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Use htsworkflow ontology to validate various RDF using components.
[htsworkflow.git]
/
htsworkflow
/
submission
/
test
/
test_condorfastq.py
diff --git
a/htsworkflow/submission/test/test_condorfastq.py
b/htsworkflow/submission/test/test_condorfastq.py
index 94df7b60b2f1e7dbca6d5e2fc2ecbacded55f30a..f4d2e2c71aef39fc8f32dbb6058fa8db71510af9 100644
(file)
--- a/
htsworkflow/submission/test/test_condorfastq.py
+++ b/
htsworkflow/submission/test/test_condorfastq.py
@@
-9,7
+9,9
@@
import unittest
from htsworkflow.submission.condorfastq import CondorFastqExtract
from htsworkflow.submission.results import ResultMap
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',
FCDIRS = [
'C02F9ACXX',
@@
-96,8
+98,13
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
@prefix seqns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
@prefix invns: <http://jumpgate.caltech.edu/wiki/InventoryOntology#> .
@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/>
<http://localhost/flowcell/30221AAXX/>
- a libns:
illumina_f
lowcell ;
+ a libns:
IlluminaF
lowcell ;
libns:read_length 33 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:read_length 33 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
@@
-112,18
+119,22
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
libns:flowcell_id "30221AAXX"@en .
<http://localhost/lane/3401>
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>
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>
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>
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 .
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 4 .
@@
-131,24
+142,28
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# read_length 33;
# status "Unknown"@en .
<http://localhost/lane/3405>
# 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>
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>
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>
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/>
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 8 .
<http://localhost/flowcell/42JUYAAXX/>
- a libns:
illumina_f
lowcell ;
+ a libns:
IlluminaF
lowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
@@
-163,22
+178,27
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
libns:flowcell_id "42JUYAAXX"@en .
<http://localhost/lane/4201>
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>
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>
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>
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>
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 .
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 5 .
@@
-186,20
+206,23
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/4206>
# 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>
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>
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/>
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 8 .
<http://localhost/flowcell/61MJTAAXX/>
- a libns:
illumina_f
lowcell ;
+ a libns:
IlluminaF
lowcell ;
libns:read_length 76 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:read_length 76 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
@@
-214,26
+237,32
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
libns:flowcell_id "61MJTAAXX"@en .
<http://localhost/lane/6601>
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>
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>
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>
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>
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>
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 .
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 6 .
@@
-241,16
+270,18
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/6607>
# 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>
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/>
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 8 .
<http://localhost/flowcell/30DY0AAXX/>
- a libns:
illumina_f
lowcell ;
+ a libns:
IlluminaF
lowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
@@
-265,34
+296,42
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
libns:flowcell_id "30DY0AAXX"@en .
<http://localhost/lane/3801>
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>
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>
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>
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>
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>
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>
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>
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 .
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 8 .
@@
-301,7
+340,7
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# status "Unknown"@en .
<http://localhost/flowcell/C02F9ACXX/>
# status "Unknown"@en .
<http://localhost/flowcell/C02F9ACXX/>
- a libns:
illumina_f
lowcell ;
+ a libns:
IlluminaF
lowcell ;
libns:read_length 101 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:read_length 101 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
@@
-310,6
+349,7
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
libns:flowcell_id "C02F9ACXX"@en .
<http://localhost/lane/12300>
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:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/12345/> ;
libns:lane_number 3 .
@@
-318,6
+358,7
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# status "Unknown"@en .
<http://localhost/lane/12500>
# 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:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 3 .
@@
-326,7
+367,7
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
# status "Unknown"@en .
<http://localhost/library/11154/>
# status "Unknown"@en .
<http://localhost/library/11154/>
- a libns:
l
ibrary ;
+ a libns:
L
ibrary ;
libns:affiliation "TSR"@en;
libns:concentration "29.7";
libns:date "2012-12-28T00:00:00"^^xsd:dateTime ;
libns:affiliation "TSR"@en;
libns:concentration "29.7";
libns:date "2012-12-28T00:00:00"^^xsd:dateTime ;
@@
-350,7
+391,7
@@
lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
<http://localhost/library/12345/>
<http://localhost/library/12345/>
- a libns:
l
ibrary ;
+ a libns:
L
ibrary ;
libns:affiliation "TSR"@en;
libns:concentration "12.345";
libns:cell_line "Unknown"@en ;
libns:affiliation "TSR"@en;
libns:concentration "12.345";
libns:cell_line "Unknown"@en ;
@@
-401,6
+442,10
@@
class TestCondorFastq(unittest.TestCase):
self.flowcelldir,
self.logdir)
load_string_into_model(self.extract.model, 'turtle', lib_turtle)
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)
def tearDown(self):
shutil.rmtree(self.tempdir)