maven pom for org.bridgedb 1.1.0

[jwhi...@gmail.com]

Hello,

While trying to build a project using maven against the 1.1.0 release, I ran into issues because BridgeDB's pom references org.restlet.jee:org.restlet.ext.servlet:jar:2.0-SNAPSHOT

While technically the problem is the fault of maven.restlet.org maintainers (the corresponding 2.0-SNAPSHOT directory there shows empty), the current stable release of the restlet library is 2.0.11 as per http://www.restlet.org/downloads/.  It seemed more worthwhile to ask BridgeDB developers to update their dependencies than to ask Restlet developers to fix their repo for the old snapshot (perhaps I should do that as well).

Thanks in advance,

Joe

[Martijn van Iersel]

Hi Joe

The pom files for BridgeDb are unmaintained, but I'd be happy to accept
a patch for this from you or any other maven user out there.

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[Christian brenninkmeijer]

Hi Joe,
I at Manchester am using the pom files fo the lastest snapshot relaease
and have not come across this issue.

Can you let me know in which package you found the file I can have a
look for you.

--
Christian Brenninkmeijer
University of Manchester
MyGrid team

[Joe Whitney]

It's actually in the bridgedb.server component; I was getting the pom from the biopax server at http://biopax.sourceforge.net/m2repo/releases/org/bridgedb/org.bridgedb.server/1.1.0/org.bridgedb.server-1.1.0.pom

I'm not sure where the "official" version lives.  But the "patch" (attached) is just one change to one version number.

Thanks,

Joe

On Tue, Mar 20, 2012 at 4:21 AM, Martijn van Iersel <mvani...@gmail.com> wrote:

Hi Joe

The pom files for BridgeDb are unmaintained, but I'd be happy to accept a patch for this from you or any other maven user out there.

--
Martijn

On 19/03/12 21:28, jwhi...@gmail.com wrote:

Hello,

While trying to build a project using maven against the 1.1.0 release, I
ran into issues because BridgeDB's pom references
org.restlet.jee:org.restlet.ext.servlet:jar:2.0-SNAPSHOT

While technically the problem is the fault of maven.restlet.org
maintainers (the corresponding 2.0-SNAPSHOT directory there shows
empty), the current stable release of the restlet library is 2.0.11 as
per http://www.restlet.org/downloads/. It seemed more worthwhile to ask
BridgeDB developers to update their dependencies than to ask Restlet
developers to fix their repo for the old snapshot (perhaps I should do
that as well).

Thanks in advance,

Joe

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[jwhi...@gmail.com]

The issue is actually with org.bridgedb.server.

Perhaps my mistake was using the repos hosted by paxtools  http://biopax.sourceforge.net/m2repo/releases/org/bridgedb/org.bridgedb.server/1.1.0/org.bridgedb.server-1.1.0.pom

(which I am also using).

What is the "official" bridgedb maven repository?  Searching always seems to land me on the trac page for the pom file.  The file there: http://www.bridgedb.org/browser/trunk/org.bridgedb.server/pom.xml

has the offending 2.0-SNAPSHOT dependency on org.restlet.jde.  But you won't see the issue unless you haven't already cached the jar in your local repository; presumably it was there at some point but I have asked and the restlet folks say no one should be using this dependency so it'd be easier if the bridgedb one could be changed.

-Joe

[Christian brenninkmeijer]

Hi Martijn,
I now agree with Joe.
The server pom does need changing as I too could not build it (once I hide the  org.restlet.jee:org.restlet.ext.servlet:jar:2.0-SNAPSHOT in my local repository)
org.restlet.jee:org.restlet.ext.servlet:jar:2.0.11 builds fine.

Do you want me to create a pull request?
Or do you want to do the change?

Hi Joe and Martijn,
I will let Martijn answer the question of where the "official" source code lives.

On 19/03/2012 21:28, jwhi...@gmail.com wrote:

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[IgorRodchenkov]

Hi all,

As far as I know, there is no official maven repository for bridgedb releases, and it's not planned...

Those artifacts in the BioPAX maven repository were modified and temporary put there, because some BioPAX projects needed them at some point. These are not guaranteed to be regularly updated; we are actually going to clean up there (definitely remove all snapshots). In the future, we will probably have to manually upload some of officially released BridgeDb JARs to the BioPAX maven repo (at least org.bridgedb and org.bridgedb.bio) rather than compile and deploy from sources.

Best,

Igor Rodchenkov

[Martijn van Iersel]

Hey Christian,

Go ahead and commit it straight to svn. You should be able to do so with
the same account as for the wiki.

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Martijn

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> University of Manchester
> MyGrid team
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[Martijn van Iersel]

The official source code is at http://svn.bigcat.unimaas.nl/bridgedb. Or
is that not what you're asking for?

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Martijn

On 20/03/12 14:09, Christian brenninkmeijer wrote:

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> University of Manchester
> MyGrid team
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[Joe Whitney]

I was asking where the official maven repo is; apparently there isn't one though (according to Igor), so I'll hope that the biopax repo maintainers will update the pom from the bridgedb SVN once it's fixed.

Thanks,

Joe

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University of Manchester
MyGrid team

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[Christian brenninkmeijer]

As it is  mainly OpenPhacts/ Manchester Univeristy who want maven I will look into placing it in one of our repsitories.
But that will probably only be for the spanshot or next release.

Christian

PS. this could take a while but feel free to ping me if it doesn't happen in a month or two.

Joe

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[IgorRodchenkov]

I removed the org.bridgedb.server 1.1.0 from the BioPAX repo (also removed 1.0 snapshots; bridgedb was temporarily put there; not required for paxtools or validator at the moment).

You might think this would be straightforward to fix, but it is not:

- it is technically "illegal" (see semver.org) to fix already released versions; much worst thing is, even if someone fixed the pom there in the repo and/or in the v1.1.0 sources, users won't get this update automatically (because it's the same, not snapshot, version); you have to figure out to clean your local m2 repo from all bridgedb artifacts...

- I guess, the root of this problem is that the 1.1.0 release has 2.0-SNAPSHOT dependency (probably, my mistake or only option at that time; as I remember, the restlet was unstable at that time...), which, seems, disappeared from public repos...

- specifically, because BridgeDb's official build system is Ant (not using Ivy), it's quite easy to care less about dependencies (whatever jars are in a "/lib" folder is OK as long as project builds ;)); so, someone using it as dependency or converting to maven must guess versions and resolve conflicts.

So, ideally, this has to be fixed in a separate branch, and the bug-fix bridgedb version v1.1.x released. Also - fix in the latest sources.

PS:

I think, until there is an official BridgeDb maven repository or it's available from the Maven Central, people should build bridgedb jars locally from sources of use only official bridgedb released binary jars, which, if required, one can wrap or manually upload to own project maven repositories (e.g., Nexus), better using different groupId and artifactId (like "my.company.org.bridgedb.server").

Sincerely,

Igor R.