convert to print_function, and start adding unicode_literals future as well

[htsworkflow.git] / encode_submission / encode3.py

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
index a77151e1ead7d2a91091a58a4451a01bcd569d72..29352d5a4d6ad561b3148a39310c8ec580ff956b 100644 (file)
--- a/encode_submission/encode3.py
+++ b/encode_submission/encode3.py
@@ -1,7 +1,8 @@
-"""Create a track hub 
+#!/usr/bin/env python
+"""Create a track hub
 """
+from __future__ import print_function, unicode_literals
 
-#!/usr/bin/env python
 from ConfigParser import SafeConfigParser
 import fnmatch
 from glob import glob
@@ -12,7 +13,7 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
-from StringIO import StringIO
+from six.moves import StringIO
 import stat
 import sys
 import time
@@ -24,18 +25,15 @@ from zipfile import ZipFile
 
 import RDF
 
-if not 'DJANGO_SETTINGS_MODULE' in os.environ:
-    os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
-
 from htsworkflow.util import api
 from htsworkflow.util.rdfhelp import \
-     dafTermOntology, \
-     fromTypedNode, \
-     get_model, \
-     get_serializer, \
-     load_into_model, \
-     sparql_query, \
-     submissionOntology
+    dafTermOntology, \
+    fromTypedNode, \
+    get_model, \
+    get_serializer, \
+    load_into_model, \
+    sparql_query, \
+    submissionOntology
 from htsworkflow.submission.daf import get_submission_uri
 from htsworkflow.submission.submission import list_submissions
 from htsworkflow.submission.results import ResultMap
@@ -46,19 +44,21 @@ logger = logging.getLogger(__name__)
 
 INDENTED = "  " + os.linesep
 
+import django
+if not 'DJANGO_SETTINGS_MODULE' in os.environ:
+    os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings.local'
+
 def main(cmdline=None):
     parser = make_parser()
     opts, args = parser.parse_args(cmdline)
     submission_uri = None
 
+    from django.conf import settings
+
     if opts.debug:
-        logging.basicConfig(level = logging.DEBUG )
+        settings.LOGGING['loggers']['level'] = 'DEBUG'
     elif opts.verbose:
-        logging.basicConfig(level = logging.INFO )
-    else:
-        logging.basicConfig(level = logging.WARNING )
-
-    apidata = api.make_auth_from_opts(opts, parser)
+        settings.LOGGING['loggers']['level'] = 'INFO'
 
     model = get_model(opts.model, opts.db_path)
 
@@ -77,7 +77,7 @@ def main(cmdline=None):
             INDENTED.join(submission_names)))
     elif len(submission_names) == 1:
         name = submission_names[0]
-        
+
     if name:
         submission_uri = get_submission_uri(name)
         logger.info('Submission URI: %s', name)
@@ -115,6 +115,7 @@ def main(cmdline=None):
         flowcells = os.path.join(opts.sequence, 'flowcells')
         extractor = CondorFastqExtract(opts.host, flowcells,
                                        model=opts.model,
+                                       compression=opts.compression,
                                        force=opts.force)
         extractor.create_scripts(results)
 
@@ -130,13 +131,13 @@ def main(cmdline=None):
 
     if opts.make_manifest:
         make_manifest(mapper, results, opts.make_manifest)
-        
+
     if opts.sparql:
         sparql_query(model, opts.sparql)
 
     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):
@@ -147,7 +148,8 @@ def make_manifest(mapper, results, filename=None):
     else:
         with open(filename, 'w') as mainifeststream:
             mainifeststream.write(manifest)
-        
+
+
 def make_parser():
     parser = OptionParser()
 
@@ -156,38 +158,40 @@ def make_parser():
     model.add_option('--db-path', default=None,
                      help="set rdf database path")
     model.add_option('--model', default=None,
-      help="Load model database")
+                     help="Load model database")
     model.add_option('--load-rdf', default=None,
-      help="load rdf statements into model")
+                     help="load rdf statements into model")
     model.add_option('--sparql', default=None, help="execute sparql query")
     model.add_option('--print-rdf', action="store_true", default=False,
-      help="print ending model state")
+                     help="print ending model state")
     parser.add_option_group(model)
     # commands
     commands = OptionGroup(parser, 'commands')
     commands.add_option('--make-link-tree-from',
-                      help="create directories & link data files",
-                      default=None)
+                        help="create directories & link data files",
+                        default=None)
     commands.add_option('--copy-tree-from',
-                      help="create directories & copy data files",
-                      default=None)
+                        help="create directories & copy data files",
+                        default=None)
     commands.add_option('--fastq', default=False, action="store_true",
                         help="generate scripts for making fastq files")
     commands.add_option('--scan-submission', default=False, action="store_true",
-                      help="Import metadata for submission into our model")
+                        help="Import metadata for submission into our model")
     commands.add_option('--make-track-hub', default=None,
                         help='web root that will host the trackhub.')
     commands.add_option('--track-hub-upload', default=None,
                         help='where to upload track hub <host>:<path>')
-    commands.add_option('--make-manifest', 
-                        help='name the manifest file name or - for stdout to create it', 
+    commands.add_option('--make-manifest',
+                        help='name the manifest file name or - for stdout to create it',
                         default=None)
 
-
     parser.add_option_group(commands)
 
     parser.add_option('--force', default=False, action="store_true",
                       help="Force regenerating fastqs")
+    parser.add_option('--compression', default=None, type='choice',
+                      choices=['gzip'],
+                      help='select compression type for fastq files')
     parser.add_option('--daf', default=None, help='specify daf name')
     parser.add_option('--library-url', default=None,
                       help="specify an alternate source for library information")
@@ -202,4 +206,6 @@ def make_parser():
     return parser
 
 if __name__ == "__main__":
+    django.setup()
+
     main()