Re: [XMLPipeDB-developer] 499 - PROBLEM - M tuberculosis xml tag importation

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

thanks and will do as directed.

My previous, last paragraph comment - A way for programming code in email
holding its format in a mail message similarly to how you can post code on
forum pages?

<code>
blah
blah
blah
</code>
thanks!

Richard
On Sun, Feb 20, 2011 at 10:05 PM, John David N. Dionisio <do...@lm...>wrote:

> Greetings,
>
> Actually, gmbuilder.properties is for the TallyEngine only.  When dealing
> with .gdb exports, look *only* at the SpeciesProfile class.  So, to find
> those 69 IDs, it is the SpeciesProfile code, and *only* the SpeciesProfile
> code, that needs to be changed.
>
> Your take on how gmbuilder.properties is used, however, is understandable.
>  It makes sense to assume that the TallyEngine code *and* the ID export code
> are based on the same characterization of the needed IDs.  This replication
> is originally a historical artifact: SpeciesProfile was done first, and then
> TallyEngine was done later by another student.
>
> However, there are other factors beyond history that sort of necessitate
> this duplication of desired IDs: (skip the two bullets below if you'd rather
> cut to the chase of the work to be done, and discuss design issues later)
>
> - The actual XML import code is a black box: this is the "canned" JAXB
> library actually in action, and not our code at all.  Plus, the XML import
> code really does not filter (nor should it), since the goal of the
> XML->relational database step is to fully capture the XML data in the
> relational database.  So, XML count is necessarily separated from XML
> import.
>
> - The notion of a declarative mechanism for extracting IDs from the
> relational database (which is what gmbuilder.properties/TallyEngine uses) is
> interesting, but at the same time there is value in the arbitrary
> computation that can be done with Java (case in point: export two versions
> of an ID, with and without periods).  This is not to say that it is
> impossible to do this declaratively, but let's just say that the procedural
> approach exists here and now, and a declarative approach will need more
> thought.
>
> These, and other factors, are good thoughts to hold onto and would be
> worthy of a good meeting discussion sometime, but bottom line for now:
> modifying the export behavior is a matter of editing the *SpeciesProfile*
> Java code, and not the gmbuilder.properties file.  Turn your attention to
> that code.
>
> Now, as to annotating your code...I'd just put in code comments  :)  Or did
> you mean something else by tagging code in e-mail?
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
>  On Feb 21, 2011, at 12:38 AM, Richard Brous wrote:
>
> > also, how do I tag code in email so it holds its formatting? I tried a
> few suggestions I found on the web but they aren't holding formatting or i'm
> just doing it wrong ;-D
> >
> > Richard
> >
> > On Sun, Feb 20, 2011 at 9:35 PM, Richard Brous <rbr...@gm...>
> wrote:
> > OK, have some updates and some suggestions:
> >
> > On Friday Dr. Dahlquist and I sat down and reviewed the gene testing
> report. We verified that XML match does indeed find 4066 unique matches - 75
> of which are not in the gdb and need to be.
> >
> > Dr. Dahlquist informed me that she was the one who completed the gene db
> testing report, not a previous student of BIO367 and had already verified
> which genes were missing and where they were to be found. I had (mistakenly)
> assumed that since a student had performed the gene database testing I had
> to redo all of the verification.
> >
> > So that said, of the 75 genes missing - 69 need to be included and 6
> excluded.
> > Per the gene db testing report: "69 of them have an "a", "b", or "d"
> suffix. They are all found in the ORF tag and need to be included in the
> gdb."
> >
> > To solve this we need to add additional search criteria into the M.
> tuberculosis section in gmbuilder.properties below:
> > # Mycobacterium tuberculosis
> >
> > mycobacteriumtuberculosis_level_amount=
> >
> > 1
> >
> > mycobacteriumtuberculosis_element_level0=
> >
> > uniprot/entry/gene/name&type&ordered locus
> >
> > mycobacteriumtuberculosis_query_level0=
> >
> > select count(*) from genenametype where type = 'ordered locus' and value
> like 'Rv%';
> >
> > mycobacteriumtuberculosis_table_name_level0=
> >
> > Ordered Locus
> > SOLUTIONS:
> >
> > 1. So am i correct in my understanding that the second line is the query
> used by TallyEngine to read the XML file? If so then this is the issue we
> need to table for the moment until we get the gbd verified and re-released.
> We will revisit this to discover why it is not only reporting incorrectly
> but also why its added a second row of Ordered Locus on the TallyEngine
> results page.
> >
> > 2. The third line is the SQL query used by postgres during the export
> from XML to gdb. To find and get the ORF tagged genes could we not add the
> following lines and change the count in the first line:
> >
> >
> > # Mycobacterium tuberculosis
> >
> > mycobacteriumtuberculosis_level_amount=2
> >
> >
> >
> mycobacteriumtuberculosis_element_level0=uniprot/entry/gene/name&type&ordered
> locus
> > mycobacteriumtuberculosis_element_level1=uniprot/entry/gene/name&type&orf
> >
> >
> > mycobacteriumtuberculosis_query_level0=
> >
> > select count(*) from genenametype where type = 'ordered locus';
> > mycobacteriumtuberculosis_query_level1=select count(*) from genenametype
> where type = 'orf';
> >
> >
> > mycobacteriumtuberculosis_table_name_level0=
> >
> > Ordered Locus
> > mycobacteriumtuberculosis_table_name_level1=Ordered Locus
> >
> >
> ----------------------------------------------------------------------------------------------------------------------------
> >
> > Of course these queries would have be manually verified prior to making
> these changes but this seems like we are moving in the right direction.
> >
> > Richard
> >
> >
> > On Thu, Feb 17, 2011 at 7:47 PM, Richard Brous <rbr...@gm...>
> wrote:
> > Just got done reading previous email and understand the change in
> priority.
> >
> > Will work on the missing ID's for now and shelve the the TalleyEngine
> issue for the moment.
> >
> > Also great about a more formalized weekly meeting. I was going to suggest
> it myself as it has been slow going so far as maybe i'm a bit too
> independent in this independent study class =D
> >
> > Will dig further into the missing ID's later tonight and during day
> tomorrow and report back.
> >
> > Richard
> >
> > On Thu, Feb 17, 2011 at 4:34 PM, John David N. Dionisio <do...@lm...>
> wrote:
> > Hi Rich,
> >
> > No problem.  The pertinent line you're referring to, for XML, is this,
> right above the line you copied:
> >
> >
>  mycobacteriumtuberculosis_element_level0=uniprot/entry/gene/name&type&ordered
> locus
> >
> > The slash-separated section is the "path" of XML tags leading to the
> element of interest; then, after the ampersand, is a name/value pair for the
> desired attribute to count.  Note that there is no hint of a *content*-based
> filter (nor is there the capability for one, as far as I can tell in the
> code).  By "content," I mean that we can't specify filters based on what's
> *between* the tags.  We can only go as far as filter by attribute value,
> e.g., type="ordered locus".
> >
> > But anyway, as mentioned in the earlier e-mail, let's have the missing
> IDs in the .gdb take precedence for now.  Please take a look at the
> tuberculosis, A. thaliana, and P. falciparum profiles to get an idea for how
> the ID output can be customized, then let me know if you have any questions
> or need to confirm anything.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> >
> > On Feb 17, 2011, at 3:04 PM, Richard Brous wrote:
> >
> > > Sorry been slammed with a programming assignment that kept needing
> continued iteration and it has been all consuming until last night. But I
> did get a chance to work with your comments and review the code again with a
> different mind set.
> > >
> > > Yes, I examined the gmbuilder.properties file ( the query is also in
> the MycobacteriumTuberculosisUniProtSpeciesProfile which I mentioned in a
> previous email ) but I don't think I see what you mean regarding the XML
> count.
> > >
> > > I understood that: mycobacteriumtuberculosis_query_level0=select
> count(*) from genenametype where type = 'ordered locus' and value like
> 'Rv%';  was the db query but don't see which is the XML count... or do they
> share the same query and you are saying that XML count doesn't recognize and
> therefore cannot use the 'Rv%' parameter?
> > >
> > > Richard
> > >
> > >
> > >
> > > On Sat, Feb 12, 2011 at 11:46 PM, John David N. Dionisio <
> do...@lm...> wrote:
> > > Hi Rich,
> > >
> > > Sorry for the delay.  Had some distractions coming into the weekend.
> > >
> > > You've looked at the code; have you looked at gmbuilder.properties?  (I
> may have mentioned it a few e-mails ago, just as you were starting to dig
> into this)
> > >
> > > On the copy I have, the M. tuberculosis block looks like this
> (indentation is mine to set it apart):
> > >
> > >        # Mycobacterium tuberculosis
> > >        mycobacteriumtuberculosis_level_amount=1
> > >
> > >
>  mycobacteriumtuberculosis_element_level0=uniprot/entry/gene/name&type&ordered
> locus
> > >
> > >        mycobacteriumtuberculosis_query_level0=select count(*) from
> genenametype where type = 'ordered locus' and value like 'Rv%';
> > >
> > >        mycobacteriumtuberculosis_table_name_level0=Ordered Locus
> > >
> > > There, I think, is the rub.  Notice that the XML count does not filter
> on RV%.  The SQL query does.
> > >
> > > Unfortunately, I don't think the TallyEngine can include selective
> filtering in the XML counts.  If the need to do selective filtering on XML
> is necessary, then I think we're looking at a new functionality for you to
> implement (or, if this throws things off too much, this may have to be noted
> somewhere, that the XML vs. database counts may be off because the database
> count is doing some text-based filtering but the XML count does not).
> > >
> > > What does xmlpipedb-match say?  That will at least tell you whether the
> 'RV%' count is indeed correct.
> > >
> > > John David N. Dionisio, PhD
> > > Associate Professor, Computer Science
> > > Loyola Marymount University
> > >
> > >
> > >
> > > On Feb 11, 2011, at 4:52 PM, Richard Brous wrote:
> > >
> > > > OK here is what I was able to put together from the past few hours of
> code review:
> > > >
> > > > MycobacteriumTuberculosisUniProtSpeciesProfile.java:
> > > > -reveals that after the 2 System table modifications are made adding
> species name and link, a PreparedStatement is instantiated which builds and
> calls the base query.
> > > >
> > > > -The base query called is: ("SELECT value, type " + "FROM
> genenametype INNER JOIN entrytype_genetype " +
> "ON(entrytype_genetype_name_hjid = entrytype_genetype.hjid) " + "WHERE type
> = 'ordered locus' and value like 'Rv%' and entrytype_gene_hjid = ?")
> > > >
> > > > -So its looking in 'ordered locus' table/column for any tuple that
> starts with Rv (followed by any substring) and entrytype_gene_hjid = ? .
> > > > The 'like' comparator and % usage are clear with the 'type'
> entrytype_gene_hjid = ?
> > > >
> > > > -To me it seems the query makes sense so the problem is likely
> elsewhere.
> > > >
> > > > GenMappBuilder.java:
> > > > -I found method doTallies() at code line 895 which:
> > > > Instantiates a Configuration called hibernateConfiguration and
> assigns to it the current hibernate configuration
> > > > Validates database settings by analyzing hibernateConfiguration
> > > > Instantiates a CriterionList for uniprot and assigns to it
> TallyType.UNIPROT
> > > > Instantiates a CriterionList for go and assigns to it TallyType.GO
> > > > Determines if both xml files exist
> > > > Then getTallyResultsXML and getTallyResultsDatabase are run on both
> xml files and their respective CriterionList
> > > > Results are then formatted for display in a table.
> > > >
> > > > -So enum TallyType which means that they are the only valid datatypes
> which TallyEngine accepts... go to know ...
> > > >
> > > > -Based on the screen shot of Tally Engine it would seem that both
> getTallyResultsXML() and getTallyResultsDatabase() are incorrectly
> returning. Likely due to both using an incorrect query (as we previously
> supposed). But where are the queries?... the more I dig the more I think
> they are in the criterial all the work is done against.
> > > >
> > > > continuing the review:
> > > > getTallyResultsXML() calls Tally Engine instance method
> getXmlFileCounts(xmlFile)
> > > > getTallyResultsDatabase() calls Tally Engine instance method
> getDbcounts(new QueryEngine(hibernateConfiguration)
> > > > Both of these instanced methods originate from TallyEngine.java...
> > > >
> > > > TallyEngine.java:
> > > >
> > > > getXmlFileCounts() calls digestXmlFile() which instantiates a
> digester then processes against criteria... but this quickly becomes
> confusing and is hard to follow
> > > >
> > > > getDbcounts() then starts a db session and executes a query but then
> I also get a bit lost with my limited db knowledge.
> > > >
> > > >
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> > > >
> > > > OVERALL I think I'm getting closer to the issues but I still feel as
> if I'm missing some understanding to proceed further. Can you pass along
> some of that Dondi insight and steer me in the right direction? =D
> > > >
> > > > -DB Tally - Not having taken databases yet certainly is limiting my
> ability determine where the "criteria" are being set and how they are
> followed during session activities. Also is the query we have been looking
> for this whole time in the criteria or someplace else?
> > > >
> > > > -XML Tally - again is the query contained within the criteria that
> digestXmlFile() uses to parse?
> > > >
> > > > Richard
> > > >
> > > >
> > > > On Mon, Feb 7, 2011 at 5:50 PM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > Right, schema issues are unlikely.  Most count discrepancies like
> this that I've seen have boiled down to forming the right query.  Then,
> knowing the right query (in both XML and SQL), it's a matter of making sure
> that TallyEngine asks that same query.
> > > >
> > > > John David N. Dionisio, PhD
> > > > Associate Professor, Computer Science
> > > > Loyola Marymount University
> > > >
> > > >
> > > > On Feb 7, 2011, at 5:48 PM, Richard Brous wrote:
> > > >
> > > > > OK, so based on your approach:
> > > > >
> > > > > 1. I'll start with reviewing the queries for xmlpipedb-match and
> sql queries needed for the respective results as you requested.
> > > > >
> > > > > I was also thinking I may need to review the schema from xml into
> postgres but the issue isn't likely a schema error. The error most likely
> lies in how xmlpipedbutils queries the data from xml source and writes to
> the tables what it returns?
> > > > >
> > > > > 2. I'll review the code: trace the entrance of tally engine in the
> gmbuilder code then follow it through the xmlpipedbutils.
> > > > >
> > > > > Richard
> > > > >
> > > > > On Sat, Feb 5, 2011 at 10:28 AM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > > Just wanted to confirm (since I wasn't sure in the first e-mail)
> --- the XMLPipeDB Utilities source code is in trunk/xmlpipedbutils in
> SourceForge's Subversion repo.
> > > > >
> > > > > John David N. Dionisio, PhD
> > > > > Associate Professor, Computer Science
> > > > > Loyola Marymount University
> > > > >
> > > > >
> > > > >
> > > > > On Feb 5, 2011, at 10:02 AM, Richard Brous wrote:
> > > > >
> > > > > > Hi Dondi,
> > > > > >
> > > > > > So I'm at the point in working with M tuberculosis that I was
> able to exactly reproduce Dr. Dahlquist's problematic TallyEngine results.
> > > > > >
> > > > > > gmb2b60 Results
> > > > > >
> > > > > >
> > > > > >
> > > > > > Now the proverbial question - What next to solve the Ordered
> Locus import/count issue?
> > > > > >
> > > > > > **********************************************
> > > > > > Here is my thought process:
> > > > > >
> > > > > > Step 1: How does the import process work at the high level?
> (obviously correct me if I'm wrong)
> > > > > >
> > > > > > I believe that basically as each XML tag is read, it is placed in
> the proper Postgres table(s) based on some criteria. There is also likely
> some sort of check that each individual tag is in valid XML format unless we
> don't care at this stage (care at export) or maybe the parser just skips
> over and goes on to the next .
> > > > > >
> > > > > > Step 2: What could be the problem?
> > > > > >
> > > > > > Either -
> > > > > > a. XML tags are being parsed incorrectly (ignored/skipped)?
> > > > > > b. Decision criteria of which table they should be added to?
> > > > > >
> > > > > > **********************************************
> > > > > >
> > > > > > I read on the sourceforge wiki:
> > > > > >
> > > > > > XMLPipeDB has a modular architecture with three components that
> may be used separately or together. XSD-to-DB reads an XSD (XML Schema
> Definition) and automatically generates an SQL schema, Java classes, and
> Hibernate mappings. XMLPipeDB Utilities provides functionality for
> configuring the database, importing data, and performing queries. GenMAPP
> Builder is based on the XMLPipeDB Utilities and exports GenMAPP-compatible
> Gene Databases based on data from UniProt and Gene Ontology (GO).
> > > > > >
> > > > > > So I should probably start with the XMLPipeDB Utilities which are
> where? I don't see any in the basic distribution or are they not standalone
> and called from the command line?
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > Richard
> > > > >
> > > > >
> > > > > <ATT00001..txt><ATT00002..txt>
> > > >
> > > >
> > > >
> ------------------------------------------------------------------------------
> > > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
> XE:
> > > > Pinpoint memory and threading errors before they happen.
> > > > Find and fix more than 250 security defects in the development cycle.
> > > > Locate bottlenecks in serial and parallel code that limit
> performance.
> > > > http://p.sf.net/sfu/intel-dev2devfeb
> > > > _______________________________________________
> > > > xmlpipedb-developer mailing list
> > > > xml...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > > >
> > > > <ATT00001..txt><ATT00002..txt>
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
> XE:
> > > Pinpoint memory and threading errors before they happen.
> > > Find and fix more than 250 security defects in the development cycle.
> > > Locate bottlenecks in serial and parallel code that limit performance.
> > > http://p.sf.net/sfu/intel-dev2devfeb
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> >
> ------------------------------------------------------------------------------
> > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> > Pinpoint memory and threading errors before they happen.
> > Find and fix more than 250 security defects in the development cycle.
> > Locate bottlenecks in serial and parallel code that limit performance.
> > http://p.sf.net/sfu/intel-dev2devfeb
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>