Using API to identify all datasets that were part of a workflow?
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 i agree on the python/java bindings being out of date, but even when i was scanning the JSON I wasnt able to see where I'd glean this information.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
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
provides a more direct indication that a set of steps was executed as
On Thu, Jun 25, 2015 at 10:04 AM, Ben Bimber <bbimber@gmail.com> wrote: that part
of a given workflow. Am I missing something?
Thanks in advance, Ben
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participants (2)
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Ben Bimber -
John Chilton