Merge changing lane_number to string and sequence finding code changes

[htsworkflow.git] / htsworkflow / submission / submission.py

diff --git a/htsworkflow/submission/submission.py b/htsworkflow/submission/submission.py
index e4ce90c73b073287913ec2f76f5f1d5f0d9bd887..2b04ff43a05ce6e70d6ccb7b20f7f17d54165699 100644 (file)
--- a/htsworkflow/submission/submission.py
+++ b/htsworkflow/submission/submission.py
@@ -83,7 +83,7 @@ class Submission(object):
                                                     rdfNS['type'])
         if file_classification is None:
             errmsg = 'Could not find class for {0}'
-            logger.warning(errmsg.format(str(file_type)))
+            LOGGER.warning(errmsg.format(str(file_type)))
             return
 
         self.model.add_statement(
@@ -126,7 +126,7 @@ class Submission(object):
 
     def link_file_to_classes(self, filename, submissionNode, submission_uri, analysis_dir):
         # add file specific information
-        fileNode = RDF.Node(RDF.Uri(submission_uri + '/' + filename))
+        fileNode = RDF.Node(RDF.Uri('file://'+ os.path.abspath(filename)))
         self.model.add_statement(
             RDF.Statement(submissionNode,
                           dafTermOntology['has_file'],
@@ -149,13 +149,44 @@ class Submission(object):
                 RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
 
     def _add_library_details_to_model(self, libNode):
+        # attributes that can have multiple values
+        set_attributes = set((libraryOntology['has_lane'],
+                              libraryOntology['has_mappings'],
+                              dafTermOntology['has_file']))
         parser = RDF.Parser(name='rdfa')
         new_statements = parser.parse_as_stream(libNode.uri)
+        toadd = []
         for s in new_statements:
+            # always add "collections"
+            if s.predicate in set_attributes:
+                toadd.append(s)
+                continue
             # don't override things we already have in the model
             targets = list(self.model.get_targets(s.subject, s.predicate))
             if len(targets) == 0:
-                self.model.append(s)
+                toadd.append(s)
+
+        for s in toadd:
+            self.model.append(s)
+
+        self._add_lane_details(libNode)
+
+    def _add_lane_details(self, libNode):
+        """Import lane details
+        """
+        query = RDF.Statement(libNode, libraryOntology['has_lane'], None)
+        lanes = []
+        for lane_stmt in self.model.find_statements(query):
+            lanes.append(lane_stmt.object)
+
+        parser = RDF.Parser(name='rdfa')
+        for lane in lanes:
+            LOGGER.debug("Importing %s" % (lane.uri,))
+            try:
+                parser.parse_into_model(self.model, lane.uri)
+            except RDF.RedlandError, e:
+                LOGGER.error("Error accessing %s" % (lane.uri,))
+                raise e
 
 
     def find_best_match(self, filename):