Hello,
I'm still relatively new to galaxy. I'm trying to use the API to identify the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job, which corresponds to one step in the workflow. Each of these has inputs/outputs. I can walk outwards and try to connect any other jobs that happen to use one of these files as an input or output; however, I am not seeing any key that provides a more direct indication that a set of steps was executed as part of a given workflow. Am I missing something?
Thanks in advance, Ben
Can you clarify one thing for me - are you attempting to break a workflow invocation into steps, and then jobs, and then inputs and outputs (so working from the workflow invocation) or are you trying to scan existing histories and find a workflow for each dataset (so working from the history id and workflow id maybe)?
I feel like this should be doable now - though blend4j and to a lesser extent even bioblend are pretty far behind what I would consider best practices for invoking workflows via the API so they may need to be updated.
-John
On Thu, Jun 25, 2015 at 10:04 AM, Ben Bimber bbimber@gmail.com wrote:
Hello,
I'm still relatively new to galaxy. I'm trying to use the API to identify the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job, which corresponds to one step in the workflow. Each of these has inputs/outputs. I can walk outwards and try to connect any other jobs that happen to use one of these files as an input or output; however, I am not seeing any key that provides a more direct indication that a set of steps was executed as part of a given workflow. Am I missing something?
Thanks in advance, Ben
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the latter. starting with a dataset, pull it's full history. therefore if it was created by running a simple single-step tool it's one step. if it was created as part of a workflow, grab that whole series of steps/inputs/outputs.
i agree on the python/java bindings being out of date, but even when i was scanning the JSON I wasnt able to see where I'd glean this information. the missing thing for me was always determining if a given dataset was connected to a larger workflow.
-ben
On Thu, Jun 25, 2015 at 7:26 AM, John Chilton jmchilton@gmail.com wrote:
Can you clarify one thing for me - are you attempting to break a workflow invocation into steps, and then jobs, and then inputs and outputs (so working from the workflow invocation) or are you trying to scan existing histories and find a workflow for each dataset (so working from the history id and workflow id maybe)?
I feel like this should be doable now - though blend4j and to a lesser extent even bioblend are pretty far behind what I would consider best practices for invoking workflows via the API so they may need to be updated.
-John
On Thu, Jun 25, 2015 at 10:04 AM, Ben Bimber bbimber@gmail.com wrote:
Hello,
I'm still relatively new to galaxy. I'm trying to use the API to
identify
the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job,
which
corresponds to one step in the workflow. Each of these has
inputs/outputs.
I can walk outwards and try to connect any other jobs that happen to use
one
of these files as an input or output; however, I am not seeing any key
that
provides a more direct indication that a set of steps was executed as
part
of a given workflow. Am I missing something?
Thanks in advance, Ben
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
Ben Bimber -
John Chilton