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 02:03:28
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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
>> > > > > > > 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>
>> > >
>> > >
>> > >
>> ------------------------------------------------------------------------------
>> > > 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
>>
>>
>
>
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