import json
import requests
import argparse

parser = argparse.ArgumentParser(
    description="Upload submission from submit.cancergenetrust.org")
parser.add_argument('file', nargs='?', default="submission.json",
                    help="Path to json file to submit")
args = parser.parse_args()

with open(args.file) as f:
    submission = json.loads(f.read())
submission["clinical"]["CGT Public ID"] = submission["patientId"]

r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                  files=[("files[]",
                          ("foundationone.json",
                           json.dumps(submission["genomic"], sort_keys=True)))],
                  data=submission["clinical"])
print(r.text)
assert(r.status_code == requests.codes.ok)

import json
import requests
import argparse

parser = argparse.ArgumentParser(
    description="Upload submission from submit.cancergenetrust.org")
parser.add_argument('file', nargs='?', default="submission.json",
                    help="Path to json file to submit")
args = parser.parse_args()

with open(args.file) as f:
    submission = json.loads(f.read())
submission["clinical"]["CGT Public ID"] = submission["patientId"]

if submission["genomic"]:
    print("Submitting clinical and genomic data")
    r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                      files=[("files[]",
                              ("foundationone.json",
                               json.dumps(submission["genomic"], sort_keys=True)))],
                      data=submission["clinical"])
else:
    print("No genomic data, submitting only clinical")
    r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                      data=submission["clinical"])
print(r.text)
assert(r.status_code == requests.codes.ok)

Handle only clinical, no genomic, submission
Handle only clinical, no genomic, submission

  import json
  import requests
  import argparse
  
  parser = argparse.ArgumentParser(
      description="Upload submission from submit.cancergenetrust.org")
  parser.add_argument('file', nargs='?', default="submission.json",
                      help="Path to json file to submit")
  args = parser.parse_args()
  
  with open(args.file) as f:
      submission = json.loads(f.read())
  submission["clinical"]["CGT Public ID"] = submission["patientId"]
  
+ if submission["genomic"]:
+     print("Submitting clinical and genomic data")
- r = requests.post("http://localhost:5000/v0/submissions?publish=true",
+     r = requests.post("http://localhost:5000/v0/submissions?publish=true",
-                   files=[("files[]",
+                       files=[("files[]",
-                           ("foundationone.json",
+                               ("foundationone.json",
-                            json.dumps(submission["genomic"], sort_keys=True)))],
+                                json.dumps(submission["genomic"], sort_keys=True)))],
-                   data=submission["clinical"])
+                       data=submission["clinical"])
+ else:
+     print("No genomic data, submitting only clinical")
+     r = requests.post("http://localhost:5000/v0/submissions?publish=true",
+                       data=submission["clinical"])
  print(r.text)
  assert(r.status_code == requests.codes.ok)
  
Handle only clinical, no genomic, submission
## Code Before:
import json
import requests
import argparse

parser = argparse.ArgumentParser(
    description="Upload submission from submit.cancergenetrust.org")
parser.add_argument('file', nargs='?', default="submission.json",
                    help="Path to json file to submit")
args = parser.parse_args()

with open(args.file) as f:
    submission = json.loads(f.read())
submission["clinical"]["CGT Public ID"] = submission["patientId"]

r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                  files=[("files[]",
                          ("foundationone.json",
                           json.dumps(submission["genomic"], sort_keys=True)))],
                  data=submission["clinical"])
print(r.text)
assert(r.status_code == requests.codes.ok)

## Instruction:
Handle only clinical, no genomic, submission
## Code After:
import json
import requests
import argparse

parser = argparse.ArgumentParser(
    description="Upload submission from submit.cancergenetrust.org")
parser.add_argument('file', nargs='?', default="submission.json",
                    help="Path to json file to submit")
args = parser.parse_args()

with open(args.file) as f:
    submission = json.loads(f.read())
submission["clinical"]["CGT Public ID"] = submission["patientId"]

if submission["genomic"]:
    print("Submitting clinical and genomic data")
    r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                      files=[("files[]",
                              ("foundationone.json",
                               json.dumps(submission["genomic"], sort_keys=True)))],
                      data=submission["clinical"])
else:
    print("No genomic data, submitting only clinical")
    r = requests.post("http://localhost:5000/v0/submissions?publish=true",
                      data=submission["clinical"])
print(r.text)
assert(r.status_code == requests.codes.ok)
