Remove entries that have no relevance to spreadsheet

EBIvariation · Sep 7, 2023 · 1806ceb · 1806ceb
1 parent fbf3bc3
commit 1806ceb
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Showing 4 changed files with 14 additions and 13 deletions.
diff --git a/cli/reporter.py b/cli/reporter.py
@@ -267,6 +267,12 @@ def convert_metadata_validation_results(self):
                 new_description = f'In sheet "{sheet}", row "{row}", column "{column}" is not populated'
             else:
                 new_description = error["description"].replace(sheet_json, sheet)
+            if column is None:
+                # We do not know this attribute. It's most likely about bioSampleObject
+                continue
+            if 'schema' in new_description:
+                # This is an error specific to json schema
+                continue
             self.results['metadata_check']['spreadsheet_errors'].append({
                 'sheet': sheet, 'row': row, 'column': column,
                 'description': new_description
@@ -290,16 +296,15 @@ def _convert_metadata_sheet(self, json_attribute, xls2json_conf):
 
     def _convert_metadata_row(self, sheet, json_row, xls2json_conf):
         if json_row is None:
-            # This is for Sheet that can only have a single entry (Project)
-            json_row = 0
+            return ''
         if 'header_row' in xls2json_conf[sheet]:
             return int(json_row) + xls2json_conf[sheet]['header_row']
         else:
             return int(json_row) + 2
 
     def _convert_metadata_attribute(self, sheet, json_attribute, xls2json_conf):
         if json_attribute is None:
-            return None
+            return ''
         attributes_dict = {}
         attributes_dict.update(xls2json_conf[sheet].get('required', {}))
         attributes_dict.update(xls2json_conf[sheet].get('optional', {}))

diff --git a/tests/resources/validation_reports/expected_report.html b/tests/resources/validation_reports/expected_report.html
diff --git a/tests/test_report.py b/tests/test_report.py
@@ -78,9 +78,7 @@
             {'property': '/analysis/0.description', 'description': "should have required property 'description'"},
             {'property': '/analysis/0.experimentType', 'description': "should have required property 'experimentType'"},
             {'property': '/analysis/0.referenceGenome', 'description': "should have required property 'referenceGenome'"},
-            {'property': '/sample/0.bioSampleAccession', 'description': "should have required property 'bioSampleAccession'"},
-            {'property': '/sample/0.bioSampleObject', 'description': "should have required property 'bioSampleObject'"},
-            {'property': '/sample/0', 'description': 'should match exactly one schema in oneOf'}
+            {'property': '/sample/0.bioSampleAccession', 'description': "should have required property 'bioSampleAccession'"}
         ],
         'report_path': '/path/to/metadata/report'
     }
@@ -98,5 +96,7 @@ def test_generate_html_report(self):
         reporter.convert_metadata_validation_results()
         validation_results = reporter.results
         report = generate_html_report(validation_results, datetime.datetime(2023, 8, 31, 12, 34, 56), "My cool project")
+        with open('report.html', 'w') as open_html:
+            assert open_html.write(report)
         with open(self.expected_report) as open_html:
             assert report == open_html.read()
diff --git a/tests/test_reporter.py b/tests/test_reporter.py
@@ -47,19 +47,15 @@ def test__collect_validation_workflow_results(self):
                     {'property': '/sample/0', 'description': 'should match exactly one schema in oneOf'}
                 ],
                 'spreadsheet_errors': [
-                    {'sheet': 'Files', 'row': 2, 'column': None, 'description': 'Sheet "Files" is missing'},
-                    {'sheet': 'Project', 'row': 2, 'column': 'Project Title',
+                    {'sheet': 'Files', 'row': '', 'column': '', 'description': 'Sheet "Files" is missing'},
+                    {'sheet': 'Project', 'row': '', 'column': 'Project Title',
                      'description': 'In sheet "Project", column "Project Title" is not populated'},
                     {'sheet': 'Analysis', 'row': 2, 'column': 'Description',
                      'description': 'In sheet "Analysis", row "2", column "Description" is not populated'},
                     {'sheet': 'Analysis', 'row': 2, 'column': 'Reference',
                      'description': 'In sheet "Analysis", row "2", column "Reference" is not populated'},
                     {'sheet': 'Sample', 'row': 3, 'column': 'Sample Accession',
                      'description': 'In sheet "Sample", row "3", column "Sample Accession" is not populated'},
-                    {'sheet': 'Sample', 'row': 3, 'column': None,
-                     'description': "should have required property 'bioSampleObject'"},
-                    {'sheet': 'Sample', 'row': 3, 'column': None,
-                     'description': 'should match exactly one schema in oneOf'}
                 ]
             }
         }