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

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

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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