Entering edit mode
14 months ago
Eliveri
▴
350
I am using the Python code example from https://www.uniprot.org/help/id_mapping to programmatically get the ID Mapping results of a list of identifiers. However the returned results are a json file.
I cannot figure out how to retrieve the results as a tsv instead.
import re
import time
import json
import zlib
from xml.etree import ElementTree
from urllib.parse import urlparse, parse_qs, urlencode
import requests
from requests.adapters import HTTPAdapter, Retry
POLLING_INTERVAL = 3
API_URL = "https://rest.uniprot.org"
retries = Retry(total=5, backoff_factor=0.25, status_forcelist=[500, 502, 503, 504])
session = requests.Session()
session.mount("https://", HTTPAdapter(max_retries=retries))
def check_response(response):
try:
response.raise_for_status()
except requests.HTTPError:
print(response.json())
raise
def submit_id_mapping(from_db, to_db, ids):
request = requests.post(
f"{API_URL}/idmapping/run",
data={"from": from_db, "to": to_db, "ids": ",".join(ids)},
)
check_response(request)
return request.json()["jobId"]
def get_next_link(headers):
re_next_link = re.compile(r'<(.+)>; rel="next"')
if "Link" in headers:
match = re_next_link.match(headers["Link"])
if match:
return match.group(1)
def check_id_mapping_results_ready(job_id):
while True:
request = session.get(f"{API_URL}/idmapping/status/{job_id}")
check_response(request)
j = request.json()
if "jobStatus" in j:
if j["jobStatus"] == "RUNNING":
print(f"Retrying in {POLLING_INTERVAL}s")
time.sleep(POLLING_INTERVAL)
else:
raise Exception(j["jobStatus"])
else:
return bool(j["results"] or j["failedIds"])
def get_batch(batch_response, file_format, compressed):
batch_url = get_next_link(batch_response.headers)
while batch_url:
batch_response = session.get(batch_url)
batch_response.raise_for_status()
yield decode_results(batch_response, file_format, compressed)
batch_url = get_next_link(batch_response.headers)
def combine_batches(all_results, batch_results, file_format):
if file_format == "json":
for key in ("results", "failedIds"):
if key in batch_results and batch_results[key]:
all_results[key] += batch_results[key]
elif file_format == "tsv":
return all_results + batch_results[1:]
else:
return all_results + batch_results
return all_results
def get_id_mapping_results_link(job_id):
url = f"{API_URL}/idmapping/details/{job_id}"
request = session.get(url)
check_response(request)
return request.json()["redirectURL"]
def decode_results(response, file_format, compressed):
if compressed:
decompressed = zlib.decompress(response.content, 16 + zlib.MAX_WBITS)
if file_format == "json":
j = json.loads(decompressed.decode("utf-8"))
return j
elif file_format == "tsv":
return [line for line in decompressed.decode("utf-8").split("\n") if line]
elif file_format == "xlsx":
return [decompressed]
elif file_format == "xml":
return [decompressed.decode("utf-8")]
else:
return decompressed.decode("utf-8")
elif file_format == "json":
return response.json()
elif file_format == "tsv":
return [line for line in response.text.split("\n") if line]
elif file_format == "xlsx":
return [response.content]
elif file_format == "xml":
return [response.text]
return response.text
def get_xml_namespace(element):
m = re.match(r"\{(.*)\}", element.tag)
return m.groups()[0] if m else ""
def merge_xml_results(xml_results):
merged_root = ElementTree.fromstring(xml_results[0])
for result in xml_results[1:]:
root = ElementTree.fromstring(result)
for child in root.findall("{http://uniprot.org/uniprot}entry"):
merged_root.insert(-1, child)
ElementTree.register_namespace("", get_xml_namespace(merged_root[0]))
return ElementTree.tostring(merged_root, encoding="utf-8", xml_declaration=True)
def print_progress_batches(batch_index, size, total):
n_fetched = min((batch_index + 1) * size, total)
print(f"Fetched: {n_fetched} / {total}")
def get_id_mapping_results_search(url):
parsed = urlparse(url)
query = parse_qs(parsed.query)
file_format = query["format"][0] if "format" in query else "json"
if "size" in query:
size = int(query["size"][0])
else:
size = 500
query["size"] = size
compressed = (
query["compressed"][0].lower() == "true" if "compressed" in query else False
)
parsed = parsed._replace(query=urlencode(query, doseq=True))
url = parsed.geturl()
request = session.get(url)
check_response(request)
results = decode_results(request, file_format, compressed)
total = int(request.headers["x-total-results"])
print_progress_batches(0, size, total)
for i, batch in enumerate(get_batch(request, file_format, compressed), 1):
results = combine_batches(results, batch, file_format)
print_progress_batches(i, size, total)
if file_format == "xml":
return merge_xml_results(results)
return results
def get_id_mapping_results_stream(url):
if "/stream/" not in url:
url = url.replace("/results/", "/results/stream/")
request = session.get(url)
check_response(request)
parsed = urlparse(url)
query = parse_qs(parsed.query)
file_format = query["format"][0] if "format" in query else "json"
compressed = (
query["compressed"][0].lower() == "true" if "compressed" in query else False
)
return decode_results(request, file_format, compressed)
job_id = submit_id_mapping(
from_db="UniProtKB_AC-ID", to_db="ChEMBL", ids=["P05067", "P12345"]
)
if check_id_mapping_results_ready(job_id):
link = get_id_mapping_results_link(job_id)
results = get_id_mapping_results_search(link)
# Equivalently using the stream endpoint which is more demanding
# on the API and so is less stable:
# results = get_id_mapping_results_stream(link)
print(results)
# {'results': [{'from': 'P05067', 'to': 'CHEMBL2487'}], 'failedIds': ['P12345']}
To follow-up on this, the available formats are listed in the documentation at Programmatic access - Retrieving entries via queries under 'What formats are available?'.
For those interested, there's a Python package for querying UniProt's new REST API, by Michael Milton(multimeric), called Unipressed; it supports formats json, tsv, list, and xml . There's example code using Unipressed here with getting
tsvandxml.Thank you for your help!