Re: [XMLPipeDB-developer] GM Builder post taxon merge
                
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      From: Richard B. <rbr...@gm...> - 2011-04-15 06:40:55
      
     | 
| also seems for some reason the fall 2010 class wiki isn't taking any of my
uploads. I'm recieving an error message saying that:
Could not rename file "/tmp/php25Gyfr" to
"public/f/f8/Mtuberculosis_OriginalRowCounts_b63_vs_b64.xls".
and it is happening for all files now...
Will send a message to Masao to see if he can check it out.
Richard
On Thu, Apr 14, 2011 at 11:22 PM, Richard Brous <rbr...@gm...> wrote:
> Well that seemed to do the trick as I was able to export out a
> Mtuberculosis gdb which is very close to our baseline gdb from b63. I will
> post both gdb's onto the wiki along with an excel doc comparison of the
> original row counts.
>
> But I'm still unclear exactly why using the general species taxon id would
> work and the taxon id for our specific species would not work?
>
> Maybe I'm still a bit weak in my understanding, but it seemed to me that
> what we wanted to do was identify the species by its taxon id to eliminate
> issues with potentially different, non-exact spellings (and tracking) of
> particual species names.
>
> Can someone clarify please? ;-D
>
> Thanks!
>
> Richard
>
>   On Thu, Apr 14, 2011 at 8:51 PM, Richard Brous <rbr...@gm...>wrote:
>
>>  No intrusion Don =D
>>
>> Thanks for the suggestion. I'll give it a try and let the distribution
>> know the findings.
>>
>> Richard
>>
>> Sent from my iPhone
>>
>> On Apr 14, 2011, at 7:07 PM, Don Murphy <djs...@gm...> wrote:
>>
>>  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
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>>>> >>>>>>>> _______________________________________________
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>>>> >>>>>>
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>>>> >>>
>>>> >>>
>>>> ------------------------------------------------------------------------------
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>>>> >>> <Tb_export_screen.jpg><ATT00001..txt><ATT00002..txt>
>>>> >>
>>>> >>
>>>> >>
>>>> ------------------------------------------------------------------------------
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>>>> Report as
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>>>> providers.
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>>>> >
>>>> >
>>>> >
>>>> ------------------------------------------------------------------------------
>>>> > 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
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