nAGCT\n>foo\nCGAT\n")

         errors = validate.validate_fastq(q)
         self.failUnlessEqual(3, errors)
 
     def test_fastq_diff_length_uniform(self):
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(3, errors)
 
     def test_fastq_diff_length_uniform(self):

-        q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n@ abcd\nAGCTT\n+\nJJJJJ\n")
+        q = StringIO("@ abc\nAGCT\n+\nBBBB\n@ abcd\nAGCTT\n+\nJJJJJ\n")

         errors = validate.validate_fastq(q, 'phred33', True)
         self.failUnlessEqual(2, errors)
 
     def test_fastq_diff_length_variable(self):
         errors = validate.validate_fastq(q, 'phred33', True)
         self.failUnlessEqual(2, errors)
 
     def test_fastq_diff_length_variable(self):

-        q = StringIO(u"@ abc\nAGCT\n+\n@@@@\n@ abcd\nAGCTT\n+\nJJJJJ\n")
+        q = StringIO("@ abc\nAGCT\n+\n@@@@\n@ abcd\nAGCTT\n+\nJJJJJ\n")

         errors = validate.validate_fastq(q, 'phred33', False)
         self.failUnlessEqual(0, errors)
 
     def test_fastq_qual_short(self):
         errors = validate.validate_fastq(q, 'phred33', False)
         self.failUnlessEqual(0, errors)
 
     def test_fastq_qual_short(self):

-        q = StringIO(u"@ abc\nAGCT\n+\nJJ\n")
+        q = StringIO("@ abc\nAGCT\n+\nJJ\n")

         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
     def test_fastq_seq_invalid_char(self):
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
     def test_fastq_seq_invalid_char(self):

-        q = StringIO(u"@ abc\nAGC\u1310\n+\nEFGH\n")
+        q = StringIO("@ abc\nAGC\u1310\n+\nEFGH\n")

         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
     def test_fastq_qual_invalid_char(self):
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
     def test_fastq_qual_invalid_char(self):

-        q = StringIO(u"+ abc\nAGC.\n+\n!@#J\n")
+        q = StringIO("+ abc\nAGC.\n+\n!@#J\n")

         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
 
 def suite():
         errors = validate.validate_fastq(q)
         self.failUnlessEqual(1, errors)
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/test/test_version.py b/htsworkflow/util/test/test_version.py
index 212f124314d5e131ec794acb7842d4c9bff16198..f1e4db0ea0e9fd104a23ab5c827245e908a98e13 100644 (file)
--- a/htsworkflow/util/test/test_version.py
+++ b/htsworkflow/util/test/test_version.py
@@ -1,4 +1,4 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 from htsworkflow.util import version
 
 
 from htsworkflow.util import version
 


@@ -11,11 +11,11 @@ class TestVersion(TestCase):
         
 
 def suite():
         
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTest(defaultTestLoader.loadTestsFromTestCase(TestVersion))
     return suite
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTest(defaultTestLoader.loadTestsFromTestCase(TestVersion))
     return suite
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/htsworkflow/util/validate.py b/htsworkflow/util/validate.py
index 959acc281db0b951d0d0dc2dec17023eddc9be47..93842c7ad4e7fe4e4d3c28c9948c6ccd6a68845e 100644 (file)
--- a/htsworkflow/util/validate.py
+++ b/htsworkflow/util/validate.py
@@ -19,7 +19,7 @@ def main(cmdline=None):
                                     opts.uniform_lengths,
                                     opts.max_errors)
             if errors > 0:
                                     opts.uniform_lengths,
                                     opts.max_errors)
             if errors > 0:

-                print "%s failed validation" % (filename,)
+                print("%s failed validation" % (filename,))

                 error_happened = True
 
         stream.close()
                 error_happened = True
 
         stream.close()


@@ -110,7 +110,7 @@ def validate_fastq(stream, format='phred33', uniform_length=False, max_errors=No
 
 def validate_re(pattern, line, line_number, errmsg):
     if pattern.match(line) is None:
 
 def validate_re(pattern, line, line_number, errmsg):
     if pattern.match(line) is None:

-        print errmsg, "[%d]: %s" % (line_number, line)
+        print(errmsg, "[%d]: %s" % (line_number, line))

         return 1
     else:
         return 0
         return 1
     else:
         return 0


@@ -123,7 +123,7 @@ def validate_length(line, line_length, line_number, errmsg):
     if line_length is None:
         line_length = len(line)
     elif len(line) != line_length:
     if line_length is None:
         line_length = len(line)
     elif len(line) != line_length:

-        print errmsg, "%d: %s" %(line_number, line)
+        print(errmsg, "%d: %s" %(line_number, line))

         error_count = 1
     return line_length, error_count
     
         error_count = 1
     return line_length, error_count
     

diff --git a/htsworkflow/util/version.py b/htsworkflow/util/version.py
index 8097edbedb8d95acddad2c9626d47050c4d92817..56a1b113513345e0fe4fcf84115d70e86c774379 100644 (file)
--- a/htsworkflow/util/version.py
+++ b/htsworkflow/util/version.py
@@ -8,13 +8,13 @@ def version():
     version = None
     try:
         import pkg_resources
     version = None
     try:
         import pkg_resources

-    except ImportError, e:
+    except ImportError as e:

         LOGGER.error("Can't find version number, please install setuptools")
         raise e
 
     try:
         version = pkg_resources.get_distribution("htsworkflow")
         LOGGER.error("Can't find version number, please install setuptools")
         raise e
 
     try:
         version = pkg_resources.get_distribution("htsworkflow")

-    except pkg_resources.DistributionNotFound, e:
+    except pkg_resources.DistributionNotFound as e:

         LOGGER.error("Package not installed")
 
     return version
         LOGGER.error("Package not installed")
 
     return version

diff --git a/scripts/rerun_eland.py b/scripts/rerun_eland.py
index 01c7a9f00361980b2627d0ba1a3b35a497810f6b..6741bca9053a37b72ccbf48291c344e2a700e26a 100644 (file)
--- a/scripts/rerun_eland.py
+++ b/scripts/rerun_eland.py
@@ -73,7 +73,7 @@ def rerun(gerald_dir, output_dir, length=25, dry_run=False):
         if not dry_run: os.mkdir(output_dir)
 
     processes = []
         if not dry_run: os.mkdir(output_dir)
 
     processes = []

-    for lane_id, lane_param in g.lanes.items():
+    for lane_id, lane_param in list(g.lanes.items()):

         eland = g.eland_results[lane_id]
 
         inpathname = eland.pathname
         eland = g.eland_results[lane_id]
 
         inpathname = eland.pathname

diff --git a/test/test_copier.py b/test/test_copier.py
index 3e26cc679605f36d45d5f24016a99f959df63b4e..e30f60452eb833ff0787822067d8e348b28e22f0 100644 (file)
--- a/test/test_copier.py
+++ b/test/test_copier.py
@@ -1,6 +1,6 @@
-from unittest2 import TestCase
+from unittest import TestCase

 
 

-from StringIO import StringIO
+from io import StringIO

 from htsworkflow.automation import copier
 from htsworkflow.automation.solexa import is_runfolder
 
 from htsworkflow.automation import copier
 from htsworkflow.automation.solexa import is_runfolder
 


@@ -76,12 +76,12 @@ notify_users: user3@example.fake
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testCopier))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py
index 9185fffde9d516d8651a5ade40723645ab82fa26..99b7ce752137359f3aa04aa5522ce40639a2a677 100644 (file)
--- a/test/test_srf2fastq.py
+++ b/test/test_srf2fastq.py
@@ -1,7 +1,7 @@
 import os
 import os

-from StringIO import StringIO
+from io import StringIO

 import sys
 import sys

-from unittest2 import TestCase
+from unittest import TestCase

 
 _module_path, _module_name = os.path.split(__file__)
 sys.path.append(os.path.join(_module_path, '..', 'scripts'))
 
 _module_path, _module_name = os.path.split(__file__)
 sys.path.append(os.path.join(_module_path, '..', 'scripts'))


@@ -137,12 +137,12 @@ IIIIB+++
 
 
 def suite():
 
 
 def suite():

-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader

     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
     return suite
 
 
 if __name__ == "__main__":
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
     return suite
 
 
 if __name__ == "__main__":

-    from unittest2 import main
+    from unittest import main

     main(defaultTest="suite")
     main(defaultTest="suite")

diff --git a/test/tree.py b/test/tree.py
index 4f666cc14a3b4f3326a66ecec138572a5a8bd05a..2d7653ec0307f82a4217672232b589ec9d51a3de 100644 (file)
--- a/test/tree.py
+++ b/test/tree.py
@@ -12,7 +12,7 @@ def make_random_string(length=8):
   """
   symbols = "abcdefhijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
   name = []
   """
   symbols = "abcdefhijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
   name = []

-  for i in xrange(length):
+  for i in range(length):

     name.append(random.choice(symbols))
   return "".join(name)
 
     name.append(random.choice(symbols))
   return "".join(name)
 


@@ -77,5 +77,5 @@ def compare_tree(root, paths, verbose=False):
   difference = experimental_set - theoretical_set
   issame = (len(difference) == 0)
   if verbose and not issame:
   difference = experimental_set - theoretical_set
   issame = (len(difference) == 0)
   if verbose and not issame:

-    print difference
+    print(difference)

   return issame
   return issame