Carlos,
The method you describe below for mapping inputs is precisely the intended
approach. One reason for the long identifier being used instead of a simple
step number is that step number (ordering as you would see in the usual run
workflow dialog) can change without it being obvious to the user. The ordering
is based on two factors- a topological sort of the workflow graph, and the
distance within the editor from the top left corner. In other words, it's
possible to edit a workflow in display position only (drag the boxes around)
and change step numbers. One approach here would be to use the step label
('label': 'Left-hand Reads') in your case and programmatically fetch and use
the input id.
For your last issue-- that library dataset is actually marked as deleted on
main, so the error is appropriate. I'm not yet sure why that is the case, but
I'll look into it. If you retry the operation on a known non-deleted library
dataset everything should work just fine.
Thanks!
Dannon
On Jan 5, 2012, at 5:35 PM, Carlos Borroto wrote:
> Hi,
>
> Looking at workflow_execute.py, it seems to me there can be only one
> input for step, is this correct? or is there a wait to map more than
> one input and match them to an specific position in a particularly
> step?
>
> This is the workaround I found.
>
> I created 'Input Dataset' boxes for all of my inputs, then I linked
> them to the step where they are needed. This is actually very
> convenient if the same input is used in more than one step, as when I
> run the workflow manually I only need to select each input once. I
> tried doing this, as each 'Input Dataset' would have his own step.
>
> This is an example workflow:
> http://main.g2.bx.psu.edu/u/cjav/w/fastq-joiner---input-datasets
>
> Initially I ran into this issue:
> $ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
> fcfa9ae643d37c32 'Fastq joiner - Input Datasets'
> '1=ldda=b4c5be159c8057c2' '2=ldda=ea0e32961d454539'
> HTTP Error 400: Bad Request
> "Workflow cannot be run because an expected input step '517620' has no
> input dataset."
>
> I then found you can do:
> $ ./display.py my_key http://main.g2.bx.psu.edu/api/workflows/fcfa9ae643d37c32
> Member Information
> ------------------
> url: /api/workflows/fcfa9ae643d37c32
> inputs: {'517620': {'value': '', 'label': 'Left-hand Reads'},
> '517622': {'value': '', 'label': 'Right-hand Reads'}}
> id: fcfa9ae643d37c32
> name: Fastq joiner - Input Datasets
>
>
> I see inputs get different keys and I can use them when executing the
> workflow:
> $ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
> fcfa9ae643d37c32 'hist_id=9fbfd3a1be8b7f8e'
> '517620=hda=8d89405199368bb0' '517622=hda=5c93f30078e5ac25'
> Response
> --------
> {'outputs': ['f7c4b0900d8f3b1b'], 'history': '9fbfd3a1be8b7f8e'}
>
> This worked perfectly. I still think it would be easier to be able to
> use the step number, but this works.
>
>
> Lastly, I did run into one issue where I had to import the datasets
> firsts, as trying to use ldda like this:
> $ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
> fcfa9ae643d37c32 'Fastq joiner - Input Datasets'
> '517620=ldda=b4c5be159c8057c2' '517622=ldda=ea0e32961d454539'
> Response
> --------
> {'outputs': ['44c033fad737acc5'], 'history': '9fbfd3a1be8b7f8e'}
>
> I got this error in the history:
> input data 1 (file:
> /galaxy/main_database/files/002/780/dataset_2780871.dat) was deleted
> before the job started
>
> This didn't happen in our local instance using galaxy-central.
>
> Thanks,
> Carlos
> ___________________________________________________________
> 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:
>
> http://lists.bx.psu.edu/
___________________________________________________________
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:
http://lists.bx.psu.edu/
