# some specific tests
if lib.id == '10981':
# test a case where there is no known status
- lane_set = {u'status': u'Unknown', u'paired_end': True, u'read_length': 75, u'lane_number': 1, u'flowcell': u'303TUAAXX', u'status_code': None}
+ lane_set = {u'status': u'Unknown',
+ u'paired_end': True,
+ u'read_length': 75,
+ u'lane_number': 1,
+ u'lane_id': 1193,
+ u'flowcell': u'303TUAAXX',
+ u'status_code': None}
self.failUnlessEqual(len(d['lane_set']), 1)
self.failUnlessEqual(d['lane_set'][0], lane_set)
elif lib.id == '11016':
# test a case where there is a status
- lane_set = {u'status': 'Good', u'paired_end': True, u'read_length': 75, u'lane_number': 5, u'flowcell': u'303TUAAXX', u'status_code': 2}
+ lane_set = {u'status': 'Good',
+ u'paired_end': True,
+ u'read_length': 75,
+ u'lane_number': 5,
+ u'lane_id': 1197,
+ u'flowcell': u'303TUAAXX',
+ u'status_code': 2}
self.failUnlessEqual(len(d['lane_set']), 1)
self.failUnlessEqual(d['lane_set'][0], lane_set)
[u'http://localhost/lane/1193'],
p=libNS['has_lane'])
+ fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
self.check_literal_object(model,
[u"303TUAAXX"],
- s=RDF.Uri('http://localhost/flowcell/303TUAAXX/'))
+ s=fc_uri, p=libNS['flowcell_id'])
def check_literal_object(self, model, values, s=None, p=None, o=None):
statements = list(model.find_statements(
cl.result_count = unicode(cl.paginator._count)
return {'library_list': records }
+
def library(request, todo_only=False):
queryset = Library.objects.filter(hidden__exact=0)
if todo_only:
c = RequestContext(request, context)
return HttpResponse( t.render(c) )
+
def library_not_run(request):
return library(request, todo_only=True)
+
def library_to_flowcells(request, lib_id):
"""
Display information about all the flowcells a library has been run on.
for lane in lib.lane_set.all():
lane_info.append( {'flowcell':lane.flowcell.flowcell_id,
'lane_number': lane.lane_number,
+ 'lane_id': lane.id,
'paired_end': lane.flowcell.paired_end,
'read_length': lane.flowcell.read_length,
'status_code': lane.status,
import types
from htsworkflow.pipelines.sequences import scan_for_sequences
+from htsworkflow.pipelines.samplekey import SampleKey
from htsworkflow.pipelines import qseq2fastq
from htsworkflow.pipelines import srf2fastq
from htsworkflow.pipelines import desplit_fastq
LOGGER = logging.getLogger(__name__)
+
class CondorFastqExtract(object):
def __init__(self, host, apidata, sequences_path,
log_path='log',
"""
template_map = {'srf': 'srf.condor',
'qseq': 'qseq.condor',
- 'split_fastq': 'split_fastq.condor'}
+ 'split_fastq': 'split_fastq.condor',
+ 'by_sample': 'lane_to_fastq.turtle',
+ }
condor_entries = self.build_condor_arguments(result_map)
for script_type in template_map.keys():
'logdir': self.log_path,
'env': os.environ.get('PYTHONPATH', None),
'args': condor_entries[script_type],
+ 'root_url': self.api.root_url,
}
-
context = Context(variables)
with open(script_type + '.condor','w+') as outstream:
condor_entries = {'srf': [],
'qseq': [],
'split_fastq': []}
+
conversion_funcs = {'srf': self.condor_srf_to_fastq,
'qseq': self.condor_qseq_to_fastq,
'split_fastq': self.condor_desplit_fastq
}
-
+ by_sample = {}
lib_db = self.find_archive_sequence_files(result_map)
needed_targets = self.find_missing_targets(result_map, lib_db)
if sources is not None:
condor_entries.setdefault(condor_type, []).append(
conversion(sources, target_pathname))
+ for s in sources:
+ by_sample.setdefault(s.lane_id,[]).append(
+ target_pathname)
else:
print " need file", target_pathname
+ condor_entries['by_sample'] = by_sample
return condor_entries
def find_archive_sequence_files(self, result_map):
for lane in lib_info['lane_set']:
lane_key = (lane['flowcell'], lane['lane_number'])
- candidate_lanes[lane_key] = lib_id
+ candidate_lanes[lane_key] = (lib_id, lane['lane_id'])
seq_dirs.add(os.path.join(self.sequences_path,
'flowcells',
lane['flowcell']))
for seq in candidate_seq_list:
lane_key = (seq.flowcell, seq.lane)
- lib_id = candidate_lanes.get(lane_key, None)
- if lib_id is not None:
+ candidate_key = candidate_lanes.get(lane_key, None)
+ if candidate_key is not None:
+ lib_id, lane_id = candidate_key
+ seq.lane_id = lane_id
lib_info = lib_db[lib_id]
lib_info['lanes'].setdefault(lane_key, set()).add(seq)
'ispaired': sources[0].paired,
}
+ def lane_rdf(self, sources, target_pathname):
+ pass
+
def make_lane_dict(lib_db, lib_id):
"""
Convert the lane_set in a lib_db to a dictionary
u'insert_size': 200,
u'lane_set': [{u'flowcell': u'30221AAXX',
u'lane_number': 4,
+ u'lane_id': 3400,
u'paired_end': False,
u'read_length': 33,
u'status': u'Unknown',
u'status_code': None},
{u'flowcell': u'42JUYAAXX',
u'lane_number': 5,
+ u'lane_id': 4200,
u'paired_end': True,
u'read_length': 76,
u'status': u'Unknown',
u'status_code': None},
{u'flowcell': u'61MJTAAXX',
u'lane_number': 6,
+ u'lane_id': 6600,
u'paired_end': False,
u'read_length': 76,
u'status': u'Unknown',
u'status_code': None},
{u'flowcell': u'30DY0AAXX',
u'lane_number': 8,
+ u'lane_id': 3800,
u'paired_end': True,
u'read_length': 76,
u'status': u'Unknown',
u'status_code': None},
{u'flowcell': u'C02F9ACXX',
u'lane_number': 3,
+ u'lane_id': 12300,
u'paired_end': True,
u'read_length': 101,
u'status': u'Unknown',
class FakeApi(object):
def __init__(self, *args, **kwargs):
- pass
+ self.root_url = 'http://localhost'
def get_library(self, libid):
lib_data = LIBDATA[libid]
return copy.deepcopy(lib_data)
+
+
class TestCondorFastq(unittest.TestCase):
def setUp(self):
self.cwd = os.getcwd()
self.failUnless('11154_NoIndex_L003_R2_002.fastq.gz' in \
arguments[1])
-
def suite():
suite = unittest.makeSuite(TestCondorFastq, 'test')
return suite
--- /dev/null
+{% for key, files in args.items %}{% for f in files %}
+<file://{{ f }}> libraryOntology:has_lane <{{host}}/lane/{{key}}> .
+{% endfor %}{% endfor %}
\ No newline at end of file
projects / htsworkflow.git / commitdiff