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From: youjun g. <you...@gm...> - 2010-02-02 21:06:39
|
Hi, Rutger, I just finished on this: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2944669&group_id=248804 The code has been committed to sourceforge, please rebuild and redeploy the TB application when you settle down. YOujun |
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From: Vladimir G. <vla...@du...> - 2010-02-02 20:23:22
|
On Jan 11, 2010, at 4:16 PM, William Piel wrote: > > The citation metadata are now available here: > > http://www.treebase.org/treebase/migration/Dec-09/citations_utf8.zip Bill, could you remind me what tools are available to handle this citation metadata? I just went through the emails since December and through the instructions at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DataDumps , and neither seemed to mention anything relevant. (I only see instructions for trees, characters, dump_utf8.txt, and taxon intelligence.) Thanks, --Vladimir |
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From: Hilmar L. <hl...@ne...> - 2010-02-02 19:02:51
|
OK so we are on now for 10am EST tomorrow, Feb 3. Good luck Rutger with the London traffic :-) -hilmar On Feb 2, 2010, at 1:16 PM, Rutger Vos wrote: > Thanks for biting the bullit, Hilmar, sorry about the mess up. > Wednesday 10AM EST works for me. > > (Still on the bus, which is now of course hopelessly stuck in > afternoon traffic.) > > On Tuesday, February 2, 2010, Hilmar Lapp <hl...@ne...> wrote: >> It sounds to me like you have enough things to think about for >> today, Rutger, so why don't we reschedule for tomorrow. My morning >> is entirely open right now until 12pm EST. What about 10am EST >> tomorrow morning? >> >> -hilmar >> >> On Feb 2, 2010, at 12:17 PM, Rutger Vos wrote: >> >> >> I'm so delayed I can't make 6 either. I've only just arrived at >> heathrow, still need to get my luggage, then take the bus to reading. >> This will take me at least another hour, if not more. Sorry, I was >> supposed to have arrived 1.5 hours ago. >> >> On Tuesday, February 2, 2010, William Piel <wil...@ya...> >> wrote: >> >> >> On Feb 2, 2010, at 11:00 AM, Hilmar Lapp wrote: >> >> >> So can we agree that we reschedule this for 1pm EST, 6pm GMT, >> today? - >> >> >> It's good with me. Youjun might be late because he's taking his kid >> to a doctor's appointment. >> >> bp >> >> >> >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in >> the business >> Choose flexible plans and management services without long-term >> contracts >> Personal 24x7 support from experience hosting pros just a phone >> call away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> 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 >> >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in >> the business >> Choose flexible plans and management services without long-term >> contracts >> Personal 24x7 support from experience hosting pros just a phone >> call away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> >> -- >> =========================================================== >> : 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-02-02 18:16:43
|
Thanks for biting the bullit, Hilmar, sorry about the mess up. Wednesday 10AM EST works for me. (Still on the bus, which is now of course hopelessly stuck in afternoon traffic.) On Tuesday, February 2, 2010, Hilmar Lapp <hl...@ne...> wrote: > It sounds to me like you have enough things to think about for today, Rutger, so why don't we reschedule for tomorrow. My morning is entirely open right now until 12pm EST. What about 10am EST tomorrow morning? > > -hilmar > > On Feb 2, 2010, at 12:17 PM, Rutger Vos wrote: > > > I'm so delayed I can't make 6 either. I've only just arrived at > heathrow, still need to get my luggage, then take the bus to reading. > This will take me at least another hour, if not more. Sorry, I was > supposed to have arrived 1.5 hours ago. > > On Tuesday, February 2, 2010, William Piel <wil...@ya...> wrote: > > > On Feb 2, 2010, at 11:00 AM, Hilmar Lapp wrote: > > > So can we agree that we reschedule this for 1pm EST, 6pm GMT, today? - > > > It's good with me. Youjun might be late because he's taking his kid to a doctor's appointment. > > bp > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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 > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > -- > =========================================================== > : 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 |
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From: William P. <wil...@ya...> - 2010-02-02 18:08:34
|
On Feb 2, 2010, at 1:03 PM, Hilmar Lapp wrote: > My morning is entirely open right now until 12pm EST me too. bp |
|
From: Hilmar L. <hl...@ne...> - 2010-02-02 18:03:25
|
It sounds to me like you have enough things to think about for today, Rutger, so why don't we reschedule for tomorrow. My morning is entirely open right now until 12pm EST. What about 10am EST tomorrow morning? -hilmar On Feb 2, 2010, at 12:17 PM, Rutger Vos wrote: > I'm so delayed I can't make 6 either. I've only just arrived at > heathrow, still need to get my luggage, then take the bus to reading. > This will take me at least another hour, if not more. Sorry, I was > supposed to have arrived 1.5 hours ago. > > On Tuesday, February 2, 2010, William Piel <wil...@ya...> > wrote: >> >> On Feb 2, 2010, at 11:00 AM, Hilmar Lapp wrote: >> >>> So can we agree that we reschedule this for 1pm EST, 6pm GMT, >>> today? - >> >> It's good with me. Youjun might be late because he's taking his kid >> to a doctor's appointment. >> >> bp >> >> >> >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in >> the business >> Choose flexible plans and management services without long-term >> contracts >> Personal 24x7 support from experience hosting pros just a phone >> call away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> 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 > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Rutger V. <rut...@gm...> - 2010-02-02 17:17:30
|
I'm so delayed I can't make 6 either. I've only just arrived at heathrow, still need to get my luggage, then take the bus to reading. This will take me at least another hour, if not more. Sorry, I was supposed to have arrived 1.5 hours ago. On Tuesday, February 2, 2010, William Piel <wil...@ya...> wrote: > > On Feb 2, 2010, at 11:00 AM, Hilmar Lapp wrote: > >> So can we agree that we reschedule this for 1pm EST, 6pm GMT, today? - > > It's good with me. Youjun might be late because he's taking his kid to a doctor's appointment. > > bp > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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: William P. <wil...@ya...> - 2010-02-02 16:55:05
|
On Feb 2, 2010, at 11:00 AM, Hilmar Lapp wrote: > So can we agree that we reschedule this for 1pm EST, 6pm GMT, today? - It's good with me. Youjun might be late because he's taking his kid to a doctor's appointment. bp |
|
From: Hilmar L. <hl...@ne...> - 2010-02-02 16:00:34
|
So can we agree that we reschedule this for 1pm EST, 6pm GMT, today? - hilmar On Feb 2, 2010, at 10:08 AM, Hilmar Lapp wrote: > 1pm, 11am, and 12pm EST all work for me. -hilmar > > On Feb 2, 2010, at 9:25 AM, William Piel wrote: > >> Whoops. forgot to send this to the whole group. >> >> >>> On Feb 2, 2010, at 3:45 AM, Rutger Vos wrote: >>> >>>> we are slated to have a conference call today at 5pm GMT. It is >>>> very >>>> likely that I will still be on the road then. Can we have it, >>>> say, one >>>> hour later? Sorry about the late notice. >>> >>> My calendar says that 5 PM GMT = 12 PM EST, whereas I thought we >>> had scheduled this for 11 AM EST. (but maybe the Standard vs >>> Savings time differences have screwed up my calendar's conversion). >>> >>> Personally, I would prefer it at 1 PM EST (which I think is 6 PM >>> London Time) or 2 PM EST (= 7 PM London). >>> >>> bp >> >> >> >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in >> the business >> Choose flexible plans and management services without long-term >> contracts >> Personal 24x7 support from experience hosting pros just a phone >> call away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-02-02 15:08:14
|
1pm, 11am, and 12pm EST all work for me. -hilmar On Feb 2, 2010, at 9:25 AM, William Piel wrote: > Whoops. forgot to send this to the whole group. > > >> On Feb 2, 2010, at 3:45 AM, Rutger Vos wrote: >> >>> we are slated to have a conference call today at 5pm GMT. It is very >>> likely that I will still be on the road then. Can we have it, say, >>> one >>> hour later? Sorry about the late notice. >> >> My calendar says that 5 PM GMT = 12 PM EST, whereas I thought we >> had scheduled this for 11 AM EST. (but maybe the Standard vs >> Savings time differences have screwed up my calendar's conversion). >> >> Personally, I would prefer it at 1 PM EST (which I think is 6 PM >> London Time) or 2 PM EST (= 7 PM London). >> >> bp > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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: William P. <wil...@ya...> - 2010-02-02 14:25:20
|
Whoops. forgot to send this to the whole group. > On Feb 2, 2010, at 3:45 AM, Rutger Vos wrote: > >> we are slated to have a conference call today at 5pm GMT. It is very >> likely that I will still be on the road then. Can we have it, say, one >> hour later? Sorry about the late notice. > > My calendar says that 5 PM GMT = 12 PM EST, whereas I thought we had scheduled this for 11 AM EST. (but maybe the Standard vs Savings time differences have screwed up my calendar's conversion). > > Personally, I would prefer it at 1 PM EST (which I think is 6 PM London Time) or 2 PM EST (= 7 PM London). > > bp |
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From: Rutger V. <rut...@gm...> - 2010-02-02 08:45:35
|
Hi all, we are slated to have a conference call today at 5pm GMT. It is very likely that I will still be on the road then. Can we have it, say, one hour later? Sorry about the late notice. Rutger -- 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: Rutger V. <rut...@gm...> - 2010-02-02 08:42:29
|
We actually never use stepmatrices, so this could very well be an
unnoticed cut-and-paste error.
On Tuesday, February 2, 2010, Vladimir Gapeyev
<vla...@du...> wrote:
> Table stepmatrixelement has an unusual name and definition of its primary key: it appears to have been copied from another table, discretecharstate. (Definitions of both are below.)Is this indeed a cut-and-paste error?
> --Vladimir
>
> CREATE TABLE stepmatrixelement( discretecharstate_id bigint NOT NULL DEFAULT nextval('discretecharstate_id_sequence'::regclass), "version" integer, transcost double precision, state1_id bigint, state2_id bigint, stepmatrix_id bigint NOT NULL, CONSTRAINT stepmatrixelement_pkey PRIMARY KEY (discretecharstate_id), CONSTRAINT fk891100af6e972a88 FOREIGN KEY (state1_id) REFERENCES discretecharstate (discretecharstate_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION, CONSTRAINT fk891100af6e979ee7 FOREIGN KEY (state2_id) REFERENCES discretecharstate (discretecharstate_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION, CONSTRAINT fk891100af9e8198e FOREIGN KEY (stepmatrix_id) REFERENCES usertype (usertype_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION)
> CREATE TABLE discretecharstate( discretecharstate_id bigint NOT NULL DEFAULT nextval('discretecharstate_id_sequence'::regclass), "version" integer, description character varying(255), notes character varying(255), symbol character(1), phylochar_id bigint NOT NULL, stateset_id bigint, ancestralstate_id bigint, CONSTRAINT discretecharstate_pkey PRIMARY KEY (discretecharstate_id), CONSTRAINT fk2eef2802163c67ce FOREIGN KEY (stateset_id) REFERENCES stateset (stateset_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION, CONSTRAINT fk2eef2802c7beaafe FOREIGN KEY (ancestralstate_id) REFERENCES ancestralstate (ancestralstate_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION, CONSTRAINT fk2eef2802fe41a723 FOREIGN KEY (phylochar_id) REFERENCES phylochar (phylochar_id) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION)
>
>
--
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: William P. <wil...@ya...> - 2010-02-02 06:05:12
|
On Jan 29, 2010, at 1:29 PM, Vladimir Gapeyev wrote: > Bill, thanks for the info! I did intend import this data in a way > similar to what you suggest. Vladimir: I just discovered a bunch of mis-wired TI records (basically, all our Wolbachia entries were pointing to the hosts instead of the parasites!). I have fixed this and have uploaded a new version to the migration directory. Please use that one, thanks. Also, I notice that our dev data has some duplicates (e.g. "Apis mellifera" has three records in the taxon table). These should disappear when the old TI data are erased and the new TI data are uploaded -- but it will be interesting to verify how the dups got in in the first place. I'll have to check that this was not in the taxon label matching process. bp |
|
From: Vladimir G. <vla...@du...> - 2010-02-02 04:28:13
|
Table stepmatrixelement has an unusual name and definition of its
primary key: it appears to have been copied from another table,
discretecharstate. (Definitions of both are below.)
Is this indeed a cut-and-paste error?
--Vladimir
CREATE TABLE stepmatrixelement
(
discretecharstate_id bigint NOT NULL DEFAULT
nextval('discretecharstate_id_sequence'::regclass),
"version" integer,
transcost double precision,
state1_id bigint,
state2_id bigint,
stepmatrix_id bigint NOT NULL,
CONSTRAINT stepmatrixelement_pkey PRIMARY KEY (discretecharstate_id),
CONSTRAINT fk891100af6e972a88 FOREIGN KEY (state1_id)
REFERENCES discretecharstate (discretecharstate_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION,
CONSTRAINT fk891100af6e979ee7 FOREIGN KEY (state2_id)
REFERENCES discretecharstate (discretecharstate_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION,
CONSTRAINT fk891100af9e8198e FOREIGN KEY (stepmatrix_id)
REFERENCES usertype (usertype_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION
)
CREATE TABLE discretecharstate
(
discretecharstate_id bigint NOT NULL DEFAULT
nextval('discretecharstate_id_sequence'::regclass),
"version" integer,
description character varying(255),
notes character varying(255),
symbol character(1),
phylochar_id bigint NOT NULL,
stateset_id bigint,
ancestralstate_id bigint,
CONSTRAINT discretecharstate_pkey PRIMARY KEY (discretecharstate_id),
CONSTRAINT fk2eef2802163c67ce FOREIGN KEY (stateset_id)
REFERENCES stateset (stateset_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION,
CONSTRAINT fk2eef2802c7beaafe FOREIGN KEY (ancestralstate_id)
REFERENCES ancestralstate (ancestralstate_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION,
CONSTRAINT fk2eef2802fe41a723 FOREIGN KEY (phylochar_id)
REFERENCES phylochar (phylochar_id) MATCH SIMPLE
ON UPDATE NO ACTION ON DELETE NO ACTION
)
|
|
From: Rutger V. <rut...@gm...> - 2010-02-01 22:11:49
|
OK, I have closed this issue in the bug tracker. On Mon, Feb 1, 2010 at 11:09 PM, William Piel <wil...@ya...> wrote: > > On Feb 1, 2010, at 4:10 PM, Rutger Vos wrote: > >> Bill, could you have a look to see if the ticket can be closed? > > > Yes, it works. I no longer get the error: > > http://treebasedb-dev.nescent.org:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=160000022316 > > bp > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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 |
|
From: William P. <wil...@ya...> - 2010-02-01 22:09:25
|
On Feb 1, 2010, at 4:10 PM, Rutger Vos wrote: > Bill, could you have a look to see if the ticket can be closed? Yes, it works. I no longer get the error: http://treebasedb-dev.nescent.org:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=160000022316 bp |
|
From: Rutger V. <rut...@gm...> - 2010-02-01 21:10:23
|
I think rebuilding and re-deploying fixed it, but I don't know which study the taxonlabel in the ticket belongs to, so I can't ascertain whether editing that particular label now also works as expected. Bill, could you have a look to see if the ticket can be closed? Thanks, Rutger On Mon, Feb 1, 2010 at 8:58 PM, youjun guo <you...@ya...> wrote: > Dear All, > > I am work on this problem: > > http://sourceforge.net/tracker/?func=detail&aid=2941145&group_id=248804&atid=1126676 > > Interestingly, this problem only appeared on > http://treebasedb-dev.nescent.org:6666/treebase-web/; > > I build a war file with most updated TB code and installed in my personal > server it work fine; > > Bill tried on the old installation at SDSC, the problem didn't show up > neither. > > So, most likely this is a build or deploy problem only exist on above > server. I expect it can be solved but a re-build and re-deployment. Rutger > can you try it out? > > My guess is a jar file related to CGLIB is missing or damaged from/in the > server. > > Youjun > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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 |
|
From: youjun g. <you...@ya...> - 2010-02-01 19:58:12
|
Dear All, I am work on this problem: http://sourceforge.net/tracker/?func=detail&aid=2941145&group_id=248804&atid=1126676 Interestingly, this problem only appeared on http://treebasedb-dev.nescent.org:6666/treebase-web/; I build a war file with most updated TB code and installed in my personal server it work fine; Bill tried on the old installation at SDSC, the problem didn't show up neither. So, most likely this is a build or deploy problem only exist on above server. I expect it can be solved but a re-build and re-deployment. Rutger can you try it out? My guess is a jar file related to CGLIB is missing or damaged from/in the server. Youjun |
|
From: Hilmar L. <hl...@ne...> - 2010-01-29 21:52:40
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Fine with me if Bill is. -hilmar On Jan 29, 2010, at 1:29 PM, Vladimir Gapeyev wrote: > Bill, thanks for the info! I did intend import this data in a way > similar to what you suggest. > > Technically, I see how to do step 4 below, but I am not clear why it > will work. (This is clearly a tangent, in the direction of data > quality, i guess.) As I understood before, the natural key in the > TAXONLABEL table is the pair (study_id, taxonlabel), and I thought the > reason was that two studies, say 981 and 1207, might use the same > label, say "Abelia", but mean different taxa by it. In this case, TB2 > should connect (981, "Abelia") and (1207, "Abelia") to different > variant_ids and taxon_ids. This, however, does not mesh with your > instruction to connect TAXONVARIANT and TAXONLABEL tables based on the > value of TAXONLABEL.taxonlabel alone, relying on the fact that > taxonlabel field is unique within the taxon_labels.tab file. Under > this arrangement, there is no way "Abelia" from different studies can > be connected to different taxonvariants! I actually expected to see a > study_id field in taxon_labels.tab. > > I misunderstood something, but what? > > --VG > > > On Jan 28, 2010, at 11:27 PM, William Piel wrote: > >> >> On Jan 28, 2010, at 6:19 PM, Vladimir Gapeyev wrote: >> >>> Here is one important piece of info I could not find: What is the >>> meaning of each column in the taxon intelligence files >>> (taxon_labels.tab, taxon_variants.tab, taxa.tab)? >> >> >> taxon: >> taxon_id (PK) >> namebankid >> namestring >> ncbi_taxid >> >> taxon_variants: >> taxon_variant_id (PK) >> taxon_id (FK) >> namebankid >> namestring >> fullnamestring >> lexicalqualifier >> >> taxon_labels: >> taxon_label_id (PK) >> taxon_variant_id (FK) >> legacy_id (from TreeBASE1) >> taxon_label (from TreeBASE1 -- useful for mapping output from >> headless Mesquite to TV table) >> >> I thing the process should go something like this: >> >> 1. In the taxonlabel table, update all values in the taxonvariant_id >> column to NULL >> 2. Delete all records in the taxonvariant and taxon tables. >> 3. The first two files can be sucked straight into the taxa and >> taxonvariant tables (the mapping among columns should be fairly >> obvious -- let me know if you have questions) >> 4. For mapping the taxonlabel table with the taxonvariant table, I'd >> suggest that you upload the third file into a temporary table, and >> then write an update statement to do the matching: use the last >> column of the taxon_labels file to match against the taxonlabel >> column in the taxonlabel table. Wherever there is a match, put the >> value of the second column in the taxon_labels file in the >> taxonvariant_id column of the taxonlabel table. Recall that in the >> third file, each value in the last column (the "taxon_label") is >> unique; by contrast, the taxonlabel column in the taxonlabel table >> are not unique. >> 5. Drop the temporary table. >> >> bp >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in the >> business >> Choose flexible plans and management services without long-term >> contracts >> Personal 24x7 support from experience hosting pros just a phone call >> away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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: Hilmar L. <hl...@ne...> - 2010-01-29 21:47:13
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On Jan 29, 2010, at 2:55 PM, William Piel wrote: > upon deletion of a tree or a matrix, the software must know to > delete any related taxon labels unless they are being used by > another matrix, rowsegment, or tree that still exists in the study. If my understanding is correct that foreign key enforcement isn't going to take care of this (due to n:n relationships), this can be done by regularly and automatically run maintenance scripts. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-01-29 19:55:32
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On Jan 29, 2010, at 12:01 PM, Hilmar Lapp wrote: > I guess that need not necessarily be resolved before the release, but it seems to me that there is a major data cleanup effort necessary at some point, combined with enforcing all possible constraints in the database. I agree that this cleanup can be done after release -- there are so few studies in question that this can be done by hand. The main thing to check before release is that there are no current bugs that are creating this mis-wiring. Once we have a working sequence and the boolean-bug is fixed, I'll upload a bunch of test datasets and then rerun these queries to check that no new mis-wiring is happening. One thing I noticed is that when I upload a tree to a submission, and then delete the tree, the taxon labels are not deleted. Over time, this will created a clutter of taxon labels that don't belong to any tree or matrix. Should we call this a bug? If so, fixing it will require some effort: upon deletion of a tree or a matrix, the software must know to delete any related taxon labels unless they are being used by another matrix, rowsegment, or tree that still exists in the study. bp |
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From: William P. <wil...@ya...> - 2010-01-29 19:39:58
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I'm okay with this. bp On Jan 29, 2010, at 2:07 PM, Vladimir Gapeyev wrote: > I am still figuring out, in consultation with Xianhua here, how to > instruct Hibernate to do what we want, but it is clear we need back a > DB instance with individual sequences. The most expedient way would > be to just re-create it from a backup. > > So, does anyone object to dropping the current treebasedev instance > (that's the one connected to 6666 as well as treebase-dev.nescent.org > front-ends)? Just in case, we will preserve a recent backup. (Would > one from yesterday or the day before suffice?) > > If that's ok, I'll ask Jon to empty treebasedev, and re-create from > the same Dec 8 backup he used for treebasestage. Depending on whether > Jon has extra space, this might cause a few hours of downtime. > > --Vladimir |
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From: William P. <wil...@ya...> - 2010-01-29 19:18:37
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On Jan 29, 2010, at 1:29 PM, Vladimir Gapeyev wrote: > Technically, I see how to do step 4 below, but I am not clear why it will work. (This is clearly a tangent, in the direction of data quality, i guess.) As I understood before, the natural key in the TAXONLABEL table is the pair (study_id, taxonlabel), and I thought the reason was that two studies, say 981 and 1207, might use the same label, say "Abelia", but mean different taxa by it. In this case, TB2 should connect (981, "Abelia") and (1207, "Abelia") to different variant_ids and taxon_ids. This, however, does not mesh with your instruction to connect TAXONVARIANT and TAXONLABEL tables based on the value of TAXONLABEL.taxonlabel alone, relying on the fact that taxonlabel field is unique within the taxon_labels.tab file. Under this arrangement, there is no way "Abelia" from different studies can be connected to different taxonvariants! I actually expected to see a study_id field in taxon_labels.tab. > > I misunderstood something, but what? Although we have taxon labels that *potentially* could point to two different TAXONVARIANT records, in no current cases do two instances of the name point to different ones. So in terms of the migrated TreeBASE1 data, we are okay. But indeed, in future, we can expect to get homonyms -- e.g. an "Aotus" as the taxon label on a tree of monkeys and an "Aotus" as the taxon label on a tree of plants. So in summary, TreeBASE1 did not allow homonyms in the entire database and did not allow homonyms within a study (hence only one record for each unique taxon label); TreeBASE2 allows homonyms in different studies but does not allow homonyms within the same study. bp |
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From: Vladimir G. <vla...@du...> - 2010-01-29 19:07:52
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I am still figuring out, in consultation with Xianhua here, how to instruct Hibernate to do what we want, but it is clear we need back a DB instance with individual sequences. The most expedient way would be to just re-create it from a backup. So, does anyone object to dropping the current treebasedev instance (that's the one connected to 6666 as well as treebase-dev.nescent.org front-ends)? Just in case, we will preserve a recent backup. (Would one from yesterday or the day before suffice?) If that's ok, I'll ask Jon to empty treebasedev, and re-create from the same Dec 8 backup he used for treebasestage. Depending on whether Jon has extra space, this might cause a few hours of downtime. --Vladimir On Jan 29, 2010, at 11:28 AM, Rutger Vos wrote: >> All this speaks in favor of the theory that TB2 Hibernate got >> confused >> by the DB2-->Postgres switch, which was done in the hope that >> Hibernate default behavior would remain the same. It appears we >> must now figure out how to explicitly instruct TB2 DAO and Hibernate >> to behave in the way that best matches their behavior back in the DB2 >> days. > > Right, and that behaviour would be that the database itself > autoincrements IDs without intervention from hibernate, as the DB2 > creation commands indicate. |
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