from htsworkflow.util.rdfhelp import \
fromTypedNode, \
geoSoftNS, \
- stripNamespace, \
+ strip_namespace, \
submissionOntology
from django.conf import settings
data = {}
for k, v in row.items():
data[k] = v
- lane = str(data['lane'])
- lanes.setdefault(lane, []).append(data)
+ library = str(data['library'])
+ lanes.setdefault(library, []).append(data)
result = []
- for lane, files in lanes.items():
+ for library, files in lanes.items():
if len(files) > 2:
errmsg = "Don't know what to do with more than 2 raw files"
raise ValueError(errmsg)
elif len(files) == 1:
is_paired = False
elif len(files) == 0:
- raise RuntimeError("Empty lane list discovered")
+ raise RuntimeError("Empty library list discovered")
files = self._format_filename(files, is_paired)
files = self._format_flowcell_type(files, is_paired)
files = self._format_read_length(files, is_paired)
def query_to_soft_dictionary(self, results, heading):
attributes = []
for r in results:
- name = stripNamespace(geoSoftNS, r['name'])
+ name = strip_namespace(geoSoftNS, r['name'])
if name is not None:
if name.lower() == heading.lower():
name = '^' + name