Re: [XMLPipeDB-developer] Plasmodium bug/task list
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Re: [XMLPipeDB-developer] Plasmodium bug/task list
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From: Richard B. <rbr...@gm...> - 2011-03-31 00:37:45
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OK, completed the merge manually and have verified that the build actually
compiles without error and the export functionality does not hang or crash.
But that said, I ran two sample exports for Mtuberculosis and Pfalciparum
and both exports seem to be bad in that they have wrong counts or are
missing all ordered locus id's etc.
Before I reach out for more help I think I will verify that I moved the
correct species changes for both and try again.
The manual merge was much easier than I thought it would be...
Richard
On Tue, Mar 29, 2011 at 5:29 PM, Richard Brous <rbr...@gm...> wrote:
> Dondi,
>
> Thanks for the chat regarding this issue.
>
> I'm in agreement that since it is significant work to either: a) create a
> new repository (with the newer file system) and dump the original contents
> inside or b) get Sourceforge to upgrade to the latest version of SVN... it
> makes sense to manually do the merge 'file by file'.
>
> I will likely start this evening and can work on it slowly during the week,
> employing the strategy of modifying the files as needed, then change the
> branch working copy files to match the trunk working copy. As discussed,
> that will allow the local compare to keep track of the remaining changes. I
> will be sure NOT TO commit any local branch changes up to the repository.
>
> Richard
>
> On Tue, Mar 29, 2011 at 1:04 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> We can do phone, but later in the afternoon. What's your schedule like
>> today?
>>
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>> On Mar 29, 2011, at 12:54 PM, Richard Brous <rbr...@gm...> wrote:
>>
>> i'm using subclipse 1.6.17 so that is up to date.
>>
>> is it possible to talk through this on the phone? I have a few questions
>> after reading through the svn tutorial of how the merge is performed within
>> Eclipse.
>>
>> richard
>>
>> On Tue, Mar 29, 2011 at 12:38 PM, John David N. Dionisio <do...@lm...>wrote:
>>
>>> 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
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > Enable your software for Intel(R) Active Management Technology to meet
>>> the
>>> > growing manageability and security demands of your customers.
>>> Businesses
>>> > are taking advantage of Intel(R) vPro (TM) technology - will your
>>> software
>>> > be a part of the solution? Download the Intel(R) Manageability Checker
>>> > today! http://p.sf.net/sfu/intel-dev2devmar
>>> >
>>> > _______________________________________________
>>> > xmlpipedb-developer mailing list
>>> > xml...@li...
>>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> >
>>> >
>>> >
>>> >
>>> > <ATT00001..txt><ATT00002..txt>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Enable your software for Intel(R) Active Management Technology to meet
>>> the
>>> growing manageability and security demands of your customers. Businesses
>>> are taking advantage of Intel(R) vPro (TM) technology - will your
>>> software
>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>> _______________________________________________
>>> xmlpipedb-developer mailing list
>>> xml...@li...
>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>>
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>>
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>>
>
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