[Debian-med-packaging] Htsjdk changed to gradle - please help (Was: Trying to update htsjdk but some tests are failing)

[Vincent Danjean]

[Adding java team in copy as they might help to complete this packaging]

  Hi,

Le 29/06/2016 à 14:28, Andreas Tille a écrit :
> Hi,
> 
> On Wed, Jun 29, 2016 at 09:24:37AM +0200, Andreas Tille wrote:
[...]
>> I'll take over and will try with the latest version (2.5.0).  If I
>> observe anything strange I'll report back.
> 
> I'm not sure whether it was a brilliant plan to go for 2.5.0 since
> upstream has changed the build system from ant to gradle.  I tried to
> cope with this but as I was afraid I did not succeeded.  I have no
> experience at all with gradle and we are probably hit by the fact that
> we need to build in offline mode but some modules need to be loaded.  I
> simply removed these modules from build.gradle but this was obviouly to
> simple and ended up in
> 
> ...
> FAILURE: Build failed with an exception.
> 
> * Where:
> Build file '/build/htsjdk-2.5.0+dfsg/build.gradle' line: 49
> 
> * What went wrong:
> A problem occurred evaluating root project 'htsjdk-2.5.0+dfsg'.
>> Could not find method gitVersion() for arguments [] on root project 'htsjdk-2.5.0+dfsg'.
> ...
> 
> Any idea from a more experienced Java / Gradle person?

  I take a look (I just discovered gradle this evening).

  First, I would say that gradle-debian-helper really did a great code.
I probably wont be able to do all my work if it were not here.
(just a remark: the README.txt in the gradle-debian-helper
source package should be installed into the binary package, IMHO)

  I successfully compiled htsjdk on my system with the following
limitation: ngs-java needs a pom file (none installed for now).
I created one manually but it must be included correctly in the
ngs-java package.
  Can someone with more java/pom experience do it?

  To test htsjdk compilation, I did:
  sudo mkdir -p /usr/share/maven-repo/gov/nih/nlm/ncbi/ngs-java/debian/
  sudo ln -fs ../../../../../../../java/ngs-java.jar /usr/share/maven-repo/gov/nih/nlm/ncbi/ngs-java/debian/ngs-java-debian.jar
  and I created /usr/share/maven-repo/gov/nih/nlm/ncbi/ngs-java/debian/ngs-java-debian.pom
  with the following contents:

<?xml version="1.0" encoding="UTF-8"?>
<!--
   Licensed to the Apache Software Foundation (ASF) under one or more
   contributor license agreements.  See the NOTICE file distributed with
   this work for additional information regarding copyright ownership.
   The ASF licenses this file to You under the Apache License, Version 2.0
   (the "License"); you may not use this file except in compliance with
   the License.  You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
        <modelVersion>4.0.0</modelVersion>
        <groupId>gov.nih.nlm.ncbi</groupId>
        <artifactId>ngs-java</artifactId>
        <version>debian</version>
        <packaging>jar</packaging>

        <name>NGS Java</name>
</project>


  Notes:
- I disabled jacoco for tests (need an agent?)
- I do not verify in a clean chroot that build-dependencies are currently
  correct
- the copyright file must be rewritten (most source files moved and are not
  catched anymore by globs, I did some modif but not all (see lintian))
- the dfsg tarball must be redone (to remove the gradle helper convenience
  library)
- it is late and I probably wont be able to work on it for a few days,
  so, Andreas, you can continue/finish

  Regards,
    Vincent