Make it possible to set a label on a track.

This works by setting a term label_template on the filename regex
block. that label_template is then expanded by searching for metadata
in from the related library for that submission.

diff --git a/htsworkflow/submission/submission.py b/htsworkflow/submission/submission.py
index 12a5154c33a01bf15d1349040e7bfd2f71f51df8..626897061ea4d9e4c78141a4cba65c4713011507 100644 (file)
--- a/htsworkflow/submission/submission.py
+++ b/htsworkflow/submission/submission.py
@@ -21,6 +21,9 @@ from htsworkflow.submission.daf import \
      ModelException, \
      get_submission_uri
 
+from django.conf import settings
+from django.template import Context, Template, loader
+
 LOGGER = logging.getLogger(__name__)
 
 class Submission(object):
@@ -121,6 +124,7 @@ class Submission(object):
         fileNode = self.make_file_node(pathname, an_analysis)
         self.add_md5s(filename, fileNode, analysis_dir)
         self.add_fastq_metadata(filename, fileNode)
+        self.add_label(file_type, fileNode, libNode)
         self.model.add_statement(
             RDF.Statement(fileNode,
                           rdfNS['type'],
@@ -182,6 +186,23 @@ class Submission(object):
             if value is not None:
                 s = RDF.Statement(fileNode, model_term, toTypedNode(value))
                 self.model.append(s)
+                
+    def add_label(self, file_type, file_node, lib_node):
+        """Add rdfs:label to a file node
+        """
+        #template_term = libraryOntology['label_template']
+        template_term = libraryOntology['label_template']
+        label_template = self.model.get_target(file_type, template_term)
+        if label_template:
+            template = loader.get_template('submission_view_rdfs_label_metadata.sparql')
+            context = Context({
+                'library': str(lib_node.uri),
+                })
+            for r in self.execute_query(template, context):
+                context = Context(r)
+                label = Template(label_template).render(context)
+                s = RDF.Statement(file_node, rdfsNS['label'], unicode(label))
+                self.model.append(s)
 
     def _add_library_details_to_model(self, libNode):
         # attributes that can have multiple values

diff --git a/htsworkflow/submission/trackhub_submission.py b/htsworkflow/submission/trackhub_submission.py
index 4720737ab924bb002cbed50db9f7f685d223ea75..7a83e8770ee39515ffe90fa223bce3ea19767e47 100644 (file)
--- a/htsworkflow/submission/trackhub_submission.py
+++ b/htsworkflow/submission/trackhub_submission.py
@@ -105,12 +105,17 @@ class TrackHubSubmission(Submission):
 
             track_subgroup = self.make_track_subgroups(subgroups, track)
 
+            if 'file_label' in track:
+                track_label = self.sanitize_name(track['file_label'])
+            else:
+                track_label = track_name
+
             newtrack = Track(
                 name=track_name,
                 tracktype = str(track['file_type']),
                 url= hub_url + str(track['relative_path']),
                 short_label=str(track['library_id']),
-                long_label=track_name,
+                long_label=str(track_label),
                 subgroups=track_subgroup,
                 )
             view.add_tracks([newtrack])
@@ -155,12 +160,11 @@ class TrackHubSubmission(Submission):
         return str(template.render(context))
 
     def make_track_name(self, track):
-        name = '{}_{}_{}'.format(
+        return '{}_{}_{}'.format(
             track['library_id'],
             track['replicate'],
             track['output_type'],
         )
-        return name
 
     def make_track_subgroups(self, subgroups, track):
         track_subgroups = {}

diff --git a/htsworkflow/templates/submission_view_rdfs_label_metadata.sparql b/htsworkflow/templates/submission_view_rdfs_label_metadata.sparql
new file mode 100644 (file)
index 0000000..0666e62
--- /dev/null
+++ b/htsworkflow/templates/submission_view_rdfs_label_metadata.sparql
@@ -0,0 +1,10 @@
+PREFIX htsw: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+PREFIX encode3: <http://jumpgate.caltech.edu/wiki/Encode3#>
+
+select ?cell_line ?assay ?protocol ?lab
+where {
+    optional { <{{ library }}> htsw:cell_line ?cell_line . }
+    optional { <{{ library }}> encode3:assay ?assay . }
+    optional { <{{ library }}> encode3:protocol ?protocol. }
+    optional { <{{ library }}> encode3:lab ?lab. }
+}

diff --git a/htsworkflow/templates/trackhub_samples.sparql b/htsworkflow/templates/trackhub_samples.sparql
index 19ce7e1d5d7f32d35b88e961c867095104dbde88..95152747b43a5ed4109e8dd8fb020edb120bfc80 100644 (file)
--- a/htsworkflow/templates/trackhub_samples.sparql
+++ b/htsworkflow/templates/trackhub_samples.sparql
@@ -1,3 +1,5 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 PREFIX htswlib: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
 PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
@@ -6,8 +8,7 @@ PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
 PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
 PREFIX encode3: <http://jumpgate.caltech.edu/wiki/Encode3#>
 
-select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol 
-
+select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol ?file_label
 WHERE {
   ?trackType geoSoft:fileTypeLabel ?file_type ;
              ucscDaf:output_type ?output_type .
@@ -15,6 +16,7 @@ WHERE {
         ucscDaf:relative_path ?relative_path ;
         htswlib:library ?library ;
         a ?trackType .
+  OPTIONAL { ?file rdfs:label ?file_label . }
   OPTIONAL { ?library htswlib:library_id ?lab_library_id }
   OPTIONAL { ?library encode3:library_id ?library_id }
   OPTIONAL { ?library htswlib:cell_line ?cell . }