wf2js.py

import datetime
import json
import os
import sys
import urllib.request

jsdefs = {}

# schema at:  https://github.com/NCATSTranslator/OperationsAndWorkflows/blob/main/schema/operation.json
raw_schema = 'https://raw.githubusercontent.com/NCATSTranslator/OperationsAndWorkflows/main/schema/operation.json'

sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../../ARAX/ARAXQuery")
from operation_to_ARAXi import WorkflowToARAXi
wf = WorkflowToARAXi()
in_arax = wf.implemented

# for local testing:
#with open('wfschema.json') as file:
#    schema = json.load(file)

with urllib.request.urlopen(raw_schema) as file:
    schema = json.loads(file.read().decode())

    for operation in schema["$defs"]:
        id = schema["$defs"][operation]['properties']['id']['enum'][0]
        print("In: "+operation+" ("+id+")")

        jsdefs[id] = {}
        jsdefs[id]['in_arax'] = id in in_arax

        all_props = []
        if 'properties' in schema["$defs"][operation]['properties']['parameters']:
            all_props.append(schema["$defs"][operation]['properties']['parameters']['properties'])
        if 'oneOf' in schema["$defs"][operation]['properties']['parameters']:
            jsdefs[id]['warning'] = 'Only one of the following sets of parameters can be used: '
            ortxt = ''
            for p in schema["$defs"][operation]['properties']['parameters']['oneOf']:
                all_props.append(p['properties'])
                jsdefs[id]['warning'] += ortxt + '['
                comma = ''
                for o in p['properties']:
                    jsdefs[id]['warning'] += comma + o
                    comma = ', '
                jsdefs[id]['warning'] += ']'
                ortxt = ' OR '

        params = {}
        for p in all_props:
            for par in p:
                if par in params:
                    del params[par]
                params[par] = {}
                ref = p[par]
                if 'required' in schema["$defs"][operation]['properties']['parameters']:
                    params[par]['is_required'] = par in schema["$defs"][operation]['properties']['parameters']['required']
                else:
                    params[par]['is_required'] = False;

                # rename and discard some fields
                if 'minimum' in ref:
                    ref['min'] = ref.pop('minimum')
                if 'maximum' in ref:
                    ref['max'] = ref.pop('maximum')
                if 'example' in ref:
                    ref['examples'] = ref.pop('example')
                if 'items' in ref:
                    del ref['items']

                # capture what we care about
                for v in ['type', 'minLength', 'enum', 'default','min', 'max', 'examples', 'description']:
                    if v in ref:
                        params[par][v] = ref.pop(v)

                for a in ref:
                    print("--------------- missed: ["+par+"]: "+a)

        jsdefs[id]['parameters'] = params


ahora = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")

file_name = 'wfoperations.js.new'
fid = open(file_name, 'w')
fid.write("// WARNING:\n")
fid.write("// This file was auto-generated by "+__file__+" on: "+ahora+"\n")
fid.write("//\n")
fid.write("var wf_operations = "+json.dumps(jsdefs,indent=2)+"\n")
fid.close()

print('\nOutput written to: '+file_name)