Menu
▾
▴
treebase-devel — TreeBASE developer mailing list
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
(1) |
Apr
(41) |
May
(41) |
Jun
(50) |
Jul
(14) |
Aug
(21) |
Sep
(37) |
Oct
(8) |
Nov
(4) |
Dec
(135) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
(145) |
Feb
(110) |
Mar
(216) |
Apr
(101) |
May
(42) |
Jun
(42) |
Jul
(23) |
Aug
(17) |
Sep
(33) |
Oct
(15) |
Nov
(18) |
Dec
(6) |
| 2011 |
Jan
(8) |
Feb
(10) |
Mar
(8) |
Apr
(41) |
May
(48) |
Jun
(62) |
Jul
(7) |
Aug
(9) |
Sep
(7) |
Oct
(11) |
Nov
(49) |
Dec
(1) |
| 2012 |
Jan
(17) |
Feb
(63) |
Mar
(4) |
Apr
(13) |
May
(17) |
Jun
(21) |
Jul
(10) |
Aug
(10) |
Sep
|
Oct
|
Nov
|
Dec
(16) |
| 2013 |
Jan
(10) |
Feb
|
Mar
(1) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2014 |
Jan
(5) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(5) |
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
|
From: William P. <wil...@ya...> - 2010-07-02 16:33:48
|
On Jul 2, 2010, at 12:13 PM, Jon Auman wrote:
> Can someone else commit it? These files belong in the WEB-INF directory
okay -- I just added the files you sent me to the WEB-INF directory.
bp
Revision: 729
http://treebase.svn.sourceforge.net/treebase/?rev=729&view=rev
Author: sfrgpiel
Date: 2010-07-02 16:30:32 +0000 (Fri, 02 Jul 2010)
Log Message:
-----------
This is Jon Auman's fix for the problem when the tuckey.org site is unavailable.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/dtd/
trunk/treebase-web/src/main/webapp/WEB-INF/dtd/urlrewrite3.2.dtd
|
|
From: Jon A. <jon...@du...> - 2010-07-02 16:13:12
|
No, they are not committed. I don't have a development environment setup on my machine nor know enough about the setup not to squash something. Normally I'd ask Vladimir to do it, but he's just started his parental leave, I believe. I'm attaching a zip file with the two changed files. Can someone else commit it? These files belong in the WEB-INF directory As Hilmar suggested, I am using the dtd downloaded from tuckey.org. Thanks, Jon On Jul 2, 2010, at 11:46 AM, William Piel wrote: > > On Jul 2, 2010, at 11:03 AM, Jon Auman wrote: > >> The fix should probably be incorporated into the build. According to the blog, it is a random error that occurs when the tuckey.org site is temporarily inaccessible, which is beyond our control. > > thanks a million! that's great. > > Are these changes committed to sourceforge as well? (if not, perhaps Vladimir could do this) > > bp > > ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Hilmar L. <hl...@ne...> - 2010-07-02 16:03:49
|
Jon - thanks a ton for researching this - any reason not to download the DTD from the URI? -hilmar On Jul 2, 2010, at 11:03 AM, Jon Auman wrote: > Ok, so I fixed this issue. You can verify by following this URL: > http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr6839 > > Please see the blog post here: > > http://notwastingtime.blogspot.com/2010/06/solved-orgtuckeywebfiltersurlrewritecon.html > > So what I did was: > > 1) updated WEB-INF/urlrewrite.xml as follows: > Changed > <!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN" > "http://tuckey.org/res/dtds/urlrewrite3.2.dtd"> > to > <!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN" > "./dtd/urlrewrite3.2.dtd"> > > 2) created dtd folder in WEB-INF folder and created > urlrewrite3.2.dtd file with contents as specified on blog: > <!ELEMENT urlrewrite ((rule|class-rule)*, outbound-rule*, catch*)> > <!ATTLIST urlrewrite > use-query-string (true|false) "false" > use-context (true|false) "false" > decode-using CDATA #IMPLIED > default-match-type (regex|wildcard) #IMPLIED> > > <!ELEMENT rule (name?, note?, condition*, from, set*, run*, to?)> > <!ATTLIST rule > enabled (true|false) "true" > match-type (regex|wildcard) #IMPLIED> > > <!ELEMENT class-rule EMPTY> > <!ATTLIST class-rule > class CDATA #IMPLIED > method CDATA "matches" > last (true|false) "true"> > > <!ELEMENT outbound-rule (name?, note?, condition*, from, set*, run*, > to?)> > <!ATTLIST outbound-rule > enabled (true|false) "true" > encodefirst (true|false) "false" > match-type (regex|wildcard) #IMPLIED> > I probably could have downloaded the dtd file from tuckey.org and > put it in the local dtd folder as well, since the example is of an > older version (3.0) > > 3) restarted Tomcat > > I was able to determine the issue by Googling the errors in this page: > http://www.treebase.org/treebase-web/rewrite-status > > The fix should probably be incorporated into the build. According to > the blog, it is a random error that occurs when the tuckey.org site > is temporarily inaccessible, which is beyond our control. > > Silly, huh? > > -Jon > > > On Jul 1, 2010, at 10:25 PM, William Piel wrote: > >> >> On Jul 1, 2010, at 2:18 PM, Jon Auman wrote: >> >>> Don't know what it means. Possibly something is hardcoded to a >>> path that only exists on dev. Production and dev are not >>> identical with regards to their location on the file system. >> >> I don't know that that's related. >> >> Basically the way this works is that this URL: >> >> http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr6839 >> >> ... gets turned into this URL: >> >> http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6839?format=nexus >> >> ... using the "Url Rewrite Filter" (http://www.tuckey.org/ >> urlrewrite/) with the remapping rules defined here: >> >> trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml >> >> ... and urlrewrite should be defined as a dependency in /treebase- >> web/porn.xml >> >> The 404 error would seem to indicate that urlrewrite is not working >> on production, for some reason. >> >> >> bp >> >> > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first_______________________________________________ > 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...> - 2010-07-02 15:46:37
|
On Jul 2, 2010, at 11:03 AM, Jon Auman wrote: > The fix should probably be incorporated into the build. According to the blog, it is a random error that occurs when the tuckey.org site is temporarily inaccessible, which is beyond our control. thanks a million! that's great. Are these changes committed to sourceforge as well? (if not, perhaps Vladimir could do this) bp |
|
From: Jon A. <jon...@du...> - 2010-07-02 15:03:51
|
Ok, so I fixed this issue. You can verify by following this URL: http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr6839 Please see the blog post here: http://notwastingtime.blogspot.com/2010/06/solved-orgtuckeywebfiltersurlrewritecon.html So what I did was: 1) updated WEB-INF/urlrewrite.xml as follows: Changed <!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN" "http://tuckey.org/res/dtds/urlrewrite3.2.dtd"> to <!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN" "./dtd/urlrewrite3.2.dtd"> 2) created dtd folder in WEB-INF folder and created urlrewrite3.2.dtd file with contents as specified on blog: <!ELEMENT urlrewrite ((rule|class-rule)*, outbound-rule*, catch*)> <!ATTLIST urlrewrite use-query-string (true|false) "false" use-context (true|false) "false" decode-using CDATA #IMPLIED default-match-type (regex|wildcard) #IMPLIED> <!ELEMENT rule (name?, note?, condition*, from, set*, run*, to?)> <!ATTLIST rule enabled (true|false) "true" match-type (regex|wildcard) #IMPLIED> <!ELEMENT class-rule EMPTY> <!ATTLIST class-rule class CDATA #IMPLIED method CDATA "matches" last (true|false) "true"> <!ELEMENT outbound-rule (name?, note?, condition*, from, set*, run*, to?)> <!ATTLIST outbound-rule enabled (true|false) "true" encodefirst (true|false) "false" match-type (regex|wildcard) #IMPLIED> I probably could have downloaded the dtd file from tuckey.org and put it in the local dtd folder as well, since the example is of an older version (3.0) 3) restarted Tomcat I was able to determine the issue by Googling the errors in this page: http://www.treebase.org/treebase-web/rewrite-status The fix should probably be incorporated into the build. According to the blog, it is a random error that occurs when the tuckey.org site is temporarily inaccessible, which is beyond our control. Silly, huh? -Jon On Jul 1, 2010, at 10:25 PM, William Piel wrote: > > On Jul 1, 2010, at 2:18 PM, Jon Auman wrote: > >> Don't know what it means. Possibly something is hardcoded to a path that only exists on dev. Production and dev are not identical with regards to their location on the file system. > > I don't know that that's related. > > Basically the way this works is that this URL: > > http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr6839 > > ... gets turned into this URL: > > http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6839?format=nexus > > ... using the "Url Rewrite Filter" (http://www.tuckey.org/urlrewrite/) with the remapping rules defined here: > > trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml > > ... and urlrewrite should be defined as a dependency in /treebase-web/porn.xml > > The 404 error would seem to indicate that urlrewrite is not working on production, for some reason. > > > bp > > ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: William P. <wil...@ya...> - 2010-07-02 02:25:56
|
On Jul 1, 2010, at 2:18 PM, Jon Auman wrote: > Don't know what it means. Possibly something is hardcoded to a path that only exists on dev. Production and dev are not identical with regards to their location on the file system. I don't know that that's related. Basically the way this works is that this URL: http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr6839 ... gets turned into this URL: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6839?format=nexus ... using the "Url Rewrite Filter" (http://www.tuckey.org/urlrewrite/) with the remapping rules defined here: trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml ... and urlrewrite should be defined as a dependency in /treebase-web/porn.xml The 404 error would seem to indicate that urlrewrite is not working on production, for some reason. bp |
|
From: Jon A. <jon...@du...> - 2010-07-01 18:19:00
|
Bill, On production, there are all sorts of files in the treebase-web/NexusFileDownload/null folder on production. On development, there are only a couple of nexus files. Here is the directory list on production: -rw-r--r-- 1 tomcat tomcat 410015 Jun 29 14:58 Combined_no_gaps.nexusorg -rw-r--r-- 1 tomcat tomcat 50000 Jun 29 15:03 T5846.xml -rw-r--r-- 1 tomcat tomcat 1973 Jun 29 15:03 T5846.nex -rw-r--r-- 1 tomcat tomcat 127214 Jun 29 15:05 M700.xml -rw-r--r-- 1 tomcat tomcat 41597 Jun 29 15:06 M700.nex -rw-r--r-- 1 tomcat tomcat 79276 Jun 29 15:08 M137.xml -rw-r--r-- 1 tomcat tomcat 6785 Jun 29 15:10 M1607.nexorg -rw-r--r-- 1 tomcat tomcat 18714 Jun 29 15:10 M703.nex -rw-r--r-- 1 tomcat tomcat 46404 Jun 29 15:15 S598.nex -rw-r--r-- 1 tomcat tomcat 117855 Jun 29 15:26 S1070.nex -rw-r--r-- 1 tomcat tomcat 132926 Jun 29 15:29 S1925.nex -rw-r--r-- 1 tomcat tomcat 721781 Jun 29 15:32 S1070.xml -rw-r--r-- 1 tomcat tomcat 39 Jun 29 16:33 M4333.nexorg -rw-r--r-- 1 tomcat tomcat 7539 Jun 29 17:03 M4627.nex -rw-r--r-- 1 tomcat tomcat 359460 Jun 29 18:06 S279.xml -rw-r--r-- 1 tomcat tomcat 554872 Jun 29 18:07 S279.rdf -rw-r--r-- 1 tomcat tomcat 117642 Jun 29 18:07 S279.nex -rw-r--r-- 1 tomcat tomcat 414351 Jun 29 18:47 M5154.nex -rw-r--r-- 1 tomcat tomcat 418724 Jun 29 18:49 AnalysisStep5868.nex -rw-r--r-- 1 tomcat tomcat 10454 Jun 29 18:50 T7818.nex -rw-r--r-- 1 tomcat tomcat 0 Jun 29 19:58 S378.rdf -rw-r--r-- 1 tomcat tomcat 127998 Jun 29 19:58 S378.nex -rw-r--r-- 1 tomcat tomcat 41548 Jun 29 19:59 M2239.nex -rw-r--r-- 1 tomcat tomcat 378210 Jun 29 19:59 M2239.rdf -rw-r--r-- 1 tomcat tomcat 8795 Jun 29 20:01 T2406.nex -rw-r--r-- 1 tomcat tomcat 15011581 Jun 29 20:53 S378.xml -rw-r--r-- 1 tomcat tomcat 11971 Jun 29 21:47 AnalysisStep4901.nex -rw-r--r-- 1 tomcat tomcat 712186 Jun 29 22:13 AnalysisStep3753.nex -rw-r--r-- 1 tomcat tomcat 310360 Jun 30 01:05 S10156.nex -rw-r--r-- 1 tomcat tomcat 608861 Jun 30 01:52 S1787.xml -rw-r--r-- 1 tomcat tomcat 225429 Jun 30 05:10 S2199.nex -rw-r--r-- 1 tomcat tomcat 161658 Jun 30 05:14 S1450.nex -rw-r--r-- 1 tomcat tomcat 388815 Jun 30 08:20 S9941.xml -rw-r--r-- 1 tomcat tomcat 216620 Jun 30 13:33 M3054.xml -rw-r--r-- 1 tomcat tomcat 10887 Jun 30 13:35 M3676.nexorg -rw-r--r-- 1 tomcat tomcat 3842 Jun 30 14:07 T825.nex -rw-r--r-- 1 tomcat tomcat 3182838 Jun 30 14:51 S423.xml -rw-r--r-- 1 tomcat tomcat 593543 Jun 30 15:09 S10420.nex -rw-r--r-- 1 tomcat tomcat 152329 Jun 30 15:21 M4245.nex -rw-r--r-- 1 tomcat tomcat 11204 Jun 30 17:14 S9941.nex -rw-r--r-- 1 tomcat tomcat 3146 Jun 30 17:32 M3438.nexorg -rw-r--r-- 1 tomcat tomcat 5102 Jun 30 17:32 M3759.nex -rw-r--r-- 1 tomcat tomcat 10073 Jun 30 17:49 T2839.nex -rw-r--r-- 1 tomcat tomcat 255372 Jun 30 17:52 T2839.xml -rw-r--r-- 1 tomcat tomcat 5472 Jun 30 17:54 S1825A7197.treorg -rw-r--r-- 1 tomcat tomcat 406225 Jun 30 18:17 T2839.rdf -rw-r--r-- 1 tomcat tomcat 708148 Jun 30 18:27 M2000.nex -rw-r--r-- 1 tomcat tomcat 160031 Jun 30 19:21 M4828.nex -rw-r--r-- 1 tomcat tomcat 45247 Jun 30 22:51 M4260.nexorg -rw-r--r-- 1 tomcat tomcat 75408 Jul 1 07:05 M2286.nexorg -rw-r--r-- 1 tomcat tomcat 204984 Jul 1 07:06 M1476.xml -rw-r--r-- 1 tomcat tomcat 627220 Jul 1 11:16 Sundue_Islam_Ranker.nexorg -rw-r--r-- 1 tomcat tomcat 12618 Jul 1 11:27 T19939.nex -rw-r--r-- 1 tomcat tomcat 4017 Jul 1 11:34 S100.nex -rw-r--r-- 1 tomcat tomcat 46691 Jul 1 11:35 S1501.nex -rw-r--r-- 1 tomcat tomcat 39 Jul 1 12:42 M4463.nexorg -rw-r--r-- 1 tomcat tomcat 231367 Jul 1 12:43 M4193.nex -rw-r--r-- 1 tomcat tomcat 460226 Jul 1 12:57 M2570.xml -rw-r--r-- 1 tomcat tomcat 247552 Jul 1 13:00 M2780.nexorg And on development: -rw-r--r-- 1 treebasedev treebase-dev 4339 Jul 1 12:50 T2026.nex -rw-r--r-- 1 treebasedev treebase-dev 2409 Jul 1 11:53 T2032.nex -rw-r--r-- 1 treebasedev treebase-dev 3577 Jul 1 12:50 T2041.nex -rw-r--r-- 1 treebasedev treebase-dev 1347 Jul 1 11:34 T3631.nex Don't know what it means. Possibly something is hardcoded to a path that only exists on dev. Production and dev are not identical with regards to their location on the file system. -Jon On Jul 1, 2010, at 2:10 PM, William Piel wrote: > > On Jul 1, 2010, at 12:00 PM, Jon Auman wrote: > >> Any ideas what to check? >> >> -Jon > > > I don't know why the dev build would work when the production build would not... > > I'll cc this to Tre...@li... in case others have ideas. > > bp > > >> On Jul 1, 2010, at 11:42 AM, William Piel wrote: >> >>> Hi Jon, >>> >>> Something seems to be broken in the PRODUCTION build of TreeBASE, but that nonetheless works okay in the DEV build. >>> >>> For example, for viewing trees in PhyloWidget, this works fine in the dev build: >>> >>> http://www.phylowidget.org/full/?tree='http://treebase-dev.nescent.org/treebase-web/tree_for_phylowidget/TB2:Tr2026' >>> >>> ... because this URL returns a NEXUS tree file: http://treebase-dev.nescent.org/treebase-web/tree_for_phylowidget/TB2:Tr2026 >>> >>> By contrast, viewing the same tree on production fails: >>> >>> http://www.phylowidget.org/full/?tree='http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr2026' >>> >>> .... because this URL returns a 404 Error: http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr2026 >>> >>> Could you look into this? >>> >>> thanks, >>> >>> Bill >>> >>> >>> >> >> ------------------------------------------------------- >> Jon Auman >> Systems Administrator >> National Evolutionary Synthesis Center >> Duke University >> http:www.nescent.org >> jon...@ne... >> ------------------------------------------------------ >> > > ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: William P. <wil...@ya...> - 2010-07-01 18:10:16
|
On Jul 1, 2010, at 12:00 PM, Jon Auman wrote: > Any ideas what to check? > > -Jon I don't know why the dev build would work when the production build would not... I'll cc this to Tre...@li... in case others have ideas. bp > On Jul 1, 2010, at 11:42 AM, William Piel wrote: > >> Hi Jon, >> >> Something seems to be broken in the PRODUCTION build of TreeBASE, but that nonetheless works okay in the DEV build. >> >> For example, for viewing trees in PhyloWidget, this works fine in the dev build: >> >> http://www.phylowidget.org/full/?tree='http://treebase-dev.nescent.org/treebase-web/tree_for_phylowidget/TB2:Tr2026' >> >> ... because this URL returns a NEXUS tree file: http://treebase-dev.nescent.org/treebase-web/tree_for_phylowidget/TB2:Tr2026 >> >> By contrast, viewing the same tree on production fails: >> >> http://www.phylowidget.org/full/?tree='http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr2026' >> >> .... because this URL returns a 404 Error: http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr2026 >> >> Could you look into this? >> >> thanks, >> >> Bill >> >> >> > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > |
|
From: William P. <wil...@ya...> - 2010-06-29 16:27:30
|
Hi Jon, Seeing as people who will be going to Rutger's talk will want to test out the API, can we have a new build-to-production done quite soon? Also, I added a new person (Junli Ping) in the "People" page, but her photo does not show through in treebase-dev.nescent.org -- I'm not sure why not. At any rate, I'll attach her pic in case it can't be found. regards, Bill |
|
From: Jon A. <ja1...@my...> - 2010-06-25 15:09:21
|
Hi all, Rutger posted a help desk request last week to open up the treebase site to allow Flash based apps access to treebase. I'm not against installing a crossdomain.xml file, but I think it needs to be done with some caution. It is strongly recommended NOT to use the least restrictive policy as advocated by the original requestor. Therefore is anyone willing to read through the docs and suggest a sane policy? Here's an excerpt from the documentation: The following is the most permissive master policy file definition (strongly not recommended). It allows any policy file on the target domain to grant permissions, allows access to any of its file, and permits any header to be sent to the server, all of this possible even through HTTPS despite the source being HTTP: Example 1.3: cross-domain-policy: Least restrictive policy <?xml version="1.0"?> <!DOCTYPE cross-domain-policy SYSTEM "http://www.adobe.com/xml/dtds/cross-domain-policy.dtd"> <cross-domain-policy> <site-control permitted-cross-domain-policies="all"/> <allow-access-from domain="*" secure="false"/> <allow-http-request-headers-from domain="*" headers="*" secure="false"/> </cross-domain-policy> The full document is located here: http://learn.adobe.com/wiki/download/attachments/64389123/CrossDomain_PolicyFile_Specification.pdf?version=1 The sourceforge request is here: https://sourceforge.net/tracker/?func=detail&aid=2977283&group_id=248804&atid=1126676 Thanks, Jon |
|
From: Hilmar L. <hl...@ne...> - 2010-06-23 17:10:19
|
This strongly smells of a misconfigured Hibernate mapping. Hibernate seems to be fooled into thinking that it needs to pull in all this information, probably due to the declaration of the relationship mappings, so that's where I would start to sleuth for the culprit. -hilmar On Jun 18, 2010, at 12:40 PM, William Piel wrote: > > On Jun 18, 2010, at 11:49 AM, Jon Auman wrote: > >> I propose 10 minutes > > Or, might it make sense to match it to the proxy time-out? (is that > 20 min?). Would a PostgreSQL-driven time-out trigger a rollback? > > I find the query a bit odd. The parts in bold don't make much sense > to me. It seems to be asking for records related to a particular > column of a particular matrix. From that column, it asks for the > PHYLOCHAR (i.e. the title for a character, e.g. "Feather color") and > then it asks for MATRIXDATATYPE of the related matrix -- i.e. type > of matrix (e.g. "morphological"), but then I think it asks for all > PHYLOCHARs that also have the same type of matrix. This would create > a very big selection (e.g. all the titles for all the characters > that belong to matrices of type morphological), and I can't imagine > why we'd want this. Likewise, after finding the related MATRIX > record, it later asks for all MATRIX records that belong to the > CHARSET that belonged to the original MATRIX record. > > So two "loops" that revisit the same tables, but arriving at > different directions and would seem to create non-sensical selections. > > Is there a way to identify which method/class/etc in the code has > called this long query? > > bp > > > > select * > from MATRIXCOLUMN matrixcolu0_ > left outer join PHYLOCHAR phylochar1_ on > matrixcolu0_.PHYLOCHAR_ID=phylochar1_.PHYLOCHAR_ID > left outer join MATRIX characterm2_ on > matrixcolu0_.MATRIX_ID=characterm2_.MATRIX_ID > left outer join MATRIXDATATYPE matrixdata3_ on > characterm2_.MATRIXDATATYPE_ID=matrixdata3_.MATRIXDATATYPE_ID > left outer join PHYLOCHAR phylochar4_ on > matrixdata3_.PHYLOCHAR_ID=phylochar4_.PHYLOCHAR_ID > left outer join ANCSTATESET ancstatese5_ on > characterm2_.ANCSTATESET_ID=ancstatese5_.ANCSTATESET_ID > left outer join CodonPositionSet codonposit6_ on > characterm2_.CODONPOSITIONSET_ID=codonposit6_.CodonPositionSet_ID > left outer join CHARSET excludedch7_ on > characterm2_.CHARSET_ID=excludedch7_.CHARSET_ID > left outer join MATRIX characterm8_ on > excludedch7_.MATRIX_ID=characterm8_.MATRIX_ID > left outer join TYPESET typeset9_ on > characterm2_.TYPESET_ID=typeset9_.TYPESET_ID > left outer join CHARWEIGHTSET charweight10_ on > characterm2_.CHARWEIGHTSET_ID=charweight10_.CHARWEIGHTSET_ID > where > matrixcolu0_.MATRIX_ID=$1 and matrixcolu0_.COLUMN_ORDER=$2 > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo_______________________________________________ > 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...> - 2010-06-22 15:17:55
|
> To access them from Java, there are helper functions in > org.cipres.treebase.TreebaseUtil You're right, I forgot to use its getPurlBase method in a location where session attributes are set for the RSS template. I've fixed that now and committed the new code. -- 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: Vladimir G. <vga...@ne...> - 2010-06-18 21:35:57
|
On Jun 16, 2010, at 5:47 PM, Rutger Vos wrote: > I've did a number of fixes on the search rss (including adding full > abstracts and fixing the safari issue). They're visible on the dev > server: > > http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.publicationName==Evolution&format=rss1 > > Two questions: i) is the purl configuration on dev undefined? It looks > like it is, resulting in broken links; Rutger, are you concerned that the links on the page above are like <link>http://localhost:8380/treebase-web/phylowsstudy/TB2:S728</ link> ? Do you use one of the two JNDI parameters to generate these URLs? Jon checked and confirmed that these parameters are set on dev as follows: <Environment name="tb2/SiteUrl" value="http://treebase-dev.nescent.org/treebase-web/" type="java.lang.String" override="false" description="The base URL from which this Treebase instance is served."/> <Environment name="tb2/PurlBase" value="http://purl.org/phylo/treebase/dev/phylows/" type="java.lang.String" override="false" description="The base URL of a PURL service that redirects to this Treebase instance."/> To access them from Java, there are helper functions in org.cipres.treebase.TreebaseUtil --VG |
|
From: William P. <wil...@ya...> - 2010-06-18 16:40:24
|
On Jun 18, 2010, at 11:49 AM, Jon Auman wrote: > I propose 10 minutes Or, might it make sense to match it to the proxy time-out? (is that 20 min?). Would a PostgreSQL-driven time-out trigger a rollback? I find the query a bit odd. The parts in bold don't make much sense to me. It seems to be asking for records related to a particular column of a particular matrix. From that column, it asks for the PHYLOCHAR (i.e. the title for a character, e.g. "Feather color") and then it asks for MATRIXDATATYPE of the related matrix -- i.e. type of matrix (e.g. "morphological"), but then I think it asks for all PHYLOCHARs that also have the same type of matrix. This would create a very big selection (e.g. all the titles for all the characters that belong to matrices of type morphological), and I can't imagine why we'd want this. Likewise, after finding the related MATRIX record, it later asks for all MATRIX records that belong to the CHARSET that belonged to the original MATRIX record. So two "loops" that revisit the same tables, but arriving at different directions and would seem to create non-sensical selections. Is there a way to identify which method/class/etc in the code has called this long query? bp select * from MATRIXCOLUMN matrixcolu0_ left outer join PHYLOCHAR phylochar1_ on matrixcolu0_.PHYLOCHAR_ID=phylochar1_.PHYLOCHAR_ID left outer join MATRIX characterm2_ on matrixcolu0_.MATRIX_ID=characterm2_.MATRIX_ID left outer join MATRIXDATATYPE matrixdata3_ on characterm2_.MATRIXDATATYPE_ID=matrixdata3_.MATRIXDATATYPE_ID left outer join PHYLOCHAR phylochar4_ on matrixdata3_.PHYLOCHAR_ID=phylochar4_.PHYLOCHAR_ID left outer join ANCSTATESET ancstatese5_ on characterm2_.ANCSTATESET_ID=ancstatese5_.ANCSTATESET_ID left outer join CodonPositionSet codonposit6_ on characterm2_.CODONPOSITIONSET_ID=codonposit6_.CodonPositionSet_ID left outer join CHARSET excludedch7_ on characterm2_.CHARSET_ID=excludedch7_.CHARSET_ID left outer join MATRIX characterm8_ on excludedch7_.MATRIX_ID=characterm8_.MATRIX_ID left outer join TYPESET typeset9_ on characterm2_.TYPESET_ID=typeset9_.TYPESET_ID left outer join CHARWEIGHTSET charweight10_ on characterm2_.CHARWEIGHTSET_ID=charweight10_.CHARWEIGHTSET_ID where matrixcolu0_.MATRIX_ID=$1 and matrixcolu0_.COLUMN_ORDER=$2 |
|
From: Rutger V. <rut...@gm...> - 2010-06-18 16:03:10
|
That seems reasonable to me. On Fri, Jun 18, 2010 at 4:49 PM, Jon Auman <jon...@du...> wrote: > I've noticed a lot of hung queries on the production treebase server over > the last couple of weeks. The hung queries consume all available memory and > CPU cycles. I propose that I put timeout limit on queries, so that postgres > will automatically kill them if they go on to long. I propose 10 minutes. > Does that seem reasonable? > FYI. the stuck query is always as follows: > select matrixcolu0_.MATRIXCOLUMN_ID as MATRIXCO1_26_10_, > matrixcolu0_.VERSION as > VERSION26_10_, matrixcolu0_.PHYLOCHAR_ID as PHYLOCHAR3_26_10_, > matrixcolu0_.MATRIX_ID as MATRIX4_26_10_, matrixcolu0_.STATEFORMAT_ID as > STATEFOR5_26_10_, phylochar1_.PHYLOCHAR_ID as PHYLOCHAR2_15_0_, > phylochar1_.VERSION as VERSION15_0_, phylochar1_.Description as > Descript4_15_0_, > phylochar1_.LowerLimit as LowerLimit15_0_, phylochar1_.UpperLimit as > UpperLimit15_0_, phylochar1_.TYPE as TYPE15_0_, characterm2_.MATRIX_ID as > MATRIX2_6_1_, characterm2_.VERSION as VERSION6_1_, characterm2_.TB_MatrixID > as > TB4_6_1_, characterm2_.MATRIXDATATYPE_ID as MATRIXD18_6_1_, > characterm2_.Description as Descript5_6_1_, characterm2_.GapSymbol as > GapSymbol6_1_, characterm2_.MATRIXKIND_ID as MATRIXKIND19_6_1_, > characterm2_.MissingSymbol as MissingS7_6_1_, characterm2_.NexusFileName as > NexusFil8_6_1_, characterm2_.Published as Published6_1_, > characterm2_.STUDY_ID > as STUDY20_6_1_, characterm2_.Symbols as Symbols6_1_, > characterm2_.TAXONLABELSET_ID as TAXONLA21_6_1_, characterm2_.Title as > Title6_1_, characterm2_.ANCSTATESET_ID as ANCSTAT22_6_1_, > characterm2_.CODONPOSITIONSET_ID as CODONPO23_6_1_, characterm2_.CHARSET_ID > as > CHARSET24_6_1_, characterm2_.TYPESET_ID as TYPESET25_6_1_, > characterm2_.CHARWEIGHTSET_ID as CHARWEI26_6_1_, characterm2_.nChar as > nChar6_1_, characterm2_.nTax as nTax6_1_, characterm2_.Aligned as > Aligned6_1_, > characterm2_.CaseSensitive as CaseSen17_6_1_, characterm2_.MATRIXTYPE as > MATRIXTYPE6_1_, matrixdata3_.MATRIXDATATYPE_ID as MATRIXDA1_27_2_, > matrixdata3_.VERSION as VERSION27_2_, matrixdata3_.PHYLOCHAR_ID as > PHYLOCHAR4_27_2_, matrixdata3_.Description as Descript3_27_2_, > phylochar4_.PHYLOCHAR_ID as PHYLOCHAR2_15_3_, phylochar4_.VERSION as > VERSION15_3_, phylochar4_.Description as Descript4_15_3_, > phylochar4_.LowerLimit > as LowerLimit15_3_, phylochar4_.UpperLimit as UpperLimit15_3_, > phylochar4_.TYPE > as TYPE15_3_, ancstatese5_.ANCSTATESET_ID as ANCSTATE1_5_4_, > ancstatese5_.VERSION as VERSION5_4_, ancstatese5_.Title as Title5_4_, > codonposit6_.CodonPositionSet_ID as CodonPos1_14_5_, codonposit6_.VERSION as > VERSION14_5_, codonposit6_.Title as Title14_5_, excludedch7_.CHARSET_ID as > CHARSET2_9_6_, excludedch7_.VERSION as VERSION9_6_, excludedch7_.MATRIX_ID > as > MATRIX5_9_6_, excludedch7_.Title as Title9_6_, characterm8_.MATRIX_ID as > MATRIX2_6_7_, characterm8_.VERSION as VERSION6_7_, characterm8_.TB_MatrixID > as > TB4_6_7_, characterm8_.MATRIXDATATYPE_ID as MATRIXD18_6_7_, > characterm8_.Description as Descript5_6_7_, characterm8_.GapSymbol as > GapSymbol6_7_, characterm8_.MATRIXKIND_ID as MATRIXKIND19_6_7_, > characterm8_.MissingSymbol as MissingS7_6_7_, characterm8_.NexusFileName as > NexusFil8_6_7_, characterm8_.Published as Published6_7_, > characterm8_.STUDY_ID > as STUDY20_6_7_, characterm8_.Symbols as Symbols6_7_, > characterm8_.TAXONLABELSET_ID as TAXONLA21_6_7_, characterm8_.Title as > Title6_7_, characterm8_.ANCSTATESET_ID as ANCSTAT22_6_7_, > characterm8_.CODONPOSITIONSET_ID as CODONPO23_6_7_, characterm8_.CHARSET_ID > as > CHARSET24_6_7_, characterm8_.TYPESET_ID as TYPESET25_6_7_, > characterm8_.CHARWEIGHTSET_ID as CHARWEI26_6_7_, characterm8_.nChar as > nChar6_7_, characterm8_.nTax as nTax6_7_, characterm8_.Aligned as > Aligned6_7_, > characterm8_.CaseSensitive as CaseSen17_6_7_, characterm8_.MATRIXTYPE as > MATRIXTYPE6_7_, typeset9_.TYPESET_ID as TYPESET1_37_8_, typeset9_.VERSION as > VERSION37_8_, typeset9_.Title as Title37_8_, charweight10_.CHARWEIGHTSET_ID > as > CHARWEIG1_11_9_, charweight10_.VERSION as VERSION11_9_, charweight10_.Title > as > Title11_9_ from MATRIXCOLUMN matrixcolu0_ left outer join PHYLOCHAR > phylochar1_ > on matrixcolu0_.PHYLOCHAR_ID=phylochar1_.PHYLOCHAR_ID left outer join MATRIX > characterm2_ on matrixcolu0_.MATRIX_ID=characterm2_.MATRIX_ID left outer > join > MATRIXDATATYPE matrixdata3_ on > characterm2_.MATRIXDATATYPE_ID=matrixdata3_.MATRIXDATATYPE_ID left outer > join > PHYLOCHAR phylochar4_ on matrixdata3_.PHYLOCHAR_ID=phylochar4_.PHYLOCHAR_ID > left > outer join ANCSTATESET ancstatese5_ on > characterm2_.ANCSTATESET_ID=ancstatese5_.ANCSTATESET_ID left outer join > CodonPositionSet codonposit6_ on > characterm2_.CODONPOSITIONSET_ID=codonposit6_.CodonPositionSet_ID left outer > join CHARSET excludedch7_ on characterm2_.CHARSET_ID=excludedch7_.CHARSET_ID > left outer join MATRIX characterm8_ on > excludedch7_.MATRIX_ID=characterm8_.MATRIX_ID left outer join TYPESET > typeset9_ > on characterm2_.TYPESET_ID=typeset9_.TYPESET_ID left outer join > CHARWEIGHTSET > charweight10_ on > characterm2_.CHARWEIGHTSET_ID=charweight10_.CHARWEIGHTSET_ID > where matrixcolu0_.MATRIX_ID=$1 and matrixcolu0_.COLUMN_ORDER=$2 > -Jon > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > 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: Jon A. <jon...@du...> - 2010-06-18 15:49:47
|
I've noticed a lot of hung queries on the production treebase server over the last couple of weeks. The hung queries consume all available memory and CPU cycles. I propose that I put timeout limit on queries, so that postgres will automatically kill them if they go on to long. I propose 10 minutes. Does that seem reasonable? FYI. the stuck query is always as follows: select matrixcolu0_.MATRIXCOLUMN_ID as MATRIXCO1_26_10_, matrixcolu0_.VERSION as VERSION26_10_, matrixcolu0_.PHYLOCHAR_ID as PHYLOCHAR3_26_10_, matrixcolu0_.MATRIX_ID as MATRIX4_26_10_, matrixcolu0_.STATEFORMAT_ID as STATEFOR5_26_10_, phylochar1_.PHYLOCHAR_ID as PHYLOCHAR2_15_0_, phylochar1_.VERSION as VERSION15_0_, phylochar1_.Description as Descript4_15_0_, phylochar1_.LowerLimit as LowerLimit15_0_, phylochar1_.UpperLimit as UpperLimit15_0_, phylochar1_.TYPE as TYPE15_0_, characterm2_.MATRIX_ID as MATRIX2_6_1_, characterm2_.VERSION as VERSION6_1_, characterm2_.TB_MatrixID as TB4_6_1_, characterm2_.MATRIXDATATYPE_ID as MATRIXD18_6_1_, characterm2_.Description as Descript5_6_1_, characterm2_.GapSymbol as GapSymbol6_1_, characterm2_.MATRIXKIND_ID as MATRIXKIND19_6_1_, characterm2_.MissingSymbol as MissingS7_6_1_, characterm2_.NexusFileName as NexusFil8_6_1_, characterm2_.Published as Published6_1_, characterm2_.STUDY_ID as STUDY20_6_1_, characterm2_.Symbols as Symbols6_1_, characterm2_.TAXONLABELSET_ID as TAXONLA21_6_1_, characterm2_.Title as Title6_1_, characterm2_.ANCSTATESET_ID as ANCSTAT22_6_1_, characterm2_.CODONPOSITIONSET_ID as CODONPO23_6_1_, characterm2_.CHARSET_ID as CHARSET24_6_1_, characterm2_.TYPESET_ID as TYPESET25_6_1_, characterm2_.CHARWEIGHTSET_ID as CHARWEI26_6_1_, characterm2_.nChar as nChar6_1_, characterm2_.nTax as nTax6_1_, characterm2_.Aligned as Aligned6_1_, characterm2_.CaseSensitive as CaseSen17_6_1_, characterm2_.MATRIXTYPE as MATRIXTYPE6_1_, matrixdata3_.MATRIXDATATYPE_ID as MATRIXDA1_27_2_, matrixdata3_.VERSION as VERSION27_2_, matrixdata3_.PHYLOCHAR_ID as PHYLOCHAR4_27_2_, matrixdata3_.Description as Descript3_27_2_, phylochar4_.PHYLOCHAR_ID as PHYLOCHAR2_15_3_, phylochar4_.VERSION as VERSION15_3_, phylochar4_.Description as Descript4_15_3_, phylochar4_.LowerLimit as LowerLimit15_3_, phylochar4_.UpperLimit as UpperLimit15_3_, phylochar4_.TYPE as TYPE15_3_, ancstatese5_.ANCSTATESET_ID as ANCSTATE1_5_4_, ancstatese5_.VERSION as VERSION5_4_, ancstatese5_.Title as Title5_4_, codonposit6_.CodonPositionSet_ID as CodonPos1_14_5_, codonposit6_.VERSION as VERSION14_5_, codonposit6_.Title as Title14_5_, excludedch7_.CHARSET_ID as CHARSET2_9_6_, excludedch7_.VERSION as VERSION9_6_, excludedch7_.MATRIX_ID as MATRIX5_9_6_, excludedch7_.Title as Title9_6_, characterm8_.MATRIX_ID as MATRIX2_6_7_, characterm8_.VERSION as VERSION6_7_, characterm8_.TB_MatrixID as TB4_6_7_, characterm8_.MATRIXDATATYPE_ID as MATRIXD18_6_7_, characterm8_.Description as Descript5_6_7_, characterm8_.GapSymbol as GapSymbol6_7_, characterm8_.MATRIXKIND_ID as MATRIXKIND19_6_7_, characterm8_.MissingSymbol as MissingS7_6_7_, characterm8_.NexusFileName as NexusFil8_6_7_, characterm8_.Published as Published6_7_, characterm8_.STUDY_ID as STUDY20_6_7_, characterm8_.Symbols as Symbols6_7_, characterm8_.TAXONLABELSET_ID as TAXONLA21_6_7_, characterm8_.Title as Title6_7_, characterm8_.ANCSTATESET_ID as ANCSTAT22_6_7_, characterm8_.CODONPOSITIONSET_ID as CODONPO23_6_7_, characterm8_.CHARSET_ID as CHARSET24_6_7_, characterm8_.TYPESET_ID as TYPESET25_6_7_, characterm8_.CHARWEIGHTSET_ID as CHARWEI26_6_7_, characterm8_.nChar as nChar6_7_, characterm8_.nTax as nTax6_7_, characterm8_.Aligned as Aligned6_7_, characterm8_.CaseSensitive as CaseSen17_6_7_, characterm8_.MATRIXTYPE as MATRIXTYPE6_7_, typeset9_.TYPESET_ID as TYPESET1_37_8_, typeset9_.VERSION as VERSION37_8_, typeset9_.Title as Title37_8_, charweight10_.CHARWEIGHTSET_ID as CHARWEIG1_11_9_, charweight10_.VERSION as VERSION11_9_, charweight10_.Title as Title11_9_ from MATRIXCOLUMN matrixcolu0_ left outer join PHYLOCHAR phylochar1_ on matrixcolu0_.PHYLOCHAR_ID=phylochar1_.PHYLOCHAR_ID left outer join MATRIX characterm2_ on matrixcolu0_.MATRIX_ID=characterm2_.MATRIX_ID left outer join MATRIXDATATYPE matrixdata3_ on characterm2_.MATRIXDATATYPE_ID=matrixdata3_.MATRIXDATATYPE_ID left outer join PHYLOCHAR phylochar4_ on matrixdata3_.PHYLOCHAR_ID=phylochar4_.PHYLOCHAR_ID left outer join ANCSTATESET ancstatese5_ on characterm2_.ANCSTATESET_ID=ancstatese5_.ANCSTATESET_ID left outer join CodonPositionSet codonposit6_ on characterm2_.CODONPOSITIONSET_ID=codonposit6_.CodonPositionSet_ID left outer join CHARSET excludedch7_ on characterm2_.CHARSET_ID=excludedch7_.CHARSET_ID left outer join MATRIX characterm8_ on excludedch7_.MATRIX_ID=characterm8_.MATRIX_ID left outer join TYPESET typeset9_ on characterm2_.TYPESET_ID=typeset9_.TYPESET_ID left outer join CHARWEIGHTSET charweight10_ on characterm2_.CHARWEIGHTSET_ID=charweight10_.CHARWEIGHTSET_ID where matrixcolu0_.MATRIX_ID=$1 and matrixcolu0_.COLUMN_ORDER=$2 -Jon ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Rutger V. <rut...@gm...> - 2010-06-17 11:53:01
|
Hi, Mike Keesey posted an issue on the bug tracker asking that we place a crossdomain.xml file in the root of the web server. This would allow flash applications on other domains to access phylows data. I think that would be awesome (I'm thinking tree viewers) so I hope you will agree to make that happen and place (something like) the attached file at http://treebase.org/crossdomain.xml Thanks, Rutger p.s. here is the tracker item: https://sourceforge.net/tracker/?func=detail&aid=2977283&group_id=248804&atid=1126676 -- 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: Rutger V. <rut...@gm...> - 2010-06-16 21:47:38
|
Hi, I've did a number of fixes on the search rss (including adding full abstracts and fixing the safari issue). They're visible on the dev server: http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.publicationName==Evolution&format=rss1 Two questions: i) is the purl configuration on dev undefined? It looks like it is, resulting in broken links; 2) can we move this fix to production? Thanks! 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 |
|
From: Hilmar L. <hl...@ne...> - 2010-06-15 20:26:28
|
On Jun 15, 2010, at 2:11 PM, Rutger Vos wrote: > So, on the topic of purls, has there been some tweaking? Not for the Linked Data issue that you brought up - you haven't responded to my last question in that regard. > I noticed there is a /dev/ path fragment that redirects to treebase- > dev.nescent.org. Nice! How long has that been there? Since April. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Rutger V. <rut...@gm...> - 2010-06-15 18:11:20
|
So, on the topic of purls, has there been some tweaking? I noticed there is a /dev/ path fragment that redirects to treebase-dev.nescent.org. Nice! How long has that been there? On Fri, Jun 4, 2010 at 7:52 PM, Hilmar Lapp <hl...@ne...> wrote: > > On Jun 4, 2010, at 11:44 AM, Rutger Vos wrote: > >>> >>> But why can't the redirection from >>> http://purl.org/phylo/treebase/phylows/tree/16354 to >>> http://treebase.org/phylows/tree/16354 be a 301 or a 302? They should >>> probably also be connected by owl:sameAs. In fact, because they are >>> owl:sameAs, shouldn't they be redirected through 301 or 302, because 303 >>> says "See also". But this is not seeAlso - they are owl:sameAs! >> >> Eh, ok, where would we make that owl:sameAs statement? > > > Well, in the RDF of course. > > So if someone dereferences http://purl.org/phylo/treebase/phylows/tree/16354 > and wants RDF, they get first redirected (using 301 or 302 in my opinion) to > http://treebase.org/phylows/tree/16354, which is resolved via 303 to > http://treebase.org/phylows/tree/16354?format=rdf through content > negotiation. In the RDF, you can say that > http://treebase.org/phylows/tree/16354 owl:sameAs > http://purl.org/phylo/treebase/phylows/tree/16354 > > -hilmar > -- > =========================================================== > : 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: Rutger V. <rut...@gm...> - 2010-06-15 17:22:35
|
On Tue, Jun 15, 2010 at 6:18 PM, William Piel <wil...@ya...> wrote: > > On Jun 15, 2010, at 1:11 PM, Jon Auman wrote: > >> I updated production with the latest build. Bill, can you check to see if the coordinates show up now? >> >> thanks, >> Jon > > it works! Sweet. -- 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...> - 2010-06-15 17:18:32
|
On Jun 15, 2010, at 1:11 PM, Jon Auman wrote: > I updated production with the latest build. Bill, can you check to see if the coordinates show up now? > > thanks, > Jon it works! Many thanks. bp |
|
From: Jon A. <jon...@du...> - 2010-06-15 17:11:34
|
I updated production with the latest build. Bill, can you check to see if the coordinates show up now? thanks, Jon On Jun 15, 2010, at 12:07 PM, Rutger Vos wrote: > There was a bug in my code that caused the coordinates to not be > attached under some (but not all, hence my initial confusion) > circumstances. I just committed a fix. When we do another deployment > the coordinates should show up in the produced output. > > On Tue, Jun 15, 2010 at 4:10 PM, Jon Auman <jon...@du...> wrote: >> Yes, they are the same version. They are exactly the same bytes in size, and >> I copied from dev instance to production. >> -Jon >> On Jun 15, 2010, at 9:36 AM, William Piel wrote: >> >> On Jun 14, 2010, at 11:22 AM, Vladimir Gapeyev wrote: >> >> Has a new build been triggered yet? It would be nice to see this on >> >> production. >> >> According to Jon, deployed to production this morning. >> >> Thanks Vladimir. >> >> This is a bit odd because the lat/longs are not showing up in the NeXML of >> these matrices: >> >> http://purl.org/phylo/treebase/phylows/matrix/TB2:M5572?format=nexml >> http://purl.org/phylo/treebase/phylows/matrix/TB2:M5212?format=nexml >> >> ... yet they should be there. >> >> Can we confirm that, indeed, the dev and prod builds are identical versions? >> >> bp >> >> >> >> ------------------------------------------------------------------------------ >> ThinkGeek and WIRED's GeekDad team up for the Ultimate >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the >> lucky parental unit. See the prize list and enter to win: >> http://p.sf.net/sfu/thinkgeek-promo >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> ------------------------------------------------------- >> Jon Auman >> Systems Administrator >> National Evolutionary Synthesis Center >> Duke University >> http:www.nescent.org >> jon...@ne... >> ------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------------ >> ThinkGeek and WIRED's GeekDad team up for the Ultimate >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the >> lucky parental unit. See the prize list and enter to win: >> http://p.sf.net/sfu/thinkgeek-promo >> _______________________________________________ >> 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 ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Rutger V. <rut...@gm...> - 2010-06-15 16:07:59
|
There was a bug in my code that caused the coordinates to not be attached under some (but not all, hence my initial confusion) circumstances. I just committed a fix. When we do another deployment the coordinates should show up in the produced output. On Tue, Jun 15, 2010 at 4:10 PM, Jon Auman <jon...@du...> wrote: > Yes, they are the same version. They are exactly the same bytes in size, and > I copied from dev instance to production. > -Jon > On Jun 15, 2010, at 9:36 AM, William Piel wrote: > > On Jun 14, 2010, at 11:22 AM, Vladimir Gapeyev wrote: > > Has a new build been triggered yet? It would be nice to see this on > > production. > > According to Jon, deployed to production this morning. > > Thanks Vladimir. > > This is a bit odd because the lat/longs are not showing up in the NeXML of > these matrices: > > http://purl.org/phylo/treebase/phylows/matrix/TB2:M5572?format=nexml > http://purl.org/phylo/treebase/phylows/matrix/TB2:M5212?format=nexml > > ... yet they should be there. > > Can we confirm that, indeed, the dev and prod builds are identical versions? > > bp > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > 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: Jon A. <jon...@du...> - 2010-06-15 16:06:38
|
I've created a custom 404 error page for treebase. If you've got better wording, please send it to me and I'll update it. Example: http://www.treebase.org/cgi-bin/treebase.pl?TaxonID=T31183&Submit=Taxon+ID An alternative wording could be: Sorry, Page, not found. :-) -Jon ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
9 messages has been excluded from this view by a project administrator.
