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

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

ah yes... i see it...

On Mon, Feb 21, 2011 at 9:33 PM, John David N. Dionisio <do...@lm...>wrote:

>  Watch your parentheses: "and" has greater precedence than "or" :)
>
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Feb 21, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
>
>   OK, so here are my query results from raw SQL:
>
> 1. using: like 'Rv%'
>
> select count (*) from genenametype where type = 'ordered locus' and value
> like 'Rv%';
> returns 3988
>
> select count (*) from genenametype where type = 'ORF' and value like 'Rv%';
> returns 70
>
> select count (*) from genenametype where type = 'ordered locus' or type =
> 'ORF' and value like 'Rv%';
> returns 7011
>
> 2. regular expression : value ~ '[Rr][Vv][0-9][0-9][0-9][0-9]*'
>
> select count (*) from genenametype where type = 'ordered locus' and value ~
> '[Rr][Vv][0-9][0-9][0-9][0-9]*';
> returns 3988
>
> select count (*) from genenametype where type = 'ordered locus' or type =
> 'ORF' and value ~ '[Rr][Vv][0-9][0-9][0-9][0-9]*';
> returns 7011
>
> select count (*) from genenametype where type = 'ORF' and value ~
> '[Rr][Vv][0-9][0-9][0-9][0-9]*';
> returns 70
>
> Conclusions:
>
> 1. It seems that querying for type = 'ORF' alone surfaces the 69 genes were
> were looking for plus one more (maybe the count for missing genes is off
> by 1?).
>
> 2. Combining the two types in a single query did not produce the results
> that I expected (7011? - how did that happen????) so this is likely not our
> solution... unless of course the query syntax isn't actually doing what I
> think it is...
>
> 3. I would think the best course of action is to serialy run two separate
> queries to capture all the required genes, then removing the one unneeded
> gene if its truly not wanted.
>
> What do you think?
>
> Richard
>
>
> On Mon, Feb 21, 2011 at 5:17 PM, John David N. Dionisio <do...@lm...>wrote:
>
>>  I don't recall the exact details of the missing 69, but if your query
>> successfully returns them in raw SQL, then this is worth a try.  You can
>> integrate into the same query as long as the same columns are returned,
>> which is the case here AFAIK, so go ahead and extend the existing query.
>>
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>   On Feb 21, 2011, at 6:56 PM, Richard Brous <rbr...@gm...> wrote:
>>
>>   So here is the appropriate code snippet from
>> MycobacteriumTuberculosisUniProtSpeciesProfile.java:
>>
>> *
>>
>> public
>> *TableManager getSystemTableManagerCustomizations(TableManager
>> tableManager, TableManager primarySystemTableManager, Date version) *
>> throws* SQLException, InvalidParameterException {
>>
>> // Build the base query; we only use "ordered locus" and we only want
>>
>> // IDs that begin with "*Rv*."
>>
>> PreparedStatement ps = ConnectionManager.*getRelationalDBConnection*
>> ().prepareStatement(
>> "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
>> = ?");
>>
>> ResultSet result;
>>
>> *for* (Row row : primarySystemTableManager.getRows()) {
>>
>> ps.setInt(1, Integer.*parseInt*(row.getValue(
>> "UID")));
>>
>> result = ps.executeQuery();
>>
>> // We actually want to keep the case where multiple ordered locus
>>
>> // names appear.
>>
>> *while* (result.next()) {
>>
>> // We want this name to appear in the OrderedLocusNames
>>
>> // system table.
>>
>> *for* (String id : result.getString("value").split("/")) {
>>
>> tableManager.submit(
>> "OrderedLocusNames", QueryType.*insert*, *new* String[][] { { "ID", id },
>> { "Species", "|" + getSpeciesName() + "|" }, { "\"Date\"",
>> GenMAPPBuilderUtilities.*getSystemsDateString*(version) }, { "UID",
>> row.getValue("UID") } });
>>
>> }
>>
>> }
>>
>> }
>>
>>
>>  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> So now we want to build the base query which uses "ordered locus" and
>> "orf" and we only want IDs that begin with "Rv".
>>
>> I know there are more comprehensive ways to search for gene ID's
>> by matching gene ID prefix but "like Rv%" seemed to work thus far, we just
>> need to tell it to search for XML tag type orf in addition to ordered locus.
>>
>> "WHERE type = 'ordered locus' and type = 'orf' and value like 'Rv%' and
>> entrytype_gene_hjid = ? "
>>
>> Here is a stab at it.... This part of our class was right as the server
>> went down and my submission for week 6 assignment I can't seem to find.
>>
>> Is it possible to have two different types in the same query or should we
>> rewrite a separate query for the orf tag?
>>
>> Richard
>>
>>
>>
>> On Sun, Feb 20, 2011 at 10:21 PM, Richard Brous < <rbr...@gm...>
>> rbr...@gm...> wrote:
>>
>>
>>> 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...>
>>> 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...>
>>>> 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...>
>>>> 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...>
>>>> 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...>
>>>> 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...>
>>>> 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...>
>>>> 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>
>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>> > > > _______________________________________________
>>>> > > > xmlpipedb-developer mailing list
>>>> > > > <xml...@li...>
>>>> xml...@li...
>>>> > > >
>>>> <https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer>
>>>> 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>
>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>> > > _______________________________________________
>>>> > > xmlpipedb-developer mailing list
>>>> > > <xml...@li...>
>>>> xml...@li...
>>>> > > <https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer>
>>>> 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>
>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>> > _______________________________________________
>>>> > xmlpipedb-developer mailing list
>>>> > <xml...@li...>
>>>> xml...@li...
>>>> > <https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer>
>>>> 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>
>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>> _______________________________________________
>>>> xmlpipedb-developer mailing list
>>>>  <xml...@li...>
>>>> xml...@li...
>>>>  <https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer>
>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>>
>>>>
>>>
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Index, Search & Analyze Logs and other IT data in Real-Time with Splunk
>> Collect, index and harness all the fast moving IT data generated by your
>> applications, servers and devices whether physical, virtual or in the
>> cloud.
>> Deliver compliance at lower cost and gain new business insights.
>> Free Software Download: <http://p.sf.net/sfu/splunk-dev2dev>
>> http://p.sf.net/sfu/splunk-dev2dev
>>
>>  _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Index, Search & Analyze Logs and other IT data in Real-Time with Splunk
>> Collect, index and harness all the fast moving IT data generated by your
>> applications, servers and devices whether physical, virtual or in the
>> cloud.
>> Deliver compliance at lower cost and gain new business insights.
>> Free Software Download: http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>>
>
> ------------------------------------------------------------------------------
> Index, Search & Analyze Logs and other IT data in Real-Time with Splunk
> Collect, index and harness all the fast moving IT data generated by your
> applications, servers and devices whether physical, virtual or in the
> cloud.
> Deliver compliance at lower cost and gain new business insights.
> Free Software Download: http://p.sf.net/sfu/splunk-dev2dev
>
>  _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> ------------------------------------------------------------------------------
> Index, Search & Analyze Logs and other IT data in Real-Time with Splunk
> Collect, index and harness all the fast moving IT data generated by your
> applications, servers and devices whether physical, virtual or in the
> cloud.
> Deliver compliance at lower cost and gain new business insights.
> Free Software Download: http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>