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 6dd630aeda90fe5ad08a96da8be610f628642b04..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'],