Hello Ben,
If I understand you correctly, you have
already committed the required code change to the BioMoby CVS
repository
Yes I did (I have an account)
I would like to move the BioMoby maven
repository to sonatype.com (public maven
repository hosting) instead, and that would solve my problem of
getting write access at the same time. I have a meeting with Mark
later today, and I will try and get his permission to do so.
If I understand the situation correctly, INB is considering to take
a responsibility for BioMoby maintenance... Mark should know
better...
I was asked whether I can fix jMoby if necessary and to get into a
build process (including Taverna plugin).
In this direction, probably, it would be better to host maven
repository in our facilities?
Kind Regards,
Dmitry
On 26/09/2011 21:27, Ben Vandervalk wrote:
On Mon, Sep 26, 2011 at 4:22 AM, Stian
Soiland-Reyes <[email protected]>
wrote:
On Mon, Sep 26, 2011 at 11:22, Dmitry <[email protected]>
wrote:
>
> Could anybody change INB repository address in BioMoby
Taverna plug-in please?
> The current plug-in points into developers repository and
not to a production one.
> I already changed it in BioMoby repository, but
unfortunately I have little knowledge how BioMoby Taverna
plug-in is built.
> As far as I understand taverna uses it's own build
scripts. Does it use BioMoby (OpenBio) repository? Why the
plug-in itself is in Taverna maven repository and not in
BioMoby maven?
Could you detail which repository should be removed, and which
should be added?
See [1] for the current setting used by Taverna at runtime -
and
[2][3] for dependencies used at build-time - repositories for
building
are declared in [4][5] - that is also our mirror [6].
Note that [6] is a (weekly) mirror of [7] due to the repeated
instability of the network connection (and future
accessibility) of
http://biomoby.org/ - done as:
#!/bin/bash
set -e # exit on error
cd /local/www/mygrid/maven/biomoby
wget --reject 'index.html*' --no-parent --random-wait --wait
0.1
--no-verbose --tries=3 --retry-connrefused
--mirror http://biomoby.org/m2repo/
Please also note that the biomoby activity is depending on a
slightly
patched version of jmoby called 1.1.4-taverna which we host in
our own
repository [8]. Only the POM has been edited compared to jmoby
1.1.4
which was provided to us by Eddie Kawas from BioMoby. I don't
know why
he did not deploy this to [9]
Also see below an email exchange with Ben Vandervalk who
volunteered
to bring our POM changes into the main jMoby codebase and do a
1.1.5
release.
[1] http://www.mygrid.org.uk/taverna/updates/2.3.0/plugins/official/activities-2.3.0-20110905.xml
[2] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/biomoby-activity/pom.xml
[3] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/biomoby-activity/pom.xml
[4] http://taverna.googlecode.com/svn/taverna/taverna-parent/trunk/pom.xml
[5] http://taverna.googlecode.com/svn/taverna/taverna-parent/branches/maintenance/pom.xml
[6] http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/
[7] http://biomoby.org/m2repo
[8] http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.4-taverna/jmoby-1.1.4-taverna.pom
[9] http://biomoby.org/m2repo/org/biomoby/jmoby/
Hi Dmitry,
I am a developer in the Wilkinson Lab and have recently taken
over responsibility for maintaining BioMoby.
Jose Rodriguez and Stian asked me to update the INB Moby
registry URL in the BioMoby code about a month ago, and to
publish a new release to the BioMoby maven repository.
Unfortunately, I have been unable to do so. The main problem
I have been having is that I can't get the people at open-bio.org
to create a BioMoby CVS account for me or to give me write
access to http://biomoby.org/m2repo/,
in spite of Mark Wilkinson's endorsement. I have asked about
five times now, but I will keep trying.
If I understand you correctly, you have already committed the
required code change to the BioMoby CVS repository (?). If so,
thank you! (I would just look for myself, but the CVS
repository seems to be down at the moment.)
Given that the network connections to the Biomoby maven
repository are flaky for some reason (I have seen it myself),
I would like to move the BioMoby maven repository to sonatype.com
(public maven repository hosting) instead, and that would
solve my problem of getting write access at the same time. I
have a meeting with Mark later today, and I will try and get
his permission to do so.
-- Ben
On Fri, Aug 26, 2011 at 15:59, Stian Soiland-Reyes
<[email protected]>
wrote:
> I believe JMoby 1.1.2, 1.1.3 and 1.1.4 was made
specifically for
> Taverna and probably not released as full Moby releases.
Until 1.1.4
> there was not a single CVS tag for any of these. They
didn't get
> deployed properly as Eddie didn't have access to the
Maven repository
> server at the time.
>
> So the next version now would be 1.1.5 - most certainly
not another 1.1.2!
>
> See attached email exchange with Eddie in the bottom of
this message.
>
>
>
> Also note that we had to make our own POM file as the
Moby team
> refused our modifications upstream. So the -taverna
versions in
> http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/
and
> friends should be bytewise equal on the .jar as supplied
by Moby, but
> with modifications of the POM.
>
> I don't remember the reason for not accepting our patch,
but I believe
> it was due to some confusion about Maven warnings. I
remember we had
> to use a different axis declarations. I think I also had
to remove a
> dependency to really old Taverna jars in jmoby-desktop.
>
> Hopefully you would be able to pull in those POM changes
for the 1.1.5
> release - you can just do a diff of the POM files from
our repository
> against what's in the CVS checkout. Feel free to ask me
any questions,
> and .. I'll try to remember or dig up the emails for why
we did it a
> certain way. Note that we no longer require Java 5
support, we use
> Java 6 now. (I assume this update is for Taverna 2.3).
>
>
> On Thu, Aug 25, 2011 at 14:34, Alan R Williams <[email protected]>
wrote:
>> Stian is looking up an e-mail exchange he had with
Eddie when the current
>> jar was created.
>>
>> Alan
>>
>>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Stian Soiland-Reyes <[email protected]>
> Date: Thu, Sep 2, 2010 at 11:24
> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496
> To: Edward Kawas <[email protected]>
> Cc: Mark Wilkinson <[email protected]>
>
>
> We've already have two builds called 1.1.2 and 1.1.3 that
I believe
> you provided. I believe 1.1.3 was just a rebuild of
1.1.2, as 1.1.2
> was compiled for Java 6 instead of Java 5.
>
> I can't find any tags for any of these versions (and
neither for
> 1.1.1) in
:pserver:[email protected]:/home/repository/moby - does
> the code live somewhere else?
>
> This is all a bit messy - we need to know what version of
jmoby to
> include in Taverna, but it seems like jMoby basically
isn't versioned.
>
> When you say that 'the bugs that are reported against
BioMoby in
> Taverna' are old bugs, which bugs do you mean?
>
> How can I verify that those bugs are fixed using the
1.1.1 JAR (or the
> build you are talking about making - would that be 1.1.4
then? From
> which code will it be built?). In which Taverna version
did this work
> as expected..?
>
>
> Mark (cc): We're trying to clear up what JAR of jMoby is
included in
> Taverna 2.2.0, and which it should be, as Eddie suspects
it is the
> wrong one.
>
>
> On Wed, Sep 1, 2010 at 15:14, Edward Kawas <[email protected]>
wrote:
>> I think that you are right about only having a
customized pom. In any case, the jar that shipped with the
latest Taverna is not the same as older versions (probably
because of the version number mess; my fault).
>>
>> I think that if you could, you should try a newer
version (I can build it for you) and we could label it version
1.1.2 and you could host it in the mygrid repository. I have
never been able to access the Biomoby.org one. I had to always
depend on someone else deploying it for me.
>>
>> The bugs that are reported regarding Biomoby in
taverna 2.2.0 are old ones and were fixed some time ago.
That's why we believe that an older version got thrown in by
accident somehow.
>>
>> Eddie
>>
>>
>>> -----Original Message-----
>>> From: [email protected]
[mailto:[email protected]]
On Behalf Of Stian
>>> Soiland-Reyes
>>> Sent: Wednesday, September 01, 2010 7:05 AM
>>> To: Edward Kawas
>>> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496
>>>
>>> On Wed, Sep 1, 2010 at 14:52, Edward Kawas <[email protected]>
>>> wrote:
>>> > Hi Stian,
>>> >
>>> > The latest one that I know about is here:
>>> http://biomoby.org/m2repo/org/biomoby/jmoby/1.1.1/
>>> >
>>> > From what I remember, Taverna is using a
custom version, hosted by you
>>> (not personally, of course, but your project)
somewhere.
>>>
>>> That matches
>>> http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.1-
>>> taverna/
>>>
>>> I don't think we have customized the JAR, just
the POM.
>>>
>>>
>>>
>>> --
>>> Stian Soiland-Reyes, myGrid team
>>> School of Computer Science
>>> The University of Manchester
>>
>>
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Stian Soiland-Reyes <[email protected]>
> Date: Fri, Sep 3, 2010 at 13:55
> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496
> To: Edward Kawas <[email protected]>
> Cc: Mark Wilkinson <[email protected]>
>
>
> On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]>
wrote:
>>> This is all a bit messy - we need to know what
version of jmoby to include in
>>> Taverna, but it seems like jMoby basically isn't
versioned.
>> I thought that there were some version tags, but if
you can't find them, I am obviously incorrect.
>
> I just had a quick look using Eclipse, tag discovery in
CVS is
> inherently tricky, so I won't claim you are incorrect :)
>
>>> When you say that 'the bugs that are reported
against BioMoby in Taverna'
>>> are old bugs, which bugs do you mean?
>> The 'too many open' files bug. I believe that this
was reported in version 1.7, but I can't find any reference to
that
>
> No, I believe it was for 2.2.0.
>
>>> How can I verify that those bugs are fixed using
the 1.1.1 JAR (or the build
>>> you are talking about making - would that be
1.1.4 then? From which code
>>> will it be built?). In which Taverna version did
this work as expected..?
>> The recent Biomoby errors in Taverna 2.2.0 won't
occur on *nix machines. The library would be built from the
latest Biomoby source. I may be wrong, but if you use an older
version of Taverna, with the same jmoby version as is shipped
with Taverna 2.2.0, the errors do not occur.
>
> So in Taverna 2.1.2 there is no problem, and the 'Moby
Objects' folder
> appear - even if the jMoby JAR there is byte-wise exactly
the same?
>
>
> Let's do a new build of jMoby, you call it 1.1.4 and make
sure it's
> tagged, and then I can add it to our repository with the
updated POM.
> We can then either wait till Taverna 2.3 (rougly
scheduled end of
> October) to release it, or do it as an online update,
which should not
> be too much work.
>
> I would suggest waiting until 2.3 if the current
installation still
> works, but just has an error-popup now and then, but if
it is true
> that the 'Moby Objects' folder is missing, we should do
it as an
> online update.
>
>
> I'm unable to reproduce on my Ubuntu, but another
colleague here has
> also seen the pop-up now and then, so we can test your
new JAR there.
>
> Just one thing - remember to compile it for Java 5, not
java 6! (From
> Taverna 2.3 Java 6-style should be OK, but not for a 2.2
update)
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Edward Kawas <[email protected]>
> Date: Thu, Sep 9, 2010 at 16:11
> Subject: RE: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496
> To: Stian Soiland-Reyes <[email protected]>
> Cc: Mark Wilkinson <[email protected]>
>
>
> Hi Stian,
>
> I added a tag to the moby cvs java/main branch and
generated 2 jars
> (target=1.5) for Taverna. I have attached them here.
>
> An immediate update would be best, because I think that
running
> Biomoby services is broken too when the error is
encountered.
>
> Please let me know if I can be of further assistance.
>
> Thanks,
>
> Eddie
>
>> -----Original Message-----
>> From: [email protected]
[mailto:[email protected]]
On Behalf Of Stian
>> Soiland-Reyes
>> Sent: Friday, September 03, 2010 5:56 AM
>> To: Edward Kawas
>> Cc: Mark Wilkinson
>> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496
>>
>> On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]>
>> wrote:
>> >> This is all a bit messy - we need to know
what version of jmoby to
>> >> include in Taverna, but it seems like jMoby
basically isn't versioned.
>> > I thought that there were some version tags, but
if you can't find them, I
>> am obviously incorrect.
>>
>> I just had a quick look using Eclipse, tag discovery
in CVS is inherently tricky,
>> so I won't claim you are incorrect :)
>>
>> >> When you say that 'the bugs that are
reported against BioMoby in
>> Taverna'
>> >> are old bugs, which bugs do you mean?
>> > The 'too many open' files bug. I believe that
this was reported in
>> > version 1.7, but I can't find any reference to
that
>>
>> No, I believe it was for 2.2.0.
>>
>> >> How can I verify that those bugs are fixed
using the 1.1.1 JAR (or
>> >> the build you are talking about making -
would that be 1.1.4 then?
>> >> From which code will it be built?). In which
Taverna version did this work
>> as expected..?
>> > The recent Biomoby errors in Taverna 2.2.0 won't
occur on *nix machines.
>> The library would be built from the latest Biomoby
source. I may be wrong,
>> but if you use an older version of Taverna, with the
same jmoby version as is
>> shipped with Taverna 2.2.0, the errors do not occur.
>>
>> So in Taverna 2.1.2 there is no problem, and the
'Moby Objects' folder
>> appear - even if the jMoby JAR there is byte-wise
exactly the same?
>>
>>
>> Let's do a new build of jMoby, you call it 1.1.4 and
make sure it's tagged, and
>> then I can add it to our repository with the updated
POM.
>> We can then either wait till Taverna 2.3 (rougly
scheduled end of
>> October) to release it, or do it as an online update,
which should not be too
>> much work.
>>
>> I would suggest waiting until 2.3 if the current
installation still works, but just
>> has an error-popup now and then, but if it is true
that the 'Moby Objects'
>> folder is missing, we should do it as an online
update.
>>
>>
>> I'm unable to reproduce on my Ubuntu, but another
colleague here has also
>> seen the pop-up now and then, so we can test your new
JAR there.
>>
>> Just one thing - remember to compile it for Java 5,
not java 6! (From Taverna
>> 2.3 Java 6-style should be OK, but not for a 2.2
update)
>>
>> --
>> Stian Soiland-Reyes, myGrid team
>> School of Computer Science
>> The University of Manchester
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
>
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
--
|
