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Hi, It looks like UniProt loaded OK, but gmb2b83 crashed during the export. Screenshot of error on this page: http://xmlpipedb.sourceforge.net/wiki/index.php/Gene_Database_Testing_Report_S._oneidensis_MR-1_2015年06月16日 Kam
> >Hi Dondi, > >One of the BioQUEST participants was interested in exporting a gdb >for Shewanella oneidensis, taxon ID ><http://www.uniprot.org/taxonomy/211586>211586 . So, I went ahead >and did it, testing report >here: >http://xmlpipedb.sourceforge.net/wiki/index.php/Gene_Database_Testing_Report_S._oneidensis_MR-1_2015年06月14日#Export_Information > >I was able to do an import/export cycle, but the UniProt XML file >only loaded partially, 350 out of 4068 entries. There is a >screenshot of the error in the console window on the wiki referenced above. > >Would you be able to take a look at this? I'll LionShare the source files. > >If I get a chance, I'll try Vibrio just to see if this is a species >problem or a general UniProt problem. > >Thanks, >Kam
Hi Dr. Dionisio, Forgot to let you know, I was able to export an L. major database on gmbuilder-2.0b82. Thank you for your help, Kevin McGee
Hi Kevin, I've completed an update to GenMAPP Builder that should be able to import L. major version 54 now. The new GenMAPP Builder version is 2.0b82. Let me know how it goes; thanks! John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University > On Feb 10, 2015, at 5:27 PM, Kevin McGee <km...@li...> wrote: > > Dr. Dionisio, > > Both Uniprot Files (The old working file and the new non working file) for L. major are on the wiki at the top of my profile. Hope that this helps. > > > Kevin McGee > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/_______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Hi Kevin,
Sorry it took me until the break to look into this. The issue is that the latest XML has again added a new element (maybe more) that the XMLPipeDB database code does not handle. I will need to update this code then produce a new release. Stand by and I will let you know when it is out.
Specifically, the new element is a 'cofactor' tag. The precise reported error is:
DefaultValidationEventHandler: [ERROR]: Unexpected element {http://uniprot.org/uniprot}:cofactor Location: line 41
Because processing aborts at this point, it is not yet known if other new elements exist. As I work to update the database code, I will seek to make sure that we cover everything that is new in this file.
John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University
> On Feb 10, 2015, at 5:27 PM, Kevin McGee <km...@li...> wrote:
>
> Dr. Dionisio,
>
> Both Uniprot Files (The old working file and the new non working file) for L. major are on the wiki at the top of my profile. Hope that this helps.
>
>
> Kevin McGee
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/_______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Dr. Dionisio, Both Uniprot Files (The old working file and the new non working file) for L. major are on the wiki at the top of my profile. Hope that this helps. Kevin McGee
Dr. Dionisio, The files are not available for download at the moment, I will be sure to put it on the wiki tomorrow. Best regards, Kevin > On Feb 3, 2015, at 10:33 PM, John David N. Dionisio <do...@lm...> wrote: > > Hi Kevin, > > OK, thanks for reporting this. Are the exact files used available for download somewhere? My first step here would be to replicate the problem so that the issue can be triaged. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > >> On Feb 3, 2015, at 5:33 PM, Kevin McGee <km...@li...> wrote: >> >> Dr. Dionisio, >> >> There appears to be a problem when trying to upload updated Uniprot files into new databases in GenMAPP Builder for both L. major and L. infantum. I downloaded them from the Uniprot site in XML format. When I uploaded either of these into GenMAPP Builder, they only need .03 minutes to upload or less. This happened last week, I re-downloaded the Uniprot file and tested it again twice today to make sure this wasn't a glitch. I also ran a tally engine test on the Uniprot file for L. major and it appeared to have everything in it. When I uploaded an older version of the Uniprot file, they took a normal amount of time. I'm not really sure whats going on with the files. I attached a screen clipping of the tally engine and the GenMAPP Builder completion message below as well as put them on my wiki. Thanks for the help! >> >> -Kevin >> <GenMAPP Builder problem 20150203.PNG><Tally Engine problem 20150203.PNG>------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming. The Go Parallel Website, >> sponsored by Intel and developed in partnership with Slashdot Media, is your >> hub for all things parallel software development, from weekly thought >> leadership blogs to news, videos, case studies, tutorials and more. Take a >> look and join the conversation now. http://goparallel.sourceforge.net/_______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Hi Kevin, OK, thanks for reporting this. Are the exact files used available for download somewhere? My first step here would be to replicate the problem so that the issue can be triaged. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University > On Feb 3, 2015, at 5:33 PM, Kevin McGee <km...@li...> wrote: > > Dr. Dionisio, > > There appears to be a problem when trying to upload updated Uniprot files into new databases in GenMAPP Builder for both L. major and L. infantum. I downloaded them from the Uniprot site in XML format. When I uploaded either of these into GenMAPP Builder, they only need .03 minutes to upload or less. This happened last week, I re-downloaded the Uniprot file and tested it again twice today to make sure this wasn't a glitch. I also ran a tally engine test on the Uniprot file for L. major and it appeared to have everything in it. When I uploaded an older version of the Uniprot file, they took a normal amount of time. I'm not really sure whats going on with the files. I attached a screen clipping of the tally engine and the GenMAPP Builder completion message below as well as put them on my wiki. Thanks for the help! > > -Kevin > <GenMAPP Builder problem 20150203.PNG><Tally Engine problem 20150203.PNG>------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/_______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Dr. Dionisio, There appears to be a problem when trying to upload updated Uniprot files into new databases in GenMAPP Builder for both L. major and L. infantum. I downloaded them from the Uniprot site in XML format. When I uploaded either of these into GenMAPP Builder, they only need .03 minutes to upload or less. This happened last week, I re-downloaded the Uniprot file and tested it again twice today to make sure this wasn't a glitch. I also ran a tally engine test on the Uniprot file for L. major and it appeared to have everything in it. When I uploaded an older version of the Uniprot file, they took a normal amount of time. I'm not really sure whats going on with the files. I attached a screen clipping of the tally engine and the GenMAPP Builder completion message below as well as put them on my wiki. Thanks for the help! -Kevin
Greetings, I don't think we've specifically coded for this...I'll have to walk through the code to determine what happens when multiple profiles are involved. I suspect it may be the last profile in the list, because this would be the last piece of code to write the link-out pattern. But this will need review. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Oct 10, 2014, at 2:35 PM, Kam Dahlquist <kda...@lm...> wrote: > Hi, > > I just wanted to let everyone know that the combined S. aureus > MRSA252 and COL gene database finished exporting. A quick look at > the gdb in access looks like the tables are full. Sarah can finish > the testing report the next time that she comes in. > > One issue that has come up, however. How does GenMAPP Builder choose > which profile to use the link out for (the link out that is listed in > the Systems table)? In this case, it looks like it used the one for > MRSA252, which won't work for COL gene IDs. In the short term, I > think we need to change the linkout for MRSA252 to EnsemblBacteria > like it is for COL, but in the long term, we probably need to ask the > user what they want to use in the wizard for exporting. > > Best, > Kam > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://p.sf.net/sfu/Zoho > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
I agree---not a bad idea. Makes things easier to reproduce. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Oct 10, 2014, at 3:21 PM, Kam Dahlquist <kda...@lm...> wrote: > Hi Dondi, > > I had a question for you. What do you think about posting the > UniProt XML, GO OBO-XML, and GOA files to the SourceForge repository > as we go forward with releasing gdb's? I'm thinking that it's > actually a little difficult to track down the older versions of > source files and this will make our work more reproducible. We would > only do this moving forward because I don't have the time to track > down all the previous versions of things. Let me know what you think. > > Kam > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://p
Hi, I noticed that the XMLPipeDB web site hasn't been updated in quite some time. I have to leave in 10 minutes, so I don't have time right now to enumerate the changes, but I wanted to get that on your radar, in case you have some time. Best, Kam
Hi Dondi, I had a question for you. What do you think about posting the UniProt XML, GO OBO-XML, and GOA files to the SourceForge repository as we go forward with releasing gdb's? I'm thinking that it's actually a little difficult to track down the older versions of source files and this will make our work more reproducible. We would only do this moving forward because I don't have the time to track down all the previous versions of things. Let me know what you think. Kam
Hi, Please find attached the S. aureus MRSA252 gdb ready for release. I've zipped together the gdb and the ReadMe. Best, Kam
Hi, I just wanted to let everyone know that the combined S. aureus MRSA252 and COL gene database finished exporting. A quick look at the gdb in access looks like the tables are full. Sarah can finish the testing report the next time that she comes in. One issue that has come up, however. How does GenMAPP Builder choose which profile to use the link out for (the link out that is listed in the Systems table)? In this case, it looks like it used the one for MRSA252, which won't work for COL gene IDs. In the short term, I think we need to change the linkout for MRSA252 to EnsemblBacteria like it is for COL, but in the long term, we probably need to ask the user what they want to use in the wizard for exporting. Best, Kam
Hi, Sarah didn't receive the reply to her last e-mail; can you check to see that she's been added to the xmlpipedb-developer list? use the e-mail sa....@gm... Thanks, Kam
Greetings Sarah, I have uploaded a new version of GenMAPP Builder, version 2.0b81, which includes a custom species profile for S. aureus COL. This version adds the taxon ID that you requested plus sets the custom link pattern. With regard to tally engine behavior, I need to dig a bit further before determining the proper fix. I figure that the discrepancy of two is due to two ordered locus records that are "slashed" IDs---i.e., they really are two IDs in a single "record," and thus both XML and PostgreSQL count them once. However, GenMAPP export separates them, and they thus add to the OrderedLocusNames count. I downloaded and searched the XML file for S. aureus COL (newer than what you have by a few days) and found the following "slashed" IDs: <name type="ordered locus">SACOL0317/SACOL0390</name> <name type="ordered locus">SACOL0081/SACOL0082</name> There are indeed two of them---explaining why OrderedLocusNames increases by 2 upon export. If this is what we want Tally Engine to take into account, then I will work to modify it accordingly then post a new version when ready. Meanwhile, I hope the new export profile creates a GenMAPP Gene Database file that is better suited for your study. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Sep 16, 2014, at 9:29 AM, Sarah Patno <sp...@li...> wrote: > Hi Dr. Dionisio, > > Please create a custom profile for this Taxon ID: 93062. > > The link out for OrderedLocusNames should be to this: > > http://ensemblgenomes.org/id/~ > > Thank you, > Sarah Patno > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk_______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Hi Sarah, OK, I can look at this. Presumably you have a testing report available with links to the original XML file? Those will be useful to have so I can get a specific handle on what needs to be changed. Please send a link to the report and/or file; thanks! John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Sep 16, 2014, at 9:33 AM, Sarah Patno <sp...@li...> wrote: > Hi Dr. Dionisio, > > When we ran the tally engine for the OrderedLocusNames ID's for SACOL we got 2678 for both the XML and the posgres database, but when we ran Match we got 2680 and we also got 2680 in the gdb. There might be some ID's that were separated by a slash and tally engine didn't separate them. Please fix this problem. > > Thank you, > Sarah Patno > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk_______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
Hi Dr. Dionisio, Please create a custom profile for this Taxon ID: 93062. The link out for OrderedLocusNames should be to this: http://ensemblgenomes.org/id/~ Thank you, Sarah Patno
Hi Dr. Dionisio, When we ran the tally engine for the OrderedLocusNames ID's for SACOL we got 2678 for both the XML and the posgres database, but when we ran Match we got 2680 and we also got 2680 in the gdb. There might be some ID's that were separated by a slash and tally engine didn't separate them. Please fix this problem. Thank you, Sarah Patno
Yes, it seems that the species filtering did not go all the way to the relationship exporting code. I will have to look at this more closely. Wow---47 GB compressed...now *that* is getting to "big data." And I agree it will probably not end up exporting a match for our needs. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Jul 1, 2014, at 2:28 PM, Dahlquist, Kam D. <Kam...@lm...> wrote: > Hi, > > The export of H. pylori from the UniProt_All postgres database crashed at the relations tables. It was stuck and I clicked the cancel button and the Fatal error message came up shown on the wiki here: > > http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014年06月27日 > > I also note that the UniProt table had only about 500 records when ~1500 were expected (judging by the single-proteome export). I am sure this is because the TrEMBL records were missing. I looked into downloading TrEMBL, but it is ~47 GB compressed! Even if we wanted to deal with that large of a file, chances are that an export from that would have many more records than the proteome and not be suitable for our needs. > > So it looks like we are stuck with the single species proteomes for now. > > However, we should maybe still look into this bug because it might potentially affect other exports when multiple species are loaded. > > I was thinking that I might start loading multiple species' proteomes into the same postgres database so that I don't have to keep loading/processing GO all the time. > > 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
Hi, The export of H. pylori from the UniProt_All postgres database crashed at the relations tables. It was stuck and I clicked the cancel button and the Fatal error message came up shown on the wiki here: http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014年06月27日 I also note that the UniProt table had only about 500 records when ~1500 were expected (judging by the single-proteome export). I am sure this is because the TrEMBL records were missing. I looked into downloading TrEMBL, but it is ~47 GB compressed! Even if we wanted to deal with that large of a file, chances are that an export from that would have many more records than the proteome and not be suitable for our needs. So it looks like we are stuck with the single species proteomes for now. However, we should maybe still look into this bug because it might potentially affect other exports when multiple species are loaded. I was thinking that I might start loading multiple species' proteomes into the same postgres database so that I don't have to keep loading/processing GO all the time. Best, Kam
Hi, I started an export of H. pylori on Friday using the UniProt_all database I made. As of today, it hasn't finished (normally takes only a couple hours). it seems to be stuck at the relationship tables; a screenshot of the console window is attached. I won't kill it just yet until you confirm it's stuck or if I come back tomorrow and it's still at the same point. Best, Kam
Hi, I'm sure this is good for now. I'll give it a try when I get the chance (not in the office today) and let you know how it goes. Best, Kam ________________________________________ From: John David N. Dionisio [do...@lm...] Sent: Friday, June 27, 2014 2:55 PM To: xml...@li... Subject: Re: [XMLPipeDB-developer] export taxon list not sorted OK, I've released GenMAPP Builder 2.0b80 to SourceForge. The species list is now sorted by taxon ID, so it should be easier to scroll to the desired species on that basis. In addition, the listing shows the species name first now, providing another alternative to finding a species---if you click on the species list, you can then start typing the name of the species and the list should take you to the matching one. Ideally, I would prefer to make this list a table now, with columns for taxon ID and species name that you can click in order to change the sort order. A typeahead filter can also make searching even faster. That would take a little more time though. However, if we decide this is worthwhile, I can go ahead and do it. I figured I'd do just this initially just so you can have at least one way to home in on a species other than scrolling around. 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 ------------------------------------------------------------------------------ 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
OK, I've released GenMAPP Builder 2.0b80 to SourceForge. The species list is now sorted by taxon ID, so it should be easier to scroll to the desired species on that basis. In addition, the listing shows the species name first now, providing another alternative to finding a species---if you click on the species list, you can then start typing the name of the species and the list should take you to the matching one. Ideally, I would prefer to make this list a table now, with columns for taxon ID and species name that you can click in order to change the sort order. A typeahead filter can also make searching even faster. That would take a little more time though. However, if we decide this is worthwhile, I can go ahead and do it. I figured I'd do just this initially just so you can have at least one way to home in on a species other than scrolling around. 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