[WIP] Development for release 3.1.3

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 title: BridgeDb
 message: 'If you use this software, please cite it as below.'
 type: software
-version: 3.1.2
-date-released: '2024-07-30'
+version: 3.1.3
+date-released: '2024-10-01'
 authors:
   - given-names: Manas
     family-names: Awasthi

README.md

@@ -15,7 +15,7 @@ Using BridgeDb dependencies
 The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to 
 [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb.
 
-Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.3`:
 
 For [Maven](https://maven.apache.org/):
 
@@ -24,27 +24,27 @@ For [Maven](https://maven.apache.org/):
     <dependency>
         <groupId>org.bridgedb</groupId>
         <artifactId>org.bridgedb.bio</artifactId>
-        <version>3.1.2</version>
+        <version>3.1.3</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.3'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.2"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.3"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.1.2'
+'org.bridgedb:org.bridgedb.bio:jar:3.1.3'
 ```
 
 
@@ -135,7 +135,7 @@ 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=3.1.2
+mvn versions:set -DnewVersion=3.1.3
 mvn clean deploy
 ```
 
@@ -145,7 +145,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.1.3-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.4-SNAPSHOT
 mvn clean deploy
 ```
 

examples/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.1.2</version>
+    <version>3.1.3</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.bridgedb.examples</groupId>
@@ -65,22 +65,10 @@
     <dependency>
     	<groupId>wsdl4j</groupId>
     	<artifactId>wsdl4j</artifactId>
-    	<version>1.6.2</version>
+    	<version>1.6.3</version>
     	<type>jar</type>
     	<scope>runtime</scope>
     </dependency>
-    <dependency>
-    	<groupId>org.apache.axis</groupId>
-    	<artifactId>axis</artifactId>
-    	<version>1.4</version>
-    	<type>jar</type>
-    </dependency>
-    <dependency>
-    	<groupId>org.apache.axis</groupId>
-    	<artifactId>axis-jaxrpc</artifactId>
-    	<version>1.4</version>
-    	<type>jar</type>
-    </dependency>
   </dependencies>
 
 </project>

org.bridgedb.bio/pom.xml

@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -32,7 +32,7 @@
             <plugin>
                 <groupId>org.apache.felix</groupId>
                 <artifactId>maven-bundle-plugin</artifactId>
-                <version>5.1.2</version>
+                <version>${felix.version}</version>
                 <extensions>true</extensions>
                 <configuration>
                     <instructions>

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

@@ -55,7 +55,6 @@ Illumina	Il	http://www.illumina.com/		ILMN_5668	probe		0	Il	ILMN_\d+	Illumina		i
 InChIKey	Ik	http://inchi.org/		QTBSBXVTEAMEQO-UHFFFAOYSA-N	metabolite		1	urn:miriam:inchikey	^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?	Standard InChIKey	P235	inchikey	metabolite
 IntAct	Ia	http://www.ebi.ac.uk/intact/	http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id	EBI-2307691	interaction		1	urn:miriam:intact	^EBI\-[0-9]+$	IntAct		intact	interaction
 InterPro	I	http://www.ebi.ac.uk/interpro/	https://www.ebi.ac.uk/interpro/entry/InterPro/$id	IPR000100	protein		1	urn:miriam:interpro	^IPR\d{6}$	InterPro	P2926	interpro	protein
-IPI	Ip	http://www.ebi.ac.uk/IPI	http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default	IPI00000001	protein		1		^IPI\d{8}$	IPI		interpro	protein
 IRGSP Gene	Ir	http://rgp.dna.affrc.go.jp/IRGSP/	https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id	Os12g0561000	gene		1	Ir	Os\d{2}g\d+	IRGSP Gene		rapdb.locus	gene
 ISBN	isbn	http://isbndb.com/	http://isbndb.com/search-all.html?kw=$id	9781584885658	publication		1	urn:miriam:isbn	^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$	ISBN	P212	isbn	publication
 ISSN	issn	https://portal.issn.org	https://portal.issn.org/resource/ISSN/$id	1776-3045	publication		1	urn:miriam:issn	^\d{4}-\d{3}[\dX]$	ISSN	P236	issn	publication

org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv

@@ -40,10 +40,11 @@ Plasmodium	falciparum	Malaria parasite	Pf	5833
 Prymnesium	parvum		Pp	97485
 Populus	trichocarpa	Western Balsam Poplar	Pi	3694
 Rattus	norvegicus	Rat	Rn	10116
+Rosmarinus	officinalis	Rosemary	Ro	39367
 Saccharomyces	cerevisiae	Yeast	Sc	4932
 Skeletonema	marinoi		Sm	267567
 Solanum	lycopersicum	Tomato	Sl	4081
-Solanum tuberosum		St	4113
+Solanum	tuberosum		St	4113
 Sorex	araneus	Shrew	Sa	42254
 Sorghum	bicolor	Sorghum	Sb	4558
 Sus	scrofa	Pig	Ss	9823

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

@@ -55,7 +55,6 @@ Illumina	Il	http://www.illumina.com/		ILMN_5668	probe		0	Il	ILMN_\d+	Illumina		i
 InChIKey	Ik	http://inchi.org/		QTBSBXVTEAMEQO-UHFFFAOYSA-N	metabolite		1	urn:miriam:inchikey	^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?	Standard InChIKey	P235	inchikey	metabolite
 IntAct	Ia	http://www.ebi.ac.uk/intact/	http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id	EBI-2307691	interaction		1	urn:miriam:intact	^EBI\-[0-9]+$	IntAct		intact	interaction
 InterPro	I	http://www.ebi.ac.uk/interpro/	https://www.ebi.ac.uk/interpro/entry/InterPro/$id	IPR000100	protein		1	urn:miriam:interpro	^IPR\d{6}$	InterPro	P2926	interpro	protein
-IPI	Ip	http://www.ebi.ac.uk/IPI	http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default	IPI00000001	protein		1		^IPI\d{8}$	IPI		interpro	protein
 IRGSP Gene	Ir	http://rgp.dna.affrc.go.jp/IRGSP/	https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id	Os12g0561000	gene		1	Ir	Os\d{2}g\d+	IRGSP Gene		rapdb.locus	gene
 ISBN	isbn	http://isbndb.com/	http://isbndb.com/search-all.html?kw=$id	9781584885658	publication		1	urn:miriam:isbn	^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$	ISBN	P212	isbn	publication
 ISSN	issn	https://portal.issn.org	https://portal.issn.org/resource/ISSN/$id	1776-3045	publication		1	urn:miriam:issn	^\d{4}-\d{3}[\dX]$	ISSN	P236	issn	publication

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

@@ -40,10 +40,11 @@ Plasmodium	falciparum	Malaria parasite	Pf	5833
 Prymnesium	parvum		Pp	97485
 Populus	trichocarpa	Western Balsam Poplar	Pi	3694
 Rattus	norvegicus	Rat	Rn	10116
+Rosmarinus	officinalis	Rosemary	Ro	39367
 Saccharomyces	cerevisiae	Yeast	Sc	4932
 Skeletonema	marinoi		Sm	267567
 Solanum	lycopersicum	Tomato	Sl	4081
-Solanum tuberosum		St	4113
+Solanum	tuberosum		St	4113
 Sorex	araneus	Shrew	Sa	42254
 Sorghum	bicolor	Sorghum	Sb	4558
 Sus	scrofa	Pig	Ss	9823

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

@@ -33,6 +33,7 @@
 import java.util.Set;
 
 import org.bridgedb.DataSource;
+import org.junit.jupiter.api.BeforeAll;
 
 
 /**
@@ -41,6 +42,11 @@
  */
 public class DataSourceTxtTest {
 
+	@BeforeAll
+	public static void setUpSources() {
+		if (DataSource.getDataSources().size() < 20) DataSourceTxt.init();
+	}
+
 	@org.junit.jupiter.api.Test
 	public void testUniqueSystemCodes() {
 		Set<String> codes = new HashSet<String>();

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

@@ -21,7 +21,7 @@ public class UniProtKBTest {
 
 	@BeforeAll
 	public static void setUpSources() {
-		DataSourceTxt.init();
+		if (DataSource.getDataSources().size() < 20) DataSourceTxt.init();
 	}
 
 	@Test

org.bridgedb.file.orthoxml/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>

org.bridgedb.gui/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -32,7 +32,7 @@
             <plugin>
                 <groupId>org.apache.felix</groupId>
                 <artifactId>maven-bundle-plugin</artifactId>
-                <version>5.1.2</version>
+                <version>${felix.version}</version>
                 <extensions>true</extensions>
                 <configuration>
                     <instructions>

org.bridgedb.rdb.construct/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -32,7 +32,7 @@
             <plugin>
                 <groupId>org.apache.felix</groupId>
                 <artifactId>maven-bundle-plugin</artifactId>
-                <version>5.1.2</version>
+                <version>${felix.version}</version>
                 <extensions>true</extensions>
                 <configuration>
                     <instructions>
@@ -80,8 +80,8 @@
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
+			<groupId>com.mysql</groupId>
+			<artifactId>mysql-connector-j</artifactId>
 			<version>${mysql.version}</version>
 			<type>jar</type>
 			<scope>runtime</scope>

org.bridgedb.rdb/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -32,7 +32,7 @@
             <plugin>
                 <groupId>org.apache.felix</groupId>
                 <artifactId>maven-bundle-plugin</artifactId>
-                <version>5.1.2</version>
+                <version>${felix.version}</version>
                 <extensions>true</extensions>
                 <configuration>
                     <instructions>
@@ -79,8 +79,8 @@
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
+			<groupId>com.mysql</groupId>
+			<artifactId>mysql-connector-j</artifactId>
 			<version>${mysql.version}</version>
 			<type>jar</type>
 			<scope>runtime</scope>
@@ -108,7 +108,7 @@
         <dependency>
             <groupId>org.junit.platform</groupId>
             <artifactId>junit-platform-launcher</artifactId>
-            <version>1.10.1</version>
+            <version>${junit5.platform.launcher.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>

org.bridgedb.rdf/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
     <build>

org.bridgedb.sql/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
         <build>
@@ -47,8 +47,8 @@
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
+			<groupId>com.mysql</groupId>
+			<artifactId>mysql-connector-j</artifactId>
 			<version>${mysql.version}</version>
 			<type>jar</type>
 			<scope>compile</scope>

org.bridgedb.tools.batchmapper/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -33,19 +33,19 @@
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb</artifactId>
-                        <version>3.1.2</version>
+                        <version>3.1.3</version>
                         <scope>compile</scope>
                 </dependency>
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb.bio</artifactId>
-			<version>3.1.2</version>
+			<version>3.1.3</version>
 			<scope>compile</scope>
 		</dependency>
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb.rdb</artifactId>
-                        <version>3.1.2</version>
+                        <version>3.1.3</version>
                         <scope>compile</scope>
                 </dependency>
 	</dependencies>

org.bridgedb.tools.info/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>

org.bridgedb.tools.qc/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.2</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -71,8 +71,8 @@
                         <version>${project.parent.version}</version>
                         <exclusions>
                                 <exclusion>
-                                        <groupId>mysql</groupId>
-                                        <artifactId>mysql-connector-java</artifactId>
+                                        <groupId>com.mysql</groupId>
+                                        <artifactId>mysql-connector-j</artifactId>
                                 </exclusion>
                         </exclusions>
                 </dependency>
@@ -82,8 +82,8 @@
                         <version>${project.parent.version}</version>
                         <exclusions>
                                 <exclusion>
-                                        <groupId>mysql</groupId>
-                                        <artifactId>mysql-connector-java</artifactId>
+                                        <groupId>com.mysql</groupId>
+                                        <artifactId>mysql-connector-j</artifactId>
                                 </exclusion>
                         </exclusions>
                 </dependency>