from pprint import pprint
import shutil
import tempfile
-import unittest
+
+from django.test import TestCase
+from django.test.utils import setup_test_environment, \
+ teardown_test_environment
+from django.db import connection
+from django.conf import settings
from htsworkflow.submission.condorfastq import CondorFastqExtract
from htsworkflow.submission.results import ResultMap
-from htsworkflow.util.rdfhelp import load_string_into_model, dump_model
+from htsworkflow.util.rdfhelp import \
+ add_default_schemas, load_string_into_model, dump_model
+from htsworkflow.util.rdfinfer import Infer
FCDIRS = [
'C02F9ACXX',
@prefix seqns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
@prefix invns: <http://jumpgate.caltech.edu/wiki/InventoryOntology#> .
+<http://localhost/library/10000/> a libns:Library .
+<http://localhost/library/1331/> a libns:Library .
+<http://localhost/library/1421/> a libns:Library .
+<http://localhost/library/1661/> a libns:Library .
+
<http://localhost/flowcell/30221AAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 33 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "30221AAXX"@en .
<http://localhost/lane/3401>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 1 .
+ libns:lane_number "1" .
<http://localhost/lane/3402>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 2 .
+ libns:lane_number "2" .
<http://localhost/lane/3403>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
<http://localhost/lane/3404>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/11154/> ;
- libns:lane_number 4 .
+ libns:lane_number "4" .
# paired_end 1;
# read_length 33;
# status "Unknown"@en .
<http://localhost/lane/3405>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 5 .
+ libns:lane_number "5" .
<http://localhost/lane/3406>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 6 .
+ libns:lane_number "6" .
<http://localhost/lane/3407>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 7 .
+ libns:lane_number "7" .
<http://localhost/lane/3408>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
- libns:lane_number 8 .
+ libns:lane_number "8" .
<http://localhost/flowcell/42JUYAAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "42JUYAAXX"@en .
<http://localhost/lane/4201>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 1 .
+ libns:lane_number "1" .
<http://localhost/lane/4202>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 2 .
+ libns:lane_number "2" .
<http://localhost/lane/4203>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
<http://localhost/lane/4204>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 4 .
+ libns:lane_number "4" .
<http://localhost/lane/4205>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/11154/> ;
- libns:lane_number 5 .
+ libns:lane_number "5" .
# paired_end 1;
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/4206>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 6 .
+ libns:lane_number "6" .
<http://localhost/lane/4207>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 7 .
+ libns:lane_number "7" .
<http://localhost/lane/4208>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
- libns:lane_number 8 .
+ libns:lane_number "8" .
<http://localhost/flowcell/61MJTAAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "61MJTAAXX"@en .
<http://localhost/lane/6601>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 1 .
+ libns:lane_number "1" .
<http://localhost/lane/6602>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 2 .
+ libns:lane_number "2" .
<http://localhost/lane/6603>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
<http://localhost/lane/6604>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 4 .
+ libns:lane_number "4" .
<http://localhost/lane/6605>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 5 .
+ libns:lane_number "5" .
<http://localhost/lane/6606>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/11154/> ;
- libns:lane_number 6 .
+ libns:lane_number "6" .
# paired_end 1;
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/6607>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 7 .
+ libns:lane_number "7" .
<http://localhost/lane/6608>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
- libns:lane_number 8 .
+ libns:lane_number "8" .
<http://localhost/flowcell/30DY0AAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "30DY0AAXX"@en .
<http://localhost/lane/3801>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 1 .
+ libns:lane_number "1" .
<http://localhost/lane/3802>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 2 .
+ libns:lane_number "2" .
<http://localhost/lane/3803>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
<http://localhost/lane/3804>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 4 .
+ libns:lane_number "4" .
<http://localhost/lane/3805>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 5 .
+ libns:lane_number "5" .
<http://localhost/lane/3806>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 6 .
+ libns:lane_number "6" .
<http://localhost/lane/3807>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
- libns:lane_number 7 .
+ libns:lane_number "7" .
<http://localhost/lane/3808>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/11154/> ;
- libns:lane_number 8 .
+ libns:lane_number "8" .
# paired_end 1;
# read_length 76;
# status "Unknown"@en .
<http://localhost/flowcell/C02F9ACXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 101 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "C02F9ACXX"@en .
<http://localhost/lane/12300>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/12345/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
# paired_end 1;
# read_length 101;
# status "Unknown"@en .
<http://localhost/lane/12500>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/11154/> ;
- libns:lane_number 3 .
+ libns:lane_number "3" .
# paired_end 1;
# read_length 101;
# status "Unknown"@en .
<http://localhost/library/11154/>
- a libns:library ;
+ a libns:Library ;
libns:affiliation "TSR"@en;
libns:concentration "29.7";
libns:date "2012-12-28T00:00:00"^^xsd:dateTime ;
libns:made_by "Gary Gygax"@en ;
libns:name "Paired Ends ASDF"@en ;
libns:replicate "1"@en;
- libns:species "Mus musculus"@en ;
+ libns:species_name "Mus musculus"@en ;
libns:stopping_point "Completed"@en ;
libns:total_unique_locations 8841201 .
# cell_line
-
<http://localhost/library/12345/>
- a libns:library ;
+ a libns:Library ;
libns:affiliation "TSR"@en;
libns:concentration "12.345";
libns:cell_line "Unknown"@en ;
libns:made_by "Gary Gygax"@en ;
libns:name "Paired Ends THING"@en ;
libns:replicate "1"@en;
- libns:species "Mus musculus"@en ;
+ libns:species_name "Mus musculus"@en ;
libns:stopping_point "Completed"@en ;
libns:total_unique_locations 8841201 .
# cell_line
"""
HOST = "http://localhost"
-class TestCondorFastq(unittest.TestCase):
+class TestCondorFastq(TestCase):
def setUp(self):
self.cwd = os.getcwd()
self.flowcelldir,
self.logdir)
load_string_into_model(self.extract.model, 'turtle', lib_turtle)
+ add_default_schemas(self.extract.model)
+ inference = Infer(self.extract.model)
+ errmsgs = list(inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
+ os.chdir(self.tempdir)
def tearDown(self):
shutil.rmtree(self.tempdir)
os.chdir(self.cwd)
- def test_find_relavant_flowcell_ids(self):
+ def test_find_relevant_flowcell_ids(self):
expected = set(('30221AAXX',
'42JUYAAXX',
'61MJTAAXX',
'30DY0AAXX',
'C02F9ACXX'))
- flowcell_ids = self.extract.find_relavant_flowcell_ids()
+ flowcell_ids = self.extract.find_relevant_flowcell_ids()
self.assertEqual(flowcell_ids, expected)
def test_find_archive_sequence(self):
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', '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')
])
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)
def suite():
- suite = unittest.makeSuite(TestCondorFastq, 'test')
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestCondorFastq))
return suite
if __name__ == "__main__":
- unittest.main(defaultTest='suite')
-
+ from unittest import main
+ main(defaultTest='suite')