Unnamed histories proliferating, can't get to my data
I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes. I just tried to "View" the history, which worked (in the middle pane) and clicked "import and start using history". This seemed to work, but I got three panes inside the middle pane! When I go back (again) to saved histories, there are 3 histories - one the imported one with 2 steps, two unnamed histories, all created < 1 minute ago. We just asked a beta tester to play with things, and he uploaded two fastqs, but had what sounds like a similar problem. Any thoughts on what's happening? Thanks, -Amir Karger Research Computing Harvard Medical School
Hi. Resending because I got no response. Can anybody suggest anything that might explain this, or tell me how I can troubleshoot? Where to look in the Python code? Whether anybody has seen anything like this? Our beta tester can't actually test anything. This occurs whether he does the "FTP-style" upload or uploads through the browser. Thanks, -Amir Karger On 10/23/12 2:42 PM, "Karger, Amir" <Amir_Karger@hms.harvard.edu> wrote:
I'm using Galaxy from June, 2012. (Sorry if there's already a fix.)
We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes.
I just tried to "View" the history, which worked (in the middle pane) and clicked "import and start using history". This seemed to work, but I got three panes inside the middle pane! When I go back (again) to saved histories, there are 3 histories - one the imported one with 2 steps, two unnamed histories, all created < 1 minute ago.
We just asked a beta tester to play with things, and he uploaded two fastqs, but had what sounds like a similar problem.
Any thoughts on what's happening?
Thanks,
-Amir Karger Research Computing Harvard Medical School
OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User->Saved Histories page), we get an error from get_history in /www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/__ init__.py The code that makes it is: # Perhaps a bot is running a tool without having logged in to get a history log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url ) So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time. Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too. Thanks, -Amir Karger
On 10/23/12 2:42 PM, "Karger, Amir" <Amir_Karger@hms.harvard.edu> wrote:
I'm using Galaxy from June, 2012. (Sorry if there's already a fix.)
We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes.
Hi Amit, I'm not understanding the original process that results in the problem. You're attempting to upload a file (as an import from an FTP dir), but that file never appears in your current history, or any of your saved histories? --nate On Nov 1, 2012, at 8:48 PM, Karger, Amir wrote:
OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User->Saved Histories page), we get an error from get_history in /www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/__ init__.py
The code that makes it is:
# Perhaps a bot is running a tool without having logged in to get a history log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url )
So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time.
Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too.
Thanks,
-Amir Karger
On 10/23/12 2:42 PM, "Karger, Amir" <Amir_Karger@hms.harvard.edu> wrote:
I'm using Galaxy from June, 2012. (Sorry if there's already a fix.)
We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes.
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On 11/5/12 3:16 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Hi Amit,
I'm not understanding the original process that results in the problem. You're attempting to upload a file (as an import from an FTP dir), but that file never appears in your current history, or any of your saved histories?
--nate
Let's ignore the FTP thing for now, as it adds unnecessary complication. Even using the regular upload tool (browse to a file and upload through HTTP), as soon as you do the upload, the system creates a new history. If you go to User->Saved Histories, you can see new unnamed histories that have been created "less than 1 minute ago". You can also see the saved history that has the uploaded files, but if you try to switch to that saved history, it gives you another new unnamed history. So you can never use the files you've uploaded. What we discovered in our troubleshooting is that get_history is failing to find the old history, so it keeps creating new ones. -Amir
On Nov 1, 2012, at 8:48 PM, Karger, Amir wrote:
OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User->Saved Histories page), we get an error from get_history in
/www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/ __ init__.py
The code that makes it is:
# Perhaps a bot is running a tool without having logged in to get a history log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url )
So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time.
Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too.
Thanks,
-Amir Karger
On 10/23/12 2:42 PM, "Karger, Amir" <Amir_Karger@hms.harvard.edu> wrote:
I'm using Galaxy from June, 2012. (Sorry if there's already a fix.)
We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes.
___________________________________________________________ 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:
participants (2)
-
Karger, Amir -
Nate Coraor