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: Don M. <djs...@gm...> - 2011-04-15 02:07:40
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Forgive my intrusion, but I have an idea of what may be the problem. In the
screenshot you provided, the only species shown in the drop down box, as
taken from the source files, is taxon id 1773. An quick Google search
reveals that 1773 is the general taxon id for Mycobacterium tuberculosis. In
the profile you created, the taxon id used is 83332, which is for M.
tuberculosis strain H37Rv. The problem seems to be that the profile you
created was for the certain strain, while your source files were for M.
tuberculosis in general. Try changing the profile to use the id 1773 and see
if that helps.
On Thu, Apr 14, 2011 at 6:53 PM, Richard Brous <rbr...@gm...> wrote:
> OK, found the method and reviewed it.
>
> It makes sense and I believe it should work as is unless I'm reading the
> code wrong.
>
> I don't see how if the taxon id is included in the Mtuberculosis species
> profile (which it is) why this shouldn't work?
>
> Help please, what am i missing?
>
> richard
>
> On Thu, Apr 14, 2011 at 11:04 AM, Richard Brous <rbr...@gm...>wrote:
>
>> Gotcha, will check it out later today as well as post gdb's up to the
>> wiki.
>>
>> Rb
>>
>> Sent from my iPhone
>>
>> On Apr 13, 2011, at 11:32 AM, "John David N. Dionisio" <do...@lm...>
>> wrote:
>>
>> > Greetings,
>> >
>> > Sorry for the delay; I ended up digging through the code a bit so I
>> would be sure of the response.
>> >
>> > getSpeciesProfilesFound does indeed feed the combo box that you want to
>> touch, but it turns out that the array returned by this method is not built
>> here.
>> >
>> > The code that builds the array returned by getSpeciesProfilesFound is
>> located in UniProtDatabaseProfile; the method is called checkRequirements.
>> This is the method that performs the query which retrieves the available
>> taxon IDs from the relational database.
>> >
>> > The intent of the method is this: if a custom species profile is found
>> that matches the taxon ID, then that species profile is added to the list.
>> If a custom species profile is *not* found, a generic species profile
>> initialized to the taxon ID is added instead.
>> >
>> > That is the method's intent. As you have seen, it may need some cleanup
>> and/or fixing. But there it is for you:
>> UniProtDatabaseProfile.checkRequirements.
>> >
>> > John David N. Dionisio, PhD
>> > Associate Professor, Computer Science
>> > Loyola Marymount University
>> >
>> >
>> >
>> > On Apr 12, 2011, at 7:03 PM, Richard Brous wrote:
>> >
>> >> OK, in ExportPanel1.java i found the following:
>> >>
>> >> 1. COMBOBOX DEFINED ON LINE 59
>> >> private
>> >>
>> >> JComboBox speciesComboBox;
>> >> 2. THEN COMBOBOX IS INSTANTIATED AND ACTION LISTENER ASSIGNED STARTING
>> ON LINE 141
>> >>
>> >> // Species | JComboBox | speciesFound | JLabel | Description
>> >>
>> >>
>> >> // | JTextField | customizable name
>> >>
>> >> speciesComboBox = new JComboBox();
>> >>
>> >> speciesComboBox.addActionListener(new ActionListener() {
>> >>
>> >> public void actionPerformed(ActionEvent arg0) {
>> >> speciesProfileSelected(
>> >>
>> >> speciesComboBox.getSelectedItem());
>> >> }
>> >>
>> >> });
>> >>
>> >> 3. NEXT CODE BLOCK ADJUSTS THE DATABASE PROFILE WHICH IS ALWAYS
>> UNIPROT, THEN BASED ON DATABASE PROFILE
>> >> IT POPULATES THE SPECIES COMBOBOX STARTING LINE 210
>> >>
>> >>
>> >> * Adjusts the dynamic content when a database profile is selected.
>> >>
>> >> *
>> >>
>> >> *
>> >>
>> >> @param selectedItem
>> >> */
>> >>
>> >>
>> >> protected void databaseProfileSelected(Object selectedItem) {
>> >>
>> >> if (selectedItem instanceof DatabaseProfile) {
>> >> DatabaseProfile selectedProfile = (DatabaseProfile)selectedItem;
>> >>
>> >> ExportToGenMAPP.setDatabaseProfile(selectedProfile);
>> >>
>> >>
>> >> profileDescriptionTextArea.setText(selectedProfile.getDescription());
>> >>
>> >> modSystemTextField.setText(selectedProfile.getMODSystem());
>> >>
>> >>
>> >> //This is populating the list of items in the speciesProfile combobox
>> >>
>> >> // based on what database was selected.
>> >>
>> >> speciesComboBox.removeAllItems();
>> >>
>> >> for (SpeciesProfile speciesProfile :
>> selectedProfile.getSpeciesProfilesFound()) {
>> >>
>> >> speciesComboBox.addItem(speciesProfile);
>> >> }
>> >>
>> >> }
>> >>
>> >> }
>> >>
>> >> SO I THINK THE METHOD I NEED TO SOURCE IS:
>> selectedProfile.getSpeciesProfilesFound())
>> >>
>> >> SOUND GOOD SO FAR??
>> >>
>> >> Richard
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Tue, Apr 12, 2011 at 6:18 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> >>
>> >> 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
>> >>>>>>>> Use the most popular FREE web apps or write code yourself;
>> >>>>>>>> WebMatrix provides all the features you need to develop and
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>> >>>>>>>> _______________________________________________
>> >>>>>>>> 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>
>> >>>>
>> >>>>
>> >>>>
>> ------------------------------------------------------------------------------
>> >>>> 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
>> 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
>> >>>
>> >>>
>> >>
>> >>> <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
>> >>
>> >>
>> >>
>> >> <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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