naturalis / biovel-nbc Goto Github PK

Travis is complaining about the project failing because there is no .travis.yml file.

Can't get the extractor to work correctly. On errors there should be a descriptive error echo'ed to the user. Perhaps this can be done using use CGI::Carp 'fatalsToBrowser';

Do you have REST endpoints implemented for this yet? (Mostly opening this issue so I know when to return to ropensci/RNeXML#55 to implement this interface). btw, the whole biovel-nbc project looks awesome!

Sun Mar 30 12:02:52 2014: Request 94317 was acted upon.
Transaction: Ticket created by SREZIC
Queue: Bio-BioVeL
Subject: Makefile.PL missing in distribution
Broken in: 0.1
Severity: (no value)
Owner: Nobody
Requestors: [email protected]
Status: new
Ticket <URL: https://rt.cpan.org/Ticket/Display.html?id=94317 >

I suspect the problems exists because "Makefile" is listed in MANIFEST.SKIP. Note that lines in MANIFEST.SKIP are interpreted as regexps, so "Makefile.PL" also matches and therefore it is skipped. If you want to skip "Makefile" then write something like "^Makefile$".

Regards,
Slaven

Can't get the extractor to work correctly. On errors there should be a descriptive error echo'ed to the user. Perhaps this can be done using use CGI::Carp 'fatalsToBrowser';

All taxon names of a matrix get replaced by an internal ID (e.g. Datum322) and it is impossible to then map back between taxon ID and taxon label.
Rows should have taxon labels instead of the internal IDs.

• need to be able to export character data + character sets
• need to be able to export Taxa in other formats, especially TSV
• need to be able to export document-level metadata, e.g. as TSV or JSON

The NeXML extractor has to be extended to extract charset data.

http://biovel.naturalis.nl/biovel?service=NeXMLExtractor&nexml=http://testjst.ba.infn.it/openacces/InputExamples/downloadAMatrix2.xml&object=Matrices&dataformat=nexus

produce a correct nexus matrix but with label name not matching label of otu in nexml or any clear ID system within the nexml file.
Best would be to give the actual label of the otu to the matrix

Can't get the extractor to work correctly. On errors there should be a descriptive error echo'ed to the user. Perhaps this can be done using use CGI::Carp 'fatalsToBrowser';

Make sure the annotations on the biodiversity catalogue (https://www.biodiversitycatalogue.org/services/70) comply with BioVeL's requirements.

Can't get the extractor to work correctly. On errors there should be a descriptive error echo'ed to the user. Perhaps this can be done using use CGI::Carp 'fatalsToBrowser';