[WIP] preparing for 3.1.5

.github/workflows/build.yml

@@ -2,13 +2,27 @@ name: build
 
 on:
   push:
-    branches: [ master ]
+    branches: [ series/3.1.0 ]
   pull_request:
-    branches: [ master ]
+    branches: [ series/3.1.0 ]
 
 jobs:
-  build:
+  java8:
+    runs-on: ubuntu-latest
 
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Java
+      uses: actions/setup-java@v4
+      with:
+        distribution: 'temurin'
+        java-version: 8
+        cache: maven
+    - name: Build with Maven
+      run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql
+
+  build:
+    needs: java8
     runs-on: ubuntu-latest
 
     steps:

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: 3.0.23
-date-released: '2023-08-07'
+version: 3.1.4
+date-released: '2024-12-19'
 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 `3.0.23`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.4`:
 
 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>3.0.23</version>
+        <version>3.1.4</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.23'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.4'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.23"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.4"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.0.23'
+'org.bridgedb:org.bridgedb.bio:jar:3.1.4'
 ```
 
 
@@ -58,6 +58,8 @@ able to compile with a simple:
 mvn clean install -Dgpg.skip
 ```
 
+When compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`.
+
 You can find the libraries in the folder called "target", in each sublibrary folder (used to be called "dist" in ant).
 
 If you want to ignore failing tests, e.g. because you are not online,
@@ -127,13 +129,13 @@ Making releases
 ---------------
 
 If it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb),
-this `README.md` and `CITATION.cff` (for Zenodo).
+this `README.md` and `CITATION.cff` (for Zenodo), as well as the `pom-java8.xml`.
 
 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=3.0.23
+mvn versions:set -DnewVersion=3.1.4
 mvn clean deploy
 ```
 
@@ -143,7 +145,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.0.23-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.5-SNAPSHOT
 mvn clean deploy
 ```
 

UPGRADE_NOTES.md

@@ -1,35 +1,49 @@
-Upgrade notes to BridgeDb 2.0
+# Upgrade notes to BridgeDb 2.0
 
-1. Initialing data sources
+## 1. Initialing data sources
 
 Replace
 
+```java
     BioDataSource.init();
+```
 
 with
 
+```java
     DataSourceTxt.init();
+```
 
-2. Getting DataSource's
+## 2. Getting DataSource's
 
 Replace
 
+```java
     DataSource ds = DataSource.getBySystemCode("Ck");
+```
 
 with
 
+```java
     DataSource ds = DataSource.getExistingBySystemCode("Ck");
+```
 
 Similarly, and more important:
 
+```java
     DataSource ds = DataSource.getByFullName("PubChem-compound");
+```
 
 with
 
+```java
     DataSource ds = DataSource.getExistingByFullName("PubChem-compound");
+```
 
-The latter two new methods throw an IllegalArgumentException if the DataSource does not exist.
+The latter two new methods throw an `IllegalArgumentException` if the `DataSource` does not exist.
 Use one of the following two methods to check first:
 
+```java
     DataSource.systemCodeExists("Ck");
     DataSource.fullNameExists("PubChem-compound");
+```

benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java

@@ -300,7 +300,7 @@ enum Connector
 		PICR ("picr", "idmapper-picr:"),
 
 		SYNERGIZER_ENSEMBL  ("synergizer(ensembl)", "idmapper-synergizer:authority=ensembl&species=Homo sapiens"),
-		BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:http://webservice.bridgedb.org/Human"),
+		BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:https://webservice.bridgedb.org/Human"),
 		BRIDGEWEBSERVICE_LOCAL ("BridgeWebservice(local)", "idmapper-bridgerest:http://localhost:8183/Human"),
 		BIOMART ("biomart", "idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl"),
 		CRONOS ("cronos", "idmapper-cronos:hsa"),

benchmarking/test/org/bridgedb/benchmarking/TestAll.java

@@ -74,7 +74,7 @@ public void testBridgeWebservice() throws IDMapperException, ClassNotFoundExcept
 		Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest");
 		Xref insr1 = new Xref ("ENSG00000171105", DataSource.getBySystemCode("EnHs"));
 		Xref insr2 = new Xref ("3643", DataSource.getBySystemCode("L"));
-		basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:http://webservice.bridgedb.org/Human", insr1, insr2);
+		basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:https://webservice.bridgedb.org/Human", insr1, insr2);
 	}
 
 	public void testFile() throws IDMapperException, ClassNotFoundException

dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl

@@ -743,7 +743,7 @@
 	%{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'], 
 				'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'", 
 					     "\'ID\|\'", "\'\|$species\|\'", "\'\'",
-					     "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", 
+					     "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", 
 					     "\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"],
 				'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
 					     'PRIMARY KEY (ID)'
@@ -863,7 +863,7 @@
 	%{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'], 
 			       'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'", 
 					    "\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
-					    "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", 
+					    "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", 
 					    "\'ftp://rgd.mcw.edu/pub/\'"],
 			       'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 
 					    'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 
@@ -916,8 +916,8 @@
         %{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'],
                                 'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'",
                                              "\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
-                                             "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
-                                             "\'http://www.gramene.org\'"],
+                                             "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
+                                             "\'https://www.gramene.org\'"],
                                 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
                                              'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
                                              'Description VARCHAR(255) DEFAULT NULL',
@@ -926,8 +926,8 @@
         %{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'],
                                 'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'",
                                              "\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
-                                             "\'http://www.gramene.org/pathway\'", "\'\'",
-                                             "\'http://www.gramene.org/pathway\'"],
+                                             "\'https://www.gramene.org/pathway\'", "\'\'",
+                                             "\'https://www.gramene.org/pathway\'"],
                                 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
                                              'Description VARCHAR(255) DEFAULT NULL',
                                              'PRIMARY KEY (ID)'

examples/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.0.23</version>
+    <version>3.1.4</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>

examples/src/org/bridgedb/examples/ChebiPubchemExample.java

@@ -15,7 +15,7 @@ public static void main (String[] args) throws ClassNotFoundException, IDMapperE
 		// We'll use the BridgeRest webservice in this case, as it does compound mapping fairly well.
 		// We'll use the human database, but it doesn't really matter which species we pick.
 		Class.forName ("org.bridgedb.webservice.bridgerest.BridgeRest");
-		IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
+		IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:https://webservice.bridgedb.org/Human");
 		DataSourceTxt.init();
 
 		// Start with defining the Chebi identifier for

examples/src/org/bridgedb/examples/ExHello.java

@@ -23,7 +23,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx
 		DataSourceTxt.init();
 
 		// now we connect to the driver and create a IDMapper instance.
-		IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
+		IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human");
 
 		// We create an Xref instance for the identifier that we want to look up.
 		// In this case we want to look up Entrez gene 3643.

examples/src/org/bridgedb/examples/ExIDSearch.java

@@ -20,7 +20,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx
 		DataSourceTxt.init();
 
 		// now we connect to the driver and create a IDMapper instance.
-		IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
+		IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human");
 
 		String query = "3643";
 

org.bridgedb.bio/pom.xml

@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.4</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>