xmlpipedb-developer Mailing List for XMLPipeDB (Page 2)
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From: John D. N. D. <do...@lm...> - 2014-06-27 18:24:23
|
Ah yes, that's true, we've never had that many species loaded up. I'll let you know when there is a new build with the sorting implemented. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 26, 2014, at 11:53 AM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > As you suggested, the export window of GenMAPP Builder lists all of the species in the Postgres database, not just the ones for which we have custom profiles. The problem is that the list is not sorted in any way, not by taxon ID, not alphabetically by the name of the species. I'm not going to be able to find one of our species for which we have a profile easily, all I can do is click through the list of maybe thousands of species. > > If this list could be sorted by taxon ID, then I could quickly scroll to the one I want. > > Best, > Kam > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
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From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-26 18:54:44
|
Hi, As you suggested, the export window of GenMAPP Builder lists all of the species in the Postgres database, not just the ones for which we have custom profiles. The problem is that the list is not sorted in any way, not by taxon ID, not alphabetically by the name of the species. I'm not going to be able to find one of our species for which we have a profile easily, all I can do is click through the list of maybe thousands of species. If this list could be sorted by taxon ID, then I could quickly scroll to the one I want. Best, Kam |
|
From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-24 18:45:17
|
OK--got it. Kam ________________________________________ From: John David N. Dionisio [do...@lm...] Sent: Tuesday, June 24, 2014 11:03 AM To: xml...@li... Subject: Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed Hi Kam, No problem, I remember about jury duty from last week...as for the fix, there are two items involved: (a) The original reported error (problem with the 'molecule' element)---this has been fixed, and was fixed by the usual XSD update (b) When I was testing the fix in (a), I encountered another problem with importing---this is the issue that I haven't isolated yet. I've tried a few approaches at getting a handle on this latter bug, but have come up short. So the issue in (b) remains, but it does not appear to be content-specific, so I decided to release this new version anyway to see what happens on your end. Let me know if that clarifies things. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 24, 2014, at 10:57 AM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > I'm at jury duty today, so I'll try the import when I get back to the office. I'll keep you posted as to whether I'll be there for Thursday's meeting. I'm not sure I understand your description of the fix below, what specifically does that mean? > > Thanks, > Kam > > ________________________________________ > From: John David N. Dionisio [do...@lm...] > Sent: Tuesday, June 24, 2014 9:55 AM > To: xml...@li... > Subject: Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed > > Hi Kam, > > I've gone ahead and released GenMAPP Builder 2.0b79. This updates UniProt code and SQL to the latest XSD libraries, but may still harbor a latent bug regarding something completely different, but which I have been unable to isolate yet. In particular, just changing the file (but retaining the data where the original XML import failed) seems to avoid the problem. Let me know what happens with your import. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > > On Jun 23, 2014, at 1:27 AM, John David N. Dionisio <do...@lm...> wrote: > >> Greetings, >> >> The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve. So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page: >> >> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22 >> >> I will look at this fresh on Monday and report back on how things go. >> >> John David N. Dionisio, PhD >> Associate Professor, Computer Science >> Associate Director, University Honors Program >> Loyola Marymount University >> >> >> >> On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: >> >>> Hi, >>> >>> I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: >>> >>> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 >>> >>> Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. >>> >>> Best, >>> Kam >>> ------------------------------------------------------------------------------ >>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions >>> Find What Matters Most in Your Big Data with HPCC Systems >>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. >>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration >>> http://p.sf.net/sfu/hpccsystems >>> _______________________________________________ >>> xmlpipedb-developer mailing list >>> xml...@li... >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
|
From: John D. N. D. <do...@lm...> - 2014-06-24 18:03:38
|
Hi Kam, No problem, I remember about jury duty from last week...as for the fix, there are two items involved: (a) The original reported error (problem with the 'molecule' element)---this has been fixed, and was fixed by the usual XSD update (b) When I was testing the fix in (a), I encountered another problem with importing---this is the issue that I haven't isolated yet. I've tried a few approaches at getting a handle on this latter bug, but have come up short. So the issue in (b) remains, but it does not appear to be content-specific, so I decided to release this new version anyway to see what happens on your end. Let me know if that clarifies things. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 24, 2014, at 10:57 AM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > I'm at jury duty today, so I'll try the import when I get back to the office. I'll keep you posted as to whether I'll be there for Thursday's meeting. I'm not sure I understand your description of the fix below, what specifically does that mean? > > Thanks, > Kam > > ________________________________________ > From: John David N. Dionisio [do...@lm...] > Sent: Tuesday, June 24, 2014 9:55 AM > To: xml...@li... > Subject: Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed > > Hi Kam, > > I've gone ahead and released GenMAPP Builder 2.0b79. This updates UniProt code and SQL to the latest XSD libraries, but may still harbor a latent bug regarding something completely different, but which I have been unable to isolate yet. In particular, just changing the file (but retaining the data where the original XML import failed) seems to avoid the problem. Let me know what happens with your import. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > > On Jun 23, 2014, at 1:27 AM, John David N. Dionisio <do...@lm...> wrote: > >> Greetings, >> >> The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve. So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page: >> >> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22 >> >> I will look at this fresh on Monday and report back on how things go. >> >> John David N. Dionisio, PhD >> Associate Professor, Computer Science >> Associate Director, University Honors Program >> Loyola Marymount University >> >> >> >> On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: >> >>> Hi, >>> >>> I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: >>> >>> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 >>> >>> Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. >>> >>> Best, >>> Kam >>> ------------------------------------------------------------------------------ >>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions >>> Find What Matters Most in Your Big Data with HPCC Systems >>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. >>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration >>> http://p.sf.net/sfu/hpccsystems >>> _______________________________________________ >>> xmlpipedb-developer mailing list >>> xml...@li... >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
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From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-24 17:58:57
|
Hi, I'm at jury duty today, so I'll try the import when I get back to the office. I'll keep you posted as to whether I'll be there for Thursday's meeting. I'm not sure I understand your description of the fix below, what specifically does that mean? Thanks, Kam ________________________________________ From: John David N. Dionisio [do...@lm...] Sent: Tuesday, June 24, 2014 9:55 AM To: xml...@li... Subject: Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed Hi Kam, I've gone ahead and released GenMAPP Builder 2.0b79. This updates UniProt code and SQL to the latest XSD libraries, but may still harbor a latent bug regarding something completely different, but which I have been unable to isolate yet. In particular, just changing the file (but retaining the data where the original XML import failed) seems to avoid the problem. Let me know what happens with your import. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 23, 2014, at 1:27 AM, John David N. Dionisio <do...@lm...> wrote: > Greetings, > > The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve. So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page: > > http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22 > > I will look at this fresh on Monday and report back on how things go. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > > On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: > >> Hi, >> >> I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: >> >> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 >> >> Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. >> >> Best, >> Kam >> ------------------------------------------------------------------------------ >> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions >> Find What Matters Most in Your Big Data with HPCC Systems >> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. >> Leverages Graph Analysis for Fast Processing & Easy Data Exploration >> http://p.sf.net/sfu/hpccsystems >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
|
From: John D. N. D. <do...@lm...> - 2014-06-24 16:55:17
|
Hi Kam, I've gone ahead and released GenMAPP Builder 2.0b79. This updates UniProt code and SQL to the latest XSD libraries, but may still harbor a latent bug regarding something completely different, but which I have been unable to isolate yet. In particular, just changing the file (but retaining the data where the original XML import failed) seems to avoid the problem. Let me know what happens with your import. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 23, 2014, at 1:27 AM, John David N. Dionisio <do...@lm...> wrote: > Greetings, > > The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve. So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page: > > http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22 > > I will look at this fresh on Monday and report back on how things go. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > > On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: > >> Hi, >> >> I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: >> >> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 >> >> Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. >> >> Best, >> Kam >> ------------------------------------------------------------------------------ >> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions >> Find What Matters Most in Your Big Data with HPCC Systems >> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. >> Leverages Graph Analysis for Fast Processing & Easy Data Exploration >> http://p.sf.net/sfu/hpccsystems >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > |
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From: John D. N. D. <do...@lm...> - 2014-06-23 08:27:13
|
Greetings, The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve. So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page: http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22 I will look at this fresh on Monday and report back on how things go. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: > > http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 > > Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. > > Best, > Kam > ------------------------------------------------------------------------------ > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://p.sf.net/sfu/hpccsystems > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
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From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-19 22:03:10
|
Hi, I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78. The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell). Screenshots of the console window with messages are on my narrative page here: http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19 Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine. Best, Kam |
|
From: John D. N. D. <do...@lm...> - 2014-06-16 08:18:28
|
Greetings, I've updated the GO database libraries to accommodate new elements found in the latest OBO XML that are not mentioned in the most recent version of the DTD. The changes are reflected in GenMAPP Builder 2.0b78; I was able to successfully import a freshly-download OBO XML file with this build so presumably the issue will also go away with your imports. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jun 9, 2014, at 5:04 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > I forgot to mention that the screenshot of the error is shown on my testing report on this page: http://xmlpipedb.sourceforge.net/wiki/index.php/Gene_Database_Testing_Report_V._cholerae_20140609 > > Best, > Kam > > ________________________________________ > From: Dahlquist, Kam D. [Kam...@lm...] > Sent: Monday, June 09, 2014 1:36 PM > To: Dahlquist, Kam D. > Subject: GO file causes null pointer exception error > > [https://lionshare.lmu.edu:443/Depts/lionshare_v2d.jpg] > > > Hi, > > Today's GO OBO-XML file seems to cause a NullPointerException error (I'll e-mail screenshot of error in another message. I'm providing link to GO file in question so you can see for yourself. > > I tried a different GO file, the one on my user page on the BioDB wiki and it seems to work fine, so it looks like it is a problem with this file. I don't want to proceed until we can clear this up--ideally, I want to run exports with the newest data possible. > > Thanks, > > Kam > > The following resources have been shared with you. > > > File Subscribe to and/or Bookmarks > /Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/_xy-465460_1> Subscribe to and/or bookmark go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/subscribeBookmark.action?entryName=/Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz> > > > Thank you, > Dahlquist, Kam D. > > This message was automatically generated. > > ------------------------------------------------------------------------------ > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://p.sf.net/sfu/hpccsystems > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
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From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-10 00:05:31
|
Hi, I forgot to mention that the screenshot of the error is shown on my testing report on this page: http://xmlpipedb.sourceforge.net/wiki/index.php/Gene_Database_Testing_Report_V._cholerae_20140609 Best, Kam ________________________________________ From: Dahlquist, Kam D. [Kam...@lm...] Sent: Monday, June 09, 2014 1:36 PM To: Dahlquist, Kam D. Subject: GO file causes null pointer exception error [https://lionshare.lmu.edu:443/Depts/lionshare_v2d.jpg] Hi, Today's GO OBO-XML file seems to cause a NullPointerException error (I'll e-mail screenshot of error in another message. I'm providing link to GO file in question so you can see for yourself. I tried a different GO file, the one on my user page on the BioDB wiki and it seems to work fine, so it looks like it is a problem with this file. I don't want to proceed until we can clear this up--ideally, I want to run exports with the newest data possible. Thanks, Kam The following resources have been shared with you. File Subscribe to and/or Bookmarks /Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/_xy-465460_1> Subscribe to and/or bookmark go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/subscribeBookmark.action?entryName=/Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz> Thank you, Dahlquist, Kam D. This message was automatically generated. |
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From: Dahlquist, K. D. <Kam...@lm...> - 2014-06-09 22:39:20
|
This didn't make it to the list the first time around. Here it is again. Best, Kam ________________________________________ From: Dahlquist, Kam D. [Kam...@lm...] Sent: Monday, June 09, 2014 1:36 PM To: Dahlquist, Kam D. Subject: GO file causes null pointer exception error [https://lionshare.lmu.edu:443/Depts/lionshare_v2d.jpg] Hi, Today's GO OBO-XML file seems to cause a NullPointerException error (I'll e-mail screenshot of error in another message. I'm providing link to GO file in question so you can see for yourself. I tried a different GO file, the one on my user page on the BioDB wiki and it seems to work fine, so it looks like it is a problem with this file. I don't want to proceed until we can clear this up--ideally, I want to run exports with the newest data possible. Thanks, Kam The following resources have been shared with you. File Subscribe to and/or Bookmarks /Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/_xy-465460_1> Subscribe to and/or bookmark go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz<https://lionshare.lmu.edu/xythoswfs/webview/subscribeBookmark.action?entryName=/Users/kdahlqui/XMLPipeDB/go_daily-termdb_release2017_06_09_2-17AM.obo-xml.gz> Thank you, Dahlquist, Kam D. This message was automatically generated. |
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From: Andrew P. <ap...@li...> - 2014-04-08 19:42:22
|
import sys
original = open(sys.argv[1])
content = original.readlines()
original.close()
file1 = open('output1.txt','w')
file2 = open('output2.txt','w')
file3 = open('output3.txt', 'w')
for index, line in enumerate(content):
if index == 0:
file1.write(line)
file2.write(line)
file3.write(line)
elif index > 0:
if index % 3 == 1:
file1.write(line)
elif index % 3 == 2:
file2.write(line)
elif index % 3 == 0:
file3.write(line)
file1.close()
file2.close()
file3.close() |
|
From: Dionisio, J. D. N. <Joh...@lm...> - 2014-04-08 07:25:00
|
Greetings, GenMAPP Builder 2.0b77 is now available from SourceForge. This release of GenMAPP Builder adds a new Leishmania infantum species profile (taxon ID 5671) to GenMAPP Builder. In the interest of time we have not yet transitioned to the synonym table approach for L. major and L. infantum; for now alternative ID versions remain exported as distinct rows. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University |
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From: Dionisio, J. D. N. <Joh...@lm...> - 2014-04-04 06:50:44
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Greetings, GenMAPP Builder 2.0b76 is now available from SourceForge. For this version we only have the SM_b/smb export variation; pending are how to handle R##### IDs (waiting on analysis of "embedded" vs. non-embedded IDs) and the use of a synonym table for L. major and infantum. Those are expected to land in a succeeding version of GenMAPP Builder. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University |
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From: Kevin M. <km...@li...> - 2014-04-01 17:16:24
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Hey Dr. Dahlquist, Just wanted to provide you with the links to the compiled raw data and the scaled and centered data for L. Major and L. Infantum. They are on lion share. They are public, but if you have any trouble accessing them just let me know! -Kevin https://lionshare.lmu.edu/Users/kmcgee3/L.majorL.infantumCompiledRawData.xls https://lionshare.lmu.edu/Users/kmcgee3/L.majorL.infantumScaledCentered.xls |
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From: Dionisio, J. D. N. <Joh...@lm...> - 2014-04-01 16:42:24
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Hi Kevin, Thanks for the clarification on the Leishmania profiles. I'll move on with those. Meanwhile, on the match question, the likely reason here is that those ID matches are appearing in parts of the XML file that Tally Engine and PostgreSQL do not cover [by default]. The process to resolve this issue is to identify those "extra" IDs and characterize what makes them different. Where in the XML file do they appear? Are they actually synonym variations of IDs that we do capture (i.e., different only due to underscores or periods)? Based on what we have seen of these IDs so far, there is a chance that the latter is the case; let's make that our current hypothesis. Spot checks on a few IDs will do the trick. You can also do a full-scale check of the uncaptured IDs using Microsoft Excel. The procedure for doing that is in the wiki: http://xmlpipedb.sourceforge.net/wiki/index.php/Using_Microsoft_Excel_to_Compare_ID_Lists Hope that helps. Let me know if there are further questions. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Apr 1, 2014, at 9:14 AM, Kevin McGee <km...@li...> wrote: > Hey Dr. Dionisio, > > I am still having trouble getting match to find the correct number of id's. I have gotten tally engine and postgress both to work, but I cannot get match to find something remotely close. Heres a picture of my code and the number of matches I am getting > <xmlipedbmatch_4_1_2014_error.PNG>------------------------------------------------------------------------------ > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
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From: Kevin M. <km...@li...> - 2014-04-01 16:04:17
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Hey Dr. Dionisio, Both these things are correct. The destination table is OrderedLocusNames and L. Infantum does get its own species profile. No worries with the hold ups, better safe than sorry! Kevin McGee On Mon, Mar 31, 2014 at 11:51 PM, Dionisio, John David N. < Joh...@lm...> wrote: > Greetings, > > I know the full additional-column instructions haven't come down yet, but > outside of that I looked into the new synonym-based approach for Leishmania > and ended up with a couple of clarification questions: > > - The destination table name should still be OrderedLocusNames, yes? I > think this is the case but wanted to be sure. > > - L. infantum should still be a species profile in its own right, but with > the exact same export logic (differing only in terms of the initial > pattern), right? > > I have a degree of confidence that these details are in fact what I think > they are, but enough doubt emerged when I started actually getting into the > code that I ended up asking. Sorry for the hold-up caused by this. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > |
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From: Dionisio, J. D. N. <Joh...@lm...> - 2014-04-01 06:51:21
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Greetings, I know the full additional-column instructions haven't come down yet, but outside of that I looked into the new synonym-based approach for Leishmania and ended up with a couple of clarification questions: - The destination table name should still be OrderedLocusNames, yes? I think this is the case but wanted to be sure. - L. infantum should still be a species profile in its own right, but with the exact same export logic (differing only in terms of the initial pattern), right? I have a degree of confidence that these details are in fact what I think they are, but enough doubt emerged when I started actually getting into the code that I ended up asking. Sorry for the hold-up caused by this. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University |
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From: Mitchell P. <mpe...@li...> - 2014-03-27 06:14:11
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I have worked on my poster revisions and would like feedback on it (see attachments; the wiki page is currently slow and not working for me) . I do not have pictures of xmlpipedb-match or an sql query at the moment, so I put in filler graphics for now to indicate the general placement of the missing screenshots later on. |
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From: Dionisio, J. D. N. <Joh...@lm...> - 2014-03-18 16:23:41
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I forgot to mention this last night...2.0b75 is now open for business :) John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University |
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From: Andrew P. <ap...@li...> - 2014-03-12 23:45:41
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To clarify, those links are for custom profiles. I also forgot to include the taxon IDs. G54: 512266 R6: 171101 On Wed, Mar 12, 2014 at 4:06 PM, Andrew Pita <ap...@li...> wrote: > Hey Dr. Dionisio, > > Here are the links that end up in the systems table of the gdb. > > G54: > http://bacteria.ensembl.org/streptococcus_pneumoniae_g54/Gene/Summary?g=~ > > R6: > http://bacteria.ensembl.org/streptococcus_pneumoniae_r6/Gene/Summary?g=~ > > Thanks, > Andrew > |
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From: Kam D. <kda...@lm...> - 2014-03-12 23:14:49
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Hi, To clarify, this is in the Database Configuration window. It does not seem to Save the port number . We are using port 5433 instead of 5432 because we have two versions of Postgres running on the computer. Best, Dr. D At 03:41 PM 3/12/2014, Andrew Pita wrote: >Hey Dr. Dionisio, > >Dr. Dahlquist and I found a small bug when configuring databases in >GenMapp Builder. When switching from one database to another (ie. >just changing the database name but leaving all the other fields >unchanged) the port number shows up as 5433. However, when you click >ok and then attempt to run an export, the database connection >problem message pops up. Upon closing that message the configure >database window returns, but the port number always says 5432. >Changing the port number back to 5433 works fine, and after doing so >everything works perfectly. I tried this a few times to make sure >and each time the same thing happened. Let me know if you need any >clarification. > >Thanks, >Andrew >------------------------------------------------------------------------------ >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 |
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From: John D. N. D. <do...@lm...> - 2014-03-12 23:10:31
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Hi Andrew, OK, thanks for this and the link updates. This is enough information for me to get going; I'll holler if I need more. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Mar 12, 2014, at 3:41 PM, Andrew Pita <ap...@li...> wrote: > Hey Dr. Dionisio, > > Dr. Dahlquist and I found a small bug when configuring databases in GenMapp Builder. When switching from one database to another (ie. just changing the database name but leaving all the other fields unchanged) the port number shows up as 5433. However, when you click ok and then attempt to run an export, the database connection problem message pops up. Upon closing that message the configure database window returns, but the port number always says 5432. Changing the port number back to 5433 works fine, and after doing so everything works perfectly. I tried this a few times to make sure and each time the same thing happened. Let me know if you need any clarification. > > Thanks, > Andrew > ------------------------------------------------------------------------------ > 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 |
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From: Andrew P. <ap...@li...> - 2014-03-12 23:08:26
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Hey Dr. Dionisio, Dr. Dahlquist and I found a small bug when configuring databases in GenMapp Builder. When switching from one database to another (ie. just changing the database name but leaving all the other fields unchanged) the port number shows up as 5433. However, when you click ok and then attempt to run an export, the database connection problem message pops up. Upon closing that message the configure database window returns, but the port number always says 5432. Changing the port number back to 5433 works fine, and after doing so everything works perfectly. I tried this a few times to make sure and each time the same thing happened. Let me know if you need any clarification. Thanks, Andrew |
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From: Andrew P. <ap...@li...> - 2014-03-12 23:06:07
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Hey Dr. Dionisio, Here are the links that end up in the systems table of the gdb. G54: http://bacteria.ensembl.org/streptococcus_pneumoniae_g54/Gene/Summary?g=~ R6: http://bacteria.ensembl.org/streptococcus_pneumoniae_r6/Gene/Summary?g=~ Thanks, Andrew |
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