xmlpipedb-developer — Mailing list for XMLPipeDB software development questions and discussions.

Re: [XMLPipeDB-developer] GenMAPP Builder Crashed

[Kam D. <kda...@lm...>]

Hi,

Kevin's second export from yesterday finished around 8:00 PM last 
night.  So probably it was the connection error that Dr. Dionisio described.

Best,
Dr. D

At 09:58 PM 3/11/2014, John David N. Dionisio wrote:
>Hi Kevin,
>
>OK, thank you for this.  I have a clarification question based on 
>this: Note in image (1) that the scroll bar is in the middle of the 
>window---that means there was more console output below the part 
>that you sent.  Was there more error information below the "... 9 
>more" line in that screenshot?  Or did you position the scroll bar 
>that way exactly because this was the error ended?
>
>If that "... 9 more" was the last line of the error report, then the 
>main thing I can determine from this is that some connectivity issue 
>with the database server took place.  Maybe someone closed pgAdmin 
>III by accident?  Or for some reason pgAdmin III quit 
>unexpectedly?  That is the scenario that the error implies.
>
>Now, if more error messages appeared below "... 9 more," then other 
>conclusions might be drawn.  But for the moment this looks like a 
>disconnection, and the main cause of that would be an unplanned 
>quitting of pgAdmin.  If this did indeed take place (pgAdmin 
>unexpectedly or unintentionally terminated), then it is safe to try 
>the export again---just make sure not to end pgAdmin.  But if 
>pgAdmin was still up and running...well, this will need more 
>investigation.  I'll take a look at the code when I make the next build.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Mar 11, 2014, at 12:41 PM, Kevin McGee <km...@li...> wrote:
>
> > Hey Dr. Dionisio,
> >
> > So while I was trying to export my database from GenMAPP builder, 
> it randomly crashed in the middle. I took a few pictures of the 
> command line window right up to where it crashed. I was wondering 
> if you could take a look at it and let me know why it happened.
> >
> > One note: I accidentally named the pictures in a confusing way. 
> Reading from the top of the command prompt window to the bottom, 
> the pictures I sent you should be read in the order 3,2,1. Sorry, I 
> only realized this after naming them this way.
> >
> > -Kevin
> > <Database Crash (1) 20140311.PNG><Database Crash (2) 
> 20140311.PNG><Database Crash (3) 
> 20140311.PNG>------------------------------------------------------------------------------
> > Learn Graph Databases - Download FREE O'Reilly Book
> > "Graph Databases" is the definitive new guide to graph databases and their
> > applications. Written by three acclaimed leaders in the field,
> > this first edition is now available. Download your free book today!
> > 
> http://p.sf.net/sfu/13534_NeoTech_______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>------------------------------------------------------------------------------
>Learn Graph Databases - Download FREE O'Reilly Book
>"Graph Databases" is the definitive new guide to graph databases and their
>applications. Written by three acclaimed leaders in the field,
>this first edition is now available. Download your free book today!
>http://p.sf.net/sfu/13534_NeoTech
>_______________________________________________
>xmlpipedb-developer mailing list
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>https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

Re: [XMLPipeDB-developer] No Use of the Capitalized Versions

[John D. N. D. <do...@lm...>]

OK, the all-caps LMJF id's might be old artifacts then.  We would need to wait on what Dr. Dahlquist finds about how GenMAPP handles LmjF IDs, but unfortunately this relies on a .gdb with those IDs.  If the error was indeed a temporary/accidental one like from my previous email, start a new export.  If not, then I will need to reinspect the code and possibly do an intermediate build to get a completed export across.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Mar 11, 2014, at 1:01 PM, Kevin McGee <km...@li...> wrote:

> Hi Dr. Dionisio, 
> 
> I have been poking around on GeneDB and on Ensembl Protists, and I cannot find any use of the LMJF version anywhere. I don't know if I should be looking anywhere else or in other databases, but judging that we have been using GeneDB and Ensembl Protists as our master reference databases, I think that there isn't really any importance to the capitalized version. 
> 
> Let me know what you think!
> Kevin
> 
> 
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

Re: [XMLPipeDB-developer] GenMAPP Builder Crashed

[John D. N. D. <do...@lm...>]

Hi Kevin,

OK, thank you for this.  I have a clarification question based on this: Note in image (1) that the scroll bar is in the middle of the window---that means there was more console output below the part that you sent.  Was there more error information below the "... 9 more" line in that screenshot?  Or did you position the scroll bar that way exactly because this was the error ended?

If that "... 9 more" was the last line of the error report, then the main thing I can determine from this is that some connectivity issue with the database server took place.  Maybe someone closed pgAdmin III by accident?  Or for some reason pgAdmin III quit unexpectedly?  That is the scenario that the error implies.

Now, if more error messages appeared below "... 9 more," then other conclusions might be drawn.  But for the moment this looks like a disconnection, and the main cause of that would be an unplanned quitting of pgAdmin.  If this did indeed take place (pgAdmin unexpectedly or unintentionally terminated), then it is safe to try the export again---just make sure not to end pgAdmin.  But if pgAdmin was still up and running...well, this will need more investigation.  I'll take a look at the code when I make the next build.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Mar 11, 2014, at 12:41 PM, Kevin McGee <km...@li...> wrote:

> Hey Dr. Dionisio,
> 
> So while I was trying to export my database from GenMAPP builder, it randomly crashed in the middle. I took a few pictures of the command line window right up to where it crashed. I was wondering if you could take a look at it and let me know why it happened.
> 
> One note: I accidentally named the pictures in a confusing way. Reading from the top of the command prompt window to the bottom, the pictures I sent you should be read in the order 3,2,1. Sorry, I only realized this after naming them this way.
> 
> -Kevin
> <Database Crash (1) 20140311.PNG><Database Crash (2) 20140311.PNG><Database Crash (3) 20140311.PNG>------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

[XMLPipeDB-developer] No Use of the Capitalized Versions

[Kevin M. <km...@li...>]

Hi Dr. Dionisio,

I have been poking around on GeneDB and on Ensembl Protists, and I cannot
find any use of the LMJF version anywhere. I don't know if I should be
looking anywhere else or in other databases, but judging that we have been
using GeneDB and Ensembl Protists as our master reference databases, I
think that there isn't really any importance to the capitalized version.

Let me know what you think!
Kevin

[XMLPipeDB-developer] GenMAPP Builder 2.0b74 is out

[John D. N. D. <do...@lm...>]

Come and get it :)  This includes the new S. meliloti link template and L. major ID export routine.  Enjoy!

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University

Re: [XMLPipeDB-developer] updated template gdb

[Kam D. <kda...@lm...>]

Trying again--attachment was rejected last time.

At 03:33 PM 3/4/2014, Kam Dahlquist wrote:
>Hi,
>
>I discovered that the links for InterPro and EMBL were outdated, so 
>I fixed them in the Gene Database Template attached.  Please use 
>this in the next build of GenMAPP Builder.
>
>Thanks,
>Kam

Re: [XMLPipeDB-developer] Deleting Files on the Wiki?

[Andrew P. <ap...@li...>]

I was just thinking that it might be helpful to include the link to the
file. Here it is:
http://xmlpipedb.sourceforge.net/wiki/index.php/File:Original_Row_Count_S_pneumoniae_G54_2014_02_26_.JPG


On Wed, Feb 26, 2014 at 3:38 PM, Andrew Pita <ap...@li...> wrote:

> Hey Dr. Dionisio,
>
> I made a mistake in the name I chose for a screen shot that I uploaded. Is
> it possible to delete uploaded files from the wiki?
>
> Thanks,
> Andrew
>

Re: [XMLPipeDB-developer] Deleting Files on the Wiki?

[John D. N. D. <do...@lm...>]

Hi Andrew,

I think there is an administrative way to do that, but I'd say just don't worry about it, and make sure nothing links to it.  Meanwhile if you tell me which image it is, I can look into truly deleting it.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Feb 26, 2014, at 3:38 PM, Andrew Pita <ap...@li...> wrote:

> Hey Dr. Dionisio, 
> 
> I made a mistake in the name I chose for a screen shot that I uploaded. Is it possible to delete uploaded files from the wiki?
> 
> Thanks,
> Andrew
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
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[XMLPipeDB-developer] Deleting Files on the Wiki?

[Andrew P. <ap...@li...>]

Hey Dr. Dionisio,

I made a mistake in the name I chose for a screen shot that I uploaded. Is
it possible to delete uploaded files from the wiki?

Thanks,
Andrew

Re: [XMLPipeDB-developer] Leishmania IDs

[John D. N. D. <do...@lm...>]

Hi  Kam,

Sounds good, thanks for the updates and details.  I'll put the queries together then work on a new versions of the profiles (new profile in the case of infantum).

I had ended my office hours a few minutes early due to an 11am meeting in UHall.  But that's over now :)

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University


> On Feb 25, 2014, at 11:41 AM, Kam Dahlquist <kda...@lm...> wrote:
> 
> Hi Dondi,
> 
> Here's a rundown of what we talked about yesterday with regards to 
> the Leishmania major IDs and some explanations:
> 
> 1.  LmjF##.#### This form is "old" according to GeneDB; we are going 
> to keep it because it is used in our microarray data.
> 
> 2.  LMJF.##.####  This form is the "official" new form according to 
> GeneDB.  Thus we need it.
> 
> 3.  LMJF_##_#### This form actually appears in UniProt records 
> although it is not in our microarray data or GeneDB.  We are going to 
> keep it because it's used by UniProt so somebody out there might be 
> using it, too. (We just figured this out this morning.)
> 
> 4.  "straggler IDs"  These are not of the above three forms, but are 
> coming from UniProt.  They are synonyms of other genes that have one 
> of the above three forms.  We are automatically capturing them with 
> our code, so we are going to just keep them instead of trying to weed 
> them out.  It's possible that somebody out there is using them since 
> they are in UniProt.  Dondi, if you would construct a query to find 
> out which UniProt records have these extra IDs, that would be 
> great.  We just want it for our documentation.
> 
> In summary, we are going to have triplicates of all the IDs with 
> forms 1, 2, and 3, + some extra number of stragglers in our 
> OrderedLocusNames table.
> 
> Let's make sure that we are capturing IDs from both the Ordered Locus 
> tag and the ORF tag (I think that's what you've been doing, but I 
> just wanted to make sure).  You might be converting IDs to one of 
> these forms, could you let us know what conversions you are doing so 
> we can have that for our documentation?
> 
> Kevin is right now in the process of documenting ID forms for 
> Leishmania infantum.  Right off the bat, it looks like we are going 
> to have the same forms of 1, 2, and 3, except the prefix will be LinJ 
> instead of LmjF.  Also, it looks like the IDs are appearing under the 
> ORF tag instead of the OrderedLocus tag (an export with a generic 
> profile turned up 0 OrderedLocus IDs), but we'd better capture from 
> both tags, just in case.
> 
> Also, we are fast-tracking the creation of an L. infantum gdb because 
> it turns out that the vast majority of IDs from the microarray data 
> are to L. infantum instead of L. major.  Once we have an infantum 
> gdb, we can create the combined gdb.  The next step would be a 
> further customization that relates the L. major IDs to the L. infantum IDs.
> 
> Finally, in the microarray data, each gene has duplicate spots 
> (duplicate rows).  Ideally, we would like to average the log fold 
> changes for these as technical replicates before doing the 
> statistics.  I think I have a script in Matlab that Dr. Fitzpatrick 
> wrote for me to split my yeast data.  I'm going to try  it on the 
> Leishmania data to see if it works.  If so, we would not need an 
> additional script to split the data.
> 
> Best,
> Kam
> 
> 
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

[XMLPipeDB-developer] Leishmania IDs

[Kam D. <kda...@lm...>]

Hi Dondi,

Here's a rundown of what we talked about yesterday with regards to 
the Leishmania major IDs and some explanations:

1.  LmjF##.#### This form is "old" according to GeneDB; we are going 
to keep it because it is used in our microarray data.

2.  LMJF.##.####  This form is the "official" new form according to 
GeneDB.  Thus we need it.

3.  LMJF_##_#### This form actually appears in UniProt records 
although it is not in our microarray data or GeneDB.  We are going to 
keep it because it's used by UniProt so somebody out there might be 
using it, too. (We just figured this out this morning.)

4.  "straggler IDs"  These are not of the above three forms, but are 
coming from UniProt.  They are synonyms of other genes that have one 
of the above three forms.  We are automatically capturing them with 
our code, so we are going to just keep them instead of trying to weed 
them out.  It's possible that somebody out there is using them since 
they are in UniProt.  Dondi, if you would construct a query to find 
out which UniProt records have these extra IDs, that would be 
great.  We just want it for our documentation.

In summary, we are going to have triplicates of all the IDs with 
forms 1, 2, and 3, + some extra number of stragglers in our 
OrderedLocusNames table.

Let's make sure that we are capturing IDs from both the Ordered Locus 
tag and the ORF tag (I think that's what you've been doing, but I 
just wanted to make sure).  You might be converting IDs to one of 
these forms, could you let us know what conversions you are doing so 
we can have that for our documentation?

Kevin is right now in the process of documenting ID forms for 
Leishmania infantum.  Right off the bat, it looks like we are going 
to have the same forms of 1, 2, and 3, except the prefix will be LinJ 
instead of LmjF.  Also, it looks like the IDs are appearing under the 
ORF tag instead of the OrderedLocus tag (an export with a generic 
profile turned up 0 OrderedLocus IDs), but we'd better capture from 
both tags, just in case.

Also, we are fast-tracking the creation of an L. infantum gdb because 
it turns out that the vast majority of IDs from the microarray data 
are to L. infantum instead of L. major.  Once we have an infantum 
gdb, we can create the combined gdb.  The next step would be a 
further customization that relates the L. major IDs to the L. infantum IDs.

Finally, in the microarray data, each gene has duplicate spots 
(duplicate rows).  Ideally, we would like to average the log fold 
changes for these as technical replicates before doing the 
statistics.  I think I have a script in Matlab that Dr. Fitzpatrick 
wrote for me to split my yeast data.  I'm going to try  it on the 
Leishmania data to see if it works.  If so, we would not need an 
additional script to split the data.

Best,
Kam

Re: [XMLPipeDB-developer] Problems with match code

[John D. N. D. <do...@lm...>]

Hi Kevin,

I'm seeing "<Leishmania Major>" in your commands there.  That's probably what's throwing off match.  Is the folder really named <Leishmania Major>, with those < > symbols?  If you're trying to accommodate the space, use double-quotes instead.  Or, just rename the folder to something without spaces.

Let me know if that helps.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Feb 25, 2014, at 9:45 AM, Kevin McGee <km...@li...> wrote:

> Hey Dr. Dionisio,
> 
> I was having trouble with match. I think my code is right but it keeps saying access denied. I was wondering if you could take a look at it.
> 
> 
> Thanks!
> Kevin McGee
> <Match Failure l.infantum 20140225.PNG>------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

[XMLPipeDB-developer] Gene ID names figured out

[Kevin M. <km...@li...>]

Hey Dr. Dionisio,

I think I have pretty much got the ID patterns figured out. Looking on
GeneDB and Ensembl Protists, they have the pattern LmjF.##.#### as the
correct way of formatting the id name. However, under synonyms, they have
another pattern LmjF##.#### and have marked it as a previously known name.
I think that these are the two patterns we want: the current up to date
pattern and the previously known pattern just in case the user of the
database has older data that was named in this way. This means that we
should get rid of the pattern LmjF_##_#### entirely and add LmjF##.#### in
its place.

Also, typing in the random straggler names on Uniprot, they have synonymous
names that follow the patterns in the coded in the database already:

L1063.01 =     LmjF23.0270 L3640.11  =    LmjF21.1780
L374.02    =    LmjF19.0670
LMAJ006828= LmjF06.1270
lmj_1130 =     LmjF21.1780


I don't know if we should change there names or what we should do with
them, but we do know they code for actual genes and it gives us the option
of including them in the coding without having to make too many
modifications.

Let me know if you have any questions or want to meet to talk about it!

-Kevin McGee

[XMLPipeDB-developer] Excel spreadsheet for Gene ID Patterns

[Kevin M. <km...@li...>]

Hey Dr. Dionisio,

I have pasted a link to lionshare for an excel file that goes through all
of the Gene ID patterns in both the microarray data and in the Database.
For the database to work in GenMAPP, the database ID code should be
LmjF##.#### The ID's of LMJF_##_#### and LMJF.##.#### are not needed and
can be removed/changed to the correct code above.

Also, if you look on the excel file, I found the stragglers on uniprot that
have synonymous names that match the Gene ID code that will work for
GenMAPP. I don't know if change or not, but now we know where/what they are.

Thanks, Kevin McGee

https://lionshare.lmu.edu/Users/kmcgee3/All%20Gene%20ID%27s%20and%20conversions.xlsx

Re: [XMLPipeDB-developer] Upload File to the Wiki Bug

[John D. N. D. <do...@lm...>]

Greetings,

I hit the right wiki this time :)  and confirmed the error.  Upon investigation this turns out to be an open ticket in SourceForge's system:

	https://sourceforge.net/p/forge/site-support/2583/

The ticket has not been officially closed, but a solution was mentioned there which I then applied.  It appears to have worked; I was able to upload an image file to the wiki.

Give it a try when you next get a chance and let me know how it goes.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jan 29, 2014, at 3:48 PM, Andrew Pita <pap...@gm...> wrote:

> I may have identified a bug when uploading a png file to the wiki. I received these upload warnings. 
> 	• Could not acquire lock for "mwstore://local-backend/local-public/c/c8".
> 	• Could not acquire lock for "mwstore://local-backend/local-public/c/c8/TallyEngine20140128.PNG".
> 
> -- Andrew
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable 
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

Re: [XMLPipeDB-developer] Upload File to the Wiki Bug

[John D. N. D. <joh...@da...>]

Greetings,

I tried a test upload on Saturday morning 2/1 and it was successful:

	https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/File:Bacterial_infections_and_involved_species.png#file

I also checked the server and did not see the typical warning signs when upload errors occur, such as disk space issues or file permission problems.

There is a chance that this error was transient---please try again and let me know how it goes.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jan 29, 2014, at 3:48 PM, Andrew Pita <pap...@gm...> wrote:

> I may have identified a bug when uploading a png file to the wiki. I received these upload warnings. 
> 	• Could not acquire lock for "mwstore://local-backend/local-public/c/c8".
> 	• Could not acquire lock for "mwstore://local-backend/local-public/c/c8/TallyEngine20140128.PNG".
> 
> -- Andrew
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable 
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

[XMLPipeDB-developer] Upload File to the Wiki Bug

[Andrew P. <pap...@gm...>]

I may have identified a bug when uploading a png file to the wiki. I
received these upload warnings.

   - Could not acquire lock for "mwstore://local-backend/local-public/c/c8".
   - Could not acquire lock for
   "mwstore://local-backend/local-public/c/c8/TallyEngine20140128.PNG".


-- Andrew

Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[John D. N. D. <do...@lm...>]

OK, gmbuilder 2.0b72 is out, integrating these taxon ID changes.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 25, 2013, at 2:46 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
> 
> Let's go ahead and make these changes.  I'll need to run the exports 
> and validate the gdb's, of course, but I think this will be better so 
> that I can actually test the custom profiles.
> 
> We don't need to do the forensics on what happened, but I don't ever 
> recall specifically calling out the taxon IDs that needed to be put 
> in the code, so maybe Rich just looked them up online and guessed.
> 
> Best,
> Kam
> 
> At 12:59 PM 11/25/2013, you wrote:
>> Greetings,
>> 
>> Here are my cross-reference results.  It turns out there were a 
>> couple more discrepancies; the rest match.  Not sure where the 
>> incorrect IDs came from at this point, but here are the pending changes:
>> 
>> - H. pylori, code: 210; wiki: 85962
>> - P. aeruginosa, code: 287; wiki: 208964
>> - S. typhimurium, code: 90371; wiki: 99287
>> 
>> Finally, the wiki notes that M. tuberculosis is 83332 but has 
>> changed to 1773; the code already has 1773 for that species profile, 
>> so presumably this can be left as is.
>> 
>> If these changes look good (i.e., code will be changed to match the 
>> wiki), then I'll send up a new release.
>> 
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>> 
>> 
>> 
>> On Nov 25, 2013, at 11:31 AM, John David N. Dionisio <do...@lm...> wrote:
>> 
>>> 
>>> OK, I will do a cross-check.  It's certainly possible that the 
>> wrong taxon IDs were mentioned; on the side I can check the version 
>> histories to see where things went wrong.
>>> 
>>> But the main task is to check the code taxon IDs with the ones on 
>> that page.  I'll make corrections then release a new version.
>>> 
>>> John David N. Dionisio, PhD
>>> Associate Professor, Computer Science
>>> Associate Director, University Honors Program
>>> Loyola Marymount University
>>> 
>>> 
>>>> On Nov 25, 2013, at 9:16 AM, Kam Dahlquist <kda...@lm...> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I don't know how 210 became the taxon ID in the code.  I checked the
>>>> ReadMe for the released version of the gdb and the tax ID for that
>>>> version is 85962.
>>>> 
>>>> I've gone through all the ReadMe's to double-check the tax IDs that I
>>>> have listed on my user page on the BiolDB wiki
>>>> here:
>>>> 
>> https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML
>>>> 
>>>> I only anticipate issues with changing tax IDs for E. coli,
>>>> Arabidopsis, and Mycobacterium tuberculosis.
>>>> 
>>>> Is it possible that when Rich (I think it was him) made the change to
>>>> putting in tax IDs instead of species names, he put in the wrong tax
>>>> ID?  If so, it's probably worth it to check all the tax IDs for the
>>>> custom profiles and make sure they match what I have put on that
>>>> page.  I think there may be issues with E. coli, Arabidopsis, and M.
>>>> tuberculosis, though.
>>>> 
>>>> Best,
>>>> Kam
>>>> 
>>>> At 11:37 PM 11/22/2013, you wrote:
>>>>> I checked the custom species profile in our code and the taxon ID
>>>>> that is associated with H. pylori is 210.  This may be another case
>>>>> of a changed taxon ID, seeing as the data reports 85962 instead, as
>>>>> seen in your attached screenshots.
>>>>> 
>>>>> John David N. Dionisio, PhD
>>>>> Associate Professor, Computer Science
>>>>> Associate Director, University Honors Program
>>>>> Loyola Marymount University
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Just started an export of H. pylori.  There were two profiles
>>>>> that showed up, both with the same taxon ID, both said they were
>>>>> generic profiles.  I'm attaching 2 screenshots.
>>>>>> 
>>>>>> Best,
>>>>>> Kam
>>>>> 
>> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
>>>>>> Shape the Mobile Experience: Free Subscription
>>>>>> Software experts and developers: Be at the forefront of tech innovation.
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>> game-changing
>>>>>> conversations that shape the rapidly evolving mobile landscape.
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>>>>> 
>>>>> 
>>>>> 
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Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[Kam D. <kda...@lm...>]

Hi,

Let's go ahead and make these changes.  I'll need to run the exports 
and validate the gdb's, of course, but I think this will be better so 
that I can actually test the custom profiles.

We don't need to do the forensics on what happened, but I don't ever 
recall specifically calling out the taxon IDs that needed to be put 
in the code, so maybe Rich just looked them up online and guessed.

Best,
Kam

At 12:59 PM 11/25/2013, you wrote:
>Greetings,
>
>Here are my cross-reference results.  It turns out there were a 
>couple more discrepancies; the rest match.  Not sure where the 
>incorrect IDs came from at this point, but here are the pending changes:
>
>- H. pylori, code: 210; wiki: 85962
>- P. aeruginosa, code: 287; wiki: 208964
>- S. typhimurium, code: 90371; wiki: 99287
>
>Finally, the wiki notes that M. tuberculosis is 83332 but has 
>changed to 1773; the code already has 1773 for that species profile, 
>so presumably this can be left as is.
>
>If these changes look good (i.e., code will be changed to match the 
>wiki), then I'll send up a new release.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Nov 25, 2013, at 11:31 AM, John David N. Dionisio <do...@lm...> wrote:
>
> >
> > OK, I will do a cross-check.  It's certainly possible that the 
> wrong taxon IDs were mentioned; on the side I can check the version 
> histories to see where things went wrong.
> >
> > But the main task is to check the code taxon IDs with the ones on 
> that page.  I'll make corrections then release a new version.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Associate Director, University Honors Program
> > Loyola Marymount University
> >
> >
> >> On Nov 25, 2013, at 9:16 AM, Kam Dahlquist <kda...@lm...> wrote:
> >>
> >> Hi,
> >>
> >> I don't know how 210 became the taxon ID in the code.  I checked the
> >> ReadMe for the released version of the gdb and the tax ID for that
> >> version is 85962.
> >>
> >> I've gone through all the ReadMe's to double-check the tax IDs that I
> >> have listed on my user page on the BiolDB wiki
> >> here:
> >> 
> https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML
> >>
> >> I only anticipate issues with changing tax IDs for E. coli,
> >> Arabidopsis, and Mycobacterium tuberculosis.
> >>
> >> Is it possible that when Rich (I think it was him) made the change to
> >> putting in tax IDs instead of species names, he put in the wrong tax
> >> ID?  If so, it's probably worth it to check all the tax IDs for the
> >> custom profiles and make sure they match what I have put on that
> >> page.  I think there may be issues with E. coli, Arabidopsis, and M.
> >> tuberculosis, though.
> >>
> >> Best,
> >> Kam
> >>
> >> At 11:37 PM 11/22/2013, you wrote:
> >>> I checked the custom species profile in our code and the taxon ID
> >>> that is associated with H. pylori is 210.  This may be another case
> >>> of a changed taxon ID, seeing as the data reports 85962 instead, as
> >>> seen in your attached screenshots.
> >>>
> >>> John David N. Dionisio, PhD
> >>> Associate Professor, Computer Science
> >>> Associate Director, University Honors Program
> >>> Loyola Marymount University
> >>>
> >>>
> >>>
> >>>> On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> Just started an export of H. pylori.  There were two profiles
> >>> that showed up, both with the same taxon ID, both said they were
> >>> generic profiles.  I'm attaching 2 screenshots.
> >>>>
> >>>> Best,
> >>>> Kam
> >>> 
> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
> >>>> Shape the Mobile Experience: Free Subscription
> >>>> Software experts and developers: Be at the forefront of tech innovation.
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> >>>> xml...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>
> >>>
> >>> 
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Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[John D. N. D. <do...@lm...>]

Greetings,

Here are my cross-reference results.  It turns out there were a couple more discrepancies; the rest match.  Not sure where the incorrect IDs came from at this point, but here are the pending changes:

- H. pylori, code: 210; wiki: 85962
- P. aeruginosa, code: 287; wiki: 208964
- S. typhimurium, code: 90371; wiki: 99287

Finally, the wiki notes that M. tuberculosis is 83332 but has changed to 1773; the code already has 1773 for that species profile, so presumably this can be left as is.

If these changes look good (i.e., code will be changed to match the wiki), then I’ll send up a new release.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 25, 2013, at 11:31 AM, John David N. Dionisio <do...@lm...> wrote:

> 
> OK, I will do a cross-check.  It's certainly possible that the wrong taxon IDs were mentioned; on the side I can check the version histories to see where things went wrong.
> 
> But the main task is to check the code taxon IDs with the ones on that page.  I'll make corrections then release a new version.
> 
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
> 
> 
>> On Nov 25, 2013, at 9:16 AM, Kam Dahlquist <kda...@lm...> wrote:
>> 
>> Hi,
>> 
>> I don't know how 210 became the taxon ID in the code.  I checked the 
>> ReadMe for the released version of the gdb and the tax ID for that 
>> version is 85962.
>> 
>> I've gone through all the ReadMe's to double-check the tax IDs that I 
>> have listed on my user page on the BiolDB wiki 
>> here: 
>> https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML
>> 
>> I only anticipate issues with changing tax IDs for E. coli, 
>> Arabidopsis, and Mycobacterium tuberculosis.
>> 
>> Is it possible that when Rich (I think it was him) made the change to 
>> putting in tax IDs instead of species names, he put in the wrong tax 
>> ID?  If so, it's probably worth it to check all the tax IDs for the 
>> custom profiles and make sure they match what I have put on that 
>> page.  I think there may be issues with E. coli, Arabidopsis, and M. 
>> tuberculosis, though.
>> 
>> Best,
>> Kam
>> 
>> At 11:37 PM 11/22/2013, you wrote:
>>> I checked the custom species profile in our code and the taxon ID 
>>> that is associated with H. pylori is 210.  This may be another case 
>>> of a changed taxon ID, seeing as the data reports 85962 instead, as 
>>> seen in your attached screenshots.
>>> 
>>> John David N. Dionisio, PhD
>>> Associate Professor, Computer Science
>>> Associate Director, University Honors Program
>>> Loyola Marymount University
>>> 
>>> 
>>> 
>>>> On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> Just started an export of H. pylori.  There were two profiles
>>> that showed up, both with the same taxon ID, both said they were 
>>> generic profiles.  I'm attaching 2 screenshots.
>>>> 
>>>> Best,
>>>> Kam
>>> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
>>>> Shape the Mobile Experience: Free Subscription
>>>> Software experts and developers: Be at the forefront of tech innovation.
>>>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>>>> conversations that shape the rapidly evolving mobile landscape.
>>> Sign up now.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> xmlpipedb-developer mailing list
>>>> xml...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> 
>>> 
>>> ------------------------------------------------------------------------------
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Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[John D. N. D. <do...@lm...>]

 OK, I will do a cross-check.  It's certainly possible that the wrong taxon IDs were mentioned; on the side I can check the version histories to see where things went wrong.

But the main task is to check the code taxon IDs with the ones on that page.  I'll make corrections then release a new version.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University


> On Nov 25, 2013, at 9:16 AM, Kam Dahlquist <kda...@lm...> wrote:
> 
> Hi,
> 
> I don't know how 210 became the taxon ID in the code.  I checked the 
> ReadMe for the released version of the gdb and the tax ID for that 
> version is 85962.
> 
> I've gone through all the ReadMe's to double-check the tax IDs that I 
> have listed on my user page on the BiolDB wiki 
> here: 
> https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML
> 
> I only anticipate issues with changing tax IDs for E. coli, 
> Arabidopsis, and Mycobacterium tuberculosis.
> 
> Is it possible that when Rich (I think it was him) made the change to 
> putting in tax IDs instead of species names, he put in the wrong tax 
> ID?  If so, it's probably worth it to check all the tax IDs for the 
> custom profiles and make sure they match what I have put on that 
> page.  I think there may be issues with E. coli, Arabidopsis, and M. 
> tuberculosis, though.
> 
> Best,
> Kam
> 
> At 11:37 PM 11/22/2013, you wrote:
>> I checked the custom species profile in our code and the taxon ID 
>> that is associated with H. pylori is 210.  This may be another case 
>> of a changed taxon ID, seeing as the data reports 85962 instead, as 
>> seen in your attached screenshots.
>> 
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>> 
>> 
>> 
>>> On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
>>> 
>>> Hi,
>>> 
>>> Just started an export of H. pylori.  There were two profiles
>> that showed up, both with the same taxon ID, both said they were 
>> generic profiles.  I'm attaching 2 screenshots.
>>> 
>>> Best,
>>> Kam
>> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
>>> Shape the Mobile Experience: Free Subscription
>>> Software experts and developers: Be at the forefront of tech innovation.
>>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>>> conversations that shape the rapidly evolving mobile landscape.
>> Sign up now.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> xmlpipedb-developer mailing list
>>> xml...@li...
>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> 
>> 
>> ------------------------------------------------------------------------------
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Re: [XMLPipeDB-developer] gmb2b71 crash during export of Vibrio

[John D. N. D. <do...@lm...>]

OK, good to know, may have been a one-off transient error then.  I think we can file this as "under observation" unless it starts recurring.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University


> On Nov 25, 2013, at 9:47 AM, Kam Dahlquist <kda...@lm...> wrote:
> 
> Hi,
> 
> The second attempt didn't crash, so I'm not sure 
> what happened the first time.  I'm on Windows 7 
> and I'm planning on updated my versions of java and postgres this week.
> 
> Best,
> Kam
> 
> At 11:31 PM 11/22/2013, you wrote:
>> This is a pretty low-level error...I'd say the 
>> first step in triaging it is to gather up 
>> versions: what version of Windows is your 
>> machine running, and what version of 
>> PostgreSQL?  Java can be seen here (6.0_43-b01).
>> 
>> The Keck lab computers on which students have 
>> been doing their exports have Windows 7, Java 7u45, and PostgreSQL 9.2.4.
>> 
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>> 
>> 
>> 
>>> On Nov 22, 2013, at 4:29 PM, Kam Dahlquist <kda...@lm...> wrote:
>>> 
>>> Hi,
>>> 
>>> My attempted export of Vibrio with gmb2b71
>> crashed.  I'm attaching a screenshot of the 
>> console window.  I tried to upload it to the wiki, but also got an error there:
>>> 
>>>      . Could not acquire lock for
>> "mwstore://local-backend/local-public/4/43".
>>>      . Could not acquire lock for
>> "mwstore://local-backend/local-public/4/43/Gmb2b71_crash_20131122.jpg".
>>> 
>>> I'm going to try an export of H. pylori, if I
>> can get it started before I leave on a 
>> different computer, although I have to get it started in the next 15 min...
>>> 
>>> Kam
>> <gmb2b71_crash_20131122.jpg>------------------------------------------------------------------------------
>>> Shape the Mobile Experience: Free Subscription
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Re: [XMLPipeDB-developer] gmb2b71 crash during export of Vibrio

[Kam D. <kda...@lm...>]

Hi,

The second attempt didn't crash, so I'm not sure 
what happened the first time.  I'm on Windows 7 
and I'm planning on updated my versions of java and postgres this week.

Best,
Kam

At 11:31 PM 11/22/2013, you wrote:
>This is a pretty low-level error...I'd say the 
>first step in triaging it is to gather up 
>versions: what version of Windows is your 
>machine running, and what version of 
>PostgreSQL?  Java can be seen here (6.0_43-b01).
>
>The Keck lab computers on which students have 
>been doing their exports have Windows 7, Java 7u45, and PostgreSQL 9.2.4.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Nov 22, 2013, at 4:29 PM, Kam Dahlquist <kda...@lm...> wrote:
>
> > Hi,
> >
> > My attempted export of Vibrio with gmb2b71 
> crashed.  I'm attaching a screenshot of the 
> console window.  I tried to upload it to the wiki, but also got an error there:
> >
> >       • Could not acquire lock for 
> "mwstore://local-backend/local-public/4/43".
> >       • Could not acquire lock for 
> "mwstore://local-backend/local-public/4/43/Gmb2b71_crash_20131122.jpg".
> >
> > I'm going to try an export of H. pylori, if I 
> can get it started before I leave on a 
> different computer, although I have to get it started in the next 15 min...
> >
> > Kam
> > 
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Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[Kam D. <kda...@lm...>]

Hi,

I don't know how 210 became the taxon ID in the code.  I checked the 
ReadMe for the released version of the gdb and the tax ID for that 
version is 85962.

I've gone through all the ReadMe's to double-check the tax IDs that I 
have listed on my user page on the BiolDB wiki 
here: 
https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML

I only anticipate issues with changing tax IDs for E. coli, 
Arabidopsis, and Mycobacterium tuberculosis.

Is it possible that when Rich (I think it was him) made the change to 
putting in tax IDs instead of species names, he put in the wrong tax 
ID?  If so, it's probably worth it to check all the tax IDs for the 
custom profiles and make sure they match what I have put on that 
page.  I think there may be issues with E. coli, Arabidopsis, and M. 
tuberculosis, though.

Best,
Kam

At 11:37 PM 11/22/2013, you wrote:
>I checked the custom species profile in our code and the taxon ID 
>that is associated with H. pylori is 210.  This may be another case 
>of a changed taxon ID, seeing as the data reports 85962 instead, as 
>seen in your attached screenshots.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
>
> > Hi,
> >
> > Just started an export of H. pylori.  There were two profiles 
> that showed up, both with the same taxon ID, both said they were 
> generic profiles.  I'm attaching 2 screenshots.
> >
> > Best,
> > Kam
> > 
> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
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Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

[John D. N. D. <do...@lm...>]

I checked the custom species profile in our code and the taxon ID that is associated with H. pylori is 210.  This may be another case of a changed taxon ID, seeing as the data reports 85962 instead, as seen in your attached screenshots.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
> 
> Just started an export of H. pylori.  There were two profiles that showed up, both with the same taxon ID, both said they were generic profiles.  I'm attaching 2 screenshots.
> 
> Best,
> Kam
> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
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