Further clean up ddf generation.

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

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index e1a9b1f113927dd431fcc43512918ea46f20f104..28f75999ce80974198a8dad9858524c06b896d71 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -20,12 +20,16 @@ from htsworkflow.util.rdfhelp import \
      submissionOntology, \
      toTypedNode, \
      fromTypedNode
+from htsworkflow.util.hashfile import make_md5sum
 
 logger = logging.getLogger(__name__)
 
 #
 class ModelException(RuntimeError): pass
-    
+class MetadataLookupException(RuntimeError):
+    """Problem accessing metadata"""
+    pass
+
 # STATES
 DAF_HEADER = 1
 DAF_VIEW = 2
@@ -154,6 +158,8 @@ def _views_to_statements(name, dafNS, views):
         view_attributes = views[view_name]
         viewSubject = viewNS[view_name]
         statements.append(RDF.Statement(subject, dafNS['views'], viewSubject))
+        statements.append(
+            RDF.Statement(viewSubject, dafNS['name'], toTypedNode(view_name)))
         for view_attribute_name in view_attributes:
             predicate = dafNS[view_attribute_name]
             obj = toTypedNode(view_attributes[view_attribute_name])
@@ -234,18 +240,6 @@ class DAFMapper(object):
         for f in submission_files:
             self.construct_file_attributes(submission_dir, libNode, f)
 
-            #attributes['md5sum'] = "None"
-            #
-            #ext = attributes["filename_re"]
-            #if attributes.get("type", None) == 'fastq':
-            #    fastqs.setdefault(ext, set()).add(f)
-            #    fastq_attributes[ext] = attributes
-            #else:
-            #    md5sum = make_md5sum(os.path.join(result_dir,f))
-            #    if md5sum is not None:
-            #        attributes['md5sum']=md5sum
-            #print attributes
-            
         
     def construct_file_attributes(self, submission_dir, libNode, pathname):
         """Looking for the best extension
@@ -263,23 +257,28 @@ class DAFMapper(object):
         if str(view) == str(libraryOntology['ignore']):
             return None
 
-        submissionName = toTypedNode(self.make_submission_name(submission_dir))
+        submission_name = self.make_submission_name(submission_dir)
         submissionNode = self.get_submission_node(submission_dir)
+        submission_uri = str(submissionNode.uri)
+        view_name = fromTypedNode(self.model.get_target(view, dafTermOntology['name']))
+        submissionView = RDF.Node(RDF.Uri(submission_uri + '/' + view_name))
+
         self.model.add_statement(
             RDF.Statement(self.submissionSet, dafTermOntology['has_submission'], submissionNode))
 
-        fileNode = RDF.Node(RDF.Uri(str(submissionNode.uri) + '/' +filename))
-        self.model.add_statement(RDF.Statement(submissionNode, submissionOntology['has_view'], view))
-        self.model.add_statement(RDF.Statement(submissionNode, submissionOntology['name'], submissionName))
+        self.model.add_statement(RDF.Statement(submissionNode, submissionOntology['has_view'], submissionView))
+        self.model.add_statement(RDF.Statement(submissionNode, submissionOntology['name'], toTypedNode(submission_name)))
         self.model.add_statement(RDF.Statement(submissionNode, rdfNS['type'], submissionOntology['submission']))
-
+        self.model.add_statement(RDF.Statement(submissionNode, submissionOntology['library'], libNode))
+        
+        # add trac specific information
         self.model.add_statement(
-            RDF.Statement(view, dafTermOntology['filename'], toTypedNode(filename)))
+            RDF.Statement(submissionView, dafTermOntology['view'], view))
         self.model.add_statement(
-            RDF.Statement(view, dafTermOntology['paired'], toTypedNode(self._is_paired(libNode))))
+            RDF.Statement(submissionView, dafTermOntology['paired'], toTypedNode(self._is_paired(libNode))))
         self.model.add_statement(
-            RDF.Statement(view, dafTermOntology['submission'], submissionNode))
-            
+            RDF.Statement(submissionView, dafTermOntology['submission'], submissionNode))
+
         # extra information 
         terms = [dafTermOntology['type'],
                  dafTermOntology['filename_re'],
@@ -290,7 +289,22 @@ class DAFMapper(object):
         for term in terms:
             value = self._get_library_attribute(libNode, term)
             if value is not None:
-                self.model.add_statement(RDF.Statement(view, term, value))
+                self.model.add_statement(RDF.Statement(submissionView, term, value))
+
+        # add file specific information
+        fileNode = RDF.Node(RDF.Uri(submission_uri + '/' + filename))
+        submission_pathname = os.path.join(submission_dir, filename)
+        md5 = make_md5sum(submission_pathname)
+        self.model.add_statement(
+            RDF.Statement(submissionView, dafTermOntology['has_file'], fileNode))
+        self.model.add_statement(
+            RDF.Statement(fileNode, dafTermOntology['filename'], filename))
+
+        if md5 is None:
+            logging.warning("Unable to produce md5sum for %s" % ( submission_pathname))
+        else:
+            self.model.add_statement(
+                RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
 
             
     def _add_library_details_to_model(self, libNode):
@@ -324,7 +338,7 @@ class DAFMapper(object):
             raise RuntimeError(
                 "Submission dir name too short: %s" %(submission_dir,))
         return submission_dir_name
-    
+        
     def get_submission_node(self, submission_dir):
         """Convert a submission directory name to a submission node
         """
@@ -423,4 +437,12 @@ class DAFMapper(object):
         elif library_type in paired:
             return True
         else:
-            raise RuntimeError("Unrecognized library type %s" % (library_type,))
+            raise MetadataLookupException(
+                "Unrecognized library type %s for %s" % \
+                (library_type, str(libNode)))
+
+    def _get_library_url(self):
+        return str(self.libraryNS[''].uri)
+    def _set_library_url(self, value):
+        self.libraryNS = RDF.NS(str(value))
+    library_url = property(_get_library_url, _set_library_url)