galaxy/scripts/api/workflow_execute_parameters.py

#!/usr/bin/env python
"""
# ---------------------------------------------- #
# PARKLAB, Author: RPARK
# ---------------------------------------------- #

Execute workflows from the command line.
Example calls:
python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value'
python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
"""
from __future__ import print_function
import os
import sys

from common import submit


def main():
    try:
        print("workflow_execute:py:")
        data = {}
        data['workflow_id'] = sys.argv[3]
        data['history'] = sys.argv[4]
        data['ds_map'] = {}

        # Trying to pass in parameter for my own dictionary
        data['parameters'] = {}

        # DBTODO If only one input is given, don't require a step
        # mapping, just use it for everything?
        for v in sys.argv[5:]:
            print("Multiple arguments ")
            print(v)

            try:
                step, src, ds_id = v.split('=')
                data['ds_map'][step] = {'src': src, 'id': ds_id}

            except ValueError:
                print("VALUE ERROR:")
                wtype, wtool, wparam, wvalue = v.split('=')
                try:
                    data['parameters'][wtool] = {'param': wparam, 'value': wvalue}
                except ValueError:
                    print("TOOL ID ERROR:")

    except IndexError:
        print('usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0]))
        sys.exit(1)
    submit( sys.argv[1], sys.argv[2], data )

if __name__ == '__main__':
    main()