Lodestar won't build: Unknown host coconut.ebi.ac.uk

[tburdett]

There is a build dependency on the repository coconut.ebi.ac.uk: this is an EBI internal server and not visible outside, causing builds to fail. Can we remove this dependency?

[sonata82]

Any progress here?

[proccaserra]

@tburdett, @olgavrou finally managed to build with stable release of Zooma bypassing EBI's internal coconut repo

STEP1: obtain virt-jena-1.8 and virt-jdbc-4.0.1 jar.

STEP2: manual installation to local .m2 repository

mvn install:install-file -DgroupId=com.openlinksw -DartifactId=virt-jena -Dpackaging=jar -Dversion=1.8 -Dfile=/path/to/virt-jena-1.8.jar -DgeneratePom=true

mvn install:install-file -DgroupId=com.openlinksw -DartifactId=virt-jdbc -Dpackaging=jar -Dversion=4.0.1 -Dfile=/path/to/virt-jdbc-4.0.1.jar -DgeneratePom=true

STEP3: edit https://github.com/EBISPOT/lodestar/blob/master/pom.xml

A. by commenting out line 97 to 113 B. by adding the following dependency at line 127:

    <dependency>
        <groupId>com.openlinksw</groupId>
        <artifactId>virt-jena</artifactId>
        <version>1.8</version>
        <scope>test</scope>
    </dependency>
    <dependency>
        <groupId>com.openlinksw</groupId>
        <artifactId>virt-jdbc</artifactId>
        <version>4.0.1</version>
        <scope>test</scope>
    </dependency> 

STEP4: edit https://github.com/EBISPOT/lodestar/blob/master/lode-virtuoso-impl/pom.xml

A. by commenting out line 46-52 (removing pointer to coconut repository) B. by correcting the dependency groupId at line 32 and 38

replace <groupId>openlinksw.com</groupId> with <groupId>com.openlinksw</groupId>

STEP5: mvn clean install -DskipTests (from zooma root)

Tested with latest 'stable' branch today.

Also, definitely requires Java 1.8, Maven 3.3+

[sonata82]

@proccaserra Thanks for your directions, but where can I obtain the virt-jena-1.8 and virt-jdbc-4.0.1.jar?

[danizen]

This is related to issue #27, because we modularize the repository location.

@sonata82 , you can obtain these JAR files from https://github.com/openlink/virtuoso-opensource/. jena drivers are in the binsrc subdirectories for each major version of Jena. I think you have to build it to get the JDBC drivers, because I don't see them under binsrc.

[simonjupp]

We have a public nexus repo at the EBI now hosting the necessary jars. I've updated lodestar poms to reference the new repository

    <repositories>
        <repository>
                <id>spot-public</id>
                <name>nexus-public</name>
                <url>https://www.ebi.ac.uk/spot/nexus/repository/maven-public/</url>
            </repository>
    </repositories>

[danizen]

@tburdett, this should be closed. EBI has the public Nexus repositories, and these are referred to through two properties in the pom:

    <properties>
        ...
        <release.repo.url>https://www.ebi.ac.uk/spot/nexus/repository/maven-releases/</release.repo.url>
        <snapshot.repo.url>https://www.ebi.ac.uk/spot/nexus/repository/maven-snapshots/</snapshot.repo.url>
    </properties>

Users can use the public repos, or they can use a profile in $HOME/.m2/settings.xml to define these properties to direct their build to a local repository (as we do).