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

[Kam D. <kda...@lm...>]

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