#!/usr/bin/env python """ # ---------------------------------------------- # # PARKLAB, Author: RPARK # ---------------------------------------------- # Execute workflows from the command line. Example calls: python workflow_execute.py /api/workflows 'hist_id=' '38=hda=' 'param=tool=name=value' python workflow_execute_parameters.py 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' """ 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(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id") sys.exit(1) submit(sys.argv[1], sys.argv[2], data) if __name__ == "__main__": main()