import types
from zipfile import ZipFile
-import RDF
-
if not 'DJANGO_SETTINGS_MODULE' in os.environ:
os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
from htsworkflow.util import api
-from htsworkflow.util.rdfhelp import \
+from htsworkflow.util.rdfns import \
dafTermOntology, \
- fromTypedNode, \
- get_model, \
- get_serializer, \
- load_into_model, \
- sparql_query, \
submissionOntology
from htsworkflow.submission.daf import \
UCSCSubmission, \
ORDER BY ?submitView"""
dag_fragments = []
- name = fromTypedNode(view_map.model.get_target(submissionNode, submissionOntology['name']))
- if name is None:
+ names = list(view_map.model.objects(submissionNode, submissionOntology['name']))
+ if len(names) == 0:
logger.error("Need name for %s" % (str(submissionNode)))
return []
- ddf_name = make_ddf_name(name)
+ ddf_name = make_ddf_name(names[0].toPython())
if outdir is not None:
outfile = os.path.join(outdir, ddf_name)
output = open(outfile,'w')
formatted_query = query_template % {'submission': str(submissionNode.uri)}
- query = RDF.SPARQLQuery(formatted_query)
- results = query.execute(view_map.model)
+ results = view_map.model.query(formatted_query)
# filename goes first
variables = view_map.get_daf_variables()
rootdir = os.getcwd()
for lib_id, result_dir in library_result_map:
submissionNode = view_map.get_submission_node(result_dir)
- nameNode = view_map.model.get_target(submissionNode,
- submissionOntology['name'])
- name = fromTypedNode(nameNode)
- if name is None:
+ nameNodes = list(view_map.model.objects(submissionNode,
+ submissionOntology['name']))
+ if len(nameNodes) == 0:
logger.error("Need name for %s" % (str(submissionNode)))
continue
+ name = nameNodes[0].toPython()
zip_name = '../{0}.zip'.format(lib_id)
os.chdir(os.path.join(rootdir, result_dir))