from htsworkflow.submission.condorfastq import CondorFastqExtract
from htsworkflow.submission.results import ResultMap
from htsworkflow.util.rdfhelp import \
- add_default_schemas, load_string_into_model, dump_model
+ add_default_schemas, dump_model
from htsworkflow.util.rdfinfer import Infer
FCDIRS = [
self.extract = CondorFastqExtract(HOST,
self.flowcelldir,
self.logdir)
- load_string_into_model(self.extract.model, 'turtle', lib_turtle)
+ self.extract.model.parse(data=lib_turtle, format='turtle')
add_default_schemas(self.extract.model)
inference = Infer(self.extract.model)
errmsgs = list(inference.run_validation())
seqs = self.extract.find_archive_sequence_files(self.result_map)
expected = set([
- (u'11154', u'42JUYAAXX', '5', 1, 76, True, 'qseq'),
- (u'11154', u'42JUYAAXX', '5', 2, 76, True, 'qseq'),
- (u'11154', u'61MJTAAXX', '6', 1, 76, False, 'qseq'),
- (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
- (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
- (u'11154', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
- (u'11154', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 1, 202, True, 'split_fastq'),
- (u'12345', u'C02F9ACXX', '3', 2, 202, True, 'split_fastq'),
- (u'11154', u'30221AAXX', '4', 1, 33, False, 'srf'),
- (u'11154', u'30DY0AAXX', '8', 1, 151, True, 'srf')
+ (u'11154', u'42JUYAAXX', u'5', 1, 76, True, 'qseq'),
+ (u'11154', u'42JUYAAXX', u'5', 2, 76, True, 'qseq'),
+ (u'11154', u'61MJTAAXX', u'6', 1, 76, False, 'qseq'),
+ (u'11154', u'C02F9ACXX', u'3', 2, 202, True, 'split_fastq'),
+ (u'11154', u'C02F9ACXX', u'3', 1, 202, True, 'split_fastq'),
+ (u'11154', u'C02F9ACXX', u'3', 1, 202, True, 'split_fastq'),
+ (u'11154', u'C02F9ACXX', u'3', 2, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 1, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 2, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 2, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 1, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 1, 202, True, 'split_fastq'),
+ (u'12345', u'C02F9ACXX', u'3', 2, 202, True, 'split_fastq'),
+ (u'11154', u'30221AAXX', u'4', 1, 33, False, 'srf'),
+ (u'11154', u'30DY0AAXX', u'8', 1, 151, True, 'srf')
])
found = set([(l.library_id, l.flowcell_id, l.lane_number, l.read, l.cycle, l.ispaired, l.filetype) for l in seqs])
self.assertEqual(expected, found)