Update test to work with species -> species_name rename.

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
new file mode 100644 (file)
index 0000000..197d7f3
--- /dev/null
+++ b/encode_submission/encode3.py
@@ -0,0 +1,182 @@
+"""Create a track hub 
+"""
+
+#!/usr/bin/env python
+from ConfigParser import SafeConfigParser
+import fnmatch
+from glob import glob
+import json
+import logging
+import netrc
+from optparse import OptionParser, OptionGroup
+import os
+from pprint import pprint, pformat
+import shlex
+from StringIO import StringIO
+import stat
+import sys
+import time
+import types
+import urllib
+import urllib2
+import urlparse
+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
+from htsworkflow.submission.daf import get_submission_uri
+from htsworkflow.submission.results import ResultMap
+from htsworkflow.submission.trackhub import TrackHubSubmission
+from htsworkflow.submission.condorfastq import CondorFastqExtract
+
+logger = logging.getLogger(__name__)
+
+def main(cmdline=None):
+    parser = make_parser()
+    opts, args = parser.parse_args(cmdline)
+    submission_uri = None
+
+    if opts.debug:
+        logging.basicConfig(level = logging.DEBUG )
+    elif opts.verbose:
+        logging.basicConfig(level = logging.INFO )
+    else:
+        logging.basicConfig(level = logging.WARNING )
+
+    apidata = api.make_auth_from_opts(opts, parser)
+
+    model = get_model(opts.model, opts.db_path)
+    mapper = None
+    if opts.name:
+        mapper = TrackHubSubmission(opts.name,  model, host=opts.host)
+        submission_uri = get_submission_uri(opts.name)
+
+
+    if opts.load_rdf is not None:
+        if submission_uri is None:
+            parser.error("Please specify the submission name")
+        load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
+
+    results = ResultMap()
+    for a in args:
+        if os.path.exists(a):
+            results.add_results_from_file(a)
+        else:
+            logger.warn("File %s doesn't exist.", a)
+
+    if opts.make_link_tree_from is not None:
+        results.make_tree_from(opts.make_link_tree_from, link=True)
+
+    if opts.copy_tree_from is not None:
+        results.make_tree_from(opts.copy_tree_from, link=False)
+
+    if opts.fastq:
+        logger.info("Building fastq extraction scripts")
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
+                                       model=opts.model,
+                                       force=opts.force)
+        extractor.create_scripts(results)
+
+    if opts.scan_submission:
+        if opts.name is None:
+            parser.error("Please define a submission name")
+        mapper.scan_submission_dirs(results)
+
+    if opts.make_hub:
+        make_hub(mapper, results, opts.make_hub)
+
+    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)
+
+
+def make_hub(mapper, results, filename=None):
+    trackdb = mapper.make_hub(results)
+
+    if filename is None or filename == '-':
+        sys.stdout.write(trackdb)
+    else:
+        with open('trackDb.txt', 'w') as trackstream:
+            trackstream.write(trackdb)
+
+def make_manifest(mapper, results, filename=None):
+    manifest = mapper.make_manifest(results)
+
+    if filename is None or filename == '-':
+        sys.stdout.write(manifest)
+    else:
+        with open(filename, 'w') as mainifeststream:
+            mainifeststream.write(manifest)
+        
+def make_parser():
+    parser = OptionParser()
+
+    model = OptionGroup(parser, 'model')
+    model.add_option('--name', help="Set submission name")
+    model.add_option('--db-path', default=None,
+                     help="set rdf database path")
+    model.add_option('--model', default=None,
+      help="Load model database")
+    model.add_option('--load-rdf', default=None,
+      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")
+    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)
+    commands.add_option('--copy-tree-from',
+                      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")
+    commands.add_option('--make-hub', default=None, 
+                        help='name the hub file 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('--daf', default=None, help='specify daf name')
+    parser.add_option('--library-url', default=None,
+                      help="specify an alternate source for library information")
+    # debugging
+    parser.add_option('--verbose', default=False, action="store_true",
+                      help='verbose logging')
+    parser.add_option('--debug', default=False, action="store_true",
+                      help='debug logging')
+
+    api.add_auth_options(parser)
+
+    return parser
+
+if __name__ == "__main__":
+    main()

diff --git a/encode_submission/trackhub.py b/encode_submission/trackhub.py
deleted file mode 100644 (file)
index 197d7f3..0000000
--- a/encode_submission/trackhub.py
+++ /dev/null
@@ -1,182 +0,0 @@
-"""Create a track hub 
-"""
-
-#!/usr/bin/env python
-from ConfigParser import SafeConfigParser
-import fnmatch
-from glob import glob
-import json
-import logging
-import netrc
-from optparse import OptionParser, OptionGroup
-import os
-from pprint import pprint, pformat
-import shlex
-from StringIO import StringIO
-import stat
-import sys
-import time
-import types
-import urllib
-import urllib2
-import urlparse
-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
-from htsworkflow.submission.daf import get_submission_uri
-from htsworkflow.submission.results import ResultMap
-from htsworkflow.submission.trackhub import TrackHubSubmission
-from htsworkflow.submission.condorfastq import CondorFastqExtract
-
-logger = logging.getLogger(__name__)
-
-def main(cmdline=None):
-    parser = make_parser()
-    opts, args = parser.parse_args(cmdline)
-    submission_uri = None
-
-    if opts.debug:
-        logging.basicConfig(level = logging.DEBUG )
-    elif opts.verbose:
-        logging.basicConfig(level = logging.INFO )
-    else:
-        logging.basicConfig(level = logging.WARNING )
-
-    apidata = api.make_auth_from_opts(opts, parser)
-
-    model = get_model(opts.model, opts.db_path)
-    mapper = None
-    if opts.name:
-        mapper = TrackHubSubmission(opts.name,  model, host=opts.host)
-        submission_uri = get_submission_uri(opts.name)
-
-
-    if opts.load_rdf is not None:
-        if submission_uri is None:
-            parser.error("Please specify the submission name")
-        load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
-
-    results = ResultMap()
-    for a in args:
-        if os.path.exists(a):
-            results.add_results_from_file(a)
-        else:
-            logger.warn("File %s doesn't exist.", a)
-
-    if opts.make_link_tree_from is not None:
-        results.make_tree_from(opts.make_link_tree_from, link=True)
-
-    if opts.copy_tree_from is not None:
-        results.make_tree_from(opts.copy_tree_from, link=False)
-
-    if opts.fastq:
-        logger.info("Building fastq extraction scripts")
-        flowcells = os.path.join(opts.sequence, 'flowcells')
-        extractor = CondorFastqExtract(opts.host, flowcells,
-                                       model=opts.model,
-                                       force=opts.force)
-        extractor.create_scripts(results)
-
-    if opts.scan_submission:
-        if opts.name is None:
-            parser.error("Please define a submission name")
-        mapper.scan_submission_dirs(results)
-
-    if opts.make_hub:
-        make_hub(mapper, results, opts.make_hub)
-
-    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)
-
-
-def make_hub(mapper, results, filename=None):
-    trackdb = mapper.make_hub(results)
-
-    if filename is None or filename == '-':
-        sys.stdout.write(trackdb)
-    else:
-        with open('trackDb.txt', 'w') as trackstream:
-            trackstream.write(trackdb)
-
-def make_manifest(mapper, results, filename=None):
-    manifest = mapper.make_manifest(results)
-
-    if filename is None or filename == '-':
-        sys.stdout.write(manifest)
-    else:
-        with open(filename, 'w') as mainifeststream:
-            mainifeststream.write(manifest)
-        
-def make_parser():
-    parser = OptionParser()
-
-    model = OptionGroup(parser, 'model')
-    model.add_option('--name', help="Set submission name")
-    model.add_option('--db-path', default=None,
-                     help="set rdf database path")
-    model.add_option('--model', default=None,
-      help="Load model database")
-    model.add_option('--load-rdf', default=None,
-      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")
-    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)
-    commands.add_option('--copy-tree-from',
-                      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")
-    commands.add_option('--make-hub', default=None, 
-                        help='name the hub file 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('--daf', default=None, help='specify daf name')
-    parser.add_option('--library-url', default=None,
-                      help="specify an alternate source for library information")
-    # debugging
-    parser.add_option('--verbose', default=False, action="store_true",
-                      help='verbose logging')
-    parser.add_option('--debug', default=False, action="store_true",
-                      help='debug logging')
-
-    api.add_auth_options(parser)
-
-    return parser
-
-if __name__ == "__main__":
-    main()

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index c7227216e42d2582129c8dae9dacc1d88638b499..7959d1e13d9a323281885d63454790f34f85c48f 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -247,7 +247,7 @@ thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
         # server is 500 for this library
         self.failUnlessEqual(gel_cut, 100)
 
-        species = daf_mapper._get_library_attribute(libNode, 'species')
+        species = daf_mapper._get_library_attribute(libNode, 'species_name')
         self.failUnlessEqual(species, "Homo sapiens")
 
         with mktempdir('analysis') as analysis_dir:

diff --git a/htsworkflow/submission/trackhub.py b/htsworkflow/submission/trackhub.py
deleted file mode 100644 (file)
index 8b7b424..0000000
--- a/htsworkflow/submission/trackhub.py
+++ /dev/null
@@ -1,78 +0,0 @@
-import logging
-import os
-
-import RDF
-
-from htsworkflow.submission.submission import Submission
-
-from htsworkflow.util.rdfhelp import \
-     fromTypedNode, \
-     geoSoftNS, \
-     stripNamespace, \
-     submissionOntology
-
-from django.conf import settings
-from django.template import Context, loader
-
-LOGGER = logging.getLogger(__name__)
-
-class TrackHubSubmission(Submission):
-    def __init__(self, name, model, host):
-        super(TrackHubSubmission, self).__init__(name, model, host)
-
-    def make_hub(self, result_map):
-        samples = []
-        for lib_id, result_dir in result_map.items():
-            an_analysis = self.get_submission_node(result_dir)
-            metadata = self.get_sample_metadata(an_analysis)
-            if len(metadata) == 0:
-                errmsg = 'No metadata found for {0}'
-                LOGGER.error(errmsg.format(str(an_analysis),))
-                continue
-            elif len(metadata) > 1:
-                errmsg = 'Confused there are more than one sample for %s'
-                LOGGER.debug(errmsg % (str(an_analysis),))
-            metadata = metadata[0]
-            samples.append(metadata)
-
-        template = loader.get_template('trackDb.txt')
-        context = Context({
-            'samples': samples,
-        })
-        return str(template.render(context))
-
-    def make_manifest(self, result_map):
-        files = []
-        for lib_id, result_dir in result_map.items():
-            an_analysis = self.get_submission_node(result_dir)
-            metadata = self.get_manifest_metadata(an_analysis)
-            files.extend(metadata)
-
-        template = loader.get_template('manifest.txt')
-        context = Context({
-            'files': files
-        })
-        return str(template.render(context))
-        
-    def get_sample_metadata(self, analysis_node):
-        """Gather information for filling out sample section of a SOFT file
-        """
-        query_template = loader.get_template('trackhub_samples.sparql')
-
-        context = Context({
-            'submission': str(analysis_node.uri),
-            'submissionSet': str(self.submissionSetNS[''].uri),
-            })
-
-        results = self.execute_query(query_template, context)
-        return results
-
-    def get_manifest_metadata(self, analysis_node):
-        query_template = loader.get_template('trackhub_manifest.sparql')
-
-        context = Context({
-            'submission': str(analysis_node.uri),
-            'submissionSet': str(self.submissionSetNS[''].uri),
-            })
-        results = self.execute_query(query_template, context)
-        return results

diff --git a/htsworkflow/submission/trackhub_submission.py b/htsworkflow/submission/trackhub_submission.py
new file mode 100644 (file)
index 0000000..8b7b424
--- /dev/null
+++ b/htsworkflow/submission/trackhub_submission.py
@@ -0,0 +1,78 @@
+import logging
+import os
+
+import RDF
+
+from htsworkflow.submission.submission import Submission
+
+from htsworkflow.util.rdfhelp import \
+     fromTypedNode, \
+     geoSoftNS, \
+     stripNamespace, \
+     submissionOntology
+
+from django.conf import settings
+from django.template import Context, loader
+
+LOGGER = logging.getLogger(__name__)
+
+class TrackHubSubmission(Submission):
+    def __init__(self, name, model, host):
+        super(TrackHubSubmission, self).__init__(name, model, host)
+
+    def make_hub(self, result_map):
+        samples = []
+        for lib_id, result_dir in result_map.items():
+            an_analysis = self.get_submission_node(result_dir)
+            metadata = self.get_sample_metadata(an_analysis)
+            if len(metadata) == 0:
+                errmsg = 'No metadata found for {0}'
+                LOGGER.error(errmsg.format(str(an_analysis),))
+                continue
+            elif len(metadata) > 1:
+                errmsg = 'Confused there are more than one sample for %s'
+                LOGGER.debug(errmsg % (str(an_analysis),))
+            metadata = metadata[0]
+            samples.append(metadata)
+
+        template = loader.get_template('trackDb.txt')
+        context = Context({
+            'samples': samples,
+        })
+        return str(template.render(context))
+
+    def make_manifest(self, result_map):
+        files = []
+        for lib_id, result_dir in result_map.items():
+            an_analysis = self.get_submission_node(result_dir)
+            metadata = self.get_manifest_metadata(an_analysis)
+            files.extend(metadata)
+
+        template = loader.get_template('manifest.txt')
+        context = Context({
+            'files': files
+        })
+        return str(template.render(context))
+        
+    def get_sample_metadata(self, analysis_node):
+        """Gather information for filling out sample section of a SOFT file
+        """
+        query_template = loader.get_template('trackhub_samples.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            'submissionSet': str(self.submissionSetNS[''].uri),
+            })
+
+        results = self.execute_query(query_template, context)
+        return results
+
+    def get_manifest_metadata(self, analysis_node):
+        query_template = loader.get_template('trackhub_manifest.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            'submissionSet': str(self.submissionSetNS[''].uri),
+            })
+        results = self.execute_query(query_template, context)
+        return results