[ome-devel] Woolz reader/writer

[Melissa Linkert]

Hi Bill,

> I think I've merged and fixed conflicts OK. It seems
> to build (using both ant & mvn) and run OK again for me now
> 
> I know you can find this stuff from git, but the following
> notes on what I did might be useful:

Looks good, thank you.  Just to confirm, can I then close this pull
request:

https://github.com/openmicroscopy/bioformats/pull/663

so that this is the one we'll review for inclusion:

https://github.com/openmicroscopy/bioformats/pull/747

Regards,
-Melissa

On Fri, Oct 18, 2013 at 04:49:47PM +0100, Bill Hill wrote:
> Melissa,
> 
> I think I've merged and fixed conflicts OK. It seems
> to build (using both ant & mvn) and run OK again for me now
> 
> I know you can find this stuff from git, but the following
> notes on what I did might be useful:
> 
> add dir components/bio-formats/src/loci/formats/out
> 
> add components/bio-formats/src/loci/formats/in/WlzReader.java
> add components/bio-formats/src/loci/formats/out/WlzWriter.java
> add components/bio-formats/src/loci/formats/services/WlzService.java
> add components/bio-formats/src/loci/formats/services/WlzServiceImpl.java
> 
> mod components/scifio/src/loci/formats/readers.txt
> mod components/bio-formats/build.properties
> mod components/bio-formats/pom.xml b/components/bio-formats/pom.xml
> mod components/loci-legacy/src/loci/common/services/services.properties
> mod components/scifio/src/loci/formats/writers.txt
> 
> Obviously to run something like:
> 
> ./tools/showinf fruit.wlz
> 
> you need your LD_LIBRAY_PATH environment variable set, eg (for
> t/csh):
> 
> setenv BFHOME   /home/bill/Build/src/bioformats
> setenv LD_LIBRARY_PATH $BFHOME/lib:$LD_LIBRARY_PATH
> 
> Cheers,
> Bill
> 
> >Hi Bill,
> >
> >>Does anyone know the status of the Woolz reader/writer in
> >>bioformats. Is this incorporated into the OMERO5 build now?
> >>If not can anyone tell if the system is waiting on me to do
> >>something?
> >>
> >>https://github.com/openmicroscopy/bioformats/pull/663
> >
> >Sorry, this just needs some final review and testing from us - we were
> >just a bit distracted by the 4.4.9 release.
> >
> >The only thing you need to do with that PR at the moment is to merge the
> >latest 'develop' branch from the openmicroscopy/bioformats repository
> >into your 'develop' branch, resolve any conflicts, and then push the
> >branch back to Github.  If you would rather not have to deal with that,
> >then I can close PR #663 and open a new one with the same commits, so
> >that I own the PR and can take care of any conflict resolution.
> >
> >Regards,
> >-Melissa
> >
> >On Fri, Oct 18, 2013 at 03:28:55PM +0100, Bill Hill wrote:
> >>Does anyone know the status of the Woolz reader/writer in
> >>bioformats. Is this incorporated into the OMERO5 build now?
> >>If not can anyone tell if the system is waiting on me to do
> >>something?
> >>
> >>https://github.com/openmicroscopy/bioformats/pull/663
> >>
> >>
> >>I see:
> >>
> >>
> >>Build
> >>     1078
> >>State
> >>     Passed
> >>Finished
> >>     about a month ago
> >>Duration
> >>     1 hr 20 min 44 sec
> >>Commit
> >>     69ffe88 (develop)
> >>Pull Request
> >>     #663 woolz add bioformats
> >>Author
> >>     Bill Hill
> >>Committer
> >>     Bill Hill
> >>Message
> >>     Fixed JWlz.jar dependency path.
> >>
> >>Cheers,
> >>Bill
> >>--
> >>Bill Hill                              : http://www.hgu.mrc.ac.uk
> >>MRC Human Genetics Unit                : http://www.emouseatlas.org
> >>MRC IGMM, University of Edinburgh      : Bill.Hill at igmm.ed.ac.uk
> >>Western General Hospital               : +44-131-3322471x2119
> >>Crewe Road, Edinburgh EH4 2XU, UK.     : +44-131-4678456
> >>
> >>The University of Edinburgh is a charitable body, registered in
> >>Scotland, with registration number SC005336.
> >>
> >>_______________________________________________
> >>ome-devel mailing list
> >>ome-devel at lists.openmicroscopy.org.uk
> >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> 
> -- 
> Bill Hill                              : http://www.hgu.mrc.ac.uk
> MRC Human Genetics Unit                : http://www.emouseatlas.org
> MRC IGMM, University of Edinburgh      : Bill.Hill at igmm.ed.ac.uk
> Western General Hospital               : +44-131-3322471x2119
> Crewe Road, Edinburgh EH4 2XU, UK.     : +44-131-4678456
> 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>