Re: [XMLPipeDB-developer] Plasmodium bug/task list
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Re: [XMLPipeDB-developer] Plasmodium bug/task list
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From: John D. N. D. <do...@lm...> - 2011-03-29 20:05:27
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We can do phone, but later in the afternoon. What's your schedule like today?
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Mar 29, 2011, at 12:54 PM, Richard Brous <rbr...@gm...> wrote:
> 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
> >
> > ------------------------------------------------------------------------------
> > 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
> >
> >
> >
> >
> > <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
>
> ------------------------------------------------------------------------------
> 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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