Continuing work on qualimap (Was: Any help?)

[Andreas Tille <andreas@an3as.eu>]

Hi Bas,

I decided to switch back to the list to make these helpful hints
available for web search.  I guess you will not mind the proof that you
are just very helpful. ;-)

For those who are missing context: Bas is helping me getting
   git://git.debian.org/git/debian-med/qualimap.git
into shape.

On Tue, Nov 24, 2015 at 01:04:55PM +0100, Bas Couwenberg wrote:
> On 2015-11-24 12:42, Andreas Tille wrote:
> >On Tue, Nov 24, 2015 at 12:59:48AM +0100, Sebastiaan Couwenberg wrote:
> >>samtools.jar is not available in the maven repository, so you'll need to
> >>install it manually in d/rules like elasticsearch did for jts:
> >>
> >>https://sources.debian.net/src/elasticsearch/1.7.3%2Bdfsg-2/debian/rules/#L34
> >>https://sources.debian.net/src/elasticsearch/1.7.3%2Bdfsg-2/debian/maven.rules/#L10
> >>
> >>miglayout.jar is likewise also not in the maven repository, but you may
> >>be able to use miglayout-parent instead.
> >
> >I added libmiglayout-java as Build-Depends.  I do not understand the hint
> >to miglayout-parent.  Any example?
> 
> Maven can only use the packaged JARs if they're available in the local Maven
> repository, to check if a Java package registers the JARs it builds with
> Maven (using maven-repo-helper) I check the package content with apt-file,
> eg.:
> 
>  $ apt-file show libmiglayout-java
>  libmiglayout-java: /usr/share/doc/libmiglayout-java/changelog.Debian.gz
>  libmiglayout-java: /usr/share/doc/libmiglayout-java/copyright
>  libmiglayout-java: /usr/share/java/miglayout-4.2.jar
>  libmiglayout-java: /usr/share/java/miglayout-core-4.2.jar
>  libmiglayout-java: /usr/share/java/miglayout-core.jar
>  libmiglayout-java: /usr/share/java/miglayout-ideutil-4.2.jar
>  libmiglayout-java: /usr/share/java/miglayout-ideutil.jar
>  libmiglayout-java: /usr/share/java/miglayout-swing-4.2.jar
>  libmiglayout-java: /usr/share/java/miglayout-swing.jar
>  libmiglayout-java: /usr/share/java/miglayout-swt-4.2.jar
>  libmiglayout-java: /usr/share/java/miglayout-swt.jar
>  libmiglayout-java: /usr/share/java/miglayout.jar
>  libmiglayout-java:
> /usr/share/maven-repo/com/miglayout/miglayout-core/4.2/miglayout-core-4.2.jar
>  libmiglayout-java:
> /usr/share/maven-repo/com/miglayout/miglayout-core/4.2/miglayout-core-4.2.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-core/debian/miglayout-core-debian.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-core/debian/miglayout-core-debian.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-ideutil/4.2/miglayout-ideutil-4.2.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-ideutil/4.2/miglayout-ideutil-4.2.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-ideutil/debian/miglayout-ideutil-debian.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-ideutil/debian/miglayout-ideutil-debian.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-parent/4.2/miglayout-parent-4.2.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-parent/debian/miglayout-parent-debian.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swing/4.2/miglayout-swing-4.2.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swing/4.2/miglayout-swing-4.2.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swing/debian/miglayout-swing-debian.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swing/debian/miglayout-swing-debian.pom
>  libmiglayout-java:
> /usr/share/maven-repo/com/miglayout/miglayout-swt/4.2/miglayout-swt-4.2.jar
>  libmiglayout-java:
> /usr/share/maven-repo/com/miglayout/miglayout-swt/4.2/miglayout-swt-4.2.pom
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swt/debian/miglayout-swt-debian.jar
>  libmiglayout-java: /usr/share/maven-repo/com/miglayout/miglayout-swt/debian/miglayout-swt-debian.pom
> 
> As you can see there is no entry in the maven-repo for the miglayout
> artifact, only the -core, -ideutil, -swing & -swg JARs.
> 
> The miglayout-parent artifact is the only one not matching a JAR by the same
> name, so I suspect it's for miglayout.jar.
> 
> To use miglayout-parent for the miglayout dependency you need to add the
> following to maven.rules to mangle the dependency defined in pom.xml:
> 
>  com.miglayout s/miglayout/miglayout-parent/ * s/.*/debian/ * *
> 
> Because the pom.xml has this dependency:
> 
>         <dependency>
>                 <groupId>com.miglayout</groupId>
>                 <artifactId>miglayout</artifactId>
>                 <version>3.7.4</version>
>         </dependency>
> 
> It will cause maven to check for /usr/share/maven-repo/com/miglayout/miglayout/3.7.4/miglayout-3.7.4.{jar,pom},
> but that isn't provided by libmiglayout-java. You need to mangle the version
> to check for /usr/share/maven-repo/com/miglayout/miglayout/debian/miglayout-debian.{jar,pom}
> at least, but that still leaves the missing artifact (miglayout vs
> miglayout-parent). With the suggested entry in maven.rules, maven will check
> for /usr/share/maven-repo/com/miglayout/miglayout-parent/debian/miglayout-parent-debian.{jar,pom}
> instead.

Thanks for your patience in explaining.  The fog becomes a bit clearer
even if it has not fully settled. ;-)

> If the -parent artifact doesn't provide the classes required for qualimap,
> they're probably provided by miglayout-core for which you'd need this entry
> in maven.rules:
> 
>  com.miglayout s/miglayout/miglayout-core/ * s/.*/debian/ * *
> 
> >>picard.jar is in the same boat as samtools.jar, and needs to be manually
> >>installed into the local maven repository.

Just to prove that I did not fully understood the principle I have now:

...
mvn --offline install:install-file \
        -Dmaven.repo.local=/build/qualimap-2.1.3+dfsg/debian/maven-repo \
        -Dfile=/usr/share/java/sam.jar \
        -DgroupId=net/sf \
        -DartifactId=samtools \
        -Dversion=fake \
        -Dpackaging=jar
[INFO] 
NOTE: Maven is executing in offline mode. Any artifacts not already in your local
repository will be inaccessible.

[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'install'.
[INFO] ------------------------------------------------------------------------
[INFO] Building qualimap
[INFO]    task-segment: [install:install-file] (aggregator-style)
[INFO] ------------------------------------------------------------------------
[INFO] [install:install-file {execution: default-cli}]
[INFO] pom.xml not found in sam.jar
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] The artifact information is incomplete or not valid:
  [0]  'groupId' with value 'net/sf' does not match a valid id pattern.
...

I'm afraid that it might be due to the fact that in sam.jar two directories
(or should I say groupIds?) reside next to each other.  I might have choosen
the wrong one or any other thing was wrong.

> This just shows that you also need to build depend on
> libmaven-install-plugin-java, because it wasn't found in the local maven
> repository used for the packaged JARs.

Damn, this was a simple one which I should have found myself ...
 
> >is not specifically connected to the maven override rules.
> >
> >I'm afraid I keep on doing things terribly wrong. :-(
> 
> You'll get the hang of it eventually :-)

I do not give up the hope. ;-)

Thanks a lot for your private support

       Andreas.
 

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