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From: Roderic P. <r....@bi...> - 2010-12-15 08:37:48
|
I've been downloading NEXML files from TreeBASE with a view to making a local copy in CouchDB. TreeBASE NEXML is pretty unpleasant to deal with, but it does give me a complete summary of a study. However, generating the NEXML file can take what seems like an age, particularly for large data sets. I've written a script to harvest NEXML for each study, but this regularly times out. Is there anyway this could be speed up, perhaps by having TreeBASE cache NEXML files so users are grabbing a text document, not forcing live queries to the database? Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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From: Arlin S. <ar...@um...> - 2010-12-04 15:04:26
|
On Nov 18, 2010, at 12:13 PM, Hilmar Lapp wrote: > Arlin - I agree completely. Would you mind adding this to the feature > tracker (or given how broken from a usability perspective this is, you > might as well add it to the bug tracker). done: https://sourceforge.net/tracker/?func=detail&aid=3127413&group_id=248804&atid=1126676 arlin > -hilmar > > On Nov 16, 2010, at 2:14 PM, Arlin Stoltzfus wrote: > >> Dear all-- >> >> I think the web-based search interface is misleading in a way that >> will frustrate users. The search is progressive, but this isn't >> advertised, and users are not accustomed to it. If a newbie issues a >> query, gets some results, and realizes from the results that she is >> searching for the wrong thing, then she is going to enter a new query >> value and try to search again. She'll see either a) a yellow warning >> bar saying "No matching studies found", followed by the list of >> studies that were found (in the previous query), or b) a result list >> that is only a subset of what she really wants, because its a subset >> of the earlier botched query. >> >> This isn't an imaginary example. It happened to me when I first >> tried >> the new query interface. Then it happened to me again because I >> forgot >> what I had learned the first time. >> >> I didn't see the "Discard all Results" button because I wasn't >> looking >> for it, and because its at the bottom of the list, which means that >> if >> you get more than 3 or 4 hits, its going to be below the browser pane >> and invisible. >> >> I would suggest to make each search independent, i.e., clear the >> results with each new query, rather than using a progressive search. >> Alternatively, the messages could be more informative and the >> "discard" button could be put at the top of the list. In any case, >> it >> wouldn't hurt to widen the layout and abbreviate the titles so that >> the results list takes up less space. >> >> Arlin >> ------- >> Arlin Stoltzfus (ar...@um...) >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST >> IBBR, 9600 Gudelsky Drive, Rockville, MD >> tel: 240 314 6208; web: www.molevol.org >> >> >> ------------------------------------------------------------------------------ >> Beautiful is writing same markup. Internet Explorer 9 supports >> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. >> Spend less time writing and rewriting code and more time creating >> great >> experiences on the web. Be a part of the beta today >> http://p.sf.net/sfu/msIE9-sfdev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
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From: Hilmar L. <hl...@ne...> - 2010-11-18 17:14:05
|
Arlin - I agree completely. Would you mind adding this to the feature tracker (or given how broken from a usability perspective this is, you might as well add it to the bug tracker). -hilmar On Nov 16, 2010, at 2:14 PM, Arlin Stoltzfus wrote: > Dear all-- > > I think the web-based search interface is misleading in a way that > will frustrate users. The search is progressive, but this isn't > advertised, and users are not accustomed to it. If a newbie issues a > query, gets some results, and realizes from the results that she is > searching for the wrong thing, then she is going to enter a new query > value and try to search again. She'll see either a) a yellow warning > bar saying "No matching studies found", followed by the list of > studies that were found (in the previous query), or b) a result list > that is only a subset of what she really wants, because its a subset > of the earlier botched query. > > This isn't an imaginary example. It happened to me when I first tried > the new query interface. Then it happened to me again because I forgot > what I had learned the first time. > > I didn't see the "Discard all Results" button because I wasn't looking > for it, and because its at the bottom of the list, which means that if > you get more than 3 or 4 hits, its going to be below the browser pane > and invisible. > > I would suggest to make each search independent, i.e., clear the > results with each new query, rather than using a progressive search. > Alternatively, the messages could be more informative and the > "discard" button could be put at the top of the list. In any case, it > wouldn't hurt to widen the layout and abbreviate the titles so that > the results list takes up less space. > > Arlin > ------- > Arlin Stoltzfus (ar...@um...) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating > great > experiences on the web. Be a part of the beta today > http://p.sf.net/sfu/msIE9-sfdev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2010-11-16 19:46:51
|
On Nov 16, 2010, at 2:14 PM, Arlin Stoltzfus wrote: > Alternatively, the messages could be more informative Yeah, this is a problem. Perhaps a warning message would be best. (e.g., the way we have yellow warning messages when you go from one tab to another). bp |
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From: Arlin S. <ar...@um...> - 2010-11-16 19:14:40
|
Dear all-- I think the web-based search interface is misleading in a way that will frustrate users. The search is progressive, but this isn't advertised, and users are not accustomed to it. If a newbie issues a query, gets some results, and realizes from the results that she is searching for the wrong thing, then she is going to enter a new query value and try to search again. She'll see either a) a yellow warning bar saying "No matching studies found", followed by the list of studies that were found (in the previous query), or b) a result list that is only a subset of what she really wants, because its a subset of the earlier botched query. This isn't an imaginary example. It happened to me when I first tried the new query interface. Then it happened to me again because I forgot what I had learned the first time. I didn't see the "Discard all Results" button because I wasn't looking for it, and because its at the bottom of the list, which means that if you get more than 3 or 4 hits, its going to be below the browser pane and invisible. I would suggest to make each search independent, i.e., clear the results with each new query, rather than using a progressive search. Alternatively, the messages could be more informative and the "discard" button could be put at the top of the list. In any case, it wouldn't hurt to widen the layout and abbreviate the titles so that the results list takes up less space. Arlin ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
|
From: William P. <wil...@ya...> - 2010-11-05 18:41:17
|
On Nov 4, 2010, at 4:59 PM, Hilmar Lapp wrote: > Smells like an abuse of the keyword field in TreeBASE to me, and should therefore be fixed in TreeBASE. Bill? Yes. I think it snuck in as part of the TB1->TB2 migration. I will produce a set of SQL command to correct this (and some other things). bp |
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From: Hilmar L. <hl...@ne...> - 2010-11-04 20:59:23
|
Smells like an abuse of the keyword field in TreeBASE to me, and
should therefore be fixed in TreeBASE. Bill?
-hilmar
On Nov 4, 2010, at 2:14 PM, Vladimir Gapeyev wrote:
> [I am cc'ing this thread to treebase-devel, per Hilmar's request]
>
> I will add to OAI record creation a keyword tokenizer that uses ","
> and ";" as delimiters.
>
> Here is another issue: Lots of entries in Treebase contain "in
> press" as the keyword, which Kevin's code on the Dryad side does not
> accept as such. Should this elimination of "in press" remain on the
> Dryad side? I.e., is "in press" a valid keyword from Treebase point
> of view? If not, should this be fixed by erasing "in press" values
> from the DB or by filtering them out of OAI records sent out?
>
> --Vladimir
>
>
> On Nov 3, 2010, at 5:10 PM, William Piel wrote:
>
>>
>> The solution of splitting the string using either commas or semi-
>> colons looks fine to me. (and why should it be a problem if the
>> string has a mix of the two? Seems to me that it should work by
>> spitting on either.) It's not impossible that some authors will use
>> other non-standard delimiters, such as the long hyphen (" — ") the
>> double hyphen ("--") and the bullet " • " but there's only so many
>> options for us to accommodate.
>>
>> bp
>>
>>
>>
>> On Nov 3, 2010, at 4:58 PM, Hilmar Lapp wrote:
>>
>>> I think Bill Piel will need to at least chime in here, and
>>> possibly others. Would you mind posting this to the treebase-devel
>>> list?
>>>
>>> -hilmar
>>>
>>> On Nov 3, 2010, at 2:56 PM, Vladimir Gapeyev wrote:
>>>
>>>> I've put this request for clarification in SF tracker, please
>>>> advise. --Vladimir
>>>>
>>>> Begin forwarded message:
>>>>
>>>>> From: "SourceForge.net" <no...@so...>
>>>>> Date: November 3, 2010 2:49:37 PM EDT
>>>>> To: no...@so...
>>>>> Subject: [Treebase-guts] [ treebase-Bugs-3079602 ] OAI records
>>>>> contain all subjects in a single field
>>>>>
>>>>>
>>>>> Initial Comment:
>>>>> In the OAI records, each <dc:subject> field contains many
>>>>> keywords, separated by commas, like this:
>>>>>
>>>>> <dc:subject>
>>>>> Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution,
>>>>> lichens, multigene phylogeny, phylogenomics, plant pathogens,
>>>>> saprobes, Tree of Life
>>>>> </dc:subject>
>>>>>
>>>>> It is best practice to put each keyword into a separate
>>>>> <dc:subject> field. This allows harvesting systems (like Dryad)
>>>>> to accurately separate the keywords, and not worry about
>>>>> keywords that may contain commas.
>>>>>
>>>>> ----------------------------------------------------------------------
>>>>>
>>>>>> Comment By: Vladimir Gapeyev (vgapeyev)
>>>>> Date: 2010-11-03 14:49
>>>>>
>>>>> Message:
>>>>> This is a request for clarification.
>>>>>
>>>>> Treebase UI offers a single field to enter keywords, text from
>>>>> which is
>>>>> stored in a single field in the database. From the data in
>>>>> treebase-dev I
>>>>> see that users used ',' or ';' to separate multiple keywords.
>>>>>
>>>>> Here is what I can do: Get Kevin's keyword-splitting code and
>>>>> place it on
>>>>> Treebase side, modifying if necessary to work with both ';' and
>>>>> ','. This
>>>>> would not work nicely if the user has a fancy to use comma-
>>>>> containing
>>>>> keywords separated by semicolons, or the other way around.
>>>>>
>>>>> Please confirm that this is what is needed.
>>
>>
>>
>>
>
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
===========================================================
|
|
From: Vladimir G. <vla...@du...> - 2010-11-04 18:14:54
|
[I am cc'ing this thread to treebase-devel, per Hilmar's request]
I will add to OAI record creation a keyword tokenizer that uses ","
and ";" as delimiters.
Here is another issue: Lots of entries in Treebase contain "in press"
as the keyword, which Kevin's code on the Dryad side does not accept
as such. Should this elimination of "in press" remain on the Dryad
side? I.e., is "in press" a valid keyword from Treebase point of
view? If not, should this be fixed by erasing "in press" values from
the DB or by filtering them out of OAI records sent out?
--Vladimir
On Nov 3, 2010, at 5:10 PM, William Piel wrote:
>
> The solution of splitting the string using either commas or semi-
> colons looks fine to me. (and why should it be a problem if the
> string has a mix of the two? Seems to me that it should work by
> spitting on either.) It's not impossible that some authors will use
> other non-standard delimiters, such as the long hyphen (" — ") the
> double hyphen ("--") and the bullet " • " but there's only so many
> options for us to accommodate.
>
> bp
>
>
>
> On Nov 3, 2010, at 4:58 PM, Hilmar Lapp wrote:
>
>> I think Bill Piel will need to at least chime in here, and possibly
>> others. Would you mind posting this to the treebase-devel list?
>>
>> -hilmar
>>
>> On Nov 3, 2010, at 2:56 PM, Vladimir Gapeyev wrote:
>>
>>> I've put this request for clarification in SF tracker, please
>>> advise. --Vladimir
>>>
>>> Begin forwarded message:
>>>
>>>> From: "SourceForge.net" <no...@so...>
>>>> Date: November 3, 2010 2:49:37 PM EDT
>>>> To: no...@so...
>>>> Subject: [Treebase-guts] [ treebase-Bugs-3079602 ] OAI records
>>>> contain all subjects in a single field
>>>>
>>>>
>>>> Initial Comment:
>>>> In the OAI records, each <dc:subject> field contains many
>>>> keywords, separated by commas, like this:
>>>>
>>>> <dc:subject>
>>>> Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution,
>>>> lichens, multigene phylogeny, phylogenomics, plant pathogens,
>>>> saprobes, Tree of Life
>>>> </dc:subject>
>>>>
>>>> It is best practice to put each keyword into a separate
>>>> <dc:subject> field. This allows harvesting systems (like Dryad)
>>>> to accurately separate the keywords, and not worry about keywords
>>>> that may contain commas.
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>>> Comment By: Vladimir Gapeyev (vgapeyev)
>>>> Date: 2010-11-03 14:49
>>>>
>>>> Message:
>>>> This is a request for clarification.
>>>>
>>>> Treebase UI offers a single field to enter keywords, text from
>>>> which is
>>>> stored in a single field in the database. From the data in
>>>> treebase-dev I
>>>> see that users used ',' or ';' to separate multiple keywords.
>>>>
>>>> Here is what I can do: Get Kevin's keyword-splitting code and
>>>> place it on
>>>> Treebase side, modifying if necessary to work with both ';' and
>>>> ','. This
>>>> would not work nicely if the user has a fancy to use comma-
>>>> containing
>>>> keywords separated by semicolons, or the other way around.
>>>>
>>>> Please confirm that this is what is needed.
>
>
>
>
|
|
From: William P. <wil...@ya...> - 2010-11-02 00:36:24
|
On Nov 1, 2010, at 7:02 PM, Hilmar Lapp wrote: > Bill - is this in the tracker already to be fixed? I just added it (artifact 3101147). bp |
|
From: Hilmar L. <hl...@ne...> - 2010-11-01 23:02:22
|
Bill - is this in the tracker already to be fixed? -hilmar On Nov 1, 2010, at 11:29 AM, William Piel wrote: > > On Nov 1, 2010, at 11:08 AM, Rutger Vos wrote: > >> To me, tree-editing seems like an odd requirement anyway. It would be >> much better for all involved if all editing is done inside client- >> side >> mesquite. > > Well.. as it is, we currently use two completely different versions > of PhyloWidget in TreeBASE. On the search/browse side, we use the > latest version of PhyloWidget from phylowidget.org(*) -- and > launched from the phylowidget.org site. On the submission side, we > use a locally (i.e. server) stored, older stripped-down version, but > modified to allow writing to the database. One solution is to > replace the search/browse links so that they point to jsPhyloSVG. > > bp > > (*) that's not entirely true, in that for trees accessed through / > phylows/, they are displayed in the older, stripped-down version -- > which, is an oversight. It would be better if that, too, used the > latest phylowidget.org version, or alternatively, jsPhyloSVG. > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America > contest > Create new apps & games for the Nokia N8 for consumers in U.S. and > Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in > marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi > Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2010-11-01 15:37:44
|
On Nov 1, 2010, at 11:24 AM, Hilmar Lapp wrote: > On Nov 1, 2010, at 11:17 AM, William Piel wrote: > >> Though, for the browse/search side of TreeBASE, editing is not needed. > > Is it needed elsewhere, e.g., for the submission process? Yes, insofar as we allow users to upload trees and then reroot them there (and save to the database). (Unfortunately, obliging people to use Mesquite from the beginning -- and having them reroot their trees in that environment -- is not easy. Lots of disoriented trees still get submitted straight from a PAUP output). bp |
|
From: William P. <wil...@ya...> - 2010-11-01 15:29:52
|
On Nov 1, 2010, at 11:08 AM, Rutger Vos wrote: > To me, tree-editing seems like an odd requirement anyway. It would be > much better for all involved if all editing is done inside client-side > mesquite. Well.. as it is, we currently use two completely different versions of PhyloWidget in TreeBASE. On the search/browse side, we use the latest version of PhyloWidget from phylowidget.org(*) -- and launched from the phylowidget.org site. On the submission side, we use a locally (i.e. server) stored, older stripped-down version, but modified to allow writing to the database. One solution is to replace the search/browse links so that they point to jsPhyloSVG. bp (*) that's not entirely true, in that for trees accessed through /phylows/, they are displayed in the older, stripped-down version -- which, is an oversight. It would be better if that, too, used the latest phylowidget.org version, or alternatively, jsPhyloSVG. |
|
From: Hilmar L. <hl...@ne...> - 2010-11-01 15:24:48
|
On Nov 1, 2010, at 11:17 AM, William Piel wrote: > Though, for the browse/search side of TreeBASE, editing is not needed. Is it needed elsewhere, e.g., for the submission process? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2010-11-01 15:17:41
|
On Nov 1, 2010, at 9:52 AM, Rutger Vos wrote: > Did you hear that jsPhyloSVG now supports NeXML? I think it's an > alternative to PhyloWidget that is worth considering, though there are > also downsides - primarily that it doesn't allow editing of trees. Though, for the browse/search side of TreeBASE, editing is not needed. bp |
|
From: William P. <wil...@ya...> - 2010-11-01 15:14:51
|
On Oct 31, 2010, at 11:20 PM, Hilmar Lapp wrote: > On Oct 29, 2010, at 11:28 AM, William Piel wrote: > >> The temporary solution for this particular study is to go through records where phylotree_id is between 9407 and 9414 and check that the string stored in the newickstring field ends in a ";". I would do this with Navicat, but I don't have access to the production database. > > Bill - shouldn't this be an SQL script that goes through the whole database? I.e., why is this more complicated than UPDATE phylotree SET newickstring = newickstring || ';' WHERE STRPOS(newickstring,';') < LENGTH(newickstring) > > -hilmar Yeah, that should work. (though, note that I'm not positive that the problem is due to a missing ";" in the newickstring field -- the database that I have access to is a version that pre-dates the addition of these problem trees) bp |
|
From: Rutger V. <rut...@gm...> - 2010-11-01 15:09:00
|
To me, tree-editing seems like an odd requirement anyway. It would be much better for all involved if all editing is done inside client-side mesquite. On Mon, Nov 1, 2010 at 2:20 PM, Hilmar Lapp <hl...@ne...> wrote: > Yeah - I thought editing is a requirement. If it's not switching to the more > lightweight jsPhyloSVG seems favorable to me too. > > -hilmar > > On Nov 1, 2010, at 9:52 AM, Rutger Vos wrote: > >> Did you hear that jsPhyloSVG now supports NeXML? I think it's an >> alternative to PhyloWidget that is worth considering, though there are >> also downsides - primarily that it doesn't allow editing of trees. >> >> On Mon, Nov 1, 2010 at 3:13 AM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> On Oct 29, 2010, at 11:28 AM, William Piel wrote: >>> >>> Why would this be the case for some trees but not others? I'm guessing >>> that >>> instead of writing the newick on the fly, TreeBASE is just grabbing the >>> newick string from a stored version (table: phylotree field: >>> newickstring), >>> and for some reason the stored version is missing a semicolon (could be >>> that >>> the authors rerooted the trees using our reroot tool, and our reroot tool >>> has a bug wherein it doesn't return a string with a semicolon -- hence >>> why >>> we don't see this problem with all trees). >>> >>> Is that bug in the tracker? Is it difficult to fix? I.e., is this more >>> complicated than finding the property setter and changing it so that it >>> makes sure that there is always a semicolon at the end? >>> -hilmar >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>> contest >>> Create new apps & games for the Nokia N8 for consumers in U.S. and >>> Canada >>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>> marketing >>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>> http://p.sf.net/sfu/nokia-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Hilmar L. <hl...@ne...> - 2010-11-01 14:20:48
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Yeah - I thought editing is a requirement. If it's not switching to the more lightweight jsPhyloSVG seems favorable to me too. -hilmar On Nov 1, 2010, at 9:52 AM, Rutger Vos wrote: > Did you hear that jsPhyloSVG now supports NeXML? I think it's an > alternative to PhyloWidget that is worth considering, though there are > also downsides - primarily that it doesn't allow editing of trees. > > On Mon, Nov 1, 2010 at 3:13 AM, Hilmar Lapp <hl...@ne...> wrote: >> >> On Oct 29, 2010, at 11:28 AM, William Piel wrote: >> >> Why would this be the case for some trees but not others? I'm >> guessing that >> instead of writing the newick on the fly, TreeBASE is just grabbing >> the >> newick string from a stored version (table: phylotree field: >> newickstring), >> and for some reason the stored version is missing a semicolon >> (could be that >> the authors rerooted the trees using our reroot tool, and our >> reroot tool >> has a bug wherein it doesn't return a string with a semicolon -- >> hence why >> we don't see this problem with all trees). >> >> Is that bug in the tracker? Is it difficult to fix? I.e., is this >> more >> complicated than finding the property setter and changing it so >> that it >> makes sure that there is always a semicolon at the end? >> -hilmar >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> ------------------------------------------------------------------------------ >> Nokia and AT&T present the 2010 Calling All Innovators-North >> America contest >> Create new apps & games for the Nokia N8 for consumers in U.S. and >> Canada >> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >> marketing >> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi >> Store >> http://p.sf.net/sfu/nokia-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-11-01 13:52:43
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Did you hear that jsPhyloSVG now supports NeXML? I think it's an alternative to PhyloWidget that is worth considering, though there are also downsides - primarily that it doesn't allow editing of trees. On Mon, Nov 1, 2010 at 3:13 AM, Hilmar Lapp <hl...@ne...> wrote: > > On Oct 29, 2010, at 11:28 AM, William Piel wrote: > > Why would this be the case for some trees but not others? I'm guessing that > instead of writing the newick on the fly, TreeBASE is just grabbing the > newick string from a stored version (table: phylotree field: newickstring), > and for some reason the stored version is missing a semicolon (could be that > the authors rerooted the trees using our reroot tool, and our reroot tool > has a bug wherein it doesn't return a string with a semicolon -- hence why > we don't see this problem with all trees). > > Is that bug in the tracker? Is it difficult to fix? I.e., is this more > complicated than finding the property setter and changing it so that it > makes sure that there is always a semicolon at the end? > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2010-11-01 03:30:44
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On Oct 29, 2010, at 11:28 AM, William Piel wrote: > Why would this be the case for some trees but not others? I'm > guessing that instead of writing the newick on the fly, TreeBASE is > just grabbing the newick string from a stored version (table: > phylotree field: newickstring), and for some reason the stored > version is missing a semicolon (could be that the authors rerooted > the trees using our reroot tool, and our reroot tool has a bug > wherein it doesn't return a string with a semicolon -- hence why we > don't see this problem with all trees). Is that bug in the tracker? Is it difficult to fix? I.e., is this more complicated than finding the property setter and changing it so that it makes sure that there is always a semicolon at the end? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-11-01 03:20:56
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On Oct 29, 2010, at 11:28 AM, William Piel wrote: > The temporary solution for this particular study is to go through > records where phylotree_id is between 9407 and 9414 and check that > the string stored in the newickstring field ends in a ";". I would > do this with Navicat, but I don't have access to the production > database. Bill - shouldn't this be an SQL script that goes through the whole database? I.e., why is this more complicated than UPDATE phylotree SET newickstring = newickstring || ';' WHERE STRPOS(newickstring,';') < LENGTH(newickstring) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-10-29 15:28:39
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On Oct 28, 2010, at 7:34 PM, Hilmar Lapp wrote: > The trees at http://www.treebase.org/treebase-web/search/study/trees.html?id=10562 > won't display in the phylowidget link. Is that specific to this > study, these trees, or do we have a general issue with PhyloWidget > right now? Looks like whenever one of these trees are downloaded, TreeBASE is neglecting to add a ";" to the end of the newick. e.g.: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr9408?format=nexus Mesquite is very forgiving, and loads the tree properly anyway. Phylowidget and TreeViewX are not so forgiving. Why would this be the case for some trees but not others? I'm guessing that instead of writing the newick on the fly, TreeBASE is just grabbing the newick string from a stored version (table: phylotree field: newickstring), and for some reason the stored version is missing a semicolon (could be that the authors rerooted the trees using our reroot tool, and our reroot tool has a bug wherein it doesn't return a string with a semicolon -- hence why we don't see this problem with all trees). The temporary solution for this particular study is to go through records where phylotree_id is between 9407 and 9414 and check that the string stored in the newickstring field ends in a ";". I would do this with Navicat, but I don't have access to the production database. bp |
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From: Hilmar L. <hl...@ne...> - 2010-10-28 23:35:08
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The trees at http://www.treebase.org/treebase-web/search/study/trees.html?id=10562 won't display in the phylowidget link. Is that specific to this study, these trees, or do we have a general issue with PhyloWidget right now? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-10-22 14:48:13
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On Oct 22, 2010, at 9:18 AM, Hilmar Lapp wrote: > That's a known issue. We delete those "by hand" mostly, where by hand is running a script. > > -hilmar Yeah... for added nuance: submissions can be deleted if the trees and matrices inside them are deleted first. Course, in your case, the added problem is that the 720 x 6309 matrix and tree are themselves reticent to delete. I did manage to get this matrix deleted in Martin Wu's account: even though there is a proxy time-out, the program seems to still grind on, eventually deleting the data. A 720 x 6309 matrix has about 5 million records to delete, and it looks like Hibernate's approach is inefficient. The tree, however, still refuses to delete, which I find weird because 720 taxa is not a big tree. But, as Hilmar mentioned, we have a perl script to delete tree blocks -- this has successfully deleted tree blocks with 5,000 trees in them of 150 taxa each, so deleting a single tree of 720 taxa shouldn't be a problem. bp |
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From: Hilmar L. <hl...@ne...> - 2010-10-22 13:18:41
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That's a known issue. We delete those "by hand" mostly, where by hand is running a script. -hilmar On Oct 22, 2010, at 9:14 AM, Arlin Stoltzfus wrote: > Dear TB developers-- > > In the past month I have uploaded several test files in order to > test the TB submission process. Overall, I'm very impressed with > the process! > > However, I find that I can't delete any of the aborted entries. I > press the "X" (end of row in the study table) to delete, then the > "Are you sure?" page loads and I press the "delete study" button. > But then I get an error message. I tried it again this morning and > got the error message below. > > I also tried it with a very large submission (720 OTUs, 6309 aa > characters). The server has not yet responded, after about 10 > minutes. > > Arlin > > Data Access Failure > > Batch update returned unexpected row count from update [0]; actual > row count: 0; expected: 1; nested exception is > org.hibernate.StaleStateException: Batch update returned unexpected > row count from update [0]; actual row count: 0; expected: 1 > > org > .springframework > .orm.hibernate3.HibernateOptimisticLockingFailureException: Batch > update returned unexpected row count from update [0]; actual row > count: 0; expected: 1; nested exception is > org.hibernate.StaleStateException: Batch update returned unexpected > row count from update [0]; actual row count: 0; expected: 1 Caused > by: org.hibernate.StaleStateException: Batch update returned > unexpected row count from update [0]; actual row count: 0; expected: > 1 at org.hibernate.jdbc.Expectations > $BasicExpectation.checkBatched(Expectations.java:61) at > org.hibernate.jdbc.Expectations > $BasicExpectation.verifyOutcome(Expectations.java:46) at > org > .hibernate > .jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:24) at > org > .hibernate > .persister > .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: > 2525) at > org > .hibernate > .persister > .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: > 2702) at > org > .hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java: > 77) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java: > 279) at > org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: > 263) at > org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: > 172) at > org > .hibernate > .event > .def > .AbstractFlushingEventListener > .performExecutions(AbstractFlushingEventListener.java:298) at > org > .hibernate > .event > .def > .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: > 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) > at org.springframework.orm.hibernate3.HibernateTemplate > $27.doInHibernate(HibernateTemplate.java:811) at > org > .springframework > .orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java: > 372) at > org > .springframework > .orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:809) > at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:158) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at > sun > .reflect > .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun > .reflect > .DelegatingMethodAccessorImpl > .invoke(DelegatingMethodAccessorImpl.java:43) at > java.lang.reflect.Method.invoke(Method.java:616) at > org > .springframework > .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: > 304) at > org > .springframework > .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: > 198) at $Proxy53.flush(Unknown Source) at > org > .cipres > .treebase > .service > .study > .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: > 428) at > org > .cipres > .treebase > .service > .study > .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: > 900) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun > .reflect > .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun > .reflect > .DelegatingMethodAccessorImpl > .invoke(DelegatingMethodAccessorImpl.java:43) at > java.lang.reflect.Method.invoke(Method.java:616) at > org > .springframework > .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: > 304) at > org > .springframework > .aop > .framework > .ReflectiveMethodInvocation > .invokeJoinpoint(ReflectiveMethodInvocation.java:182) at > org > .springframework > .aop > .framework > .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: > 149) at > org > .springframework > .transaction > .interceptor > .TransactionInterceptor.invoke(TransactionInterceptor.java:106) at > org > .springframework > .aop > .framework > .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: > 171) at > org > .springframework > .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: > 204) at $Proxy81.deleteSubmission(Unknown Source) at > org > .cipres > .treebase > .web > .controllers > .DeleteStudyController.onSubmit(DeleteStudyController.java:71) at > org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission > (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission > (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal > (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest > (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle > (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch > (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService > (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest > (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost > (FrameworkServlet.java:441) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 269) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .tuckey > .web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) > at > org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java: > 141) at > org > .tuckey > .web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java: > 90) at > org > .tuckey > .web > .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java: > 406) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .displaytag > .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: > 125) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .springframework > .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: > 70) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .springframework > .orm > .hibernate3 > .support > .OpenSessionInViewFilter > .doFilterInternal(OpenSessionInViewFilter.java:198) at > org > .springframework > .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: > 75) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > com > .opensymphony > .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at > com > .opensymphony > .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at > org > .acegisecurity > .intercept > .web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: > 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter > (FilterSecurityInterceptor.java:72) at > org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at > org > .acegisecurity > .ui > .ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java: > 110) at org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at > org > .acegisecurity > .wrapper > .SecurityContextHolderAwareRequestFilter > .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at > org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at > org > .acegisecurity > .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: > 217) at org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at > org > .acegisecurity > .context > .HttpSessionContextIntegrationFilter > .doFilter(HttpSessionContextIntegrationFilter.java:191) at > org.acegisecurity.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at > org > .acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: > 148) at > org > .acegisecurity > .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .apache > .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: > 213) at > org > .apache > .catalina.core.StandardContextValve.invoke(StandardContextValve.java: > 172) at > org > .apache > .catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org > .apache > .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org > .apache > .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: > 108) at > org > .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: > 174) at > org > .apache.coyote.http11.Http11Processor.process(Http11Processor.java: > 873) at org.apache.coyote.http11.Http11BaseProtocol > $Http11ConnectionHandler.processConnection(Http11BaseProtocol.java: > 665) at > org > .apache > .tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java: > 528) at > org > .apache > .tomcat > .util > .net > .LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java: > 81) at org.apache.tomcat.util.threads.ThreadPool > $ControlRunnable.run(ThreadPool.java:689) at > java.lang.Thread.run(Thread.java:636) « Back > > > ------- > Arlin Stoltzfus (ar...@um...) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America > contest > Create new apps & games for the Nokia N8 for consumers in U.S. and > Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in > marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi > Store > http://p.sf.net/sfu/nokia-dev2dev_______________________________________________ > 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: Arlin S. <ar...@um...> - 2010-10-22 13:14:11
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Dear TB developers-- In the past month I have uploaded several test files in order to test the TB submission process. Overall, I'm very impressed with the process! However, I find that I can't delete any of the aborted entries. I press the "X" (end of row in the study table) to delete, then the "Are you sure?" page loads and I press the "delete study" button. But then I get an error message. I tried it again this morning and got the error message below. I also tried it with a very large submission (720 OTUs, 6309 aa characters). The server has not yet responded, after about 10 minutes. Arlin Data Access Failure Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1; nested exception is org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 org .springframework .orm.hibernate3.HibernateOptimisticLockingFailureException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1; nested exception is org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 Caused by: org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 at org.hibernate.jdbc.Expectations $BasicExpectation.checkBatched(Expectations.java:61) at org.hibernate.jdbc.Expectations $BasicExpectation.verifyOutcome(Expectations.java:46) at org .hibernate.jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java: 24) at org .hibernate .persister .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 2525) at org .hibernate .persister .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 2702) at org .hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java: 77) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 263) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:172) at org .hibernate .event .def .AbstractFlushingEventListener .performExecutions(AbstractFlushingEventListener.java:298) at org .hibernate .event .def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at org.springframework.orm.hibernate3.HibernateTemplate $27.doInHibernate(HibernateTemplate.java:811) at org .springframework .orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:372) at org .springframework .orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:809) at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:158) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 57) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 43) at java.lang.reflect.Method.invoke(Method.java:616) at org .springframework .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: 304) at org .springframework .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:198) at $Proxy53.flush(Unknown Source) at org .cipres .treebase .service .study .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 428) at org .cipres .treebase .service .study .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 900) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 57) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 43) at java.lang.reflect.Method.invoke(Method.java:616) at org .springframework .aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java: 304) at org .springframework .aop .framework .ReflectiveMethodInvocation .invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org .springframework .aop .framework .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 149) at org .springframework .transaction .interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java: 106) at org .springframework .aop .framework .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 171) at org .springframework .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy81.deleteSubmission(Unknown Source) at org.cipres.treebase.web.controllers.DeleteStudyController.onSubmit (DeleteStudyController.java:71) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost (FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 269) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java: 164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java: 141) at org .tuckey .web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java: 90) at org .tuckey .web .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java: 406) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .displaytag .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: 125) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .springframework .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 70) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .springframework .orm .hibernate3 .support .OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java: 198) at org .springframework .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 75) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com .opensymphony .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com .opensymphony .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org .acegisecurity .intercept .web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter (FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .ui .ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java: 110) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .wrapper .SecurityContextHolderAwareRequestFilter .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 217) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .context .HttpSessionContextIntegrationFilter .doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: 148) at org .acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java: 90) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .apache .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: 213) at org .apache .catalina.core.StandardContextValve.invoke(StandardContextValve.java: 172) at org .apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java: 127) at org .apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 117) at org .apache .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: 174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java: 873) at org.apache.coyote.http11.Http11BaseProtocol $Http11ConnectionHandler.processConnection(Http11BaseProtocol.java: 665) at org .apache .tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java: 528) at org .apache .tomcat .util .net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java: 81) at org.apache.tomcat.util.threads.ThreadPool $ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) « Back ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
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