Merge pull request #1227 from alliance-genome/SCRUM-4823

SCRUM-4823 Update hard-coded assembly names to current versions

Author: markquintontulloch

agr_api/src/test/groovy/org/alliancegenome/api/tests/integration/QueryMatchIntegrationSpec.groovy

@@ -113,7 +113,7 @@ class QueryMatchIntegrationSpec extends Specification {
         "AGR-2072" | "MGI:1856689"          | "8:g.11226343C>A"
         "AGR-2072" | "MGI:1856689"          | "RefSeq:XM_017312555.2:c.1879G>T"
         "AGR-2072" | "MGI:1856689"          | "RefSeq:XP_017168044.1:p.Gly627Trp"
-        "AGR-1893" | "RGD:11568041"         | "(Rnor_6.0)X:154703661_154703782del"
+        "AGR-1893" | "RGD:11568041"         | "(mRatBN7.2)X:154703661_154703782del"
         "AGR-1893" | "ZFIN:ZDB-ALT-000412-8" | "(GRCz11)7:30341642C>T"
         "AGR-1893" | "ZFIN:ZDB-ALT-000621-2" | "(GRCz11)20:43717424A>G"
         "AGR-1893" | "WB:WBVar00089581"      | "(WBcel235)I:152331C>T"

agr_api/src/test/java/org/alliancegenome/api/tests/integration/VariantIT.java

@@ -177,7 +177,7 @@ public void checkVariantHgvsDuplication() {
 		Variant variant = variants.get(0);
 		assertEquals(variants.size(), 2);
 		String variantNames = String.join(",", variant.getHgvsG());
-		List<String> expectedNames = List.of("(GRCm38)3:115711821_115711824delinsCCGC", "3:g.115711821_115711824delinsCCGC");
+		List<String> expectedNames = List.of("(GRCm39)3:115711821_115711824delinsCCGC", "3:g.115711821_115711824delinsCCGC");
 		expectedNames.forEach(name -> assertTrue(name + " does not exist", variantNames.contains(name)));
 		String unexpectedName = "3:g.115711833T>C";
 		assertFalse(unexpectedName + " exists but should not on this transcript", variantNames.contains(unexpectedName));

agr_java_core/src/main/java/org/alliancegenome/neo4j/entity/SpeciesType.java

@@ -16,8 +16,8 @@
 @Getter
 @AllArgsConstructor
 public enum SpeciesType {
-	HUMAN("Homo sapiens", "HUMAN", "NCBITaxon:9606", "Hsa", "HUMAN", "Human", "9606", 1, "GRCh38"), RAT("Rattus norvegicus", "RGD", "NCBITaxon:10116", "Rno", "RGD", "Rat Genome Database", "10116", 2, "Rnor_6.0"),
-	MOUSE("Mus musculus", "MGI", "NCBITaxon:10090", "Mmu", "MGD", "Mouse Genome Database", "10090", 3, "GRCm38"), AFRCLAWFROG("Xenopus laevis", "XBXL", "NCBITaxon:8355", "Xla", "XB", "Xenbase", "8355", 4, "XL9.2"),
+	HUMAN("Homo sapiens", "HUMAN", "NCBITaxon:9606", "Hsa", "HUMAN", "Human", "9606", 1, "GRCh38"), RAT("Rattus norvegicus", "RGD", "NCBITaxon:10116", "Rno", "RGD", "Rat Genome Database", "10116", 2, "mRatBN7.2"),
+	MOUSE("Mus musculus", "MGI", "NCBITaxon:10090", "Mmu", "MGD", "Mouse Genome Database", "10090", 3, "GRCm39"), AFRCLAWFROG("Xenopus laevis", "XBXL", "NCBITaxon:8355", "Xla", "XB", "Xenbase", "8355", 4, "XL9.2"),
 	WESTCLAWFROG("Xenopus tropicalis", "XBXT", "NCBITaxon:8364", "Xtr", "XB", "Xenbase", "8364", 5, "XT9.1"), ZEBRAFISH("Danio rerio", "ZFIN", "NCBITaxon:7955", "Dre", "ZFIN", "Zebrafish Information Network", "7955", 6, "GRCz11"),
 	FLY("Drosophila melanogaster", "FB", "NCBITaxon:7227", "Dme", "FB", "Fly Base", "7227", 7, "R6"), WORM("Caenorhabditis elegans", "WB", "NCBITaxon:6239", "Cel", "WB", "Worm Base", "6239", 8, "WBcel235"),
 	YEAST("Saccharomyces cerevisiae", "SGD", "NCBITaxon:559292", "Sce", "SGD", "Saccharomyces Genome Database", "559292", 9, "R64-2-1"), COVID("SARS-CoV-2", // Must be the same as the DB due to lookup from the database