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Re: [Obi-devel] OBI-svn re-organisation
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From: Daniel S. <sc...@eb...> - 2008-03-25 16:48:45
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Hi all. This is fine with me as well. We decided to do the svn restructuring after the release, because we all had more urgent stuff to do and we wanted to do the restructuring in a more 'svn quiet' time. I would suggest Alan implements what is on the wiki and then we comment and refine where necessary. Cheers, Daniel. Alan Ruttenberg wrote: > We are set to move with the structure described at > http://docs.google.com/View?docid=dzprnmw_11cfp3w8cx > > -Alan > > On Tue, Mar 25, 2008 at 9:57 AM, frank gibson <Fra...@nc... > <mailto:Fra...@nc...>> wrote: > > Did we come to a conclusion on the svn re-structuring or has it > stalled? > > Frank > > On Fri, Feb 22, 2008 at 11:13 PM, Alan Ruttenberg > <ala...@gm... <mailto:ala...@gm...>> wrote: > > > > On Feb 22, 2008, at 4:48 AM, Daniel Schober wrote: > > >> On Thu, Feb 21, 2008 at 11:08 AM, Daniel Schober > > >> <sc...@eb... <mailto:sc...@eb...>> wrote: > > >> Hi all, > > >> here the proposal for the OBI-svn re-organisation: > > >> (if directories mentioned are not currently in existence, I will > > >> create > > >> them where needed) > > >> > > >> > > >> obi\branchDevelopment\trunk\sourcecodes > > >> move into > > >> obi\ > > >> > > >> > > >> obi\branchDevelopment\trunk\sourcecodes\xl2owl > > >> move into > > >> obi\tools\format_converters\ > > > > In sourcecodes there is also a format converter - the lisp one used > > to import some of the spreadsheets. In addition, in xl2owl, > there is > > some source code. > > > > Thinking a bit further: > > > > A common arrangement of a project such as this is something like: > > > > trunk > > src/ > > bin/ > > examples/ > > dist/ > > test/ > > .... > > README > > buildscript (e.g. ant or Makefile). > > > > Currently we have a number of directories below obi, each of which > > has its own trunk. Perhaps a simpler organization that follows the > > convention above: > > > > below obi/trunk > > src/ > > ontology/ > > branches/ > > spreadsheets/ > > in/ > > out/ > > tools/ > > format-converters/ > > lsw/ > > xl2owl/ > > build/ > > (join and merge scripts go here, etc.) > > examples/ > > tests/ > > bin/ (xl2owl binaries go here) > > dist/ (where scripted builds of OBI for distribution are created) > > > > then obi/tags and obi/branches are the usual place one makes > > subversion checkpoints. > > > > Some further comments in line below. > > > > > > >> obi\branchDevelopment\trunk\spreadsheets-exported > > >> obi\branchDevelopment\trunk\spreadsheets-imported > > >> move into > > >> obi\tools\format_converters\xls2owl\ > > > > Sigh, it's hard to be an ontologist. A spreadsheet isn't a format > > converter, it is input to one. I suppose it could be > > "format_conversion", and that would work, but see proposal above, > > suggesting src/ontology/spreadsheets/ > > > > > > >> obi\tools\OBIBatchTermLoader > > >> if this is not working, we might remove it, > > >> otherwise put under obi\tools\format_converters\ > > > > Perhaps, for posterity, obi/trunk/obsolete > > > > > > >> obi\branchDevelopment\trunk\older > > >> is this needed? > > > > no. > > > > > > >> obi\branchDevelopment\trunk\bfo > > >> move into > > >> obi\branchDevelopment\trunk\external\ > > >> AND align import statements in files to reflect that. > > >> (Alan, was there a reason for not having bfo under > /external ?) > > > > No good one :) > > Above suggests src/ontology/external/ > > > > > > >> obi\branchDevelopment\trunk\gather-class-uris.pl > > >> move into > > >> obi\sourcecodes\ > > > > src/build/ > > > > > > >> obi\branchDevelopment\trunk\reasoner-example-workshop-2007- > > >> July.owl > > >> move into > > >> > obi\branchDevelopment\trunk\development-examples\reasoner-example\ > > > > examples/development/ > > > > > > >> all under \obi\branchDevelopment\trunk\development-examples > > >> move to > > >> > > >> \obi\branchDevelopment\trunk\development-examples > > >> \object_top_level_example > > > > examples/development/object_top_level > > > > > > >> obi\branchDevelopment\trunk\obi-liver.owl > > >> move to > > >> obi\branchDevelopment\trunk\development-examples > > >> (what is this obi-liver.owl anyway? Can it be deleted ?) > > > > From workshop. To examples/development > > > > > > >> > > >> obi\branchDevelopment\trunk\obi-owl-full.owl > > >> looks quite outdated, delete? Or put under > > >> obi\branchDevelopment\trunk\development-examples > > > > Needed to keep any owl full bits of OBI. Currently range for the > > annotation property curation_status. Presumably this should now be > > adjusted in light of our decision about appropriate values. > > to: src/ontology/branches/ > > > > > > >> obi\branchDevelopment\trunk\external.owl > > >> obi\branchDevelopment\trunk\externalDerived.owl > > >> what are they? Maybe put under > > >> obi\branchDevelopment\trunk\development-examples ? > > Needed. See http://obi-biomaterial.googlegroups.com/web/ > > importsDocumentation_v1.0.doc > > to: src/ontology/branches/ > > > > > > >> regarding the imported external ontologies... shouldn't > we import > > >> from their websites via URI to always get the latest updated > > >> versions? > > >> Or are these automatically piped into our \external folder? > > > > I prefer to have a stable copy in our development folder and make > > careful updates so as to be not subject to random things breaking. > > However, people can adjust their .repository files to not use these > > if they want. So, not automatically. Deliberately copied there. > > > > -Alan > > > > > > > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Obi-devel mailing list > > Obi...@li... > <mailto:Obi...@li...> > > https://lists.sourceforge.net/lists/listinfo/obi-devel > > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 > > -- __________________________________________________________________________________________ Dr. Daniel Schober NET Project - Ontologist The European Bioinformatics Institute email: sc...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) Project page: www.ebi.ac.uk/net-project Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ |