from htsworkflow.util.rdfhelp import \
blankOrUri, \
- dafTermOntology, \
dump_model, \
+ fromTypedNode, \
get_model, \
- libraryOntology, \
- owlNS, \
- rdfNS, \
- submissionLog, \
- submissionOntology, \
- toTypedNode, \
- fromTypedNode
+ stripNamespace, \
+ toTypedNode
+from htsworkflow.util.rdfns import *
from htsworkflow.util.hashfile import make_md5sum
from htsworkflow.submission.fastqname import FastqName
from htsworkflow.submission.daf import \
d[key] = fromTypedNode(value)
results.append(d)
return results
+
+
+def list_submissions(model):
+ """Return generator of submissions in this model.
+ """
+ query_body = """
+ PREFIX subns: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
+
+ select distinct ?submission
+ where { ?submission subns:has_submission ?library_dir }
+ """
+ query = RDF.SPARQLQuery(query_body)
+ rdfstream = query.execute(model)
+ for row in rdfstream:
+ s = stripNamespace(submissionLog, row['submission'])
+ if s[-1] in ['#', '/', '?']:
+ s = s[:-1]
+ yield s