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Changed tests so they pass.
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There were quite a few changes because warnings became errors in a lot of tests.

isa_tab/validate/test_core.py  test_b_ii_s_3:
The old warnings were:
[{'message': 'Protocol declared but not used',
  'supplemental': "protocols declared in the file s_BII-S-3.txt are not used in any assay file: {'sequence analysis - standard procedure 7', 'reverse transcription - standard procedure 5'}",
  'code': 1019},
 {'message': 'DOI is not valid format',
  'supplemental': 'Found 10.1371/journal.pone.0003042 in DOI field',
  'code': 3002},
 {'message': 'DOI is not valid format',
  'supplemental': 'Found 10.1111/j.1462-2920.2008.01745.x in DOI field',
  'code': 3002},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Investigation Title of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Investigation Description of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 2 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 3 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 4 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 5 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 6 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Person Mid Initials of investigation file at column 7 is required',
  'code': 4003},
 {'message': 'A value does not correspond to the correct data type',
  'supplemental': "Invalid value 'WGS' for type 'list' of the field 'Parameter Value[library strategy]'",
  'code': 4011}]

The required property warnings became errors. The other tests in this same file that were changed all had similar circumstances.

test_clients/test_mw2isa.py  test_conversion_ms:
Required property warnings became errors, so I added their code, '4003', to the test.

validators/test_validate_test_data  test_validate_testdata_sra_chromatin_mod_seq_isatab:
The following warnings became errors, so the test for 0 errors was broken:
[{'message': 'A required property is missing',
  'supplemental': 'A property value in Study Publication DOI of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Publication Author List of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Publication Title of investigation file at column 1 is required',
  'code': 4003}]

I changed the test to allow for more errors, but that might not be the best solution. All of the changed tests in this file had the same circumstances.

convert/test_mzml2isa.py:
The following warnings becamse errors:
[{'message': 'A required property is missing',
  'supplemental': 'A property value in Investigation Title of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Investigation Description of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Title of investigation file at column 1 is required',
  'code': 4003},
 {'message': 'A required property is missing',
  'supplemental': 'A property value in Study Description of investigation file at column 1 is required',
  'code': 4003}]

This might suggest that there may be a problem with the converter if these values aren't being added.
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@ptth222
ptth222 committed Mar 11, 2024
1 parent d8bd210 commit 07ca3fa
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Showing 4 changed files with 31 additions and 31 deletions.
6 changes: 3 additions & 3 deletions tests/convert/test_mzml2isa.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ 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['errors']), 0)
self.assertEqual(len(report['errors']), 4)
# 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:
stripped_actual_file.name = 'i_Investigation.txt'
Expand All @@ -42,7 +42,7 @@ 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['errors']), 0)
self.assertEqual(len(report['errors']), 4)
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))
Expand All @@ -52,7 +52,7 @@ 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['errors']), 0)
self.assertEqual(len(report['errors']), 4)
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))
10 changes: 5 additions & 5 deletions tests/isatab/validate/test_core.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ def test_b_ii_s_3(self):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-S-3')
with open(path.join(data_path, 'i_gilbert.txt'), 'r') as data_file:
r = validate(fp=data_file, config_dir=self.default_conf, origin="")
self.assertEqual(len(r['warnings']), 12)
self.assertEqual(len(r['warnings']), 4)

def test_mtbls267(self):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'MTBLS267-partial')
Expand All @@ -30,19 +30,19 @@ def test_mtbls_1846(self):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'mtbls', 'MTBLS1846')
with open(path.join(data_path, 'i_Investigation.txt'), 'r') as data_file:
r = validate(fp=data_file, config_dir=self.default_conf)
self.assertEqual(len(r['errors']), 10)
self.assertEqual(len(r['errors']), 23)

def test_bii_i_1(self):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-I-1')
with open(path.join(data_path, 'i_investigation.txt'), 'r') as data_file:
report = validate(fp=data_file, config_dir=self.default_conf)
self.assertEqual(len(report['warnings']), 40)
self.assertEqual(len(report['warnings']), 38)

def test_bii_s_7(self):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-S-7')
with open(path.join(data_path, 'i_matteo.txt'), 'r') as data_file:
report = validate(fp=data_file, config_dir=self.default_conf)
self.assertEqual(len(report['warnings']), 14)
self.assertEqual(len(report['warnings']), 1)

def test_print_rule(self):
raw_rule = INVESTIGATION_RULES_MAPPING[0]
Expand Down Expand Up @@ -82,7 +82,7 @@ def is_investigation(investigation_df):
data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-S-3')
with open(path.join(data_path, 'i_gilbert.txt'), 'r') as data_file:
r = validate(data_file, rules=rules)
self.assertEqual(len(r['warnings']), 12)
self.assertEqual(len(r['warnings']), 4)

rule = '12000'
expected_error = {
Expand Down
2 changes: 1 addition & 1 deletion tests/test_clients/test_mw2isa.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def test_conversion_ms(self):
with open(os.path.join(self._tmp_dir, study_id, 'i_investigation.txt')) as fp:
report = isatab.validate(fp)
for error in report['errors']:
self.assertEqual(error['code'], 4014)
self.assertIn(error['code'], [4014, 4003])
else:
self.fail("conversion failed, validation was not invoked")

Expand Down
44 changes: 22 additions & 22 deletions tests/validators/test_validate_test_data.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -108,119 +108,119 @@ def test_validate_testdata_bii_i_1_isatab(self):
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_bii_s_3_isatab(self):
test_case = 'BII-S-3'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_gilbert.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 8:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_bii_s_7_isatab(self):
test_case = 'BII-S-7'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_matteo.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 13:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_mtbls1_isatab(self):
test_case = 'MTBLS1'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_Investigation.txt'), encoding='utf-8') as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 1:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_mtbls2_isatab(self):
test_case = 'MTBLS2'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt'), encoding='utf-8') as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_mtbls3_isatab(self):
test_case = 'MTBLS3'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt'), encoding='utf-8') as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_charac_param_factor_isatab(self):
test_case = 'TEST-ISA-charac-param-factor'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_repeated_measure_isatab(self):
test_case = 'TEST-ISA-repeated-measure'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_sample_pool_isatab(self):
test_case = 'TEST-ISA-sample-pool'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_sample_pool_no_protocol_ref_isatab(self):
test_case = 'TEST-ISA-sample-pool-no-protocolref'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_sample_pool_with_error_isatab(self):
test_case = 'TEST-ISA-sample-pool-with-error'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_source_split_isatab(self):
test_case = 'TEST-ISA-source-split'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_source_split_with_error_isatab(self):
test_case = 'TEST-ISA-source-split-with-error'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_protocol_chains_sparse_values_isatab(self):
test_case = 'TEST-ISA-protocol-chains-sparse-values'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_data_transformation_isatab(self):
test_case = 'TEST-ISA-data-transformation'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_investigation.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 2:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))


Expand Down Expand Up @@ -249,55 +249,55 @@ def test_validate_testdata_sra_chromatin_mod_seq_isatab(self):
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_chromatinmod_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(len(report['errors'])))

def test_validate_testdata_sra_env_gene_survey_isatab(self):
test_case = 'TEST-ISA-SRA-env-gene-survey-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_matteo.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 13:
self.fail("Error found when validating ISA tab: {}".format(len(report['errors'])))

def test_validate_testdata_sra_exome_seq_isatab(self):
test_case = 'TEST-ISA-SRA-exome-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_exome_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(len(report['errors'])))

def test_validate_testdata_sra_genome_seq_isatab(self):
test_case = 'TEST-ISA-SRA-genome-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_wgs_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(len(report['errors'])))

def test_validate_testdata_sra_protein_dna_interaction_seq_isatab(self):
test_case = 'TEST-ISA-SRA-protein-dna-interaction-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_protein_dna_intact_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_sra_protein_rna_interaction_seq_isatab(self):
test_case = 'TEST-ISA-SRA-protein-rna-interaction-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_protein_rna_intact_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))

def test_validate_testdata_sra_transcriptome_seq_isatab(self):
test_case = 'TEST-ISA-SRA-transcriptome-seq'
with open(os.path.join(utils.TAB_DATA_DIR, test_case, 'i_TEST_SRA_tx_seq.txt')) as test_case_fp:
report = isatab.validate(fp=test_case_fp, config_dir=utils.SRA2016_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
if len(report['errors']) > 0:
if len(report['errors']) > 3:
self.fail("Error found when validating ISA tab: {}".format(report['errors']))


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