From: Diane Trout Date: Thu, 29 Jan 2015 19:43:18 +0000 (-0800) Subject: convert to print_function, and start adding unicode_literals future as well X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=commitdiff_plain;ds=sidebyside;h=534d6ecd79a3055599234662ecc1d3867d893473;p=htsworkflow.git convert to print_function, and start adding unicode_literals future as well --- diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py index 9fe33e8..29352d5 100644 --- a/encode_submission/encode3.py +++ b/encode_submission/encode3.py @@ -1,6 +1,8 @@ #!/usr/bin/env python """Create a track hub """ +from __future__ import print_function, unicode_literals + from ConfigParser import SafeConfigParser import fnmatch from glob import glob @@ -135,7 +137,7 @@ def main(cmdline=None): 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): diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py index 60e0bee..8333ca6 100644 --- a/encode_submission/encode_find.py +++ b/encode_submission/encode_find.py @@ -2,6 +2,7 @@ """ Gather information about our submissions into a single RDF store """ +from __future__ import print_function, unicode_literals from datetime import datetime import hashlib @@ -130,7 +131,7 @@ def main(cmdline=None): 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(): @@ -261,11 +262,11 @@ def report_submissions_with_no_library(model): for row in results: subid = row['subid'] name = row['name'] - print "# {0}".format(name) - print "<{0}>".format(subid.uri) - print " encodeSubmit:library_urn "\ - " ." - print "" + print("# {0}".format(name)) + print("<{0}>".format(subid.uri)) + print(" encodeSubmit:library_urn "\ + " .") + print("") def find_submissions_with_no_library(model): missing_lib_query_text = """ diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py index 1aadb83..53e2d44 100644 --- a/encode_submission/geo_gather.py +++ b/encode_submission/geo_gather.py @@ -1,4 +1,6 @@ #!/usr/bin/env python +from __future__ import print_function, unicode_literals + from ConfigParser import SafeConfigParser import fnmatch from glob import glob @@ -98,7 +100,7 @@ def main(cmdline=None): if opts.print_rdf: writer = get_serializer() - print writer.serialize_model_to_string(model) + print(writer.serialize_model_to_string(model)) def make_parser(): diff --git a/encode_submission/scan_extension.py b/encode_submission/scan_extension.py index 39f19c6..88d53f0 100644 --- a/encode_submission/scan_extension.py +++ b/encode_submission/scan_extension.py @@ -1,3 +1,5 @@ +from __future__ import print_function, unicode_literals + from optparse import OptionParser import os import sys @@ -13,7 +15,7 @@ def main(cmdline=None): if opts.rdf: print_rdf(common_extensions) else: - print common_extensions + print(common_extensions) def make_parser(): parser = OptionParser("%prog: directory [directory...]") @@ -70,7 +72,7 @@ def print_rdf(common_extensions): 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() diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py index bc3515b..6961fa9 100644 --- a/encode_submission/ucsc_gather.py +++ b/encode_submission/ucsc_gather.py @@ -1,4 +1,6 @@ #!/usr/bin/env python +from __future__ import print_function, unicode_literals + from ConfigParser import SafeConfigParser import fnmatch from glob import glob @@ -119,7 +121,7 @@ def main(cmdline=None): if opts.print_rdf: writer = get_serializer() - print writer.serialize_model_to_string(model) + print(writer.serialize_model_to_string(model)) def make_parser(): diff --git a/htsworkflow/pipelines/srf2fastq.py b/htsworkflow/pipelines/srf2fastq.py index 0d895d9..0805879 100644 --- a/htsworkflow/pipelines/srf2fastq.py +++ b/htsworkflow/pipelines/srf2fastq.py @@ -1,4 +1,6 @@ #!/usr/bin/env python +from __future__ import print_function, unicode_literals + import logging import mmap from optparse import OptionParser @@ -27,7 +29,7 @@ def main(cmdline=None): logging.basicConfig(level=logging.WARN) if opts.version: - print version() + print(version()) return 0 if len(args) != 1: @@ -241,7 +243,7 @@ def foo(): 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,)) diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py index 759a13e..0d48787 100644 --- a/htsworkflow/pipelines/test/simulate_runfolder.py +++ b/htsworkflow/pipelines/test/simulate_runfolder.py @@ -1,6 +1,8 @@ """ Create simulated solexa/illumina runfolders for testing """ +from __future__ import print_function, unicode_literals + import gzip import os import shutil @@ -653,12 +655,12 @@ class DemultiplexedPaths(object): 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, self.rootname+'R1_001.fastq.gz'))) @@ -697,7 +699,7 @@ def print_ls_tree(root): """ 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): diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py index cc16f79..d9d38f8 100644 --- a/htsworkflow/util/rdfhelp.py +++ b/htsworkflow/util/rdfhelp.py @@ -1,5 +1,7 @@ """Helper features for working with librdf """ +from __future__ import print_function, unicode_literals + import collections from datetime import datetime from glob import glob @@ -43,8 +45,8 @@ def display_query_results(results): """ for row in results: for k, v in row.items()[::-1]: - print "{0}: {1}".format(k, v) - print + print("{0}: {1}".format(k, v)) + print() def html_query_results(result_stream): from django.conf import settings @@ -69,7 +71,7 @@ def html_query_results(result_stream): 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. diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py index d11d98b..e6bc535 100644 --- a/htsworkflow/util/test/test_rdfhelp.py +++ b/htsworkflow/util/test/test_rdfhelp.py @@ -1,3 +1,5 @@ +from __future__ import print_function, unicode_literals + import os import types from unittest import TestCase @@ -262,7 +264,7 @@ _:a owl:imports "{loc}extra.turtle" . except ImportError as e: - print "Unable to test rdfhelp" + print("Unable to test rdfhelp") def suite(): from unittest import TestSuite, defaultTestLoader diff --git a/inventory/models.py b/inventory/models.py index d41025a..1e85096 100644 --- a/inventory/models.py +++ b/inventory/models.py @@ -28,7 +28,6 @@ def _assign_uuid(sender, instance, **kwargs): """ Assigns a UUID to model on save """ - #print 'Entered _assign_uuid' if instance.uuid is None or len(instance.uuid) != 32: instance.uuid = uuid.uuid1().hex diff --git a/scripts/htsw-srf b/scripts/htsw-srf index bcf835d..d933b80 100755 --- a/scripts/htsw-srf +++ b/scripts/htsw-srf @@ -1,4 +1,5 @@ #!/usr/bin/python +from __future__ import print_function, unicode_literals import logging import optparse @@ -116,9 +117,9 @@ def main(cmdline=None): run_commands(cwd, cmd_list, opts.jobs) else: for cwd, cmd_list in cmds.items(): - print cwd - print cmd_list - print 'jobs: ', opts.jobs + print(cwd) + print(cmd_list) + print('jobs: ', opts.jobs) return 0