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

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

OK, here is the deal with Pfalciparum:

5 Uniprot ids are missing from the b64 export of Pfalciparum gdb.
The gdb export was done using taxon id = 36329


Using excel match I located the following 5 UniProt ids:

   Q25820 O00806 P21421 P21422 Q25802

These UniProt ids are attached to the other taxon id = 5833 which is why
they were excluded.

How would you like to proceed forward on this for the short term?

Should I modify the XML to replace any instance of taxon id = 5833 with
taxon id = 36329?

I expect it would capture all the ids when exporting to *.gdb.

As previously discussed it seems that we may need to solve the multiple
strains/taxon ids issue sooner rather than later.

Richard


On Wed, Apr 27, 2011 at 4:11 PM, Richard Brous <rbr...@gm...> wrote:

> Surfaced the missing Ordered Locus id's for Mtuberculosis and noticed
> that I must have excluded the previous query changes I made during the
> merge... which is why the counts were off. I corrected this error and am
> running an export now, then will update the status.
>
> Will start on the Uniprot id issue for Pfalciparum next.
>
> Richard
>
>   On Mon, Apr 25, 2011 at 5:33 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> Hi Rich,
>>
>> Thanks for the various updates.  My main question on the ID differential
>> is --- have you tried issuing the SQL queries directly in PostgreSQL, and
>> comparing results between the original, non-taxon-ID-filtering queries and
>> the new, taxon-ID-filtering ones?  That's where I would start.  The former
>> type of query must necessarily be based on a single-species database, so
>> hopefully you still have those lying around.
>>
>> You can potentially also do comparisons at the XML level --- look for
>> blocks that don't have a taxon ID tag, or have a different taxon ID value.
>>  But I think you'll be closer to home if you start at PostgreSQL.
>>
>> Hope this helps...
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>>
>>  On Apr 25, 2011, at 1:55 PM, Richard Brous wrote:
>>
>> > I have added all the taxon id's to beta64 and posted it to the
>>  GMBuilder branch 'name2taxon' 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 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
>> > >> >>>>>>>>
>> > >> >>>>>>>> <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
>> > >>
>> > >>
>> > >>
>> ------------------------------------------------------------------------------
>> > >> 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
>> >
>> >
>> >
>> >
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>>  _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>
>