Re: [XMLPipeDB-developer] Plasmodium bug/task list
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Re: [XMLPipeDB-developer] Plasmodium bug/task list
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From: Richard B. <rbr...@gm...> - 2011-03-29 19:54:47
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i'm using subclipse 1.6.17 so that is up to date.
is it possible to talk through this on the phone? I have a few questions
after reading through the svn tutorial of how the merge is performed within
Eclipse.
richard
On Tue, Mar 29, 2011 at 12:38 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> The unknown with this error is whether this is a limitation on the server
> side (SourceForge) or client side (your copy of Subclipse/Subversion). If
> the former, that will need some investigation. Let's try with the latter
> case first:
>
> - Make sure you have the latest Subclipse/Subversion. According to
> Subclipse, they are at 1.6.17.
>
> - You might need to re-check out the projects if you updated Subclipse
> versions.
>
> - Try again.
>
> If the error persists, then this may be a server side issue, in which the
> action may be to *downgrade* the Subversion version. But we'll cross that
> bridge if/when we get to it.
>
> Hope this helps...
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Mar 29, 2011, at 10:13 AM, Richard Brous wrote:
>
> > Hi Dondi,
> >
> > I'm working on the merge and have located the merge functionality under
> the team menu in Eclipse.
> >
> > The first menu requests a choice regarding the type of merge required.
> > I would expect the correct selection to be reintegrate branch.
> >
> > I then select the branch to merge and ask for conflicts of all types be
> noted for later review.
> >
> > Click finish and it attempts to merge but I receive an error message of
> the following:
> > org.tigris.subversion.javahl.ClientException: Trying to use an
> unsupported feature
> > svn: Querying mergeinfo requires version 3 of the FSFS filesystem schema;
> filesystem '/nfs/sf-svn-symlinks/xmlpipedb/db' uses only version 2
> > org.tigris.subversion.javahl.ClientException: Trying to use an
> unsupported feature
> > svn: Querying mergeinfo requires version 3 of the FSFS filesystem schema;
> filesystem '/nfs/sf-svn-symlinks/xmlpipedb/db' uses only version 2
> > Help please!
> >
> > Thanks.
> >
> > Richard
> > On Fri, Mar 25, 2011 at 3:50 PM, Richard Brous <rbr...@gm...>
> wrote:
> > ok, beta 63 is up on sourceforge.
> >
> > Richard
> >
> > On Fri, Mar 25, 2011 at 2:55 PM, Richard Brous <rbr...@gm...>
> wrote:
> > will do. i'll send out an email when completed.
> >
> > On Fri, Mar 25, 2011 at 11:30 AM, Kam Dahlquist <kda...@lm...>
> wrote:
> > Hi,
> >
> > I've checked the gdb and it looks OK. Richard, will you release a build
> of GenMAPP Builder with these changes so that I can test the export on one
> of my machines? I am going to work on the ReadMe for this gdb so we can
> release it.
> >
> > Once I've validated that the new version of GenMAPP Builder works, we'll
> be ready to move on to the code merge.
> >
> > Best,
> > Dr. D
> >
> >
> > At 09:15 PM 3/24/2011, you wrote:
> >> Sorry for the late reply... been laid up with a cold and barely
> functioning on cold medicine...
> >>
> >> I believe I have the Pfalciparum solved by using the following code:
> >>
> >>
> >> /**
> >>
> >> *
> >>
> >> @see
> edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile#getSystemTableManagerCustomizations(edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager,
> edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager,
> java.util.Date)
> >>
> >> */
> >>
> >> @Override
> >>
> >> public TableManager getSystemTableManagerCustomizations(TableManager
> tableManager, TableManager primarySystemTableManager, Date version) throws
> SQLException, InvalidParameterException {
> >>
> >> // Start with the default OrderedLocusNames behavior.
> >>
> >> TableManager result =
> >> super .getSystemTableManagerCustomizations(tableManager,
> primarySystemTableManager, version);
> >>
> >> // Next, we add IDs from the other gene/name tags, but ONLY if they
> match
> >>
> >> // the pattern PF[A-Z][0-9]{4}[a-z].
> >>
> >> //final String pfID = "PF[A-Z][0-9][0-9][0-9][0-9][a-z]";
> >>
> >> //final String pfID2 = "PF[0-9][0-9]_[0-9][0-9][0-9][0-9]";
> >>
> >> //final String pfID3 = "MAL[0-9]*P1.[0-9]*";
> >>
> >> String sqlQuery =
> >> "select d.entrytype_gene_hjid as hjid, c.value " +
> >>
> >> "from genenametype c inner join entrytype_genetype d " +
> >>
> >> "on (c.entrytype_genetype_name_hjid = d.hjid) " +
> >>
> >> //"where (c.value similar to ? " +
> >>
> >> "where c.type = 'ORF'" +
> >>
> >> //"or c.value similar to ? " +
> >>
> >> //"or c.value similar to ?) " +
> >>
> >> //"and type <> 'ordered locus names' " +
> >>
> >> //"and type <> 'ORF' " +
> >>
> >> "group by d.entrytype_gene_hjid, c.value";
> >>
> >> String dateToday =
> GenMAPPBuilderUtilities.getSystemsDateString(version);
> >>
> >> Connection c = ConnectionManager.getRelationalDBConnection();
> >>
> >> PreparedStatement ps;
> >>
> >> ResultSet rs;
> >>
> >> try {
> >>
> >> // Query, iterate, add to table manager.
> >>
> >> ps = c.prepareStatement(sqlQuery);
> >>
> >> //ps.setString(1, pfID);
> >>
> >> //ps.setString(2, pfID2);
> >>
> >> //ps.setString(3, pfID3);
> >>
> >> rs = ps.executeQuery();
> >>
> >> while (rs.next()) {
> >>
> >> String hjid = Long.valueOf(rs.getLong(
> >> "hjid" )).toString();
> >>
> >> // capture unmodified value in string variable id
> >>
> >> // We want to remove the '_' here but also add id's with the '_'
> >>
> >> String id = rs.getString(
> >> "value" );
> >>
> >> // condition if id matched pattern "PFA_"
> >>
> >> if (id.matches("PFA_.*" )) {
> >>
> >> String[] substrings = id.split("/" );
> >>
> >> String new_id = null;
> >>
> >> String old_id = id;
> >>
> >> for (int i = 0; i < substrings.length ; i++) {
> >>
> >> new_id = substrings[i].replace("_" , "");
> >>
> >> _Log.debug( "Remove '_' from " + id + " to create: " + new_id + " for
> surrogate " + hjid);
> >>
> >> result.submit( "OrderedLocusNames", QueryType.insert , new String[][] {
> { "ID", new_id }, { "Species" , "|" + getSpeciesName() + "|" }, { "\"Date\""
> , dateToday }, { "UID", hjid } });
> >>
> >> _Log.debug( "Keep '_' from " + id + " to create: " + old_id + " for
> surrogate " + hjid);
> >>
> >> result.submit( "OrderedLocusNames", QueryType.insert , new String[][] {
> { "ID", old_id }, { "Species" , "|" + getSpeciesName() + "|" }, { "\"Date\""
> , dateToday }, { "UID", hjid } });
> >>
> >> }
> >>
> >> }
> >>
> >> // otherwise process as normal
> >>
> >> else {
> >>
> >> _Log .debug("Processing raw ID: " + id + " for surrogate " + hjid);
> >>
> >> tableManager.submit(
> >> "OrderedLocusNames" , QueryType.insert , new String[][] { { "ID", id },
> { "Species" , "|" + getSpeciesName() + "|" }, { "\"Date\"" , dateToday }, {
> "UID", hjid } });
> >>
> >> }
> >>
> >> }
> >>
> >> }
> >> catch (SQLException sqlexc) {
> >>
> >> logSQLException(sqlexc, sqlQuery);
> >>
> >> }
> >>
> >> return result;
> >>
> >> }
> >>
> >> I have exported a gdb which contains 5472 gene id's as compared to the
> previous 5338. The 134 gene id's with the prefix PFA_ are included plus
> their underscore removed form.
> >>
> >> Zipped up and attached here and will later post to the wiki.
> >>
> >> Richard
> >
> >
> ------------------------------------------------------------------------------
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> the
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> > are taking advantage of Intel(R) vPro (TM) technology - will your
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> >
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
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