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

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

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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>