{"action":"created","comment":{"url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/comments/229073701","pull_request_review_id":169486720,"id":229073701,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIyOTA3MzcwMQ==","diff_hunk":"@@ -70,92 +98,215 @@\n \tEntity chebiEntity2;\n \t\n \t@InjectMocks\n-\tChebiUpdater updator = new ChebiUpdater(adaptor, true, 12345L);\n+\tChebiUpdater updator = new ChebiUpdater(adaptor, true, PERSON_ID, false);\n+\t\n+\t@Mock\n+\tGKInstance person;\n \t\n \t@Mock\n \tResultSet duplicateResults;\n \t\n+\t@Mock\n+\tSchema schema;\n+\t\n+\t@Mock\n+\tGKSchemaClass refMolSchemaClass;\n+\t\n+\t@Mock\n+\tGKSchemaClass simpleEntitySchemaClass;\n+\t\n+\t@Mock\n+\tGKSchemaClass chemicalDrugSchemaClass;\n+\t\n+\t@Mock\n+\tGKInstance createdInstance;\n+\t\n+\t@Mock\n+\tGKSchemaAttribute attribute;\n+\t\n \t@Before\n-\tvoid setupMolecule() throws InvalidAttributeException, Exception\n+\tpublic void setupMolecule() throws InvalidAttributeException, Exception\n \t{\n \t\tMockitoAnnotations.initMocks(this);\n+\t\t\n+\t\t\n+\t\twhen(attribute.isMultiple()).thenReturn(false);\n+\t\t\n+\t\twhen(refMolSchemaClass.getName()).thenReturn(ReactomeJavaConstants.ReferenceMolecule);\n+\t\twhen(simpleEntitySchemaClass.getName()).thenReturn(ReactomeJavaConstants.SimpleEntity);\n+\t\twhen(chemicalDrugSchemaClass.getName()).thenReturn(ReactomeJavaConstants.ChemicalDrug);\n+\t\tPowerMockito.mockStatic(InstanceEditUtils.class);\n+\t\twhen(adaptor.fetchInstance(PERSON_ID)).thenReturn(person);\n+\t\t\n+\t\twhen(adaptor.getSchema()).thenReturn(schema);\n+\n+\t\twhen(schema.getClassByName(ReactomeJavaConstants.ReferenceMolecule)).thenReturn(refMolSchemaClass);\n+\t\twhen(person.getDbAdaptor()).thenReturn(adaptor);\n+\t\twhen(createdInstance.getAttributeValue(ReactomeJavaConstants.author)).thenReturn(person);\n+\t\t\n+\t\twhen(InstanceEditUtils.createInstanceEdit(adaptor, PERSON_ID, updator.getClass().getCanonicalName())).thenReturn(person);\n+\t\t\n+\t\twhen(chebiRefDB.getDBID()).thenReturn(123456L);\n+\t\twhen(adaptor.fetchInstanceByAttribute(\"ReferenceDatabase\", \"name\", \"=\", \"ChEBI\")).thenReturn(Arrays.asList(chebiRefDB)) ;\n+\n \t}\n \t\n \t@Test\n-\t@MockitoSettings(strictness = Strictness.WARN)\n-\tpublic void testUpdateMolecules() throws Exception\n+\tpublic void testUpdateMolecules()\n+\t{\n+\t\ttry\n+\t\t{\n+\t\t\t\n+\t\t\twhen(chebiEntity1.getChebiAsciiName()).thenReturn(\"NAME1\");\n+\t\t\twhen(chebiEntity2.getChebiAsciiName()).thenReturn(\"NAME-2\");\n+\t\t\t\n+\t\t\twhen(chebiEntity1.getChebiId()).thenReturn(\"CHEBI:112233\");\n+\t\t\twhen(chebiEntity2.getChebiId()).thenReturn(\"CHEBI:332211-2\");\n+\t\t\t\n+\t\t\tDataItem d = new DataItem();\n+\t\t\td.setData(\"H2\");\n+\t\t\twhen(chebiEntity1.getFormulae()).thenReturn(Arrays.asList( d ));\n+\t\t\twhen(chebiEntity2.getFormulae()).thenReturn(Arrays.asList( d ));\n+\t\t\t\n+\t\t\twhen(chebiClient.getCompleteEntity(\"112233\")).thenReturn(chebiEntity1);\n+\t\t\twhen(chebiClient.getCompleteEntity(\"332211\")).thenReturn(chebiEntity2);\n+\t\t\twhen(chebiClient.getCompleteEntity(\"445566\")).thenReturn(null);\n+\t\t\twhen(chebiClient.getCompleteEntity(\"778899\")).thenReturn(chebiEntity1);\n+\t\t\t\n+\t\t\twhen(molecule1.getAttributeValue(\"identifier\")).thenReturn(\"112233\");\n+\t\t\twhen(molecule1.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"NAME1\")));\n+\t\t\twhen(molecule1.getAttributeValue(\"formula\")).thenReturn(\"H3\");\n+\t\t\twhen(molecule1.getDBID()).thenReturn(123L);\n+\t\t\twhen(molecule1.getSchemClass()).thenReturn(refMolSchemaClass);\n+\t\t\twhen(adaptor.fetchInstance(123L)).thenReturn(molecule1);\n+\t\t\t\n+\t\t\twhen(molecule2.getAttributeValue(\"identifier\")).thenReturn(\"332211\");\n+\t\t\twhen(molecule2.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"NAME2\")));\n+\t\t\twhen(molecule2.getDBID()).thenReturn(456L);\n+\t\t\twhen(molecule2.getSchemClass()).thenReturn(refMolSchemaClass);\n+\t\t\twhen(adaptor.fetchInstance(456L)).thenReturn(molecule2);\n+\t\t\t\n+\t\t\twhen(molecule3.getAttributeValue(\"identifier\")).thenReturn(\"445566\");\n+\t\t\t\n+\t\t\twhen(molecule4.getAttributeValue(\"identifier\")).thenReturn(\"778899\");\n+\t\t\twhen(molecule4.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"NAME1\")));\n+\t\t\twhen(molecule4.getAttributeValue(\"formula\")).thenReturn(\"H2\");\n+\t\t\twhen(molecule4.getSchemClass()).thenReturn(refMolSchemaClass);\n+\t\t\twhen(molecule4.getDBID()).thenReturn(444L);\n+\t\t\twhen(adaptor.fetchInstance(444L)).thenReturn(molecule4);\n+\t\t\t\n+\t\t\twhen(refEnt1.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"OTHERNAME\", \"NAME1\", \"BLAH\")));\n+\t\t\twhen(refEnt1.getSchemClass()).thenReturn(simpleEntitySchemaClass);\n+\t\t\twhen(refEnt2.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"TEST\", \"NAME2\")));\n+\t\t\twhen(refEnt2.getSchemClass()).thenReturn(simpleEntitySchemaClass);\n+\t\t\twhen(refEnt3.getAttributeValuesList(\"name\")).thenReturn(new ArrayList<String>(Arrays.asList(\"NAME-2\", \"ASDFQ@#$FASFASDF\",\"NOPE\")));\n+\t\t\twhen(refEnt1.getSchemClass()).thenReturn(chemicalDrugSchemaClass);","path":"chebi-update/src/test/java/org/reactome/release/test/chebiupdate/ChebiUpdaterTest.java","position":193,"original_position":193,"commit_id":"e0495059b81b6ed9ba6984b2773253e0ad792e79","original_commit_id":"e0495059b81b6ed9ba6984b2773253e0ad792e79","user":{"login":"jweiser","id":2857592,"node_id":"MDQ6VXNlcjI4NTc1OTI=","avatar_url":"https://avatars3.githubusercontent.com/u/2857592?v=4","gravatar_id":"","url":"https://api.github.com/users/jweiser","html_url":"https://github.com/jweiser","followers_url":"https://api.github.com/users/jweiser/followers","following_url":"https://api.github.com/users/jweiser/following{/other_user}","gists_url":"https://api.github.com/users/jweiser/gists{/gist_id}","starred_url":"https://api.github.com/users/jweiser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jweiser/subscriptions","organizations_url":"https://api.github.com/users/jweiser/orgs","repos_url":"https://api.github.com/users/jweiser/repos","events_url":"https://api.github.com/users/jweiser/events{/privacy}","received_events_url":"https://api.github.com/users/jweiser/received_events","type":"User","site_admin":false},"body":"Should this be refEnt3 returning chemicalDrugSchemaClass?","created_at":"2018-10-29T19:50:56Z","updated_at":"2018-10-29T19:50:56Z","html_url":"https://github.com/reactome/data-release-pipeline/pull/10#discussion_r229073701","pull_request_url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/10","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/comments/229073701"},"html":{"href":"https://github.com/reactome/data-release-pipeline/pull/10#discussion_r229073701"},"pull_request":{"href":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/10"}}},"pull_request":{"url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/10","id":224080582,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI0MDgwNTgy","html_url":"https://github.com/reactome/data-release-pipeline/pull/10","diff_url":"https://github.com/reactome/data-release-pipeline/pull/10.diff","patch_url":"https://github.com/reactome/data-release-pipeline/pull/10.patch","issue_url":"https://api.github.com/repos/reactome/data-release-pipeline/issues/10","number":10,"state":"open","locked":false,"title":"Feature/ch ebi update","user":{"login":"SolomonShorser-OICR","id":10213802,"node_id":"MDQ6VXNlcjEwMjEzODAy","avatar_url":"https://avatars1.githubusercontent.com/u/10213802?v=4","gravatar_id":"","url":"https://api.github.com/users/SolomonShorser-OICR","html_url":"https://github.com/SolomonShorser-OICR","followers_url":"https://api.github.com/users/SolomonShorser-OICR/followers","following_url":"https://api.github.com/users/SolomonShorser-OICR/following{/other_user}","gists_url":"https://api.github.com/users/SolomonShorser-OICR/gists{/gist_id}","starred_url":"https://api.github.com/users/SolomonShorser-OICR/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SolomonShorser-OICR/subscriptions","organizations_url":"https://api.github.com/users/SolomonShorser-OICR/orgs","repos_url":"https://api.github.com/users/SolomonShorser-OICR/repos","events_url":"https://api.github.com/users/SolomonShorser-OICR/events{/privacy}","received_events_url":"https://api.github.com/users/SolomonShorser-OICR/received_events","type":"User","site_admin":false},"body":"@jweiser @cookersjs Looking for general feedback and comments on this.\r\n\r\nThis is a Re-implementation of the ChEBI Update code and algorithm. It is *not* the same as the Perl algorithm.","created_at":"2018-10-18T19:59:26Z","updated_at":"2018-10-29T19:50:56Z","closed_at":null,"merged_at":null,"merge_commit_sha":"f9cc42539c3bc1da1bf2dc071dc098e22219bca5","assignee":{"login":"jweiser","id":2857592,"node_id":"MDQ6VXNlcjI4NTc1OTI=","avatar_url":"https://avatars3.githubusercontent.com/u/2857592?v=4","gravatar_id":"","url":"https://api.github.com/users/jweiser","html_url":"https://github.com/jweiser","followers_url":"https://api.github.com/users/jweiser/followers","following_url":"https://api.github.com/users/jweiser/following{/other_user}","gists_url":"https://api.github.com/users/jweiser/gists{/gist_id}","starred_url":"https://api.github.com/users/jweiser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jweiser/subscriptions","organizations_url":"https://api.github.com/users/jweiser/orgs","repos_url":"https://api.github.com/users/jweiser/repos","events_url":"https://api.github.com/users/jweiser/events{/privacy}","received_events_url":"https://api.github.com/users/jweiser/received_events","type":"User","site_admin":false},"assignees":[{"login":"jweiser","id":2857592,"node_id":"MDQ6VXNlcjI4NTc1OTI=","avatar_url":"https://avatars3.githubusercontent.com/u/2857592?v=4","gravatar_id":"","url":"https://api.github.com/users/jweiser","html_url":"https://github.com/jweiser","followers_url":"https://api.github.com/users/jweiser/followers","following_url":"https://api.github.com/users/jweiser/following{/other_user}","gists_url":"https://api.github.com/users/jweiser/gists{/gist_id}","starred_url":"https://api.github.com/users/jweiser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jweiser/subscriptions","organizations_url":"https://api.github.com/users/jweiser/orgs","repos_url":"https://api.github.com/users/jweiser/repos","events_url":"https://api.github.com/users/jweiser/events{/privacy}","received_events_url":"https://api.github.com/users/jweiser/received_events","type":"User","site_admin":false},{"login":"cookersjs","id":19961210,"node_id":"MDQ6VXNlcjE5OTYxMjEw","avatar_url":"https://avatars0.githubusercontent.com/u/19961210?v=4","gravatar_id":"","url":"https://api.github.com/users/cookersjs","html_url":"https://github.com/cookersjs","followers_url":"https://api.github.com/users/cookersjs/followers","following_url":"https://api.github.com/users/cookersjs/following{/other_user}","gists_url":"https://api.github.com/users/cookersjs/gists{/gist_id}","starred_url":"https://api.github.com/users/cookersjs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cookersjs/subscriptions","organizations_url":"https://api.github.com/users/cookersjs/orgs","repos_url":"https://api.github.com/users/cookersjs/repos","events_url":"https://api.github.com/users/cookersjs/events{/privacy}","received_events_url":"https://api.github.com/users/cookersjs/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/10/commits","review_comments_url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/10/comments","review_comment_url":"https://api.github.com/repos/reactome/data-release-pipeline/pulls/comments{/number}","comments_url":"https://api.github.com/repos/reactome/data-release-pipeline/issues/10/comments","statuses_url":"https://api.github.com/repos/reactome/data-release-pipeline/statuses/e0495059b81b6ed9ba6984b2773253e0ad792e79","head":{"label":"reactome:feature/ChEBI_Update","ref":"feature/ChEBI_Update","sha":"e0495059b81b6ed9ba6984b2773253e0ad792e79","user":{"login":"reactome","id":5891396,"node_id":"MDEyOk9yZ2FuaXphdGlvbjU4OTEzOTY=","avatar_url":"https://avatars1.githubusercontent.com/u/5891396?v=4","gravatar_id":"","url":"https://api.github.com/users/reactome","html_url":"https://github.com/reactome","followers_url":"https://api.github.com/users/reactome/followers","following_url":"https://api.github.com/users/reactome/following{/other_user}","gists_url":"https://api.github.com/users/reactome/gists{/gist_id}","starred_url":"https://api.github.com/users/reactome/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/reactome/subscriptions","organizations_url":"https://api.github.com/users/reactome/orgs","repos_url":"https://api.github.com/users/reactome/repos","events_url":"https://api.github.com/users/reactome/events{/privacy}","received_events_url":"https://api.github.com/users/reactome/received_events","type":"Organization","site_admin":false},"repo":{"id":130117984,"node_id":"MDEwOlJlcG9zaXRvcnkxMzAxMTc5ODQ=","name":"data-release-pipeline","full_name":"reactome/data-release-pipeline","private":false,"owner":{"login":"reactome","id":5891396,"node_id":"MDEyOk9yZ2FuaXphdGlvbjU4OTEzOTY=","avatar_url":"https://avatars1.githubusercontent.com/u/5891396?v=4","gravatar_id":"","url":"https://api.github.com/users/reactome","html_url":"https://github.com/reactome","follo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