[Biojava-dev] biojava3-core release candidate

[PATERSON Trevor]

Regarding the parent POM dependency 
-----------------------------------

- when you do a real release I think the parent shouldn't be a snapshot version...

I think using a parent pom dependency can be a bit problematic - we usually do the same thing and run into various problems. I wonder whether it is better to separate out the modularisation architecture (directory structure) from the pom attributes that need to be inherited in the modules, and put them in a pom project at the same level as the children. The maven documentation suggests that you should then reference the parent by a relative path - but if it is itself a module in the project, that doesn't appear to be necessary..

  <parent>
    <groupId>com.mycompany.app</groupId>
    <artifactId>my-app</artifactId>
    <version>1</version>
    <!-- ??? <relativePath>../parent/pom.xml</relativePath> -->
  </parent>

You still have a pom in the directory containing the modules, but it only specifyies the modules to be built - and not the setting/properties etc to be inherited - which are in the new parent module 

Its worth remembering that the 'module' pom can of course be any where - it doesn't have to be in a a parent directory as the modules can be referenced by relative links 
e.g.   
  <modules>
    <module>../my-module</module>
  </modules>

Of course both the 'parent; and the 'module' pom need to be specified as <packaging>pom</packaging> 


Regarding SVN
-------------

I managed to pull down the svn repo from github today - albeit with an error code at the end

It is a bit flaky and throws errors if I run update on it tho..

But at least I can grab the code!

Regards 

Trevor


Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
The Royal (Dick) School of Veterinary Studies
University of Edinburgh
Scotland EH25 9PS
phone +44 (0)131 5274197


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-----Original Message-----
From: andreas.prlic at gmail.com  On Behalf Of Andreas Prlic
Sent: 21 October 2010 16:56
To: PATERSON Trevor
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] biojava3-core release candidate

Hi  Trevor,

> We can pull the artifact down down and use it fine - the only snafoo was that the parent pom is a SNAPSHOT and our local mirror archive is configured to ignore snapshots - so I had to pull it down directly.

anything we can change on our side? I believe the biojava.pom should have the correct version.

> Do you plan on deploying source jars alongside the release artifacts, and perhaps javadoc jars? Source jars matching the release artifact would be extremely useful...

I believe they should already be available.


> There is still something (?missing?) in the biojava and github subversion trees that breaks subversion checkouts for us - so I use the github zip download for source code - and obviously that may not match the artifact release version.

hm. github is using a developer SVN connection, so it should not suffer from the same issues as the anonymous SVN server. What was the problem with it?


> The BioJava DNAsequence functionality that we rely on in our Ensembl Java API (jensembl) demo code works fine - now that access to the ProxySequenceReader is allowed. So I will update our sourceforge project to use the biojava3-core-3.0-alpha1 dependency.

great, glad to hear it works for you,

Andreas



> We have used our jensembl demo to write a Java plug-in for the Savant genome browser - which allows it to pull in chromosomes and annotations from recent releases of ensembl and ensemblgenomes. The sequence can also be uploaded and displayed in the browser - using the BioJava functionality.
>
> We plan on writing this work up - to show the potential for an Ensembl Java API, allowing integration of Ensembl datasources with Java visualisation applications - and obviously integration with BioJava will be another big plus. If we can manage to get funding to continue this work we will implement far more functionality in the demo API, and would doubtless use many more BioJava features.
>
> Savant LINK: compbio.cs.toronto.edu/savant/index.html
> jensembl LINKS: jensembl.sourceforge.net  
> sourceforge.net/projects/jensembl
>
> Thanks for all the good work done by the whole biojava3 team.
>
> Trevor
>
>
>
> Trevor Paterson PhD
> new email trevor.paterson at roslin.ed.ac.uk
>
> Bioinformatics
> The Roslin Institute
> The Royal (Dick) School of Veterinary Studies University of Edinburgh 
> Scotland EH25 9PS phone +44 (0)131 5274197
>
> bioinformatics.roslin.ed.ac.uk
>
> Please consider the environment before printing this e-mail
>
> The University of Edinburgh is a charitable body, registered in 
> Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
>
>
> --
> The University of Edinburgh is a charitable body, registered in 
> Scotland, with registration number SC005336.
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org

>



--
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego
(+1) 858.246.0526
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