BridgeDb 3.0.13

Updated dependencies for log4j (2.17.1), OpenRDF (2.7.16), Apache CFX (3.2.14), and some dependency cleanup.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.13</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.13'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.13"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.13'

BridgeDb 3.0.10

Updated dependencies. Everyone using BridgeDb in a (web)service context should upgrade as soon as possible.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.10</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.10'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.10"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.10'

BridgeDb 3.0.9

This release is mostly identical to BridgeDb 3.0.8 but should have better OSGi support.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.9</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.9'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.9"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.9'

BridgeDb 3.0.8

This release updates the URL patterns for the CAS database, adds Brassica napus as species, outputs info from Derby databases with the quality control (QC) tool, and adds Guide to Pharmacology Targets as data source.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.8</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.8'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.8"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.8'

BridgeDb 3.0.7

This release updates a few dependencies, including jaxws-ri, log4j, and org.apache.cxf.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.7</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.7'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.7"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.7'

BridgeDb 3.0.6

Another minor release doing a bit of code clean up and improves the output of the QC tool for readability.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.6</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.6'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.6"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.6'

BridgeDb 3.0.5

Minor release that addresses a few data source inconsistencies and adds the DataSource.getCompactIdentifierPrefix() method.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.5</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.5'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.5"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.5'

BridgeDb 3.0.4

First public release of BridgeDb 3.0, a major version upgrade. It includes all the many small updates in the 2.3 seriese, but also introduces new features: support for secondary identifiers (identifiers that are not removed or deleted yet, but which have a better identifier), compact identifier support, no longer has the main copy of datasources.tsv, updates the versions of many dependencies, and a tool for create VoID header files. Java 8 and 11 are supported

This version has now seen several months of use in production and everyone is recommended to upgrade to BridgeDb 3.0.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.4</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.4'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.4"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.4'

BridgeDb 2.3.10

This larger minor release updates removes the Ant build system, and can now generate OSGi bundles with Maven (for five modules). It also gives more informative error messages when loading a Derby files goes bad, e.g. when BridgeDb 3 Derby files are attempted to be opened. Furthermore, it adds two Daphnia species and an Unspecified to the Organism enumeration.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>2.3.10</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.10'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.10"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.3.10'

BridgeDb 2.3.9

This minor release updates the URL pattern for Scholia and bumps the versions of two dependencies, Apache Velocity and Google's Guava.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>2.3.9</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.9'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.9"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.3.9'