Fix export pipeline and OLS tests

pipelines/export_curation_spreadsheet.nf

@@ -43,8 +43,8 @@ workflow {
     )
 
     if (params.with_feedback) {
-        generateZoomaFeedback(addMappingsHeader.out.finalMappings)
-        updateLinks(addMappingsHeader.out.finalMappings, generateZoomaFeedback.out.zoomaFeedback)
+        generateZoomaFeedback(createLatestMappings.out.finalMappings)
+        updateLinks(createLatestMappings.out.finalMappings, generateZoomaFeedback.out.zoomaFeedback)
     }
 }
 

tests/trait_mapping/test_ols.py

@@ -118,7 +118,7 @@ def test_get_ols_search_results():
         target_ontology='EFO',
         preferred_ontologies=['mondo', 'hp']
     )
-    assert len(results) == 4
+    assert len(results) == 5
     top_ranked_result = next(iter(sorted(results, reverse=True)))
     assert top_ranked_result.label == 'hemophilia A'
     assert top_ranked_result.get_match_type() == MatchType.EXACT_MATCH_SYNONYM

tests/trait_mapping/test_trait_processing.py

@@ -33,14 +33,14 @@ def test_ols_exact_match(self):
         # Only goes through OLS as it finds an exact match in EFO
         trait = Trait('chédiak-higashi syndrome', None, None)
         processed_trait = self.run_process_trait(trait)
-        assert len(processed_trait.ols_result_list) == 7
+        assert len(processed_trait.ols_result_list) == 8
         assert processed_trait.is_finished
 
     def test_previous_mapping(self):
         # Finds nothing exact via OLS, so checks previous mappings and finds a current result
         trait = Trait('11p partial monosomy syndrome', None, None)
         processed_trait = self.run_process_trait(trait)
-        assert len(processed_trait.ols_result_list) == 5
+        assert len(processed_trait.ols_result_list) == 6
         assert len(processed_trait.previous_mapping_list) == 1
         assert processed_trait.is_finished