Changed missing required properties to error

isatools/isatab/validate/rules/rules_40xx.py

@@ -26,29 +26,16 @@ def check_investigation_against_config(i_df_dict, configs):
     code = 4003
     message = "A required property is missing"
 
-    # def add_warning(index, column, value_index):
-    #     if index > 0:
-    #         spl = "A property value in {}.{} of investigation file at column {} is required"
-    #         spl = spl.format(column, index + 1, value_index + 1)
-    #         validator.add_warning(message=message, supplemental=spl, code=code)
-    #         log.warning("(W) {}".format(spl))
-    #     else:
-    #         spl = "A property value in {} of investigation file at column {} is required"
-    #         spl = spl.format(column, value_index + 1)
-    #         validator.add_warning(message=message, supplemental=spl, code=code)
-    #         log.warning("(W) {}".format(spl))
-
     def add_error(index, column, value_index):
         if index > 0:
             spl = "A property value in {}.{} of investigation file at column {} is required"
             spl = spl.format(column, index + 1, value_index + 1)
-            validator.add_error(message=message, supplemental=spl, code=code)
-            log.error("(E) {}".format(spl))
         else:
             spl = "A property value in {} of investigation file at column {} is required"
             spl = spl.format(column, value_index + 1)
-            validator.add_error(message=message, supplemental=spl, code=code)
-            log.error("(E) {}".format(spl))
+        validator.add_error(message=message, supplemental=spl, code=code)
+        log.error("(E) {}".format(spl))
+
 
     def check_section_against_required_fields_one_value(section, required, i=0):
         fields_required = [i for i in section.columns if i in required]

tests/convert/test_mzml2isa.py

@@ -22,7 +22,6 @@ def test_mzml2isa_convert_investigation(self):
         study_id = 'MTBLS267'
         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']), 8)
         self.assertEqual(len(report['errors']), 5)
 
@@ -43,9 +42,9 @@ def test_mzml2isa_convert_study_table(self):
         study_id = 'MTBLS267'
         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']), 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))
@@ -54,9 +53,9 @@ def test_mzml2isa_convert_assay_table(self):
         study_id = 'MTBLS267'
         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']), 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/validate/test_core.py

@@ -19,7 +19,6 @@ def test_b_ii_s_3(self):
             r = validate(fp=data_file, config_dir=self.default_conf, origin="")
         self.assertEqual(len(r['warnings']), 2)
 
-
     def test_mtbls267(self):
         data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'MTBLS267-partial')
         with open(path.join(data_path, 'i_Investigation.txt'), 'r') as data_file:
@@ -33,6 +32,7 @@ def test_mtbls_1846(self):
             r = validate(fp=data_file, config_dir=self.default_conf)
         self.assertEqual(len(r['errors']), 33)
 
+
     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:
@@ -85,7 +85,6 @@ def is_investigation(investigation_df):
             r = validate(data_file, rules=rules)
         self.assertEqual(len(r['warnings']), 2)
 
-
         rule = '12000'
         expected_error = {
             'message': 'Unknown/System Error',

tests/test_clients/test_mw2isa.py

@@ -31,12 +31,8 @@ def test_conversion_ms(self):
             log.info("conversion successful, invoking the validator for " + study_id)
             with open(os.path.join(self._tmp_dir, study_id, 'i_investigation.txt')) as fp:
                 report = isatab.validate(fp)
-                # print(report)
-                # for error in report['errors']:
-                    # print("ERROR:", error)
-                    # self.assertEqual(error['code'], 4014)
-                    # self.assertIn(error['code'], [4003, 4014])
-                self.assertTrue(len(report['errors']) > 0)
+                for error in report['errors']:
+                    self.assertIn(error['code'], [4014, 4003])
         else:
             self.fail("conversion failed, validation was not invoked")