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Change unittest2 back into unittest.
[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 24d6e4982018dd23ac8e8746d7ade1856ae3d4e7..2d232715e5289d93c17b68da92c7dfdac45f6b04 100644 (file)
--- a/htsworkflow/submission/test/test_condorfastq.py
+++ b/htsworkflow/submission/test/test_condorfastq.py
@@ -5,11 +5,18 @@ import os
 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',
@@ -96,8 +103,13 @@ 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#> .
 
+<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;
@@ -112,43 +124,51 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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;
@@ -163,43 +183,51 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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;
@@ -214,43 +242,51 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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;
@@ -265,43 +301,51 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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;
@@ -310,23 +354,25 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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 ;
@@ -343,14 +389,13 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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 ;
@@ -364,14 +409,14 @@ lib_turtle = """@prefix : <http://www.w3.org/1999/xhtml> .
         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()
 
@@ -401,39 +446,44 @@ class TestCondorFastq(unittest.TestCase):
                                           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)
@@ -441,7 +491,7 @@ class TestCondorFastq(unittest.TestCase):
     def test_find_needed_targets(self):
         lib_db = self.extract.find_archive_sequence_files(self.result_map)
 
-        needed_targets = self.extract.find_missing_targets(self.result_map,
+        needed_targets = self.extract.update_fastq_targets(self.result_map,
                                                            lib_db)
         self.assertEqual(len(needed_targets), 9)
         srf_30221 = needed_targets[
@@ -631,9 +681,11 @@ class TestCondorFastq(unittest.TestCase):
 
 
 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')
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