From 5a693575bd33a87f7c04585c436e934143fdcf47 Mon Sep 17 00:00:00 2001
From: Philippe Rocca-Serra <proccaserra@gmail.com>
Date: Mon, 9 Sep 2024 15:01:39 +0100
Subject: [PATCH] adding a check on parameter values in write_study and
 write_assay methods

---
 isatools/isatab/dump/write.py | 15 ++++---
 tests/isatab/test_isatab.py   | 77 +++++++++++++++++++++++++++++++++++
 2 files changed, 87 insertions(+), 5 deletions(-)

diff --git a/isatools/isatab/dump/write.py b/isatools/isatab/dump/write.py
index bce3c2fb..51d7cbd3 100644
--- a/isatools/isatab/dump/write.py
+++ b/isatools/isatab/dump/write.py
@@ -151,9 +151,11 @@ def write_study_table_files(inv_obj, output_dir):
                     protocol_in_path_count += 1
                     df_dict[olabel][-1] = node.executes_protocol.name
                     for pv in node.parameter_values:
-                        pvlabel = "{0}.Parameter Value[{1}]".format(
-                            olabel, pv.category.parameter_name.term)
-                        write_value_columns(df_dict, pvlabel, pv)
+                        if pv.category:
+                            pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term)
+                            write_value_columns(df_dict, pvlabel, pv)
+                        else:
+                            raise(ValueError, "Protocol Value has no valid parameter_name")
                     if node.date is not None:
                         df_dict[olabel + ".Date"][-1] = node.date
                     if node.performer is not None:
@@ -405,8 +407,11 @@ def pbar(x):
                         if node.performer is not None:
                             df_dict[olabel + ".Performer"][-1] = node.performer
                         for pv in node.parameter_values:
-                            pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term)
-                            write_value_columns(df_dict, pvlabel, pv)
+                            if pv.category:
+                                pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term)
+                                write_value_columns(df_dict, pvlabel, pv)
+                            else:
+                                raise(ValueError, "Protocol Value has no valid parameter_name")
                         for co in node.comments:
                             colabel = "{0}.Comment[{1}]".format(olabel, co.name)
                             df_dict[colabel][-1] = co.value
diff --git a/tests/isatab/test_isatab.py b/tests/isatab/test_isatab.py
index b7bef7c5..1e83d03e 100644
--- a/tests/isatab/test_isatab.py
+++ b/tests/isatab/test_isatab.py
@@ -512,6 +512,83 @@ def test_simple_investigation(self):
         self.assertEqual(i2.studies[0].samples[0].characteristics[0].value,
                          investigation.studies[0].samples[0].characteristics[0].value)
 
+    def test_simple_investigation_protocol_well_formed_parameter_value_use(self):
+        unit_source = OntologySource(name='UO', description='Unit Ontology')
+        investigation = Investigation(ontology_source_references=[unit_source])
+        unit = OntologyAnnotation(term='mg', term_source=unit_source)
+        concentration_category = OntologyAnnotation(term='concentration', term_source=unit_source)
+        concentration = Characteristic(
+            value=500,
+            unit=unit,
+            category=concentration_category
+        )
+        protocol = Protocol(name="protest", protocol_type=OntologyAnnotation(term="extraction"))
+        parameter = ProtocolParameter(parameter_name="param_test")
+        protocol.parameters.append(parameter)
+        source = Source(name="source_1", id_="#isatest/source_1")
+        sample = Sample(
+            name='sample1',
+            id_="#isatest/sample1",
+            characteristics=[concentration]
+        )
+        pv = ParameterValue(category=parameter, value="T4")
+        ps1 = Process(executes_protocol=protocol, parameter_values=[pv], inputs=[source], outputs=[sample])
+        study = Study(
+            title='study1',
+            sources=[source],
+            samples=[sample],
+            units=[unit],
+            characteristic_categories=[concentration_category],
+            protocols=[protocol],
+            process_sequence=[ps1]
+        )
+        investigation.studies = [study]
+        i_dict = investigation.to_dict()
+
+        i2 = Investigation()
+        i2.from_dict(i_dict)
+        self.assertEqual(i2.studies[0].samples[0].characteristics[0].value,
+                         investigation.studies[0].samples[0].characteristics[0].value)
+        self.assertEqual(i2.studies[0].process_sequence[0].parameter_values[0].value.term, "T4")
+
+
+    def test_simple_investigation_protocol_badly_formed_parameter_value_use(self):
+        unit_source = OntologySource(name='UO', description='Unit Ontology')
+        investigation = Investigation(ontology_source_references=[unit_source])
+        unit = OntologyAnnotation(term='mg', term_source=unit_source)
+        concentration_category = OntologyAnnotation(term='concentration', term_source=unit_source)
+        concentration = Characteristic(
+            value=500,
+            unit=unit,
+            category=concentration_category
+        )
+        protocol = Protocol(name="protest", protocol_type=OntologyAnnotation(term="extraction"))
+        parameter = ProtocolParameter(parameter_name="param_test")
+        protocol.parameters.append(parameter)
+        source = Source(name="source_1", id_="#isatest/source_1")
+        sample = Sample(
+            name='sample1',
+            id_="#isatest/sample1",
+            characteristics=[concentration]
+        )
+        pv = ParameterValue(value="T4") # declaration of a parameter value without a catogory
+        ps1 = Process(executes_protocol=protocol, parameter_values=[pv], inputs=[source], outputs=[sample])
+        study = Study(
+            title='study1',
+            sources=[source],
+            samples=[sample],
+            units=[unit],
+            characteristic_categories=[concentration_category],
+            protocols=[protocol],
+            process_sequence=[ps1]
+        )
+        investigation.studies = [study]
+
+        with self.assertRaises(ValueError):
+            isatab.dump(investigation, self._tmp_dir, i_file_name='i_investigation.txt')
+            # my_json_report_isa_flux = isatab.validate(open(os.path.join(self._tab_data_dir, "issue-569", "i_investigation.txt")))
+            # print(my_json_report_isa_flux)
+
     def test_isatab_dump_investigation_with_assay(self):
         # Create an empty Investigation object and set some values to the
         # instance variables.