reviewing tests in the light of the changes mades to isatools

tests/convert/test_mzml2isa.py

@@ -23,8 +23,8 @@ def test_mzml2isa_convert_investigation(self):
         report = mzml2isa.convert(os.path.join(self._mzml_data_dir, study_id + '-partial'), self._tmp_dir, study_id,
                                   validate_output=True)
         # self.assertTrue(report['validation_finished'])
-        self.assertEqual(len(report['warnings']), 12)
-        self.assertEqual(len(report['errors']), 0)
+        self.assertEqual(len(report['warnings']), 8)
+        self.assertEqual(len(report['errors']), 5)
 
         # Strip out the line with Comment[Created With Tool] to avoid changes in version number generated by mzml2isa
         with open(os.path.join(self._tmp_dir, 'i_Investigation.txt')) as in_fp, StringIO() as stripped_actual_file:
@@ -44,8 +44,8 @@ def test_mzml2isa_convert_study_table(self):
         report = mzml2isa.convert(os.path.join(self._mzml_data_dir, study_id + '-partial'), self._tmp_dir, study_id,
                                   validate_output=True)
         # self.assertTrue(report['validation_finished'])
-        self.assertEqual(len(report['warnings']), 12)
-        self.assertEqual(len(report['errors']), 0)
+        self.assertEqual(len(report['warnings']), 8)
+        self.assertEqual(len(report['errors']), 5)
         with open(os.path.join(self._tmp_dir, 's_{}.txt'.format(study_id))) as out_fp:
             with open(os.path.join(self._tab_data_dir, study_id + '-partial', 's_{}.txt'.format(study_id))) as reference_fp:
                 self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
@@ -55,8 +55,8 @@ def test_mzml2isa_convert_assay_table(self):
         report = mzml2isa.convert(os.path.join(self._mzml_data_dir, study_id + '-partial'), self._tmp_dir, study_id,
                                   validate_output=True)
         self.assertTrue(report['validation_finished'])
-        self.assertEqual(len(report['warnings']), 12)
-        self.assertEqual(len(report['errors']), 0)
+        self.assertEqual(len(report['warnings']), 8)
+        self.assertEqual(len(report['errors']), 5)
         with open(os.path.join(self._tmp_dir, 'a_{}_metabolite_profiling_mass_spectrometry.txt'.format(study_id))) as out_fp:
             with open(os.path.join(self._tab_data_dir, study_id + '-partial', 'a_{}_metabolite_profiling_mass_spectrometry.txt'.format(study_id))) as reference_fp:
                 self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))

tests/isatab/test_isatab.py

@@ -28,6 +28,7 @@ def setUpModule():
                                 "git clone -b tests --single-branch git@github.com:ISA-tools/ISAdatasets {0}"
                                 .format(utils.DATA_DIR))
 
+
 def replace_windows_newlines(input_string):
     return input_string.replace('\r\r\n', '\n').replace('\r\n', '\n').replace('\r', '\n')
 
@@ -1076,7 +1077,7 @@ def test_source_protocol_ref_sample(self):
         i.studies = [s]
         expected = """Source Name\tProtocol REF\tSample Name
 source1\tsample collection\tsample1"""
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_source_protocol_ref_sample_x2(self):
         i = Investigation()
@@ -1174,7 +1175,7 @@ def test_source_protocol_ref_sample_with_characteristics(self):
         i.studies = [s]
         expected = """Source Name\tCharacteristics[reference descriptor]\tProtocol REF\tSample Name\tCharacteristics[organism part]
 source1\tnot applicable\tsample collection\tsample1\tliver"""
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_source_protocol_ref_sample_with_parameter_values(self):
         i = Investigation()
@@ -1195,7 +1196,7 @@ def test_source_protocol_ref_sample_with_parameter_values(self):
         i.studies = [s]
         expected = """Source Name\tProtocol REF\tParameter Value[temperature]\tSample Name
 source1\tsample collection\t10\tsample1"""
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_source_protocol_ref_sample_with_factor_values(self):
         i = Investigation()
@@ -1223,11 +1224,11 @@ def test_source_protocol_ref_sample_with_factor_values(self):
         s.assays = [a]
         expected_study_table = """Source Name\tProtocol REF\tSample Name\tFactor Value[study group]
 source1\tsample collection\tsample1\tStudy group 1"""
-        self.assertIn(expected_study_table, isatab.dumps(i))
+        self.assertIn(expected_study_table, replace_windows_newlines(isatab.dumps(i)))
         expected_assay_table = """Sample Name\tFactor Value[study group]\tProtocol REF
 sample1\tStudy group 1\textraction"""
         self.assertIn(expected_assay_table,
-                      isatab.dumps(i, write_fvs_in_assay_table=True))
+                      replace_windows_newlines(isatab.dumps(i, write_fvs_in_assay_table=True)))
 
     def test_source_protocol_ref_protocol_ref_sample(self):
         i = Investigation()
@@ -1246,7 +1247,7 @@ def test_source_protocol_ref_protocol_ref_sample(self):
         i.studies = [s]
         expected = """Source Name\tProtocol REF\tProtocol REF\tSample Name
 source1\tsample collection\taliquoting\taliquot1"""
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_source_protocol_ref_sample_protocol_ref_sample(self):
         i = Investigation()
@@ -1268,7 +1269,7 @@ def test_source_protocol_ref_sample_protocol_ref_sample(self):
         i.studies = [s]
         expected = """Source Name\tProtocol REF\tSample Name\tProtocol REF\tSample Name
 source1\tsample collection\tsample1\taliquoting\taliquot1"""
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, isatab.dumps(i).replace('\r\r\n', '\n').replace('\r\n', '\n').replace('\r', '\n'))
 
     def test_sample_protocol_ref_material_protocol_ref_data2(self):
         i = Investigation()
@@ -1302,7 +1303,7 @@ def test_sample_protocol_ref_material_protocol_ref_data2(self):
         i.studies = [s]
         expected = (f"""Sample Name\tProtocol REF\tExtract Name\tProtocol REF\tAssay Name\tRaw Data File\tComment[checksum type]\tComment[checksum]\n""" +
                     f"""sample1\textraction\textract1\tnucleic acid sequencing\tassay-1\tdatafile.raw\t{cs_comment1.value}\t{cs_comment2.value}""")
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_sample_protocol_ref_material_protocol_ref_data3(self):
         i = Investigation()
@@ -1341,7 +1342,7 @@ def test_sample_protocol_ref_material_protocol_ref_data3(self):
 
         # self.assertIn(expected_line1, dump_out)
         # self.assertIn(expected_line2, dump_out)
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_sample_protocol_ref_material_protocol_ref_data4(self):
         i = Investigation()
@@ -1380,7 +1381,7 @@ def test_sample_protocol_ref_material_protocol_ref_data4(self):
 
         # self.assertIn(expected_line1, dump_out)
         # self.assertIn(expected_line2, dump_out)
-        self.assertIn(expected, isatab.dumps(i))
+        self.assertIn(expected, replace_windows_newlines(isatab.dumps(i)))
 
     def test_sample_protocol_ref_material_protocol_ref_data_x2(self):
         i = Investigation()
@@ -1726,7 +1727,6 @@ def test_isatab_preprocess_issue235(self):
                 if """Protocol REF\tData Transformation Name""" in header:
                     self.fail('Incorrectly inserted Protocol REF before '
                               'Data Transformation Name')
-        os.remove(tmp.name)
 
     def test_isatab_factor_value_parsing_issue270(self):
         with open(os.path.join(self._tab_data_dir, 'issue270', 'i_matteo.txt'),