[WIP] release 4.0.0

.github/workflows/build.yml

@@ -2,26 +2,24 @@ name: build
 
 on:
   push:
-    branches: [ series/4.0 ]
   pull_request:
-    branches: [ series/4.0 ]
 
 jobs:
   build:
 
     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: 'temurin'
         java-version: 17
         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 }}

README.md

@@ -7,15 +7,15 @@ BridgeDb
 [![codecov](https://codecov.io/gh/bridgedb/BridgeDb/branch/master/graph/badge.svg?token=F0kJdoEt0x)](https://codecov.io/gh/bridgedb/BridgeDb)
 [![NWO](https://img.shields.io/badge/NWO%20Open%20Science-203.001.121-orange)](https://www.nwo.nl/en/projects/203001121)
 
-BridgeDb is currently tested with Java 11 and higher (3.0.x releases and master branch).
+BridgeDb is currently tested with Java 17 and higher (4.0.x releases).
 
 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.
+[Maven Central](https://search.maven.org/artifact/org.bridgedb/bridgedb-bundle), 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 `3.1.0`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `4.0.0`:
 
 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>3.1.0</version>
+        <version>4.0.0</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.0'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '4.0.0'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.0"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="4.0.0"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.1.0'
+'org.bridgedb:org.bridgedb.bio:jar:4.0.0'
 ```
 
 
@@ -133,7 +133,7 @@ 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=3.1.0
+mvn versions:set -DnewVersion=4.0.0
 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");
+```

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)'

org.bridgedb.bio/pom.xml

@@ -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>