Re: [XMLPipeDB-developer] Plasmodium bug/task list

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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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