Merge pull request #550 from ptth222/511-testing-changes

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ISA-tools · Mar 11, 2024 · 6d30dc2 · 6d30dc2
2 parents e5f6fd2 + 0f9214f
commit 6d30dc2
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/tests/isatab/test_isatab.py b/tests/isatab/test_isatab.py
@@ -440,7 +440,7 @@ def test_isatab_dump_source_sample_char_quant(self):
         s.process_sequence = [sample_collection_process]
         s.samples.append(sample1)
         i.studies = [s]
-        actual = isatab.dumps(i)
+        actual = replace_windows_newlines(isatab.dumps(i))
         expected = """Source Name\tMaterial Type\tCharacteristics[organism]\tTerm Source REF\tTerm Accession Number\tCharacteristics[body weight]\tUnit\tTerm Source REF\tTerm Accession Number\tProtocol REF\tParameter Value[vessel]\tTerm Source REF\tTerm Accession Number\tParameter Value[storage temperature]\tUnit\tTerm Source REF\tTerm Accession Number\tSample Name\tCharacteristics[organism part]\tTerm Source REF\tTerm Accession Number\tCharacteristics[specimen mass]\tUnit\tTerm Source REF\tTerm Accession Number
 source1\tspecimen\tHuman\tNCBITAXON\thttp://purl.bioontology.org/ontology/STY/T016\t72\tkilogram\tUO\thttp://purl.obolibrary.org/obo/UO_0000009\tsample collection\teppendorf tube\tOBI\tpurl.org\t-20\tdegree Celsius\tUO\thttp://purl.obolibrary.org/obo/UO_0000027\tsample1\tliver\tUBERON\thttp://purl.obolibrary.org/obo/UBERON_0002107\t450.5\tmilligram\tUO\thttp://purl.obolibrary.org/obo/UO_0000022"""
         self.assertIn(expected, actual)

diff --git a/tests/validators/test_validate_test_data.py b/tests/validators/test_validate_test_data.py
@@ -305,7 +305,7 @@ class TestIsaJsonCreateTestData(unittest.TestCase):
 
     def setUp(self):
         self._reporting_level = logging.ERROR
-        self.v2_create_schemas_path = pathlib.PurePosixPath(
+        self.v2_create_schemas_path = pathlib.Path(
             pathlib.Path(__file__).parents[0], '..', '..', 'isatools', 'resources', 'schemas',
             'isa_model_version_2_0_schemas', 'create')
 
@@ -315,7 +315,7 @@ def test_validate_testdata_sampleassayplan_json(self):
             with open(os.path.join(self.v2_create_schemas_path,
                                    'sample_assay_plan_schema.json')) as fp:
                 sample_assay_plan_schema = json.load(fp)
-                res_path = pathlib.PurePosixPath("file://", self.v2_create_schemas_path,
+                res_path = pathlib.Path("file://", self.v2_create_schemas_path,
                              'sample_assay_plan_schema.json').as_uri()
                 resolver = RefResolver(res_path, sample_assay_plan_schema)
             validator = Draft4Validator(sample_assay_plan_schema,
@@ -342,7 +342,7 @@ def test_validate_testdata_treatment_sequence_json(self):
             with open(os.path.join(self.v2_create_schemas_path,
                                    'treatment_sequence_schema.json')) as fp:
                 treatment_sequence_schema = json.load(fp)
-            res_path = pathlib.PurePosixPath("file://", self.v2_create_schemas_path,
+            res_path = pathlib.Path("file://", self.v2_create_schemas_path,
                          'treatment_sequence_schema.json').as_uri()
             resolver = RefResolver(res_path, treatment_sequence_schema)
             validator = Draft4Validator(treatment_sequence_schema,