Issue240 pr

.github/workflows/build.yml

@@ -12,16 +12,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
-        distribution: 'adopt'
+        distribution: 'temurin'
         java-version: 11
         cache: maven
     - name: Build with Maven
       run: mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql
     - name: push JaCoCo stats to codecov.io
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv

@@ -85,7 +85,7 @@ NASC Gene	N	http://arabidopsis.info/		ATMG00960-TAIR-G	gene	Arabidopsis thaliana
 NCBI Protein	Np	http://www.ncbi.nlm.nih.gov/protein	http://www.ncbi.nlm.nih.gov/protein/$id	CAA71118.1	protein		1	urn:miriam:ncbiprotein	^\w+\d+(\.\d+)?$	NCBI Protein		ncbiprotein	protein
 NCI Pathway Interaction Database	Pid	http://pid.nci.nih.gov/	http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id	pi3kcipathway	pathway		1	urn:miriam:pid.pathway	^\w+$	NCI Pathway Interaction Database		pid.pathway	pathway
 OMIM	Om	http://omim.org/	http://omim.org/entry/$id	603903	gene		0	urn:miriam:mim	^[*#+%^]?\d{6}$	OMIM	P492	omim	gene,disease
-OpenTargets	Opt	https://www.opentargets.org/	https://genetics.opentargets.org/gene/$id	ENSG00000169174	gene		1		^ENS[A-Z]*[FPTG]\d{11}$			ensembl	gene
+OpenTargets	Opt	https://www.opentargets.org/	https://genetics.opentargets.org/gene/$id	ENSG00000169174	gene		1		^ENS[A-Z]*[FPTG]\d{11}$				gene
 ORCID	orcid	https://orcid.org	https://orcid.org/$id	0000-0002-5355-2576	other	Homo sapiens	1	urn:miriam:orcid	^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$	ORCID	P496	orcid	other,author
 Orphanet	On	http://www.orpha.net/consor/	https://identifiers.org/orphanet:$id	85163	other	Homo sapiens	1	urn:miriam:orphanet	^\d+$	Bio2RDF		orphanet	other
 Oryzabase	Ob	http://www.shigen.nig.ac.jp/rice/oryzabase	http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id	468	gene	Oryza sativa	1	Ob		Oryzabase		oryzabase.gene	gene

org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java

@@ -42,7 +42,7 @@ public class DataSourceTxtTest {
 
 	@BeforeAll
 	public static void setUpSources() {
-		DataSourceTxt.init();
+		if (DataSource.getDataSources().size() == 0) DataSourceTxt.init();
 	}
 
 	@org.junit.jupiter.api.Test

org.bridgedb.bio/src/test/java/org/bridgedb/bio/XrefTest.java

@@ -0,0 +1,25 @@
+package org.bridgedb.bio;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import org.bridgedb.DataSource;
+import org.bridgedb.Xref;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+public class XrefTest {
+
+	@BeforeAll
+	public static void setUpSources() {
+		if (DataSource.getDataSources().size() == 0) DataSourceTxt.init();
+	}
+
+	@Test
+	public void testCheckCorrectBioregistryIdentifier() {
+		Xref xref = Xref.fromBioregistryIdentifier("ensembl:ENSGALG00000007562");
+		assertNotNull(xref);
+		assertEquals("En:ENSGALG00000007562:T", xref.toString());
+	}
+
+}

org.bridgedb/src/test/java/org/bridgedb/XrefTest.java

@@ -19,8 +19,6 @@
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNotSame;
 import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
@@ -196,4 +194,5 @@ public void testToString() {
 	public void testGetKnownUrl() {
 		System.out.println(new Xref("CHEBI:17855", CHEBI, true).getKnownUrl());
 	}
+
 }