[WIP] preparing for 3.1.5

README.md

@@ -135,7 +135,8 @@ To make the release, run the following commands. Mind you, this requires you
 to have an approved Sonatype (http://oss.sonatype.org/) account with push rights:
 
 ```shell
-mvn versions:set -DnewVersion=3.1.4
+mvn versions:set -DnewVersion=3.1.5
+mvn -f pom-java8.xml versions:set -DnewVersion=3.1.5
 mvn clean deploy
 ```
 
@@ -145,7 +146,8 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.1.5-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.6-SNAPSHOT
+mvn -f pom-java8.xml versions:set -DnewVersion=3.1.6-SNAPSHOT
 mvn clean deploy
 ```
 

org.bridgedb.bio/pom.xml

@@ -56,7 +56,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <configuration>
                     <archive>
                         <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>

org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java

@@ -97,7 +97,9 @@ public enum Organism {
 
 	RattusNorvegicus("Rattus norvegicus", "Rn", "Rat", 10116),
 	SaccharomycesCerevisiae("Saccharomyces cerevisiae", "Sc", "Yeast", 4932),
+	SalviaFruticosa("Salvia fruticosa", "Sf", "Greek sage", 268906),
 	SolanumLycopersicum("Solanum lycopersicum", "Sl", "Tomato", 4081),
+	SolanumTuberosum("Solanum tuberosum", "St", "potato", 4113),
 	SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567),
 
 	SorexAraneus ("Sorex araneus", "Sa", "Shrew", 42254),

org.bridgedb.gui/pom.xml

@@ -57,7 +57,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <configuration>
                     <archive>
                         <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>

org.bridgedb.rdb.construct/pom.xml

@@ -57,7 +57,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <configuration>
                     <archive>
                         <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>

org.bridgedb.rdb/pom.xml

@@ -56,7 +56,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <configuration>
                     <archive>
                         <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>

org.bridgedb.sql/pom.xml

@@ -21,7 +21,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.uri.api/pom.xml

@@ -32,7 +32,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.uri.sql/pom.xml

@@ -32,7 +32,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.uri.ws.core/pom.xml

@@ -33,7 +33,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.utils/pom.xml

@@ -32,7 +32,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.ws.core/pom.xml

@@ -33,7 +33,6 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
                 <executions>
                     <execution>
                         <goals>

org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java

@@ -169,12 +169,12 @@ public void testListDataSourceBean() throws ClassNotFoundException, IDMapperExce
 		assertEquals("class org.bridgedb.ws.bean.DataSourceBean",dsBean.getClass().toString());
 		assertEquals("S",dsBean.getIdExample());
 		assertEquals("S",dsBean.getSysCode());
-		assertEquals("Uniprot-TrEMBL",dsBean.getFullName());
+		assertEquals("UniProtKB",dsBean.getFullName());
 		assertEquals("http://www.uniprot.org/",dsBean.getMainUrl());
 		assertEquals("protein",dsBean.getType().toString());
 		assertEquals("http://www.uniprot.org/uniprot/$id", dsBean.getUrlPattern());
 		assertEquals("urn:miriam:uniprot", dsBean.getUrnBase());
-		assertEquals("S:Uniprot-TrEMBL", dsBean.toString());
+		assertEquals("S:UniProtKB", dsBean.toString());
 		assertEquals("sysCode = dsEnsembl", testdsBean.toString());
 		assertEquals("sysCode = Ensembl", testdsBean2.toString());
 

org.bridgedb/src/main/java/org/bridgedb/DataSource.java

@@ -666,6 +666,10 @@ public Builder description(String description){
 	 * @return Builder that can be used for adding detailed information.
 	 */
 	public static Builder register(String sysCode, String fullName){
+		if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) {
+			fullName = "UniProtKB";
+		}
+
         if (!isSuitableKey(sysCode)) {
             throw new IllegalArgumentException ("Unsuitable sysCode " + sysCode + " with " + fullName);
         }
@@ -683,14 +687,22 @@ public static Builder register(String sysCode, String fullName){
 	 * @return Builder that can be used for adding detailed information.
 	 */
 	public static Builder mock(String sysCode, String fullName){
+		if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) {
+			fullName = "UniProtKB";
+		}
+
 		return new Builder(new DataSource (sysCode, fullName));
     }
 
     private static Builder findOrRegister(String sysCode, String fullName)
 	{
  		DataSource current = null;
 		if (fullName == null && sysCode == null) throw new NullPointerException();
-
+
+		if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) {
+			fullName = "UniProtKB";
+		}
+
 		if (byFullName.containsKey(fullName))
 		{
 			current = byFullName.get(fullName);
@@ -823,6 +835,9 @@ public static DataSource getExistingByFullName(String fullName)
      * @since Version 2.0.0
      */
     public static boolean fullNameExists(String fullName){
+        if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) {
+			fullName = "UniProtKB";
+		}
         return byFullName.containsKey(fullName);
     }
 

org.bridgedb/src/main/resources/version.props

@@ -1,2 +1,2 @@
 # Current version of BridgeDb
-bridgedb.version=3.1.3
+bridgedb.version=3.1.5-SNAPSHOT

org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java

@@ -505,4 +505,13 @@ public void testBioregistry() {
 		assertFalse(DataSource.bioregistryPrefixExists("unifrot"));
 	}
 
+	@Test
+	public void testFullNameExists() {
+		DataSource.register("S", "UniProtKB")
+	    	.bioregistryPrefix("uniprot")
+	    	.asDataSource();
+	    assertTrue(DataSource.fullNameExists("Uniprot-TrEMBL"));;
+	    assertTrue(DataSource.fullNameExists("Uniprot-SwissProt"));;
+	    assertTrue(DataSource.fullNameExists("UniProtKB"));;
+	}
 }

pom-java8.xml

@@ -4,7 +4,7 @@
   <groupId>org.bridgedb</groupId>
   <artifactId>bridgedb-bundle-pv</artifactId>
   <packaging>pom</packaging>
-  <version>3.1.4</version>
+  <version>3.1.5-SNAPSHOT</version>
   <name>BridgeDb 4 PathVisio bundle</name>
 	<description>
 		BridgeDb is a framework for finding and mapping equivalent database

pom.xml

@@ -49,8 +49,8 @@
         <felix.version>5.1.9</felix.version>
         <hamcrest.version>3.0</hamcrest.version>
         <jersey.version>1.10</jersey.version>
-        <log4j.version>2.22.0</log4j.version>
-        <mysql.version>9.0.0</mysql.version>
+        <log4j.version>2.25.0</log4j.version>
+        <mysql.version>9.5.0</mysql.version>
         <netbeans.hint.deploy.server>Tomcat</netbeans.hint.deploy.server>
         <owlapi-api.version>3.4</owlapi-api.version>
         <rdf4j.version>4.3.8</rdf4j.version>
@@ -59,7 +59,7 @@
         <derby.version>10.15.2.0</derby.version>
         <junit-platform-surefire-provider>1.3.2</junit-platform-surefire-provider>
         <junit5.platform.launcher.version>1.11.0</junit5.platform.launcher.version>
-        <junit5.jupiter.version>5.11.0</junit5.jupiter.version>
+        <junit5.jupiter.version>5.11.4</junit5.jupiter.version>
         <junit5.excludeGroups>mysql</junit5.excludeGroups>
         <junit5.groups />
     </properties>
@@ -95,7 +95,30 @@
 			</testResource>
 		</testResources>
         <plugins>
-          <plugin>
+        <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-enforcer-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                        <execution>
+                                <id>enforce-maven</id>
+                                <goals>
+                                        <goal>enforce</goal>
+                                </goals>
+                                <configuration>
+                                        <rules>
+                                                <requireMavenVersion>
+                                                        <version>3.6.3</version>
+                                                </requireMavenVersion>
+                                                <!-- requireJavaVersion>
+                                                        <version>11</version>
+                                                </requireJavaVersion -->
+                                        </rules>
+                                </configuration>
+                        </execution>
+                </executions>
+        </plugin>
+        <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-source-plugin</artifactId>
             <version>3.2.1</version>