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Merged
merged 4 commits into from
Sep 17, 2025
Merged

Add HTTP Request timeout and error handling #18

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cccafc3
Fix timeout errors
shashankbrgowda Sep 16, 2025
5e8119b
fix
shashankbrgowda Sep 16, 2025
e7ad0d1
fixes
shashankbrgowda Sep 16, 2025
3476c70
fix
shashankbrgowda Sep 16, 2025
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65 changes: 39 additions & 26 deletions app/api/resources/rapid_view.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,21 +41,34 @@ async def resolve_rapid_stable_id(request: Request, stable_id: str):
)
return HTMLResponse(generate_rapid_id_page(res))

matches = search_results.get("matches")
metadata_results = get_metadata(matches)
try:
matches = search_results.get("matches")
metadata_results = get_metadata(matches)

stable_id_resolver_response = StableIdResolverResponse(
stable_id=stable_id,
code=308,
rapid_archive_url=rapid_archive_url
)
results = build_stable_id_resolver_content(metadata_results)
stable_id_resolver_response.content = results
stable_id_resolver_response = StableIdResolverResponse(
stable_id=stable_id,
code=308,
rapid_archive_url=rapid_archive_url
)
results = build_stable_id_resolver_content(metadata_results)
stable_id_resolver_response.content = results

if is_json_request(request):
return results
if is_json_request(request):
return results

return HTMLResponse(generate_rapid_id_page(stable_id_resolver_response))
return HTMLResponse(generate_rapid_id_page(stable_id_resolver_response))
except Exception as e:
logging.error(f"Error: {e}")
if is_json_request(request):
return response_error_handler({"status": 500})
res = StableIdResolverResponse(
stable_id=stable_id,
code=500,
message=str(e),
content=None,
rapid_archive_url=rapid_archive_url
)
return HTMLResponse(generate_rapid_id_page(res))


@router.get("/info/{subpath:path}", name="Resolve rapid help page")
Expand Down Expand Up @@ -94,19 +107,19 @@ async def resolve_species(
)
return rapid_resolved_response(response, request)

assembly_accession_id = format_assembly_accession(species_url_name)

if assembly_accession_id is None:
input_error_response = RapidResolverResponse(
response_type=RapidResolverHtmlResponseType.ERROR,
code=422,
resolved_url=f"{ENSEMBL_URL}/species-selector",
message="Invalid input accession ID",
species_name=species_url_name,
)
return rapid_resolved_response(input_error_response, request)

try:
assembly_accession_id = format_assembly_accession(species_url_name)

if assembly_accession_id is None:
input_error_response = RapidResolverResponse(
response_type=RapidResolverHtmlResponseType.ERROR,
code=422,
resolved_url=f"{ENSEMBL_URL}/species-selector",
message="Invalid input accession ID",
species_name=species_url_name,
)
return rapid_resolved_response(input_error_response, request)

genome_object = get_genome_id_from_assembly_accession_id(assembly_accession_id)

if genome_object and genome_object != {}:
Expand All @@ -131,7 +144,7 @@ async def resolve_species(
else:
raise HTTPException(status_code=404, detail="Genome not found")
except HTTPException as e:
logging.debug(e)
logging.error(f"HTTP Error: {e.detail}")
response = RapidResolverResponse(
response_type=RapidResolverHtmlResponseType.ERROR,
code=e.status_code,
Expand All @@ -141,7 +154,7 @@ async def resolve_species(
)
return rapid_resolved_response(response, request)
except Exception as e:
logging.debug(f"Unexpected error occurred: {e}")
logging.error(f"Error: {e}")
response = RapidResolverResponse(
species_name=species_url_name,
response_type=RapidResolverHtmlResponseType.ERROR,
Expand Down
48 changes: 30 additions & 18 deletions app/api/resources/resolver_view.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,26 +41,38 @@ async def resolve(
)
return HTMLResponse(generate_resolver_id_page(res))

matches = search_results.get("matches")
try:
matches = search_results.get("matches")

# Get metadata for all genomes
metadata_results = get_metadata(matches)
# Get metadata for all genomes
metadata_results = get_metadata(matches)

stable_id_resolver_response = StableIdResolverResponse(
stable_id=stable_id,
code=308,
)
results = build_stable_id_resolver_content(metadata_results)
stable_id_resolver_response.content = results
stable_id_resolver_response = StableIdResolverResponse(
stable_id=stable_id,
code=308,
)
results = build_stable_id_resolver_content(metadata_results)
stable_id_resolver_response.content = results

if is_json_request(request):
return results
if is_json_request(request):
return results

if len(results) == 1:
if app == "entity-viewer":
resolved_url = results[0].entity_viewer_url
if len(results) == 1:
if app == "entity-viewer":
resolved_url = results[0].entity_viewer_url
else:
resolved_url = results[0].genome_browser_url
return RedirectResponse(resolved_url)
else:
resolved_url = results[0].genome_browser_url
return RedirectResponse(resolved_url)
else:
return HTMLResponse(generate_resolver_id_page(stable_id_resolver_response))
return HTMLResponse(generate_resolver_id_page(stable_id_resolver_response))
except Exception as e:
logging.error(f"Error: {e}")
if is_json_request(request):
return response_error_handler({"status": 500})
res = StableIdResolverResponse(
stable_id=stable_id,
code=500,
message=str(e),
content=None
)
return HTMLResponse(generate_resolver_id_page(res))
2 changes: 1 addition & 1 deletion app/api/resources/templates/shared/id_content.html
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<span class="search-param-label">Gene</span>
<span class="search-param-value">{{ response.stable_id }}</span>
</div>
{% if response.code == 404 and response.message %}
{% if (response.code == 404 or response.code == 500) and response.message %}
Copy link

@azangru azangru Sep 16, 2025 •
edited
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The id_content.html isn't really well-suited for showing the 500 error. For that matter, it doesn't really fit the 404 error either. The Venn diagram doesn't make sense here. There isn't a 'redirect' happening.

Image Image

Also, I realise that the 404 page says:

You will be redirected to the new Ensembl website, where you will find the latest genomic information

which isn't correct (the 404 page isn't redirecting user anywhere).

I don't have any concrete solutions for this; just pointing this out. I wouldn't say that this is a blocker.

<div class="error-message">
{{ response.message }}
</div>
Expand Down
22 changes: 7 additions & 15 deletions app/api/utils/metadata.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
from loguru import logger
import requests
from typing import List

Expand All @@ -15,19 +14,16 @@ def get_metadata(matches: List[SearchMatch] = []):
try:
session = requests.Session()
with session.get(
url=f"{ENSEMBL_URL}/api/metadata/genome/{genome_id}/details"
url=f"{ENSEMBL_URL}/api/metadata/genome/{genome_id}/details",
timeout=10
) as response:
response.raise_for_status()
metadata_results[genome_id] = response.json()
metadata_results[genome_id]["unversioned_stable_id"] = match.get(
"unversioned_stable_id"
)
except requests.exceptions.HTTPError as HTTPError:
logger.error(f"HTTPError: {HTTPError}")
raise HTTPError
except Exception as e:
logger.exception(e)
raise e
except Exception:
raise Exception("Failed to fetch data from metadata service")

return metadata_results

Expand All @@ -38,12 +34,8 @@ def get_genome_id_from_assembly_accession_id(accession_id: str):
metadata_api_url = (
f"{ENSEMBL_URL}/api/metadata/genomeid?assembly_accession_id={accession_id}"
)
with session.get(url=metadata_api_url) as response:
with session.get(url=metadata_api_url, timeout=10) as response:
response.raise_for_status()
return response.json()
except requests.exceptions.HTTPError as HTTPError:
logger.error(f"HTTPError: {HTTPError}")
raise HTTPError
except Exception as e:
logger.exception(e)
raise e
except Exception:
raise Exception("Failed to fetch data from metadata service")
11 changes: 3 additions & 8 deletions app/api/utils/rapid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,20 +15,15 @@ def get_assembly_accession_from_ncbi(accession_id: str):
f"{NCBI_DATASETS_URL}/genome/accession/{accession_id}/dataset_report"
)

with session.get(url=ncbi_dataset_api_url) as response:
with session.get(url=ncbi_dataset_api_url, timeout=10) as response:
response.raise_for_status()
response_json = response.json()
if response_json and response_json["reports"]:
return response_json["reports"][0]
else:
return None

except requests.exceptions.HTTPError as HTTPError:
logger.error(f"HTTPError: {HTTPError}")
raise HTTPError
except Exception as e:
logger.exception(e)
raise e
except Exception:
raise Exception("Failed to fetch data from NCBI")


def format_assembly_accession(species_url_name: str):
Expand Down