Changed missing required properties to error

isatools/isatab/validate/rules/rules_40xx.py

@@ -24,17 +24,15 @@ def check_investigation_against_config(i_df, configs):
     code = 4003
     message = "A required property is missing"
 
-    def add_warning(index, column, value_index):
+    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_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))
+        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]
@@ -45,10 +43,10 @@ def check_section_against_required_fields_one_value(section, required, i=0):
                     required_value = required_values.iloc[x]
                     if isinstance(required_value, float):
                         if isnan(required_value):
-                            add_warning(i, col, x)
+                            add_error(i, col, x)
                     else:
                         if required_value == '' or 'Unnamed: ' in required_value:
-                            add_warning(i, col, x)
+                            add_error(i, col, x)
 
     config_fields = configs[('[investigation]', '')].get_isatab_configuration()[0].get_field()
     required_fields = [i.header for i in config_fields if i.is_required]

isatools/resources/config/xml/investigation.xml

@@ -93,7 +93,7 @@
             <default-value><![CDATA[]]></default-value>
         </field>
         <field header="Investigation Person Mid Initials" data-type="String" is-file-field="false"
-            is-multiple-value="false" is-required="true" is-hidden="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
             is-forced-ontology="false" section="INVESTIGATION CONTACTS">
             <description><![CDATA[The mid initial of the contact.]]></description>
             <default-value><![CDATA[]]></default-value>
@@ -231,7 +231,7 @@
             <default-value><![CDATA[]]></default-value>
         </field>
         <field header="Study Person Mid Initials" data-type="String" is-file-field="false"
-            is-multiple-value="false" is-required="true" is-hidden="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
             is-forced-ontology="false" section="STUDY CONTACTS">
             <description><![CDATA[The mid initial of the contact.]]></description>
             <default-value><![CDATA[]]></default-value>

tests/convert/test_mzml2isa.py

@@ -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'
@@ -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))
@@ -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))

tests/isatab/validate/test_core.py

@@ -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')
@@ -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]
@@ -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 = {

tests/test_clients/test_mw2isa.py

@@ -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")