History items get REMOVED when using the API to run workflows
Hi, I am continueing to struggle with the API.... I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api). When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there! This is very bizarre....Any ideas what is going on here? I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples... Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com LinkedIn Profile
I see the bug you're running into. As a temporary solution, executing workflows via the API with 'no_add_to_history' in the payload should work as expected. I'll have a permanent fix out shortly. -Dannon On Jul 5, 2012, at 5:12 PM, Thon Deboer wrote:
Hi,
I am continueing to struggle with the API....
I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api).
When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there!
This is very bizarre....Any ideas what is going on here? I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples...
Regards,
Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com LinkedIn Profile
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Thanks for the fast reply... How do I add this to the "payload"? Is it part of ds_map or something else? data['workflow_id'] = data['history'] = data['ds_map'] = {} data['no_add_to_history']="True" ? or is it part of the actual definition of the input step? Thanks Thon Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com LinkedIn Profile On Jul 5, 2012, at 2:12 PM, Thon Deboer wrote:
Hi,
I am continueing to struggle with the API....
I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api).
When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there!
This is very bizarre....Any ideas what is going on here? I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples...
Regards,
Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com LinkedIn Profile
___________________________________________________________ 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:
WOW...I guess I know how you guys that designed the API think :) Small other question...Is it possible (yet) to pass a parameter to the API yet, that is NOT an input step? Things that get defined in the workflow step such as {Analysis_Run} that get filled in at runtime? Now it reverts to "X__oc__Analysis_Run__cc__" but I would like to change this at runtime through the API... Thanks Thon On Jul 05, 2012, at 02:34 PM, Dannon Baker <dannonbaker@me.com> wrote: On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote:
data['no_add_to_history']="True" ?
Should do it.
On Jul 5, 2012, at 5:40 PM, Anthonius deBoer wrote:
WOW...I guess I know how you guys that designed the API think :)
Small other question...Is it possible (yet) to pass a parameter to the API yet, that is NOT an input step? Things that get defined in the workflow step such as {Analysis_Run} that get filled in at runtime? Now it reverts to "X__oc__Analysis_Run__cc__" but I would like to change this at runtime through the API...
Not yet. If I remember correctly, the tool API currently allows this (passing a dictionary of parameters to the tool at runtime), and it's definitely the plan that the functionality will eventually be available from the workflow API as well. -Dannon
OK...I tried this and it no longer removes the entries from the history...Thanks! I do see that each of the new histories I create still have a reference to some of the other files I pick up from the library (such as dbSNP) but those entries in the history have the number "None" in stead of the usual 1,2 3 etc. that each file in a history has.... I guess that is an artifact and it does not really bother me, although it makes it hard to run a tool again that uses one of those files later manually, but since that is not the point of running through the API it is fine for now, but it just looks scary... Thon On Jul 05, 2012, at 02:34 PM, Dannon Baker <dannonbaker@me.com> wrote: On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote:
data['no_add_to_history']="True" ?
Should do it.
participants (3)
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Anthonius deBoer -
Dannon Baker -
Thon Deboer