Re: [XMLPipeDB-developer] GM Builder post taxon merge
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From: Richard B. <rbr...@gm...> - 2011-04-28 01:09:13
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Lets discuss tomorrow during our call at 12:30pm... Dr. D mentioned she might not be back from an appointment so I can either call you on your cell or you can call mine. The species change I'm sure is doable but I'm concerned about adding that right at the end of the semester... finals start next week and I was hoping that we were winding down. I want to be able to commit to specific deliverables by end of this week, then have time to write up my paper recounting the semester. Richard On Wed, Apr 27, 2011 at 5:23 PM, John David N. Dionisio <do...@lm...>wrote: > Greetings, > > Yes, I would say that this moves the multiple taxon ID support issue up the > pipeline. This means that the species profiles should produce collections > of taxon IDs instead of a single one, and that all SQL queries extracting > taxon ID data should be in the form of "taxonid in ('nnnn', 'oooo', ....)" > or "(taxonid = 'nnnn') or (taxonid = 'oooo') or ...." The former is more > readable but might be specific to PostgreSQL --- you can do a quick search > of the SQL specification and/or PostgreSQL documentation to verify. > > There are some implications to this change when multiple species are loaded > into the same relational database. For example, what if a user loaded > species A and species B into the database, both of which have species > profiles, where species A has taxon IDs 1 and 2, while species B has taxon > IDs 2 and 3? An export based on "taxonid = '1' or taxonid = '2'" will mix > in some species B records, and vice versa for "taxonid = '2' or taxonid = > '3'" and species A records. > > This aspect may be worth further discussion, though I don't think it is a > blocker issue, as after all it is a very specific combination of > circumstances. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Loyola Marymount University > > > On Apr 27, 2011, at 5:11 PM, Richard Brous wrote: > > > 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> > > > >> >>>>>>>> > > > >> >>>>>>>> > > > >> >>>>>>>> > ------------------------------------------------------------------------------ > > > >> >>>>>>>> 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 > > > >> >> > > > >> >> > > > >> >> > > > >> >> <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. 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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. 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