Re: [XMLPipeDB-developer] GM Builder post taxon merge

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

I have added all the taxon id's to beta64 and posted it to the  GMBuilder
branch 'name2taxon'
merge<https://www.cs.lmu.edu/biodb/fall2010/index.php/GMBuilder_branch_%27name2taxon%27_merge>
 page.

Still working on sourcing the query issue surrounding the missing ids.

Richard

On Wed, Apr 20, 2011 at 1:54 PM, Richard Brous <rbr...@gm...> wrote:

> Completed exports for Msmegmatis and the comparison between b63 and b64
> show that the gdb's are idential in regards to original row counts!
>
> We have one species off the list!
>
> Richard
>
>   On Wed, Apr 20, 2011 at 12:03 PM, Richard Brous <rbr...@gm...>wrote:
>
>> OK, couple things.
>>
>> 1.
>> Spoke with Dr. D regarding Mtuberculosis and it seems the reason 1773 is
>> specified in the xml is that there has been much legacy work done with Mt
>> and it is referenced to the general taxon id, not the particular strains
>> which may have a more recent taxon id. That said, (and per Don's
>> observation) the species profile was adjusted to 1773 from the taxon id
>> reported in the released gdb readme. Export wizard did recognize the species
>> by the 1773 id and exported completed successfully.
>>
>> 2.
>> I have added taxon id's to the following species using the information
>> posted by Dr. D to date on the GMBuilder branch 'name2taxon' merge<https://www.cs.lmu.edu/biodb/fall2010/index.php/GMBuilder_branch_%27name2taxon%27_merge>page:
>> Msmegmatis = 246196
>> Mtuberculosis = 1773
>> Pfalciparum = 36329 (xml also references taxon id 5833)
>> Vcholerae = 666
>> Hpylori = 210
>>
>> Don's code was tested with the following two species:
>> Paeruginosa = 287
>> Saureus = 282458
>>
>> 3.
>> Performed comparison analysis between b63 and b64 (post name2taxon merge)
>> for the following species:
>> Mtuberculosis - excel comparison linked to page
>> Pfalciparum - excel comparison linked to page
>> Msmegmatis - underway atm
>>
>> **overall the general pattern seems to be that the beta 64 version of
>> GMBuilder is exporting slightly less id's in each category when compared
>> with b63 baseline gdbs.**
>>
>> I'm hopeful that the fix is global which will correct for all species as
>> opposed to individual tweaks for each species... but we shall see.
>>
>> Richard
>>
>>
>> On Fri, Apr 15, 2011 at 12:04 AM, Richard Brous <rbr...@gm...>wrote:
>>
>>> No, unfortunetely i haven't done the query or looked at the original xml
>>> file yet but those will be my first steps when I start digging into this
>>> again tomorrow.
>>>
>>> Richard
>>>
>>>   On Thu, Apr 14, 2011 at 11:38 PM, John David N. Dionisio <
>>> do...@lm...> wrote:
>>>
>>>> Hi Rich,
>>>>
>>>> Did you do the aforementioned "lower level" investigation, which was to
>>>> query all of the available taxon IDs directly from PostgreSQL, to see what
>>>> taxon IDs were there?
>>>>
>>>> Alternatively, you can look at the original UniProt XML file that was
>>>> imported into PostgreSQL, and examine the taxon IDs in that file.
>>>>
>>>> Essentially, the program won't match a species profile if that species
>>>> profile's declared taxon ID cannot be found in the relational database.  So,
>>>> you need to know what taxon IDs found their way into the relational database
>>>> to begin with, then work from there.
>>>>
>>>> John David N. Dionisio, PhD
>>>> Associate Professor, Computer Science
>>>> Loyola Marymount University
>>>>
>>>>
>>>>
>>>>  On Apr 14, 2011, at 11:22 PM, Richard Brous 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>
>>>> >> >>>>>>>>
>>>> >> >>>>>>>>
>>>> >> >>>>>>>>
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>>>> >> >>> 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
>>>> >>
>>>> >>
>>>> >>
>>>> ------------------------------------------------------------------------------
>>>> >> Benefiting from Server Virtualization: Beyond Initial Workload
>>>> >> Consolidation -- Increasing the use of server virtualization is a top
>>>> >> priority.Virtualization can reduce costs, simplify management, and
>>>> improve
>>>> >> application availability and disaster protection. Learn more about
>>>> boosting
>>>> >> the value of server virtualization.
>>>> http://p.sf.net/sfu/vmware-sfdev2dev
>>>> >> _______________________________________________
>>>> >> xmlpipedb-developer mailing list
>>>> >> xml...@li...
>>>> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>> >>
>>>> >>
>>>> >>
>>>> ------------------------------------------------------------------------------
>>>> >> Benefiting from Server Virtualization: Beyond Initial Workload
>>>> >> Consolidation -- Increasing the use of server virtualization is a top
>>>> >> priority.Virtualization can reduce costs, simplify management, and
>>>> improve
>>>> >> application availability and disaster protection. Learn more about
>>>> boosting
>>>> >> the value of server virtualization.
>>>> http://p.sf.net/sfu/vmware-sfdev2dev
>>>> >> _______________________________________________
>>>> >> xmlpipedb-developer mailing list
>>>> >> xml...@li...
>>>> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>> >
>>>> > <ATT00001..txt><ATT00002..txt>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Benefiting from Server Virtualization: Beyond Initial Workload
>>>> Consolidation -- Increasing the use of server virtualization is a top
>>>> priority.Virtualization can reduce costs, simplify management, and
>>>> improve
>>>> application availability and disaster protection. Learn more about
>>>> boosting
>>>> the value of server virtualization.
>>>> http://p.sf.net/sfu/vmware-sfdev2dev
>>>> _______________________________________________
>>>> xmlpipedb-developer mailing list
>>>> xml...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>>
>>>
>>>
>>
>