How to resolve 400 Client Error when mapping uniprot IDs programatically? - python-3.x

Question

Here's the code:
API_URL = "https://rest.uniprot.org"
def submit_id_mapping(from_db, to_db, ids):
request = requests.get(
f"{API_URL}/idmapping/run",
data={"from": from_db, "to": to_db, "ids": ",".join(ids)},
)
#request.raise_for_status()
return request.json()
submit_id_mapping(from_db="UniProtKB_AC-ID", to_db="ChEMBL", ids=["P05067", "P12345"])
Taken directly from the official example
And returning the following 404 client error. I tried accessing the url myself and it doesn't seem to work. Given that this is the official documentation I don't really know what to do. Any suggestions are welcomed.
{'url': 'http://rest.uniprot.org/idmapping/run',
'messages': ['Internal server error']}
I also have another script for this but it no longer works! And I don't know why :(
in_f = open("filename")
url = 'https://www.uniprot.org/uploadlists/'
ids=in_f.read().splitlines()
ids_s=" ".join(ids)
params = {
'from': 'PDB_ID',
'to': 'ACC',
'format': 'tab',
'query': ids_s
}
data = urllib.parse.urlencode(params)
data = data.encode('utf-8')
req = urllib.request.Request(url, data)
with urllib.request.urlopen(req) as f:
response = f.read()
print(response.decode('utf-8'))
Error:
urllib.error.HTTPError: HTTP Error 405: Not Allowed

Answer 1

Try to change .get to .post:
import requests
API_URL = "https://rest.uniprot.org"
def submit_id_mapping(from_db, to_db, ids):
data = {"from": from_db, "to": to_db, "ids": ids}
request = requests.post(f"{API_URL}/idmapping/run", data=data)
return request.json()
result = submit_id_mapping(
from_db="UniProtKB_AC-ID", to_db="ChEMBL", ids=["P05067", "P12345"]
)
print(result)
Prints:
{'jobId': 'da05fa39cf0fc3fb3ea1c4718ba094b8ddb64461'}