On 21 May 2012 07:32, Egon Willighagen <egon.willighagen@...> wrote:
> Dear Tomáš,
> On Sun, May 20, 2012 at 7:06 AM, Tomas Pluskal <pluskal@...> wrote:
> > That said, I would also like to share some hurdles we have experienced
> > with embedding your projects into MZmine and perhaps make a few
> > suggestions how to improve it.
> Please do. As must be clear, the CDK project does not receive direct
> (yet) for development, which means that all developed is primarily
> triggered by specific needs by people using the CDK, rather than user
> needs... I say primarily, because user support is in fact what the
> community does get to too...
> > First, the hurdles. It's basically two issues.
> > 1) We use maven to build MZmine. According to your website
> > (
> > there are two maven repositories holding CDK. Unfortunately, the
> > Cambridge repository only contains CDK 1.4.7 and no JChemPaint
> > release.
> Yeah, I am looking into in installing Jenkins here in Maastricht, but
> no one in the group has time at right this moment (education, etc)...
> we actually have an open vacancy for a good/eager sysadmin :)
> > The Ambit repository is down at the moment.
> I asked Nina... it is confirmed; problems with a faulty network
> configuration... it is being looked into.
Just to clarify, Ambit repository was down Sat night, 2012-05-19 18:00 CEST
until till 2012-05-20 8:30 CEST (Sunday), and is online since. It was down
due to a network problem at the hosting university, but as it was weekend
night time in Europe, we didn't envisage major obstacles. I apologize for
the inconveniences in other parts of the world !
Let me know if you still have troubles accessing it.
> > The last time it
> > was online, I saw it contained JChemPaint 3.3.0, while the official
> > download page for JChemPaint
> > (http://sourceforge.net/projects/cdk/files/JChemPaint/) has the latest
> > version of 3.2.0. Is 3.3.0 an official release? The versioning seems a
> > bit unclear.
> I am not sure about that. That is a question that Christoph should
The JChempaint maven artifact is compiled from the JChemPaint 3.3.0 trunk
against CDK 1.4.8 and CDK 1.4.9 . We provide three artifacts, JCP + CDK ,
JCP compiled against CDK 1.4.8 without CDK dependencies and JCP compiled
against CDK 1.4.8 without CDK dependencies.
The JCP source was compiled as follows:
git clone git://github.com/cdk/cdk.git
git checkout -b cdk-1.4.5-copy cdk-1.4.5
git remote add ebicdk http://www.ebi.ac.uk/steinbeck-srv/git/cdk
git fetch ebicdk
git log ebicdk/ebiPatches ^master
mv index.html?view=tar jcp.tar.gz
gunzip < jcp.tar.gz | tar xvf -
cp ant.properties.template ant.properties
nano ant.properties (set cdk.dir=/home/vedrin/jcp/20120405/cdk)
nano build.xml (set <include name="org/openscience/jchempaint/**" /> for
> > 2) It is quite hard to find where the source code comes from. The
> > SourceForge's CDK project has both SVN and git repositories. These
> > contain some duplicate content.
> Indeed. We do not like deleting history, but git is the main
> repository. The SourceForge and GitHub git repositories are mirrored,
> with GitHub being the more up to date one (patches go there first).
The CDK and CDK-JCP maven artifacts are created and deployed only for
releases, which are available for download at the sourceforge.net. The
1) download a release
2) compile by
3) Use https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/cdk-maven to
generate and deploy the artifacts.
> > It is unclear where the code for a
> > particular version of CDK comes from,
> They all come from the git repository. There are two branches of
> interest: cdk-1.4.x and master.
> > and it is even more unclear in
> > the case of JChemPaint, because it requires a patched version of CDK
> > (CDK-JChemPaint), which seems to have its own versioning.
> Yes. The CDK-JChemPaint is the development project, and like a
> development branch. It is versioned indeed.
> > Last time I
> > tried to to find what CDK version is embedded into JChemPaint 3.2.0, I
> > failed (http://sourceforge.net/mailarchive/message.php?msg_id=28118123).
> The JChemPaint applet is done by the EBI team, and I do not know such
> things either, and do not currently have the time to personally
> investigate it... I am happy enough to get my own CDK/CDK-JChemPaint
> (current) work progressing... like cleaning up code to meet the
> standards of the main CDK library...
> > Speaking for people who embed CDK or JChemPaint into their
> > applications like us, I think it would make our lives much easier if
> > you/your team could implement a few changes:
> > 1) Separate CDK and JChemPaint completely. Make CDK a library and
> > JChemPaint an application that is using the library as a dependency.
> That is in fact the case... but I also know the situation is complex.
> That is historical.
The JChemPaint 3.3.0 artifacts are tested to work with CDK 1.4.8 and 1.4.9
(in fact we use and distribute them in our own software).
> > The CDK-JChemPaint patch should be integrated completely into
> > JChemPaint code base, as - correct me if I am wrong - it contains
> > mostly additional code to CDK.
> It's more complicated... if you need both the JChemPaint
> applet/application code and the latest CDK, your in an unlucky
You could safely use cdk-jchempaint artifact 25
with cdk 1.4.8 and cdk 1.4.9, and cdk-jchempaint 18 with earlier cdk
> The full story is a conflict of interest, causing a (temporary) fork
> almost two
> years ago... they are not really compatible, but we haven't had the
> resources yet to merge the forks again. I do not know if
> Christoph has the resources to update the JChemPaint
> applet/application right now... if there are others who like to help,
> that is most welcome, and we should synchronize efforts...
> > It seems that someone has already created a patch to separate the CDK
> > and JChemPaint build
> > (http://sourceforge.net/mailarchive/message.php?msg_id=28891512), so
> > the issue is mostly about integrating this into the official tree.
> I do not know the current state of the JChemPaint
> applet/application... but I do know this:
> there is the CDK library, and the CDK-JChemPaint patch... the latter I
> maintain, and consists of code *extending* (not changing) the CDK
> library... the major part of the rendering stack has now been cleared
> and is part of CDK 1.4.10... I will very soon release a new
> CDK-JChemPaint which will then only contain all the code for editing
> and editing feedback...
> The JChemPaint applet/application uses a forked code base of
> CDK-JChemPaint (the rendering/controller stack), and is not
> easily rebased on either of the above... instead, this will require to
> look at individual patches and decide what to do with it: ignore or
On the positive side, the JChemPaint 3.3.0 trunk compiles with just few
warnings against CDK 1.4.8 and 1.4.9.
And this is what we already did, tested, and deployed as fully functional
JCP maven artifacts.
We'll be glad to provide further help.
> > 2) Use only git (or only SVN) for the code trees of both CDK and
> The CDK library only uses git at this moment.
> > JChemPaint,
> I have to check how JChemPaint is developed, but am not the maintainer
> of that, and not the person to decide of git or svn should be used...
> > and remove the obsolete code repositories,
> That won't work, as there are older code (branches) that I do not want
> to remove.
> What I can do instead, is add files to mark where they should be
> looking instead for more up to date code... would that help?
> Additionally, we should update wiki pages more... but again, we're
> very much resource constrained, and then bug fixing takes priority...
> > because these tend to confuse people. Everyone is busy, and although I
> would like to
> > occasionally submit a small patch/bugfix to CDK, the difficulty of
> > finding the right source tree with the latest code base simply turns
> > me off..
> Understood. Sad story is that without a pile of money, the CDK project
> cannot prioritize these things...
> > 3) Publish new releases of both CDK and JChemPaint into the Maven OSS
> > Central repository
> > (
> > This would make it much easier for everyone, as the Ambit repository
> > has been turning offline and online in a nondeterministic manner over
> > last few months..
> I do not know how to do this. You're making many suggestions now
> that I will not have time for, but others may. By discussing it on
> this list, everyone can see what is to be done, and who is doing what
> already. That way, small contributions are worthwhile.
> > What do you think about this? I would be very happy to contribute some
> > manpower to achieve these goals, if you decide to implement them.
> I am sorry to inform you that it works the other way around: if you
> contribute manpower, you are most welcome to implement your goals. All
> comments touch on good points, but maintaining a project of this size
> takes a lot of effort, and it cannot work other than people
> contributing what they can... the current Maven support comes from
> other volunteers, and I am sure if you talk to them you can come to a
> mutual goal...
I agree the overall setup of the CDK & JChemPaint is complicated, but we
hope the maven artifacts provide an easier way to use stable releases. We
are discussing the possibility of maintaining snapshot releases of the
development branch as well.
I am glad the Maven repository is becoming an useful resource for the CDK
community. I realise the information about how maven artifacts are
generated is missing (provided that CDK build is ant based), and we'll make
this information online shortly. Your feedback is very much appreciated!
> So, I am very happy with your interest!
> PS. Nina told me she will as soon as possible upload 1.4.10 to the
> Maven repository...
Yes, it is ready for deployment, just needs to be completed with the
CDK-JCP release. Will be online by tomorrow.
We'll then try to compile JChemPaint trunk with 1.4.10. Help by JCP
developers is very much welcome!
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> Cdk-devel mailing list