[ome-devel] v3draw writer branch

Melissa Linkert melissa at glencoesoftware.com
Wed Mar 19 21:10:17 GMT 2014 

Hi Brian,

> My .v3draw writer is now in a branch forked from the develop branch of bioformats:
> 
> 
> https://github.com/berl/bioformats
> 
> and I just submitted a pull request as Melissa described and I look forward to any feedback the OME team can provide.

Thank you for submitting a pull request.  We will review it, and any
questions or comments will be added to the PR.

> With regards to the building problems I had earlier, it's probably some beginner User Error with Netbeans: basically, with the master branch, I could just 'build with dependencies' on the main project and end up with a functioning loci-tools.jar for use with bfconvert.  With the develop branch, I had to build from the command line ( ant clean jars tools and then mvn to build the project), or else the bioformats-package.jar didn't know about some basic classes that did exist, they just weren't packaged in the .jar.   In any case, this can likely be ignored unless others report the same problem.
> 
> 
> I do get errors in the mvn build, but they didn't cause me subsequent errors (but I didn't try reading these formats, so who knows?).  they look like this:
> 
> ...
> 	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:74) [surefire-booter-2.12.jar:2.12]
> 2014-03-17 20:10:26,261 [main] ERROR loci.formats.ClassList - "loci.formats.in.SBIGReader" is not valid.
> 2014-03-17 20:10:26,262 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.HRDGDFReader
> java.lang.ClassNotFoundException: loci.formats.in.HRDGDFReader
> ...
> 	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:74) [surefire-booter-2.12.jar:2.12]
> 2014-03-17 20:10:26,265 [main] ERROR loci.formats.ClassList - "loci.formats.in.BrukerReader" is not valid.
> 2014-03-17 20:10:26,267 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.CanonRawReader
> ...
> 
> and similar lines for different formats.  

That is expected output when Maven is running the unit tests in
components/formats-api and/or components/formats-bsd, and so can be safely
ignored.

Regards,
-Melissa

On Tue, Mar 18, 2014 at 03:42:39AM +0000, Brian Long wrote:
> Hi All,
> 
> My .v3draw writer is now in a branch forked from the develop branch of bioformats:
> 
> 
> https://github.com/berl/bioformats
> 
> and I just submitted a pull request as Melissa described and I look forward to any feedback the OME team can provide.
> 
> With regards to the building problems I had earlier, it's probably some beginner User Error with Netbeans: basically, with the master branch, I could just 'build with dependencies' on the main project and end up with a functioning loci-tools.jar for use with bfconvert.  With the develop branch, I had to build from the command line ( ant clean jars tools and then mvn to build the project), or else the bioformats-package.jar didn't know about some basic classes that did exist, they just weren't packaged in the .jar.   In any case, this can likely be ignored unless others report the same problem.
> 
> 
> I do get errors in the mvn build, but they didn't cause me subsequent errors (but I didn't try reading these formats, so who knows?).  they look like this:
> 
> ...
> 	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:74) [surefire-booter-2.12.jar:2.12]
> 2014-03-17 20:10:26,261 [main] ERROR loci.formats.ClassList - "loci.formats.in.SBIGReader" is not valid.
> 2014-03-17 20:10:26,262 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.HRDGDFReader
> java.lang.ClassNotFoundException: loci.formats.in.HRDGDFReader
> ...
> 	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:74) [surefire-booter-2.12.jar:2.12]
> 2014-03-17 20:10:26,265 [main] ERROR loci.formats.ClassList - "loci.formats.in.BrukerReader" is not valid.
> 2014-03-17 20:10:26,267 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.CanonRawReader
> ...
> 
> and similar lines for different formats.  
> 
> 
> Thanks so much!
> -Brian
> 
> 
> ________________________________________
> From: Melissa Linkert [] on behalf of Melissa Linkert []
> Sent: Friday, March 14, 2014 5:50 AM
> To: Brian Long
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] v3draw writer branch
> 
> Hi Brian,
> 
> > I've added a .v3draw writer to the bioformats develop branch here:
> >
> > https://github.com/berl/v3draw-bioformats
> >
> > I'd like to get this reviewed and incorporated into the main bioformats branch- what's the next step?
> 
> The next step is to open a pull request from that branch against the
> 'develop' branch of openmicroscopy/bioformats.  We can then review the
> code and make sure that it passes all of the tests in our continuous
> integration systems.
> 
> > Also, with the master branch, I can directly build in NetBeans and everything works fine, but the develop branch seemed to require command-line building to get a functional ImageConverter class.  This is probably something basic, but I'd like to understand how/why it works this way.
> 
> Do you see an error in NetBeans when building the develop branch?  If
> so, what is it?  The only thing I can think of is that Genshi is needed
> to build on develop (but not on master), so if NetBeans isn't picking
> that up then you would likely see an error similar to what is here:
> 
> https://github.com/openmicroscopy/bioformats/issues/472
> 
> Regards,
> -Melissa
> 
> 
> On Fri, Mar 14, 2014 at 05:10:20PM +0000, Brian Long wrote:
> > I've added a .v3draw writer to the bioformats develop branch here:
> >
> > https://github.com/berl/v3draw-bioformats
> >
> > I'd like to get this reviewed and incorporated into the main bioformats branch- what's the next step?
> >
> > Also, with the master branch, I can directly build in NetBeans and everything works fine, but the develop branch seemed to require command-line building to get a functional ImageConverter class.  This is probably something basic, but I'd like to understand how/why it works this way.
> >
> > Thanks!
> >
> > Brian Long
> > Scientist-I
> > Allen Institute for Brain Science
> > Seattle, WA
> > USA
> 
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> 
> 
> ________________________________________
> From: Melissa Linkert [] on behalf of Melissa Linkert []
> Sent: Friday, March 14, 2014 5:50 AM
> To: Brian Long
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] v3draw writer branch
> 
> Hi Brian,
> 
> > I've added a .v3draw writer to the bioformats develop branch here:
> >
> > https://github.com/berl/v3draw-bioformats
> >
> > I'd like to get this reviewed and incorporated into the main bioformats branch- what's the next step?
> 
> The next step is to open a pull request from that branch against the
> 'develop' branch of openmicroscopy/bioformats.  We can then review the
> code and make sure that it passes all of the tests in our continuous
> integration systems.
> 
> > Also, with the master branch, I can directly build in NetBeans and everything works fine, but the develop branch seemed to require command-line building to get a functional ImageConverter class.  This is probably something basic, but I'd like to understand how/why it works this way.
> 
> Do you see an error in NetBeans when building the develop branch?  If
> so, what is it?  The only thing I can think of is that Genshi is needed
> to build on develop (but not on master), so if NetBeans isn't picking
> that up then you would likely see an error similar to what is here:
> 
> https://github.com/openmicroscopy/bioformats/issues/472
> 
> Regards,
> -Melissa
> 
> 
> On Fri, Mar 14, 2014 at 05:10:20PM +0000, Brian Long wrote:
> > I've added a .v3draw writer to the bioformats develop branch here:
> >
> > https://github.com/berl/v3draw-bioformats
> >
> > I'd like to get this reviewed and incorporated into the main bioformats branch- what's the next step?
> >
> > Also, with the master branch, I can directly build in NetBeans and everything works fine, but the develop branch seemed to require command-line building to get a functional ImageConverter class.  This is probably something basic, but I'd like to understand how/why it works this way.
> >
> > Thanks!
> >
> > Brian Long
> > Scientist-I
> > Allen Institute for Brain Science
> > Seattle, WA
> > USA
> 
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>

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