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 .
<http://localhost/lane/3402>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
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 .
<http://localhost/lane/3404>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 4 .
# 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 .
<http://localhost/lane/3406>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
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 .
<http://localhost/lane/3408>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
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 .
<http://localhost/lane/4202>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
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 .
<http://localhost/lane/4204>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
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 .
# 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 .
<http://localhost/lane/4207>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
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 .
<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 .
<http://localhost/lane/6602>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
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 .
<http://localhost/lane/6604>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
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 .
<http://localhost/lane/6606>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 6 .
# 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 .
<http://localhost/lane/6608>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
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 .
<http://localhost/lane/3802>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
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 .
<http://localhost/lane/3804>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
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 .
<http://localhost/lane/3806>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
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 .
<http://localhost/lane/3808>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 8 .
# 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 .
# 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 .
# 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 ;
<http://localhost/library/12345/>
- a libns:library ;
+ a libns:Library ;
libns:affiliation "TSR"@en;
libns:concentration "12.345";
libns:cell_line "Unknown"@en ;
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)
def tearDown(self):
shutil.rmtree(self.tempdir)