Merge pull request #548 from ptth222/ontology-source-check-fix

Fix rule and check.
ISA-tools · Mar 11, 2024 · 16ccc00 · 16ccc00
2 parents 01dffc7 + 9a5fb86
commit 16ccc00
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git a/isatools/isatab/validate/rules/core.py b/isatools/isatab/validate/rules/core.py
@@ -54,7 +54,7 @@ def execute(self, validator_params: dict) -> None:
         try:
             response = self.rule(*params)
             if self.identifier == '3008':
-                validator_params['term_source_refs'] = response[0]
+                validator_params['term_source_refs'] = response
             if self.identifier == '4001':
                 validator_params['configs'] = response
             self.executed = True

diff --git a/isatools/isatab/validate/rules/rules_30xx.py b/isatools/isatab/validate/rules/rules_30xx.py
@@ -150,20 +150,22 @@ def check_single_field(cell_value, source, acc, config_field, filename):
         :param filename: Filename of the table
         :return: True if OK, False if not OK
         """
+        return_value = True
         if ((cell_has_value(cell_value) and not cell_has_value(source) and cell_has_value(acc))
                 or not cell_has_value(cell_value)):
             msg = "Missing Term Source REF in annotation or missing Term Source Name"
             spl = ("Incomplete values for ontology headers, for the field '{}' in the file '{}'. Check that all the "
                    "label/accession/source are provided.").format(config_field.header, filename)
             validator.add_warning(message=msg, supplemental=spl, code=3008)
             log.warning("(W) {}".format(spl))
-            if source not in tsrs:
-                spl = ("Term Source REF, for the field '{}' in the file '{}' does not refer to a declared "
-                       "Ontology Source.").format(config_field.header, filename)
-                validator.add_warning(message="Term Source REF reference broken", supplemental=spl, code=3011)
-                log.warning("(W) {}".format(spl))
-            return False
-        return True
+            return_value = False
+        if cell_has_value(source) and source not in tsrs:
+            spl = ("Term Source REF, for the field '{}' in the file '{}' does not refer to a declared "
+                   "Ontology Source.").format(cfield.header, filename)
+            validator.add_warning(message="Term Source REF reference broken", supplemental=spl, code=3011)
+            log.warning("(W) {}".format(spl))
+            return_value = False
+        return return_value
 
     result = True
     nfields = len(table.columns)