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

[Richard B. <rbr...@gm...>]

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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>>
>