self.sequences_path = sequences_path
self.log_path = log_path
self.force = force
+ LOGGER.info("CondorFastq host={0}".format(self.host))
+ LOGGER.info("CondorFastq sequences_path={0}".format(self.sequences_path))
+ LOGGER.info("CondorFastq log_path={0}".format(self.log_path))
def create_scripts(self, result_map ):
"""
flowcell_ids = self.find_relavant_flowcell_ids()
self.import_sequences(flowcell_ids)
+
query = RDF.SPARQLQuery("""
prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
flowcell_ids = set()
for r in flowcell_query.execute(self.model):
flowcell_ids.add( fromTypedNode(r['flowcell_id']) )
- LOGGER.debug("Flowcells = %s" %(unicode(flowcell_ids)))
+ LOGGER.debug("Flowcells = %s" %(unicode(flowcell_ids)))
+ flowcell_test = RDF.Statement(r['flowcell'],
+ rdfNS['type'],
+ libraryOntology['illumina_flowcell'])
+ if not self.model.contains_statement(flowcell_test):
+ # we probably lack full information about the flowcell.
+ load_into_model(self.model, 'rdfa', r['flowcell'])
return flowcell_ids
def import_sequences(self, flowcell_ids):
- seq_dirs = ( os.path.join(self.sequences_path, f)
- for f in flowcell_ids )
+
+ seq_dirs = []
+ for f in flowcell_ids:
+ seq_dirs.append(os.path.join(self.sequences_path, str(f)))
sequences = scan_for_sequences(seq_dirs)
for seq in sequences:
- seq.save_to_model(self.model)
+ seq.save_to_model(self.model, self.host)
update_model_sequence_library(self.model, self.host)
def find_missing_targets(self, result_map, raw_files):