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[WIP] preparing for 3.1.5 #253

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[WIP] preparing for 3.1.5 #253

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94e9edd
Open for development
egonw Dec 28, 2024
82e3996
Don't forget to update the Java8 pom too
egonw Dec 28, 2024
f3445db
Also handle old UniProt names here
egonw Dec 28, 2024
c83bce1
Updated for new UniProtKB data source full name
egonw Dec 28, 2024
2532a86
Also backwards compatibility in fullNameExists()
egonw Dec 28, 2024
d75afa2
Register the expected resource
egonw Dec 30, 2024
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6 changes: 4 additions & 2 deletions README.md
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Expand Up @@ -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
```

Expand All @@ -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
```

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2 changes: 1 addition & 1 deletion examples/pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bridgedb.examples</groupId>
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2 changes: 1 addition & 1 deletion org.bridgedb.bio/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.file.orthoxml/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.gui/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdb.construct/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdb/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdf/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.sql/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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8 changes: 4 additions & 4 deletions org.bridgedb.tools.batchmapper/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -33,19 +33,19 @@
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb</artifactId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.bio</artifactId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb</artifactId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.info/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.qc/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.voidtool/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.api/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.loader/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<dependencies>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.sql/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.client/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.core/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.server/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.utils/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.webservice.biomart/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.webservice.bridgerest/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.ws.client/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.ws.core/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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4 changes: 2 additions & 2 deletions org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java
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Expand Up @@ -172,12 +172,12 @@ 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());

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2 changes: 1 addition & 1 deletion org.bridgedb.ws.server/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb/pom.xml
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Expand Up @@ -33,7 +33,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
</parent>

<build>
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17 changes: 16 additions & 1 deletion org.bridgedb/src/main/java/org/bridgedb/DataSource.java
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Expand Up @@ -666,6 +666,10 @@
* @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);
}
Expand All @@ -683,14 +687,22 @@
* @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";

Check warning on line 703 in org.bridgedb/src/main/java/org/bridgedb/DataSource.java

View check run for this annotation

Codecov / codecov/patch

org.bridgedb/src/main/java/org/bridgedb/DataSource.java#L703 

Added line #L703 was not covered by tests
}

if (byFullName.containsKey(fullName))
{
current = byFullName.get(fullName);
Expand Down Expand Up @@ -823,6 +835,9 @@
* @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);
}

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2 changes: 1 addition & 1 deletion org.bridgedb/src/main/resources/version.props
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@@ -1,2 +1,2 @@
# Current version of BridgeDb
bridgedb.version=3.1.3
bridgedb.version=3.1.5
9 changes: 9 additions & 0 deletions org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java
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Expand Up @@ -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"));;
}
}
2 changes: 1 addition & 1 deletion pom-java8.xml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -4,7 +4,7 @@
<groupId>org.bridgedb</groupId>
<artifactId>bridgedb-bundle</artifactId>
<packaging>pom</packaging>
<version>3.1.4</version>
<version>3.1.5-SNAPSHOT</version>
<name>BridgeDb bundle</name>
<description>
BridgeDb is a framework for finding and mapping equivalent database
Expand Down
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