ModelException, \
get_submission_uri
+from django.conf import settings
+from django.template import Context, Template, loader
+
LOGGER = logging.getLogger(__name__)
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'],
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
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])
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 = {}
--- /dev/null
+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. }
+}
+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#>
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 .
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 . }