From baa667274268459a70eebb856935a1e6f9c337a4 Mon Sep 17 00:00:00 2001 From: supun Date: Thu, 11 Apr 2024 16:28:51 +0100 Subject: [PATCH 1/2] remove xrefs --- .../META-INF/drlineconfiguration.json | 39 ------------------- 1 file changed, 39 deletions(-) diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json index 2672aa0c8..24721f3a8 100644 --- a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json +++ b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json @@ -539,13 +539,6 @@ "category": "GVD", "uriLink": "https://www.ncbi.nlm.nih.gov/snp/%id" }, - - { - "name": "COMPLUYEAST-2DPAGE", - "displayName": "COMPLUYEAST-2DPAGE", - "category": "2DG", - "uriLink": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=%id" - }, { "name": "DOSAC-COBS-2DPAGE", "displayName": "DOSAC-COBS-2DPAGE", @@ -564,26 +557,6 @@ "category": "2DG", "uriLink": "http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?%id" }, - { - "name": "SWISS-2DPAGE", - "displayName": "SWISS-2DPAGE", - "category": "2DG", - "uriLink": "https://world-2dpage.expasy.org/swiss-2dpage/%id" - }, - { - "name": "UCD-2DPAGE", - "displayName": "UCD-2DPAGE", - "category": "2DG", - "uriLink": "https://proteomics-portal.ucd.ie/cgi-bin/2d/2d.cgi?%id" - }, - { - "name": "World-2DPAGE", - "displayName": "World-2DPAGE", - "category": "2DG", - "uriLink": "https://world-2dpage.expasy.org/repository/%id", - "idMappingName": "WORLD_2DPAGE_ID" - }, - { "name": "CPTAC", "displayName": "CPTAC", @@ -1558,18 +1531,6 @@ } ] }, - { - "name": "Genevisible", - "displayName": "Genevisible", - "category": "GEP", - "uriLink": "https://genevisible.com/tissues/%OrganismId/UniProt/%id", - "attributes": [ - { "name": "OrganismId", - "xmlTag":"organism ID" - } - ] - }, - { "name": "CDD", "displayName": "CDD", From 16570750803baa6a0bc2e2843d0b6ec46d5d4a94 Mon Sep 17 00:00:00 2001 From: supun Date: Fri, 12 Apr 2024 09:16:43 +0100 Subject: [PATCH 2/2] fixed tests --- .../cv/xdb/UniProtKBDatabaseTypesTest.java | 18 ++++-------------- 1 file changed, 4 insertions(+), 14 deletions(-) diff --git a/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java b/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java index b63f6e3b9..c258e33f3 100644 --- a/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java +++ b/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java @@ -1,8 +1,6 @@ package org.uniprot.cv.xdb; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.jupiter.api.Assertions.*; import static org.uniprot.core.cv.xdb.UniProtDatabaseCategory.*; import java.util.List; @@ -128,15 +126,7 @@ void testdbSNPType() { @Test void testSwiss2dpageType() { - UniProtDatabaseDetail opType = - UniProtDatabaseTypes.INSTANCE.getDbTypeByName("SWISS-2DPAGE"); - - assertEquals("SWISS-2DPAGE", opType.getName()); - assertEquals("SWISS-2DPAGE", opType.getDisplayName()); - assertEquals(D2_GEL_DATABASES, opType.getCategory()); - assertEquals("https://world-2dpage.expasy.org/swiss-2dpage/%id", opType.getUriLink()); - assertEquals(1, opType.getAttributes().size()); - verifyAttribute(opType.getAttributes().get(0), "Description", "description", null); + assertThrows(IllegalArgumentException.class,()->UniProtDatabaseTypes.INSTANCE.getDbTypeByName("SWISS-2DPAGE")); } @Test @@ -302,7 +292,7 @@ void testDatabaseFieldSize() { verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PTM_DATABASES), 10); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENERIC_VARIATION_DATABASES), 6); - verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 7); + verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 3); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 12); verifyGroupSize( @@ -322,7 +312,7 @@ void testDatabaseFieldSize() { 10); verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(MISCELLANEOUS), 15); verifyGroupSize( - UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENE_EXPRESSION_DATABASES), 5); + UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENE_EXPRESSION_DATABASES), 4); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(FAMILY_AND_DOMAIN_DATABASES), 16);