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From: Rutger V. <rut...@gm...> - 2012-07-25 14:27:09
|
I see. I think that means that, in principle, this ought to work.
-- Famous last words, Rutger Vos, 2012
On Wed, Jul 25, 2012 at 3:36 PM, Mattison Ward
<mat...@ne...> wrote:
> The web server would load balance by session such that a session would
> always be handled by the same tomcat instance (unless the instance
> failed).
>
> On Wed, Jul 25, 2012 at 9:11 AM, Rutger Vos <rut...@gm...> wrote:
>> I think there is a potential for problems with uploads/submissions
>> (where physical files are being processed by mesquite). In the
>> scenario that you're describing, how are sessions managed? I.e. would
>> a session be handled from start to finish by the same tomcat instance?
>>
>> On Wed, Jul 25, 2012 at 2:52 PM, Mattison Ward
>> <mat...@ne...> wrote:
>>> Is treebase written in such a way that having multiple tomcat
>>> application servers would work?
>>>
>>> Is all data written to and read from the database or does curation
>>> involve files in a directory somewhere?
>>>
>>> If we maintained one web server and one database server, but multiple
>>> tomcat servers then a problem with one of the tomcat servers would not
>>> make the site stop responding for everyone.
>>>
>>> The site has been pretty stable for the last few weeks, but during
>>> certain periods, certain file uploads and downloads cause tomcat to
>>> stop responding until restarted. I have automated the restarting as
>>> much as possible, but load balancing is an option we might want to
>>> consider for the future.
>>>
>>> Regards,
>>>
>>> Mattison Ward
>>> NESCent at Duke University
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Bioinformaticist
>> NCB Naturalis
>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
>> http://rutgervos.blogspot.com
>
>
>
> --
> Mattison Ward
> NESCent at Duke University
> 2024 W. Main Street, Suite A200
> Durham, NC 27705-4667
> 919-668-4585 (desk)
> 919-668-4551 (alternate)
> 919-668-9198 (fax)
--
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com
|
|
From: Mattison W. <mat...@ne...> - 2012-07-25 13:37:36
|
The web server would load balance by session such that a session would always be handled by the same tomcat instance (unless the instance failed). On Wed, Jul 25, 2012 at 9:11 AM, Rutger Vos <rut...@gm...> wrote: > I think there is a potential for problems with uploads/submissions > (where physical files are being processed by mesquite). In the > scenario that you're describing, how are sessions managed? I.e. would > a session be handled from start to finish by the same tomcat instance? > > On Wed, Jul 25, 2012 at 2:52 PM, Mattison Ward > <mat...@ne...> wrote: >> Is treebase written in such a way that having multiple tomcat >> application servers would work? >> >> Is all data written to and read from the database or does curation >> involve files in a directory somewhere? >> >> If we maintained one web server and one database server, but multiple >> tomcat servers then a problem with one of the tomcat servers would not >> make the site stop responding for everyone. >> >> The site has been pretty stable for the last few weeks, but during >> certain periods, certain file uploads and downloads cause tomcat to >> stop responding until restarted. I have automated the restarting as >> much as possible, but load balancing is an option we might want to >> consider for the future. >> >> Regards, >> >> Mattison Ward >> NESCent at Duke University >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com -- Mattison Ward NESCent at Duke University 2024 W. Main Street, Suite A200 Durham, NC 27705-4667 919-668-4585 (desk) 919-668-4551 (alternate) 919-668-9198 (fax) |
|
From: Rutger V. <rut...@gm...> - 2012-07-25 13:11:37
|
I think there is a potential for problems with uploads/submissions (where physical files are being processed by mesquite). In the scenario that you're describing, how are sessions managed? I.e. would a session be handled from start to finish by the same tomcat instance? On Wed, Jul 25, 2012 at 2:52 PM, Mattison Ward <mat...@ne...> wrote: > Is treebase written in such a way that having multiple tomcat > application servers would work? > > Is all data written to and read from the database or does curation > involve files in a directory somewhere? > > If we maintained one web server and one database server, but multiple > tomcat servers then a problem with one of the tomcat servers would not > make the site stop responding for everyone. > > The site has been pretty stable for the last few weeks, but during > certain periods, certain file uploads and downloads cause tomcat to > stop responding until restarted. I have automated the restarting as > much as possible, but load balancing is an option we might want to > consider for the future. > > Regards, > > Mattison Ward > NESCent at Duke University > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
|
From: Mattison W. <mat...@ne...> - 2012-07-25 13:00:47
|
Is treebase written in such a way that having multiple tomcat application servers would work? Is all data written to and read from the database or does curation involve files in a directory somewhere? If we maintained one web server and one database server, but multiple tomcat servers then a problem with one of the tomcat servers would not make the site stop responding for everyone. The site has been pretty stable for the last few weeks, but during certain periods, certain file uploads and downloads cause tomcat to stop responding until restarted. I have automated the restarting as much as possible, but load balancing is an option we might want to consider for the future. Regards, Mattison Ward NESCent at Duke University |
|
From: Hilmar L. <hl...@ne...> - 2012-07-03 19:45:00
|
I wonder, too. Keep in mind though that that would only complicate the picture in regard to migrating the wiki content. -hilmar On Jul 3, 2012, at 3:43 PM, Rutger Vos wrote: > Might this be something that pushes us towards github, I wonder? > > On Tue, Jul 3, 2012 at 4:44 PM, Hilmar Lapp <hl...@ne...> wrote: >> Some others here have probably received this, too. Nonetheless, to make sure we're all aware, the MediaWiki for TreeBASE will be going away on Sep 1. The migration to "project web space" isn't documented yet, but we should be on the lookout for that. >> >> -hilmar >> >> Begin forwarded message: >> >>> From: "SourceForge.net Team" <no...@so...> >>> Subject: Hosted Apps Retirement >>> Date: July 3, 2012 10:17:46 AM EDT >>> To: hl...@dr... >>> >>> In case you missed it ... >>> >>> We wanted to be sure you were aware of some upcoming changes to the >>> SourceForge project hosting service. >>> >>> One or more of your projects use the Hosted Apps service. On September 1, >>> 2012, the Hosted Apps service will reach the end of its life and be shut >>> down. The reasons for this are discussed in the blog post, at >>> http://sourceforge.net/blog/hosted-apps-retirement/ and in the wiki, at >>> https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/ >>> >>> >>> Over the coming days, we'll be publishing more documents about how to >>> migrate your apps to your own project web space, so that none of your data >>> is lost in this transition. We want to be sure that your project can >>> continue to operate without interruption, so if you have any concerns, >>> difficulty with migration, or just want to chat, please send us a note >>> (com...@so...). >>> >>> Please watch the wiki page >>> (https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/) >>> for further updates about this process. We'll be back in touch as it gets >>> closer to the deadline, or if anything about the plan changes. >>> >>> Thanks again for being part of the SourceForge community. >>> >>> ---------------------------------------------------------------------- >>> SourceForge.net has made this mailing to you as a registered user of >>> the SourceForge.net site to convey important information regarding >>> your SourceForge.net account or your use of SourceForge.net services. >>> >>> We make a small number of directed mailings to registered users each >>> year regarding their account or data, to help preserve the security of >>> their account or prevent loss of data or service access. >>> >>> If you have concerns about this mailing please contact our Support >>> team per: http://sourceforge.net/support >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Rutger V. <rut...@gm...> - 2012-07-03 19:43:36
|
Might this be something that pushes us towards github, I wonder? On Tue, Jul 3, 2012 at 4:44 PM, Hilmar Lapp <hl...@ne...> wrote: > Some others here have probably received this, too. Nonetheless, to make sure we're all aware, the MediaWiki for TreeBASE will be going away on Sep 1. The migration to "project web space" isn't documented yet, but we should be on the lookout for that. > > -hilmar > > Begin forwarded message: > >> From: "SourceForge.net Team" <no...@so...> >> Subject: Hosted Apps Retirement >> Date: July 3, 2012 10:17:46 AM EDT >> To: hl...@dr... >> >> In case you missed it ... >> >> We wanted to be sure you were aware of some upcoming changes to the >> SourceForge project hosting service. >> >> One or more of your projects use the Hosted Apps service. On September 1, >> 2012, the Hosted Apps service will reach the end of its life and be shut >> down. The reasons for this are discussed in the blog post, at >> http://sourceforge.net/blog/hosted-apps-retirement/ and in the wiki, at >> https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/ >> >> >> Over the coming days, we'll be publishing more documents about how to >> migrate your apps to your own project web space, so that none of your data >> is lost in this transition. We want to be sure that your project can >> continue to operate without interruption, so if you have any concerns, >> difficulty with migration, or just want to chat, please send us a note >> (com...@so...). >> >> Please watch the wiki page >> (https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/) >> for further updates about this process. We'll be back in touch as it gets >> closer to the deadline, or if anything about the plan changes. >> >> Thanks again for being part of the SourceForge community. >> >> ---------------------------------------------------------------------- >> SourceForge.net has made this mailing to you as a registered user of >> the SourceForge.net site to convey important information regarding >> your SourceForge.net account or your use of SourceForge.net services. >> >> We make a small number of directed mailings to registered users each >> year regarding their account or data, to help preserve the security of >> their account or prevent loss of data or service access. >> >> If you have concerns about this mailing please contact our Support >> team per: http://sourceforge.net/support > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
|
From: Hilmar L. <hl...@ne...> - 2012-07-03 14:44:16
|
Some others here have probably received this, too. Nonetheless, to make sure we're all aware, the MediaWiki for TreeBASE will be going away on Sep 1. The migration to "project web space" isn't documented yet, but we should be on the lookout for that. -hilmar Begin forwarded message: > From: "SourceForge.net Team" <no...@so...> > Subject: Hosted Apps Retirement > Date: July 3, 2012 10:17:46 AM EDT > To: hl...@dr... > > In case you missed it ... > > We wanted to be sure you were aware of some upcoming changes to the > SourceForge project hosting service. > > One or more of your projects use the Hosted Apps service. On September 1, > 2012, the Hosted Apps service will reach the end of its life and be shut > down. The reasons for this are discussed in the blog post, at > http://sourceforge.net/blog/hosted-apps-retirement/ and in the wiki, at > https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/ > > > Over the coming days, we'll be publishing more documents about how to > migrate your apps to your own project web space, so that none of your data > is lost in this transition. We want to be sure that your project can > continue to operate without interruption, so if you have any concerns, > difficulty with migration, or just want to chat, please send us a note > (com...@so...). > > Please watch the wiki page > (https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/) > for further updates about this process. We'll be back in touch as it gets > closer to the deadline, or if anything about the plan changes. > > Thanks again for being part of the SourceForge community. > > ---------------------------------------------------------------------- > SourceForge.net has made this mailing to you as a registered user of > the SourceForge.net site to convey important information regarding > your SourceForge.net account or your use of SourceForge.net services. > > We make a small number of directed mailings to registered users each > year regarding their account or data, to help preserve the security of > their account or prevent loss of data or service access. > > If you have concerns about this mailing please contact our Support > team per: http://sourceforge.net/support -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2012-06-21 20:20:01
|
On Jun 21, 2012, at 3:00 PM, Michael Jones wrote: > There is no thesis option for the "Citation Type" field on the > "Citation Information" tab of TreeBASE. For now, I'm guessing I should > upload data from theses as "Book Sections"? Yes -- book section is the best match for thesis, if for a specific chapter. bp |
|
From: Michael J. <mic...@gm...> - 2012-06-21 19:00:12
|
There is no thesis option for the "Citation Type" field on the "Citation Information" tab of TreeBASE. For now, I'm guessing I should upload data from theses as "Book Sections"? |
|
From: Hilmar L. <hl...@ne...> - 2012-06-20 21:30:38
|
I guess the NeXML example file should then be documented so as not to be mistaken as a sample of something one would actually obtain from TreeBASE. -hilmar On Jun 20, 2012, at 4:20 PM, Rutger Vos wrote: > Hi Hilmar, > > that example file was generated using this unit test: > > http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlAnalysisConverterTest.java?revision=1095&view=markup > > I am very sorry but I don't have the time right now to deploy this on > TreeBASE, but it wouldn't be hard to do - it would need to be folded > into the document writer here: > > http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java?revision=1095&view=markup > > Cheers, > > Rutger > > On Wed, Jun 20, 2012 at 6:04 PM, Hilmar Lapp <hl...@ne...> wrote: >> There is an example NeXML file in the examples folder that suggests that it is reproduced from TreeBASE (and its study number is actually a valid one): >> >> http://nexml.org/nexml/examples/treebase-record.xml >> >> However, this differs significantly from the one returned by TreeBASE for this study: >> >> http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml >> >> Specifically, the analysis input and output connections between trees and matrices are gone in the TreeBASE-produced version. This is rather unfortunate (at least from a MIAPA standpoint), because there doesn't seem to be any other way to connect characters and trees through an analysis with one as the input and the other as the output. Although Both characters and trees elements reference otus elements, referencing the same otus element doesn't have to mean that they are connected through one analysis. >> >> Are there plans to also capture the analysis input/output in the TreeBASE NeXML? >> >> -hilmar >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Hilmar L. <hl...@ne...> - 2012-06-20 21:28:55
|
On Jun 20, 2012, at 4:46 PM, William Piel wrote: > But separately, as you point out, something called "tb:identifier.study" is defined in the NeXML with just the number "794" -- which is the ID number for the row in the study table. > > Perhaps this should be changed to the fully qualified 'http://purl.org/phylo/treebase/phylows/study/TB2:S794' ? I think so. There may be room for two identifiers - one the globally unique URI, and two the TreeBASE internal identifier or "accession number", and the tb:identifier.study predicate should reference one of them. But right now there are more than that being advertised (794, S794, TB2:S794, http://purl.org/phylo/treebase/phylows/study/TB2:S794) and it's confusing as a consumer what to make of the value of the tb:identifier.study property. So based on the PhyloWS pattern the TreeBASE internal accession number is "TB2:S794", which through TreeBASE's support of PhyloWS gives rise to the globally unique identifier http://purl.org/phylo/treebase/phylows/study/TB2:S794. For the sake of clarity, no other variants should be exposed through the data or metadata exports (though of course it's nice that one can also search by 'S794' or even '794'). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2012-06-20 20:46:54
|
On Jun 20, 2012, at 11:44 AM, Hilmar Lapp wrote: > It seems that the studyID in TreeBASE's NeXML output is given with the leading 'S', although everywhere else the studyID is quoted with the leading 'S'. For example for study S794: > > <meta content="794" datatype="xsd:string" id="meta901" property="tb:identifier.study" xsi:type="nex:LiteralMeta"/> > > http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml > > I notice that I can search either variant through the UI and it finds the study. However, this URL does *not* work: > > http://purl.org/phylo/treebase/phylows/study/TB2:794?format=nexml > > What does this mean semantically? Are S794 and 794 as studyIDs synonymous or not? And shouldn't the <meta> attribute give the ID with the leading 'S' if that's also the ID exposed everywhere else? I guess some of this is a legacy of the older TreeBASE, in which we encouraged people to prefix numbers with a letter so that it's clear what they're referring to. e.g. SN12345 = "submission number" S12345 = study ID number M12345 = matrix ID number etc. With TreeBASE2 the idea was that each study would be identified using a long globally unique string that itself is resolvable to some metadata about the object, and the chosen format looks like: 'http://purl.org/phylo/treebase/phylows/study/TB2:S794'. That is supposed to be the identifier that will continue to work regardless of any new migrations to TreeBASE3, TreeBASE4, etc. -- i.e. it's our version of a Dryad data DOI without having to pay for one. If we dissect this identifier, we can see the id for the record in the study table is somewhere in there (794) with the 'S' tradition retained. Perhaps the UI should be designed to match on /(.+S|S)*\d+$/ so that it hits on both fully qualified and semi-qualified versions of the full identifier, e.g.: 'http://purl.org/phylo/treebase/phylows/study/TB2:S794', 'TB2:S794', 'S794', '794'. For the NeXML, the xml:base is defined: xml:base="http://purl.org/phylo/treebase/phylows/study/TB2:" thus expecting to append 'S794' via an xlink:href value of "S794" or a "#S794" value. So that would be in keeping with the idea that the real identifier is the long, globally unique string. But separately, as you point out, something called "tb:identifier.study" is defined in the NeXML with just the number "794" -- which is the ID number for the row in the study table. Perhaps this should be changed to the fully qualified 'http://purl.org/phylo/treebase/phylows/study/TB2:S794' ? bp |
|
From: Rutger V. <rut...@gm...> - 2012-06-20 20:21:01
|
Hi Hilmar, that example file was generated using this unit test: http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlAnalysisConverterTest.java?revision=1095&view=markup I am very sorry but I don't have the time right now to deploy this on TreeBASE, but it wouldn't be hard to do - it would need to be folded into the document writer here: http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java?revision=1095&view=markup Cheers, Rutger On Wed, Jun 20, 2012 at 6:04 PM, Hilmar Lapp <hl...@ne...> wrote: > There is an example NeXML file in the examples folder that suggests that it is reproduced from TreeBASE (and its study number is actually a valid one): > > http://nexml.org/nexml/examples/treebase-record.xml > > However, this differs significantly from the one returned by TreeBASE for this study: > > http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml > > Specifically, the analysis input and output connections between trees and matrices are gone in the TreeBASE-produced version. This is rather unfortunate (at least from a MIAPA standpoint), because there doesn't seem to be any other way to connect characters and trees through an analysis with one as the input and the other as the output. Although Both characters and trees elements reference otus elements, referencing the same otus element doesn't have to mean that they are connected through one analysis. > > Are there plans to also capture the analysis input/output in the TreeBASE NeXML? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
|
From: Hilmar L. <hl...@ne...> - 2012-06-20 16:04:53
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There is an example NeXML file in the examples folder that suggests that it is reproduced from TreeBASE (and its study number is actually a valid one): http://nexml.org/nexml/examples/treebase-record.xml However, this differs significantly from the one returned by TreeBASE for this study: http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml Specifically, the analysis input and output connections between trees and matrices are gone in the TreeBASE-produced version. This is rather unfortunate (at least from a MIAPA standpoint), because there doesn't seem to be any other way to connect characters and trees through an analysis with one as the input and the other as the output. Although Both characters and trees elements reference otus elements, referencing the same otus element doesn't have to mean that they are connected through one analysis. Are there plans to also capture the analysis input/output in the TreeBASE NeXML? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2012-06-20 15:44:43
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It seems that the studyID in TreeBASE's NeXML output is given with the leading 'S', although everywhere else the studyID is quoted with the leading 'S'. For example for study S794: <meta content="794" datatype="xsd:string" id="meta901" property="tb:identifier.study" xsi:type="nex:LiteralMeta"/> http://purl.org/phylo/treebase/phylows/study/TB2:S794?format=nexml I notice that I can search either variant through the UI and it finds the study. However, this URL does *not* work: http://purl.org/phylo/treebase/phylows/study/TB2:794?format=nexml What does this mean semantically? Are S794 and 794 as studyIDs synonymous or not? And shouldn't the <meta> attribute give the ID with the leading 'S' if that's also the ID exposed everywhere else? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Mattison W. <mat...@ne...> - 2012-06-19 20:54:09
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---------- Forwarded message ---------- From: Michael Jones <mjo...@gm...> Date: Tue, Jun 19, 2012 at 4:30 PM Subject: Re: [Treebase-devel] treebase file download issues To: Mattison Ward <mat...@ne...> P.S. I sent an email to Hilmar asking if TreeBASE was down for maintenance at 1:28. I had tried to download something, realized it was taking a really long time, reloaded, and then reattempted downloading. Then I got a site unavailable error. Cheers, Micael On Tue, Jun 19, 2012 at 4:27 PM, Michael Jones <mjo...@gm...> wrote: > Hi Mattison, > I'm not sure how much traffic there is on TreeBASE, but I was using > the production site when it crashed (under the username jonesmcc). I > can't remember specifically, but I was definitely working on one of my > "In Progress" submissions and think I was attempting to diagnose some > taxa labeling issues while interconverting between nex and NeXML > formats. > Let me know if you would like any further information. > Cheers, > Michael > > On Tue, Jun 19, 2012 at 4:03 PM, Mattison Ward > <mat...@ne...> wrote: >> Sorry for the repeat message to some folks, but I wanted to send this >> to the whole list. >> >> Occasionally the tomcat process on the production or development site >> will go through the roof for cpu usage and stop responding until >> killed and restarted. I have searched through the error logs, but >> haven't found anything obvious to me. I am starting to suspect that >> trying to download certain studies in nexml format precipitates the >> problem. If several of these nexml files in a row start to pile up, >> memory usage by the JVM keeps increasing and the server stops >> responding. >> >> You can see this yourself if you try to download the nexml file from >> http://treebase-dev.nescent.org/treebase-web/search/study/summary.html?id=12742 >> >> The nexus file for that study downloads almost immediately. >> >> You can see in the screenshot one that I left running for over 10 >> minutes. It maybe if I left these running long enough they would >> complete, but in practice these requests can overwhelm the server if >> they are not serial (like in my test). >> >> Other "problem" study ids between 12800 and 11753 >> 12201 killed after 10 minutes (killed nexus download after 10 >> minutes,but database was busy rather than java/tomcat) >> 12156 killed after 10 minutes (5 seconds for nexus) >> 12064 = 5 minutes (3 seconds for nexus) >> 12032 = 4 minutes (1 second for nexus) >> 11872 = 10 minutes (52 seconds for nexus) >> 11811 killed after 10 minutes (35 seconds for nexus) >> >> Note that I turned Apache caching off for these tests and will leave >> it off for anyone else to test. >> >> Could timeouts for uploading and downloading files be implemented so >> too many concurrent downloads don't disable the site? >> >> Maybe some studies are too large to be converted to nexml in a >> workable amount of time? >> >> Is treebase written in such a way that we could deploy many tomcat >> instances pointed to a common database so that if one client requested >> many downloads, it would only tie up one tomcat instance while the >> other 7 would keep serving requests happily? >> >> -- >> Mattison >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> -- Mattison Ward NESCent at Duke University 2024 W. Main Street, Suite A200 Durham, NC 27705-4667 919-668-4585 (desk) 919-668-4551 (alternate) 919-668-9198 (fax) |
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From: Mattison W. <mat...@ne...> - 2012-06-19 20:03:58
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Sorry for the repeat message to some folks, but I wanted to send this to the whole list. Occasionally the tomcat process on the production or development site will go through the roof for cpu usage and stop responding until killed and restarted. I have searched through the error logs, but haven't found anything obvious to me. I am starting to suspect that trying to download certain studies in nexml format precipitates the problem. If several of these nexml files in a row start to pile up, memory usage by the JVM keeps increasing and the server stops responding. You can see this yourself if you try to download the nexml file from http://treebase-dev.nescent.org/treebase-web/search/study/summary.html?id=12742 The nexus file for that study downloads almost immediately. You can see in the screenshot one that I left running for over 10 minutes. It maybe if I left these running long enough they would complete, but in practice these requests can overwhelm the server if they are not serial (like in my test). Other "problem" study ids between 12800 and 11753 12201 killed after 10 minutes (killed nexus download after 10 minutes,but database was busy rather than java/tomcat) 12156 killed after 10 minutes (5 seconds for nexus) 12064 = 5 minutes (3 seconds for nexus) 12032 = 4 minutes (1 second for nexus) 11872 = 10 minutes (52 seconds for nexus) 11811 killed after 10 minutes (35 seconds for nexus) Note that I turned Apache caching off for these tests and will leave it off for anyone else to test. Could timeouts for uploading and downloading files be implemented so too many concurrent downloads don't disable the site? Maybe some studies are too large to be converted to nexml in a workable amount of time? Is treebase written in such a way that we could deploy many tomcat instances pointed to a common database so that if one client requested many downloads, it would only tie up one tomcat instance while the other 7 would keep serving requests happily? -- Mattison |
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From: Hilmar L. <hl...@ne...> - 2012-06-19 16:55:45
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You can use "svn copy" with the -r parameter to specify the date or revision at which you want to retroactively branch off. However, in this case it sounds like you want to maintain the more "conservative code" (i.e., the code without some new features) on the main trunk, and the new feature on the branch. In that case I would branch off (svn copy) from trunk/ now (without using -r), which keeps all the new code on that branch. Then on the main trunk undo the commits that introduced the for now unwanted functionality using reverse merge: http://svnbook.red-bean.com/en/1.2/svn.branchmerge.commonuses.html#svn.branchmerge.commonuses.undo BTW any reason why this wasn't on the developers list? -hilmar > ---------- Forwarded message ---------- > From: Rutger Vos <rut...@gm...> > Date: Tue, Jun 19, 2012 at 12:30 PM > Subject: Re: New commits > To: William Piel <wil...@ya...> > Cc: Mattison Ward <mat...@ne...>, Harry Shyket > <har...@ya...> > > > Hi Bill, > > you're right, it would be nice if the new search functionality was on > a separate branch so that other fixes can continue more easily. I'm > afraid I'm actually not experienced with creating branches > retroactively, does anyone else know? > > Rutger > > On Tue, Jun 19, 2012 at 5:47 PM, William Piel <wil...@ya...> wrote: >> >> Hi Rutger, >> >> I guess I'm a little conflicted about the new changes you've made: on the >> one hand, the one-field system is has a nice Zen to it, on the other hand we >> will be losing the ability to do more sophisticated searches. I wonder if we >> can "shelve" this new interface for a little while until we have an >> opportunity to have the best of both worlds: i.e. a radio-button that would >> allow building queries or de-novo queries. On the other hand, some minor >> fixes are being made and those cannot be pushed to production. >> >> What do people think about the possibility of forking your changes >> temporarily so that these newer minor changes can be applied to production, >> and then at a later date (once the radio-button has been fixed) reconcile >> the fork back into production? >> >> bp >> >> >> >> On May 29, 2012, at 4:06 AM, Rutger Vos wrote: >> >> Do you think it's possible to have a radio-button switch somewhere in the >> >> header: "New queries applied to previous results vs. New queries are always >> >> de novo" ? >> >> >> Sure, that would definitely be possible, but I'm afraid I don't really >> have the time this week or the next to make it so. Can we put it in >> the issue tracker? >> >> > > > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Michael J. <mjo...@gm...> - 2012-06-15 14:12:49
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Hi Bill, A day or so after sending this email, I went back and resolved all of the names by googling them. Ergo, I changed the Hystrix label to Hystrix africaeaustralis, as it was shown in the paper. The hyperlink in my previous message entitled, "validate by hand", still links to the error message that presented for me, however, and I think I've run into this error message a few more times. The next time I run into this error (if at all), I will make sure preserve it as an example and bring it to your attention. Cheers, Michael On Tue, Jun 12, 2012 at 2:05 PM, William Piel <wil...@ya...> wrote: > > On Jun 12, 2012, at 11:47 AM, Michael Jones wrote: > > Hello, > Upon attempting to resolve some taxa labelling issues for TreeBASE > submission 12826 (Sustained high levels of neuregulin-1 in the > longest-lived rodents; a key determinant of rodent longevity, by Edrey, > Casper et al.), I was presented with the error message: "Hystrix appears > to be a homonym; defaulted to first hit, but please validate by hand<http://www.treebase.org/treebase-web/user/editTaxonLabel.html?taxonlabelid=811236> > ." When I clicked the hyperlink, I was presented with a null pointer > exception error message with the header, "Uncaught Exception Encountered". > Furthermore, I found that I was unable to resolve the error message even by > going straight to the Taxon Label Editor for the the Hystrix taxa label. > Michael > > > hmm.. I don't see any "Hystrix" there, or, for that matter, a homonym > alert message. I do see a "Hystrix africaeaustralis" -- but no error or > homonym alert. > > bp > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Hilmar L. <hl...@ne...> - 2012-06-13 23:48:03
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It's a phylogenetic tree, so I don't know why it wouldn't fit under TreeBASE scope. It shouldn't matter that the tips aren't taxa - they're still OTUs. -hilmar Sent with a tap. On Jun 13, 2012, at 11:00 AM, Michael Jones <mjo...@gm...> wrote: > Hi all, > I've come across an interesting Dryad submission, available http://datadryad.org/resource/doi:10.5061/dryad.8081, which includes mitochondrial nucleotide sequences for several subgroups of Canis along with sequences for canine transmissible venereal tumor (CTVT). I was wondering if this sort of data should be included in TreeBASE. Since CTVT is a cell line instead of taxa, I'm guessing I shouldn't upload it, but I just wanted to make sure. > Thanks, > Michael > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: William P. <wil...@ya...> - 2012-06-13 15:20:43
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I think it would be a great addition. The taxon labels need editing, and they might get a bit long. e.g.: Canis_lupus_lupus_Russia (for the correct subspecies, see here) Canis_lupus_familiaris_Cocker_Spaniel Canis_lupus_familiaris_Line_h42M Canis_lupus_familiaris_Line_62C_67C_68C (etc). bp On Jun 13, 2012, at 11:00 AM, Michael Jones wrote: > Hi all, > I've come across an interesting Dryad submission, available http://datadryad.org/resource/doi:10.5061/dryad.8081, which includes mitochondrial nucleotide sequences for several subgroups of Canis along with sequences for canine transmissible venereal tumor (CTVT). I was wondering if this sort of data should be included in TreeBASE. Since CTVT is a cell line instead of taxa, I'm guessing I shouldn't upload it, but I just wanted to make sure. > Thanks, > Michael > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Michael J. <mjo...@gm...> - 2012-06-13 15:00:27
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Hi all, I've come across an interesting Dryad submission, available http://datadryad.org/resource/doi:10.5061/dryad.8081, which includes mitochondrial nucleotide sequences for several subgroups of Canis along with sequences for canine transmissible venereal tumor (CTVT). I was wondering if this sort of data should be included in TreeBASE. Since CTVT is a cell line instead of taxa, I'm guessing I shouldn't upload it, but I just wanted to make sure. Thanks, Michael |
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From: William P. <wil...@ya...> - 2012-06-12 18:05:47
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On Jun 12, 2012, at 11:47 AM, Michael Jones wrote: > Hello, > Upon attempting to resolve some taxa labelling issues for TreeBASE submission 12826 (Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity, by Edrey, Casper et al.), I was presented with the error message: "Hystrix appears to be a homonym; defaulted to first hit, but please validate by hand." When I clicked the hyperlink, I was presented with a null pointer exception error message with the header, "Uncaught Exception Encountered". Furthermore, I found that I was unable to resolve the error message even by going straight to the Taxon Label Editor for the the Hystrix taxa label. > Michael hmm.. I don't see any "Hystrix" there, or, for that matter, a homonym alert message. I do see a "Hystrix africaeaustralis" -- but no error or homonym alert. bp |
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From: Hilmar L. <hl...@ne...> - 2012-06-12 17:00:31
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Hi Michael, that looks like a bad bug - can you put that into the bug tracker on SourceForge? -hilmar On Jun 12, 2012, at 11:47 AM, Michael Jones wrote: > Hello, > Upon attempting to resolve some taxa labelling issues for TreeBASE submission 12826 (Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity, by Edrey, Casper et al.), I was presented with the error message: "Hystrix appears to be a homonym; defaulted to first hit, but please validate by hand." When I clicked the hyperlink, I was presented with a null pointer exception error message with the header, "Uncaught Exception Encountered". Furthermore, I found that I was unable to resolve the error message even by going straight to the Taxon Label Editor for the the Hystrix taxa label. > Michael > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Michael J. <mjo...@gm...> - 2012-06-12 15:47:40
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Hello, Upon attempting to resolve some taxa labelling issues for TreeBASE submission 12826 (Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity, by Edrey, Casper et al.), I was presented with the error message: "Hystrix appears to be a homonym; defaulted to first hit, but please validate by hand<http://www.treebase.org/treebase-web/user/editTaxonLabel.html?taxonlabelid=811236> ." When I clicked the hyperlink, I was presented with a null pointer exception error message with the header, "Uncaught Exception Encountered". Furthermore, I found that I was unable to resolve the error message even by going straight to the Taxon Label Editor for the the Hystrix taxa label. Michael |
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