Re: [XMLPipeDB-developer] GM Builder post taxon merge
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Re: [XMLPipeDB-developer] GM Builder post taxon merge
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From: Richard B. <rbr...@gm...> - 2011-04-13 01:18:13
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OK, I'll look around and attempt to sniff out the code regarding populating
the drop down menu on the first export screen.
But that said, I was surprised it didn't work since the functionality
'seemed' to be in place for the two working species (P_a and S_a). And I
noticed that the working species don't always show in the drop down box, so
figured they likely aren't hard coded in.
Richard
On Tue, Apr 12, 2011 at 6:04 PM, John David N. Dionisio <do...@lm...>wrote:
> Greetings,
>
> First off, recall that the taxon ID that is given to the species profile is
> not involved in building the dropdown menu; it is used to match the chosen
> taxon ID from that menu with a species profile to use. That dropdown menu
> is built from a database query that retrieves all available taxon IDs and
> species names in the PostgreSQL database.
>
> With that in mind, I would tackle this as follows:
>
> - First, track down the code that builds the data displayed in that
> JComboBox. It should be trackable from the wizard panel code. If you're
> having trouble finding it, let me know and I can take a stab at following
> the breadcrumbs, or you can ask Don.
>
> This code should ultimately lead you to the database query that derives the
> overall list of available taxon IDs and species names in the PostgreSQL
> database.
>
> - Now, armed with this database query, you can verify the validity of this
> query directly in PostgreSQL. Essentially you need to make sure that this
> query does indeed retrieve the list of all taxon IDs and species names that
> are present in the PostgreSQL database.
>
> If the query is correct, then the issue is in the way the JComboBox is put
> together. This may need a little more knowledge of Swing that you have, in
> which case send the issue my way and I can take a look.
>
> If the query is incorrect, then it should be corrected. If the Swing code
> is correct, then things should work. If the Swing code is also incorrect,
> then you are at the previous case, and the Swing code now needs to be
> addressed (safe in the knowledge that the data part has been fixed).
>
> Let me know how that plan sounds to you.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Apr 12, 2011, at 5:56 PM, Richard Brous wrote:
>
> > Great, glad we are on the same page!
> >
> > I went ahead and added the taxon id to the Mtuberculosis species profile,
> recompiled and initiated an export but the expected taxon id didn't show in
> the species drop down box.
> >
> > The coded modified is (as shown above):
> >
> >
> > public MycobacteriumTuberculosisUniProtSpeciesProfile() {
> >
> > super("Mycobacterium tuberculosis", 83332,
> >
> > "This profile customizes the GenMAPP Builder export for Mycobacterium
> Tuberculosis data loaded from a UniProt XML file.");
> > }
> >
> > Attached is a ss of the dialog box.
> >
> > I also checked to make sure the species was listed in the
> UniProtDatabaseProfile and Mtuberculosis and the rest of the newer species
> are present.
> >
> > Any idea where i should look next aside from assuring that the change is
> actually in my working build?
> >
> > Thanks!
> >
> > Richard
> >
> >
> >
> >
> > On Tue, Apr 12, 2011 at 3:40 PM, John David N. Dionisio <do...@lm...>
> wrote:
> >
> > Hi Rich,
> >
> > Thanks for the update. I agree that we can move past the merge stage
> now.
> >
> > Regarding the species constructor, yes, having the required change
> consist solely of the addition of the taxon ID really was the goal.
> "Separation of concerns" and "don't repeat yourself" and all that :) Note
> how, in the end, the designation of the taxon ID is truly the only piece of
> additional information that is required of species profiles in order to get
> the work done. So, this ideal is reflected in the code.
> >
> > Of course, there is a possibility that certain types of customizations
> may require additional work; however that depends on the type of
> customization involved and the way the species profile implements it. We
> can approach those on a per-species-profile basis.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> >
> >
> > On Apr 11, 2011, at 11:57 PM, Richard Brous wrote:
> >
> > > Hi all,
> > >
> > > I recreated a multispecies postgres db for P_aeruginosa and S_aureus
> and reimported the species xml files:
> > > P_aeruginosa UniProtXML
> > > P_aeruginosa goa
> > >
> > > S_aureus UniProtXML
> > > S_aureus goa
> > >
> > > GO xml
> > > processed go data
> > >
> > > I then exported P_aeruginosa .gdb using both Don's name2taxon code and
> the new trunk (b64): both gdb's original row counts are identical
> > > Also exported S_aureus using both Don's name2taxon code and the new
> trunk (b64) : both gdb's original row counts are identical
> > >
> > > I think we can safely say that Don's name2taxon changes are working at
> the point where he left off and the successful merge into the trunk is now
> verfied.
> > >
> > >
> =============================================================================
> > >
> > > Now to move to species I am familiar with and ensure they still match
> the base line gdb's generated from b63.
> > >
> > > The first species I will work on is Mtuberculosis. From the readme file
> of the gdb previously posted, the taxon id is 83332.
> > >
> > > I will go ahead and make the change to the Mtuberculosis species
> profile which is to add the taxon id in the form:
> > >
> > >
> > > public MycobacteriumTuberculosisUniProtSpeciesProfile() {
> > >
> > > super("Mycobacterium tuberculosis", 83332,
> > >
> > > "This profile customizes the GenMAPP Builder export for Mycobacterium
> Tuberculosis data loaded from a UniProt XML file.");
> > > }
> > >
> > > When comparing to S_aereus species profile, it was the only change to
> make in the Mtuberculosis species profile.
> > >
> > > I rechecked my notes from this morning and don't see any other changes
> needed to enable our newer species to work with the post merge constructor.
> > >
> > > I'll attempt an export tomorrow and see what happens.
> > >
> > > Richard
> > >
> > > On Fri, Apr 1, 2011 at 12:51 PM, John David N. Dionisio <do...@lm...>
> wrote:
> > > Follow the way the name2taxon “branch” was done. Put a gmbuilder/
> directory under tags/ if it is not already there, and make sure that the
> copied/tagged/branched subdirectory under that corresponds to the top-level
> directory of a gmbuilder project (i.e., it contains the build.xml, other
> top-level directories, etc.).
> > >
> > > Subversion copies are “cheap:” it is OK to copy deep trees of files.
> You only start using additional storage space if the files themselves get
> modified. Otherwise, they are just references to their original versions.
> > >
> > > John David N. Dionisio, PhD
> > > Associate Professor, Computer Science
> > > Loyola Marymount University
> > >
> > >
> > >
> > > On Apr 1, 2011, at 12:47 PM, Richard Brous wrote:
> > >
> > > > ok, so should I start at the gmbuilder directory Or the src
> directory?
> > > >
> > > > On Fri, Apr 1, 2011 at 11:42 AM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > Yes, in Subversion what they did is collapse both activities into a
> single operation called "Copy." Whether you use the copy as a branch for
> modifications, or use it as a tag for posterity, is left to the developer
> and not the system.
> > > >
> > > > This functional change is the subject of some debate in the
> community. Some folks still feel that "enforced" tags have their benefits.
> But in the end, this is how Subversion conducts things, so we'll just have
> to go with it.
> > > >
> > > > John David N. Dionisio, PhD
> > > > Associate Professor, Computer Science
> > > > Loyola Marymount University
> > > >
> > > >
> > > > On Apr 1, 2011, at 12:38 PM, Richard Brous wrote:
> > > >
> > > > > ok, makes sense because when I went through the process (without
> clicking finish) there was really no difference between the two... not even
> a specification to say this this is a "tag" vs "branch" unless I can only do
> that in the comments.
> > > > >
> > > > > On Fri, Apr 1, 2011 at 11:35 AM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > > Yes, tags and branches are structurally identical in Subversion.
> The only difference between a “tag” and a “branch” is that the developers
> have agreed to *not* touch a tag after it has been copied out.
> > > > >
> > > > > In other words, “tags” and “branches” are only different in
> Subversion by consensus. The distinction is not system-enforced.
> > > > >
> > > > > John David N. Dionisio, PhD
> > > > > Associate Professor, Computer Science
> > > > > Loyola Marymount University
> > > > >
> > > > >
> > > > >
> > > > > On Apr 1, 2011, at 12:32 PM, Richard Brous wrote:
> > > > >
> > > > > > tagging is really creating a new branch for posterity?
> > > > > >
> > > > > > On Fri, Apr 1, 2011 at 10:56 AM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > > > You'll want to tag from the repository, since your local copy has
> been modified. If you issue the tag command from the SVN Repository Viewing
> perspective, that should happen server-side.
> > > > > >
> > > > > > If you want to play it really safe, you can even do the tagging
> from a completely separate Eclipse workspace that does not have your local
> copies loaded up.
> > > > > >
> > > > > > John David N. Dionisio, PhD
> > > > > > Associate Professor, Computer Science
> > > > > > Loyola Marymount University
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Apr 1, 2011, at 11:54 AM, Richard Brous wrote:
> > > > > >
> > > > > > > Am I tagging in my local project or in the repository?
> > > > > > >
> > > > > > > On Fri, Apr 1, 2011 at 10:51 AM, John David N. Dionisio <
> do...@lm...> wrote:
> > > > > > > Hi Rich,
> > > > > > >
> > > > > > > I think it's OK to commit to the trunk, with one tweak for easy
> management: before committing, copy out ("tag") what is in the trunk right
> now, and put it in /tags/gmbuilder/before-name2taxon-merge (or something
> like that). This way, you have an easy basis for comparison if you need to
> go back to how the trunk was before name2taxon came along.
> > > > > > >
> > > > > > > Also, it will save some time if your before- and after- .gdbs
> are available. Running our own exports, while of course doable as you said,
> would require things like getting old versions, building them, etc.
> > > > > > >
> > > > > > > Happy digital forensics...
> > > > > > >
> > > > > > > John David N. Dionisio, PhD
> > > > > > > Associate Professor, Computer Science
> > > > > > > Loyola Marymount University
> > > > > > >
> > > > > > >
> > > > > > > On Apr 1, 2011, at 11:42 AM, Richard Brous wrote:
> > > > > > >
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > Started a new thread since this is Pfalciparum specific.
> > > > > > > >
> > > > > > > > I have double checked my manual merge to confirm that in fact
> my edits were correctly included for Mtuberculosis and Pfalciparum.
> > > > > > > >
> > > > > > > > So when running gdb exports for each I determined that in
> fact something broke in the merge.
> > > > > > > >
> > > > > > > > Before I start digging into this further I want to ask a
> couple questions:
> > > > > > > >
> > > > > > > > 1. Should I commit the changes up to Sourceforge yet or leave
> them locally on my laptop while troubleshooting? I know we can revert to
> earlier versions if needed but wanted to be sure we were all on same page.
> > > > > > > >
> > > > > > > > 2. I have before and after exports of Mtuberculosis and
> Pfalciparum on my laptop. Would you like me to post them for review or will
> you be running your own anyway?
> > > > > > > >
> > > > > > > > Richard
> > > > > > > > <ATT00001..txt><ATT00002..txt>
> > > > > > >
> > > > > > >
> > > > > > >
> ------------------------------------------------------------------------------
> > > > > > > Create and publish websites with WebMatrix
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> > > > > > > _______________________________________________
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> > > > > > > xml...@li...
> > > > > > >
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > > > > > >
> > > > > > > <ATT00001..txt><ATT00002..txt>
> > > > > >
> > > > > >
> > > > > >
> ------------------------------------------------------------------------------
> > > > > > Create and publish websites with WebMatrix
> > > > > > Use the most popular FREE web apps or write code yourself;
> > > > > > WebMatrix provides all the features you need to develop and
> > > > > > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> > > > > > _______________________________________________
> > > > > > xmlpipedb-developer mailing list
> > > > > > xml...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > > > > >
> > > > > > <ATT00001..txt><ATT00002..txt>
> > > > >
> > > > >
> > > > >
> ------------------------------------------------------------------------------
> > > > > Create and publish websites with WebMatrix
> > > > > Use the most popular FREE web apps or write code yourself;
> > > > > WebMatrix provides all the features you need to develop and
> > > > > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> > > > > _______________________________________________
> > > > > xmlpipedb-developer mailing list
> > > > > xml...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > > > >
> > > > > <ATT00001..txt><ATT00002..txt>
> > > >
> > > >
> > > >
> ------------------------------------------------------------------------------
> > > > Create and publish websites with WebMatrix
> > > > Use the most popular FREE web apps or write code yourself;
> > > > WebMatrix provides all the features you need to develop and
> > > > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> > > > _______________________________________________
> > > > xmlpipedb-developer mailing list
> > > > xml...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > > >
> > > > <ATT00001..txt><ATT00002..txt>
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > Create and publish websites with WebMatrix
> > > Use the most popular FREE web apps or write code yourself;
> > > WebMatrix provides all the features you need to develop and
> > > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> >
> ------------------------------------------------------------------------------
> > Forrester Wave Report - Recovery time is now measured in hours and
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> > not days. Key insights are discussed in the 2010 Forrester Wave Report as
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> vision.
> > Read this report now! http://p.sf.net/sfu/ibm-webcastpromo
> >
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <Tb_export_screen.jpg><ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Read this report now! http://p.sf.net/sfu/ibm-webcastpromo
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
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