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
participants (2)
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Neil.Burdett＠csiro.au -
Peter Cock