Great. I'm glad it's working and thanks for your patience, Sascha.
On Mon, Jan 7, 2013 at 5:35 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hi Carl!
My holidays were good, indeed. Hope you did have some time to relax, too.
Thanks for your last update! Everything works as expected now! Thanks thanks thanks!
Have a nice week!
Cheers,
Sascha
Hello, Sascha
I’ve added some better handling for new datasets and now refresh the history panel when a job completes with the force_history_refresh.
If you update to the latest revision, does your tool work as expected now?
Hope your holidays were good,
C
On Fri, Dec 21, 2012 at 5:33 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hey Carl!
Thanks for this information and your work. I will be on holidays the next two weeks. Therefore I cannot reply if you need more information or testing from me. I wish you a Merry Christmas and a Happy New Year!
Cheers,
Sascha
Hello Sascha,
I wanted to let you know this issue is still being worked on and that I have some leads as to what’s going on. I may have a fix for this soon. I appreciate your patience.
C
On Mon, Dec 10, 2012 at 3:41 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
- How many datasets does your tool produce (in your test case)?
- Two files
- Does your tool produce datasets over time (that’s my assumption from
the errors we’ve had)?
- My tool submits selected workflows and the datasets from the tools in
these worflow are added to
the same history as where the submit-tool datasets are
- If I understand, your first dataset appears, shows running, and (now)
goes green?
- Yes, exactly
- You’re other datasets never appear?
- No, they appear. But I have to refresh the history manually >>
force_history_refresh="True" does not work
anymore.
S
On Thu, Dec 6, 2012 at 4:35 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hi Carl!
It looks like you are getting closer. Now the output of the tool gets green as soon as the job has finished but
the history did not refresh automatically (force_history_refresh is set to True).
If you need any further information let me know!
Thanks,
Sascha
Original Message
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Subject:
Re: [galaxy-dev] History will not refresh after workflow submission via the API
Sent:
Mittwoch, 5. Dezember 2012 19:03
From:
Carl Eberhard (carlfeberhard@gmail.com)
Hello again, Sascha
I’ve committed a change to galaxy-central that more gracefully handles sync’ing histories and the HDAs they contain.
Can you update to the latest galaxy-central revision and try your tool again?
Thanks,
C
On Fri, Nov 30, 2012 at 1:47 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Don’t worry, Carl!
Thanks for you assistance and your quick response.
Cheers,
Sascha
Original Message
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Subject:
Re: [galaxy-dev] History will not refresh after workflow submission via the API
Sent:
Donnerstag, 29. November 2012 20:38
From:
Carl Eberhard (carlfeberhard@gmail.com)
Sorry for the delay, Sascha.
I think I’ve figured out what’s going on here. I’ll work on a fix which should be available in central soon.
Thanks for your patience.
C
On Wed, Nov 28, 2012 at 2:22 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
This line is output right before the Job is running on the Cluster:
The following ids have changed state: ["e721f81135f1bdf1", "79b6b0e08a33fb04"]
Then come some "normal" information lines, and finally:
The following ids have changed state:
[
"84f49fe0eab77e89"
,
"c7ed15b882f70e0c"
,
"a2fd9a049c3c1244"
,
"f2f5d3b2414fcb33"
,
"6a7868e6e99a9a29"
,
"7eefa465e388c990"
,
"f37a392459dba1d7"
,
"6a73de8a9c82cb0e"
]
historyItem is undefined (line 277)...
Cheers, Sascha
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Subject:
Re: Re: Re: [galaxy-dev] History will not refresh after workflow submission via the API
Sent:
Dienstag, 27. November 2012 17:01
From:
Carl Eberhard (carlfeberhard@gmail.com)
That’s a good lead. Thanks.
It looks like some of the dataset ids in the history aren’t mapping correctly. That line is looking up a particular dataset in the history by it’s id. Galaxy uses two styles of ids: raw (e.g. ’12’) and encoded (e.g. ’65hf39ef19’). The problem may be there.
Is this a local installation of Galaxy? In other words, can you alter the code being used?
If so, can you add the following to line 170 in static/scripts/mvc/history/history-model.js:
console.warn( ’The following ids have changed state:’, changedIds );
and try your workflow again (hopefully this isn’t too time-consuming)?
I’ll add some better error handling in that section.
On Tue, Nov 27, 2012 at 10:33 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Here it comes:
historyItem is undefined (line 277)
[image: [image]]
historyItem.fetch();
http://192.168.30.78:5454/static/scripts/mvc/dataset/hda-model.js?v=13540287...
Original Message
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Subject:
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Sent:
Dienstag, 27. November 2012 15:08
From:
Carl Eberhard (carlfeberhard@gmail.com)
Good. As a start, that should allow you to see any errors in Galaxy’s javascript (a client-side programming language) that might occur.
If you start firebug (by hitting F12) and run your workflow, do you see any errors?
On Tue, Nov 27, 2012 at 2:17 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Firebug is installed!
Original Message
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Re: [galaxy-dev] History will not refresh after workflow submission via the API
Sent:
Montag, 26. November 2012 16:33
From:
Carl Eberhard (carlfeberhard@gmail.com)
Great! Do you have Firebug installed?
If not, could you install it, please? It will allow us to find javascript errors more easily.
On Mon, Nov 26, 2012 at 10:22 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hello Carl!
Thanks for your personal assistance :-)
I am using Firefox 13.0.1
Cheers,
Sascha
Original Message
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Sent:
Montag, 26. November 2012 16:15
From:
Carl Eberhard (carlfeberhard@gmail.com)
Hello, Sascha
So let’s see what the problem might be.
Which browser are you currently using?
On Thu, Nov 22, 2012 at 4:01 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hi Carl,
I have updated to the latest revison but the error still occurs.
Cheers,
Sascha
Original Message
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Subject:
Re: [galaxy-dev] History will not refresh after workflow submission via the API
Sent:
Mittwoch, 21. November 2012 17:54
From:
Carl Eberhard (carlfeberhard@gmail.com)
Hi Sascha,
This may be due to the recent history panel changes. Can you update to the latest revision and see if the error still occurs?
Thanks,
Carl
On Tue, Nov 20, 2012 at 2:22 AM, MSc. Sascha Kastens < s.kastens@gatc-biotech.com> wrote:
Hi devs!
After updating my local instance to changeset 19cbbaf566216cb46ecc6a6d17e0f1e0ab52978e my tool which submits a workflow via the
API and set force_history_refresh to TRUE does not refresh the history anymore.
The job is submit via DRMAA to SGE. Unfortunately the job seems to run forever because it is still in yellow state (even after SGE tells Galaxy that the job has finished. As soon as I refresh the history manually the according history entries get green and all entries for the submitted workflow are shown.
I have no idea where I can have a look at. If you need any further information let me know!
Thanks for your help in advance!
Cheers,
Sascha
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Carl Eberhard