History not updating for multiple instances of Galaxy
Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and "Get Data" and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/tool_runner/upload_async_message HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_message" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:29,261 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:29 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342323 galaxy.tools.actions.upload_common INFO 2013-02-21 13:16:30,841 tool upload1 created job id 4 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/index HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:30 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:31,347 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:31 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342324 galaxy.jobs.manager DEBUG 2013-02-21 13:16:33,263 (4) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-02-21 13:16:38,574 (4) Working directory for job is: /home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4 galaxy.jobs.handler DEBUG 2013-02-21 13:16:38,574 dispatching job 4 to local runner galaxy.jobs.handler INFO 2013-02-21 13:16:38,837 (4) Job dispatched galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,130 executing: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,549 execution finished: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs DEBUG 2013-02-21 13:16:39,590 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-02-21 13:16:39,900 job 4 ended So some reason the history isn't getting updated for multiple instances of Galaxy Thanks Neil
Further, when I try "register" I add an email address and password, but the system still doesn't log me in Maybe this is a database configuration issue? I didn't think I'd need to state any specific entries in universe as I am using physically separate directories i.e. /home/galaxy/galaxy-cte/ .... i.e. /home/galaxy/galaxy-Newcastle/ .... Cheers Neil From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Thursday, 21 February 2013 1:19 PM To: galaxy-dev@lists.bx.psu.edu Cc: galaxy-user@lists.bx.psu.edu Subject: History not updating for multiple instances of Galaxy Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and "Get Data" and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/tool_runner/upload_async_message HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_message" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:29,261 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:29 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342323 galaxy.tools.actions.upload_common INFO 2013-02-21 13:16:30,841 tool upload1 created job id 4 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/index HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:30 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:31,347 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:31 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342324 galaxy.jobs.manager DEBUG 2013-02-21 13:16:33,263 (4) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-02-21 13:16:38,574 (4) Working directory for job is: /home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4 galaxy.jobs.handler DEBUG 2013-02-21 13:16:38,574 dispatching job 4 to local runner galaxy.jobs.handler INFO 2013-02-21 13:16:38,837 (4) Job dispatched galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,130 executing: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,549 execution finished: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs DEBUG 2013-02-21 13:16:39,590 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-02-21 13:16:39,900 job 4 ended So some reason the history isn't getting updated for multiple instances of Galaxy Thanks Neil
On Thursday, February 21, 2013, wrote:
Further, when I try “register” I add an email address and password, but the system still doesn’t log me in****
** **
Maybe this is a database configuration issue?****
** **
I didn’t think I’d need to state any specific entries in universe as I am using physically separate directories****
** **
i.e. /home/galaxy/galaxy-cte/ ....****
i.e. /home/galaxy/galaxy-Newcastle/ ....****
** **
Cheers****
Neil****
The logging in problem sounds like a cookie path issue to me, I had something similar when I added second public Galaxy to our server (in my case, a live on and a dev one). Peter
<untested> maybe the cookie path for each instance defined in universe_wsgi.ini needs to be distinguishable if you're swapping between authenticated instances ? </untested> # If proxy-prefix is enabled and you're running more than one Galaxy instance # behind one hostname, you will want to set this to the same path as the prefix # in the filter above. This value becomes the "path" attribute set in the # cookie so the cookies from each instance will not clobber each other. cookie_path = /galaxy On Thu, Feb 21, 2013 at 7:07 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Thursday, February 21, 2013, wrote:
Further, when I try “register” I add an email address and password, but the system still doesn’t log me in****
** **
Maybe this is a database configuration issue?****
** **
I didn’t think I’d need to state any specific entries in universe as I am using physically separate directories****
** **
i.e. /home/galaxy/galaxy-cte/ ....****
i.e. /home/galaxy/galaxy-Newcastle/ ....****
** **
Cheers****
Neil****
The logging in problem sounds like a cookie path issue to me, I had something similar when I added second public Galaxy to our server (in my case, a live on and a dev one).
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
Thanks all that solved the problem. I also deleted my cache and cookies Thanks for the help Neil From: Ross [mailto:ross.lazarus@gmail.com] Sent: Thursday, 21 February 2013 8:27 PM To: Peter Cock; Burdett, Neil (ICT Centre, Herston - RBWH); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] History not updating for multiple instances of Galaxy <untested> maybe the cookie path for each instance defined in universe_wsgi.ini needs to be distinguishable if you're swapping between authenticated instances ? </untested> # If proxy-prefix is enabled and you're running more than one Galaxy instance # behind one hostname, you will want to set this to the same path as the prefix # in the filter above. This value becomes the "path" attribute set in the # cookie so the cookies from each instance will not clobber each other. cookie_path = /galaxy On Thu, Feb 21, 2013 at 7:07 PM, Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote: On Thursday, February 21, 2013, wrote: Further, when I try "register" I add an email address and password, but the system still doesn't log me in Maybe this is a database configuration issue? I didn't think I'd need to state any specific entries in universe as I am using physically separate directories i.e. /home/galaxy/galaxy-cte/ .... i.e. /home/galaxy/galaxy-Newcastle/ .... Cheers Neil The logging in problem sounds like a cookie path issue to me, I had something similar when I added second public Galaxy to our server (in my case, a live on and a dev one). Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
participants (3)
-
Neil.Burdett＠csiro.au -
Peter Cock -
Ross