[galaxy-dev] (New) error in Galaxy Reports
Hi all, a similar error with this one ( http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html) has appeared in Galaxy reports after the last update. It also occurs only when I'm trying to view the completed jobs in a certain day. Thanks in advance. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (New) error in Galaxy Reports
False alarm, the error went away when I restated the webapp. 2014-04-24 15:36 GMT+02:00 Nikos Sidiropoulos nikos.sid...@gmail.com: Hi all, a similar error with this one ( http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html) has appeared in Galaxy reports after the last update. It also occurs only when I'm trying to view the completed jobs in a certain day. Thanks in advance. Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Help Galaxy
Hello, Galaxy workflow and history structure is stored in Galaxy's database vs. flat files so you can't just find the representation of those on the file system. I actually don't know if there is any documentation about the JSON structure for those artifacts - I've CC'd the -dev mailing list so someone there might know (btw, emailing the -dev list is preferred with questions like these because your question get more exposure). In the mean time, you can explore the API documentation (available herehttp://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.workflowsand herehttps://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController) because that's where JSON objects can be retrieved. Hope this helps, Enis On Thu, Apr 24, 2014 at 3:33 PM, yattara Moussa moussayatta...@yahoo.frwrote: Hello, I'm working at South Paris University (Université Paris-Sud) Computer Science Research Laboratory (LRI), France. I'm working on Galaxy. I need to know about Galaxy syntax for worklfow internal structure description with JSON, and Galaxy workflow history. *if you have any technical document describing the JSON syntax used for the storage of Galaxy workflow and Galaxy history, it will be very nice if you can send it to me. *I installed Galaxy on ubuntu, In which directory can I find workflow histories files ?. Thank you for your considération, I look forward to hearing from you. Moussa YATTARA. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] user account
Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for operations.append and item.deleted and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make delete user function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Help Galaxy
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on
your local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my local
instance results in
https://gist.github.com/martenson/6b8e1d402fa193c914a5
Nice tool for calling API from browser is Postman http://www.getpostman.com/
M.
On Thu, Apr 24, 2014 at 10:49 AM, Enis Afgan afg...@gmail.com wrote:
Hello,
Galaxy workflow and history structure is stored in Galaxy's database vs.
flat files so you can't just find the representation of those on the file
system.
I actually don't know if there is any documentation about the JSON
structure for those artifacts - I've CC'd the -dev mailing list so someone
there might know (btw, emailing the -dev list is preferred with questions
like these because your question get more exposure). In the mean time, you
can explore the API documentation (available
herehttp://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.workflowsand
herehttps://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController)
because that's where JSON objects can be retrieved.
Hope this helps,
Enis
On Thu, Apr 24, 2014 at 3:33 PM, yattara Moussa
moussayatta...@yahoo.frwrote:
Hello,
I'm working at South Paris University (Université Paris-Sud) Computer
Science Research Laboratory (LRI), France.
I'm working on Galaxy.
I need to know about Galaxy syntax for worklfow internal structure
description with JSON, and Galaxy workflow history.
*if you have any technical document describing the JSON syntax used for
the storage of Galaxy workflow and Galaxy history, it will be very nice if
you can send it to me.
*I installed Galaxy on ubuntu, In which directory can I find workflow
histories files ?.
Thank you for your considération, I look forward to hearing from you.
Moussa YATTARA.
___
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To search Galaxy mailing lists use the unified search at:
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___
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Re: [galaxy-dev] user account
Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] cleaning up job_working_directory
Greetings, Currently my group has set our universe_wsgi.ini's cleanup_job to onsuccess, allowing us to troubleshoot failed runs. However, now failed job folders are beginning to accumulate in the job_working_directory. Is there a way to clean this up? Preferably, a means that can be automated, like with the cleanup_datasets scripts. -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] the dataset update time
Greetings, Just have a conceptual question regarding the dataset object's field update time. What events trigger this field to get modified? For example, I know that using admin_cleanup_datasets.py will update the dataset's update time if it matches the given parameters. What other triggers are there? Are there any actions via UI that will update the update time, such as downloading or even just viewing the dataset's contents? -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user account
Hi Martin I am using Postgresql. Best regards! Jun From: emulato...@gmail.com [mailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 5:21 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Help Galaxy
Hi,
Thanks, great !, i'll try it.
Moussa.
Le Jeudi 24 avril 2014 17h47, Martin Čech mar...@bx.psu.edu a écrit :
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on your
local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my local instance
results in
https://gist.github.com/martenson/6b8e1d402fa193c914a5
Nice tool for calling API from browser is Postman http://www.getpostman.com/
M.
On Thu, Apr 24, 2014 at 10:49 AM, Enis Afgan afg...@gmail.com wrote:
Hello,
Galaxy workflow and history structure is stored in Galaxy's database vs. flat
files so you can't just find the representation of those on the file system.
I actually don't know if there is any documentation about the JSON structure
for those artifacts - I've CC'd the -dev mailing list so someone there might
know (btw, emailing the -dev list is preferred with questions like these
because your question get more exposure). In the mean time, you can explore
the API documentation (available here and here) because that's where JSON
objects can be retrieved.
Hope this helps,
Enis
On Thu, Apr 24, 2014 at 3:33 PM, yattara Moussa moussayatta...@yahoo.fr
wrote:
Hello,
I'm working at South Paris University (Université Paris-Sud) Computer Science
Research Laboratory (LRI), France.
I'm working on Galaxy.
I need to know about Galaxy syntax for worklfow internal structure
description with JSON, and Galaxy workflow history.
*if you have any technical document describing the JSON syntax used for the
storage of Galaxy workflow and Galaxy history, it will be very nice if you
can send it to me.
*I installed Galaxy on ubuntu, In which directory can I find workflow
histories files ?.
Thank you for
your considération, I look forward to hearing from you.
Moussa YATTARA.
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] user account
Hi Martin, Thanks for the hint. After setting track_jobs_in_database to True, the status of the new upload is waiting to run, which should be the behavior expected. Luckily when I modified the setting in universal_wsgi.ini, I noticed that there is an option allow_user_deletion = True which enables the user deletion in UI. The problem is that even I deleted and purged one email, I still can re-register with that email. What is the solution to this? Direct SQL operation? Best regards! Jun From: emulato...@gmail.com [mailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 9:50 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, the account activation is meant for multi-processor environments and these have to have the following option turned on in the configuration: track_jobs_in_database = True Please try to change it. thank you Martin On Thu, Apr 24, 2014 at 4:27 PM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi Martin I am using Postgresql. Best regards! Jun From: emulato...@gmail.commailto:emulato...@gmail.com [mailto:emulato...@gmail.commailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 5:21 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy - Cloudman
Hey Alessia,
I'd love to help, but I need a little more context here. Where are you
seeing this error, what exactly are you doing when it appears, and can you
tell me a little bit more about the Galaxy configuration you're working
with?
-Dannon
On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Posting to the galaxy-...@bx.psu.edu mailing list.
https://wiki.galaxyproject.org/MailingLists
My instance of Galaxy seems to be stuck (same place since last night)
and I have received the error message several times now.
Pasting the error message below:
*Details*
user
username
adeglincer
quota_percent
68
total_disk_usage
184947273683
nice_total_disk_usage
172.2 GB
email
xxx
is_admin
false
tags_used
model_class
User
id
xxx
source
HDACollection(xxx)
xhr
readyState
4
responseText
{err_msg: Uncaught exception in exposed API method:, err_code: 0}
responseJSON
err_msg
Uncaught exception in exposed API method:
err_code
0
status
500
statusText
Internal Server Error
responseHeaders
Date
Thu, 24 Apr 2014 20:51:39 GMT
cache-control
max-age=0,no-cache,no-store
Server
nginx/1.4.7
Connection
keep-alive
Transfer-Encoding
chunked
Content-Type
application/json
options
data
parse
true
emulateHTTP
false
emulateJSON
false
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To search Galaxy mailing lists use the unified search at:
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___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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