Fix: Frequent timeouts from TDR (#7452) #7623

dsotirho-ucsc · 2025-12-08T19:27:44Z

Linked issues: #7452

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codecov · 2025-12-08T19:42:47Z

Codecov Report

❌ Patch coverage is 61.53846% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.83%. Comparing base (ca6fa2d) to head (66b5dab).

Files with missing lines	Patch %	Lines
src/azul/chalice.py	70.00%	3 Missing ⚠️
src/azul/http.py	50.00%	1 Missing ⚠️
src/azul/service/source_controller.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7623      +/-   ##
===========================================
- Coverage    84.84%   84.83%   -0.02%     
===========================================
  Files          157      157              
  Lines        22871    22880       +9     
===========================================
+ Hits         19405    19410       +5     
- Misses        3466     3470       +4

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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coveralls · 2025-12-08T19:43:35Z

coverage: 85.021% (-0.03%) from 85.047%
when pulling f009376 on issues/dsotirho-ucsc/7452-tdr-timeout
into 158e524 on develop.

dsotirho-ucsc · 2025-12-11T18:21:48Z

IT was run before adding the drop! commit which causes TDR requests to timeout by dropping the timeout threshold to 0.1 seconds.

7623_IT_2025-12-11.txt

Before adding the `drop!` commit

$ curl -v 'https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/sources?catalog=dcp3'
...
> GET /repository/sources?catalog=dcp3 HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.7.1
> Accept: */*
>
* Request completely sent off
< HTTP/2 200
< content-type: application/json
< content-length: 17128
< date: Thu, 11 Dec 2025 17:51:17 GMT
< x-amzn-trace-id: Root=1-693b0494-65c44d940957b2351e684f3a;Parent=65aef77bec749fc5;Sampled=0;Lineage=1:18704a40:0
< x-amzn-requestid: 4ba7f2d6-1f59-4d0a-850a-3556113c8d73
< referrer-policy: strict-origin-when-cross-origin
< x-xss-protection: 1; mode=block
< access-control-allow-origin: *
< strict-transport-security: max-age=63072000; includeSubDomains; preload
< access-control-allow-headers: Authorization,Content-Type,X-Amz-Date,X-Amz-Security-Token,X-Api-Key
< x-frame-options: DENY
< content-security-policy: default-src 'self';img-src 'self' data:;script-src 'self';style-src 'self';frame-ancestors 'none';form-action 'self'
< x-amz-apigw-id: Vb2nUHR1IAMEoJw=
< cache-control: no-store
< x-content-type-options: nosniff
< x-cache: Miss from cloudfront
< via: 1.1 f1f1587942b30c5e9c37a190f21c30ba.cloudfront.net (CloudFront)
< x-amz-cf-pop: SFO53-P1
< x-amz-cf-id: _4UC33HDARdviu-LeBMmMmi0Mb3x95hWvcwbleeDxU6fAqyYLyxsYw==
<
{"sources":[{"sourceId":"c6e19201-4fae-4213-a16c-edfd0cc11335","sourceSpec":...

After adding the `drop!` commit

(note 307 response returned along with a location header)

$ curl -v 'https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/sources?catalog=dcp3'
...
> GET /repository/sources?catalog=dcp3 HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.7.1
> Accept: */*
>
* Request completely sent off
< HTTP/2 307
< content-type: application/json
< content-length: 157
< location: https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/sources?catalog=dcp3
< date: Thu, 11 Dec 2025 17:57:49 GMT
< x-amzn-trace-id: Root=1-693b061d-6c4c647622c74b4e7fc1ca8d;Parent=5e1e44c4679fdffe;Sampled=0;Lineage=1:18704a40:0
< x-amzn-requestid: d3864aa1-206e-4ef6-bd12-d3d874eb677b
< referrer-policy: strict-origin-when-cross-origin
< x-xss-protection: 1; mode=block
< access-control-allow-origin: *
< strict-transport-security: max-age=63072000; includeSubDomains; preload
< access-control-allow-headers: Authorization,Content-Type,X-Amz-Date,X-Amz-Security-Token,X-Api-Key
< x-frame-options: DENY
< content-security-policy: default-src 'self';img-src 'self' data:;script-src 'self';style-src 'self';frame-ancestors 'none';form-action 'self'
< x-amz-apigw-id: Vb3kpF2voAMEiEQ=
< cache-control: no-store
< x-content-type-options: nosniff
< retry-after: 30
< x-cache: Miss from cloudfront
< via: 1.1 f21e2ffc4473de4703e807b6f2df3d0e.cloudfront.net (CloudFront)
< x-amz-cf-pop: SFO53-P1
< x-amz-cf-id: 30exdNHZgCBSiyWZibZm1MMgI4IwlsCBpUvOJBK2XTGLlYD1YZEXfQ==
<
* Connection #0 to host service.daniel.dev.singlecell.gi.ucsc.edu left intact
{"Code":"TerraTimeoutError","Message":"No response from https://jade.datarepo-dev.broadinstitute.org/api/repository/v1/snapshots/roleMap within 0.1 seconds"}

achave11-ucsc

Looks good! ✅

hannes-ucsc

#7452 (comment)

In order to more quickly iterate over different solutions it would be helpful to use a instance of the Data Browser running locally on the assignee's machine. Assignee to figure out how to do that, potentially asking CC for help.

What's the status of this aspect?

hannes-ucsc · 2025-12-12T18:29:43Z

src/azul/chalice.py

+    def _retry_after(self, event, get_response):
        """
-        Add a retry-after header to 503 responses
+        Add a retry-after header to the response based on the response type.


Suggested change

Add a retry-after header to the response based on the response type.

Add a retry-after header to the response based on its type.

hannes-ucsc · 2025-12-12T18:32:31Z

src/azul/chalice.py

+            location = furl(self.base_url,
+                            path=event.context['path'],
+                            args=event.query_params)
+            response.headers.setdefault('Location', location.url)


Suggested change

response.headers.setdefault('Location', location.url)

response.headers.setdefault('Location', str(location))

is what we typically use.

It's also a bit odd that we compute the header value only to discard it if the header is already present.

hannes-ucsc · 2025-12-12T18:36:05Z

src/azul/chalice.py

+            # When a client's request fails due to an internal request to TDR
+            # timing out, we want the client to retry their request, so we
+            # return a 307 response along with a location header containing the
+            # URL the client had just requested.


Maybe also explain why we don't want a 503.

hannes-ucsc · 2025-12-12T18:42:17Z

src/azul/chalice.py

+        if status in [307, 503]:
            response.headers.setdefault('Retry-After', '30')
+        if status == 307:
+            # When a client's request fails due to an internal request to TDR


Suggested change

# When a client's request fails due to an internal request to TDR

# When a client's request fails due to an internal request to Terra

Or change the name of the exception

dsotirho-ucsc self-assigned this Dec 8, 2025

dsotirho-ucsc linked an issue Dec 8, 2025 that may be closed by this pull request

Frequent timeouts from TDR #7452

Open

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7452-tdr-timeout branch 4 times, most recently from 5833fe1 to 311b240 Compare December 11, 2025 16:52

dsotirho-ucsc assigned achave11-ucsc Dec 11, 2025

achave11-ucsc previously approved these changes Dec 12, 2025

View reviewed changes

achave11-ucsc marked this pull request as ready for review December 12, 2025 05:19

achave11-ucsc requested a review from hannes-ucsc as a code owner December 12, 2025 05:19

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Dec 12, 2025

hannes-ucsc reviewed Dec 12, 2025

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hannes-ucsc unassigned dsotirho-ucsc Dec 12, 2025

hannes-ucsc added the 1 review [process] Lead requested changes once label Dec 12, 2025

hannes-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Dec 12, 2025

dsotirho-ucsc dismissed achave11-ucsc’s stale review via 4365a09 December 16, 2025 01:42

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7452-tdr-timeout branch 7 times, most recently from 9d544c1 to e23ba1e Compare December 19, 2025 17:47

dsotirho-ucsc added 2 commits January 5, 2026 11:29

Fix: Frequent timeouts from TDR (#7452)

cee4d2f

fixup! Fix: Frequent timeouts from TDR (#7452)

bffa854

drop! Make TDR requests raise a LimitedTimeoutException

f009376

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7452-tdr-timeout branch 2 times, most recently from f009376 to bffa854 Compare January 6, 2026 18:06

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Fix: Frequent timeouts from TDR (#7452) #7623

Fix: Frequent timeouts from TDR (#7452) #7623

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edited by achave11-ucsc

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	Add a retry-after header to the response based on the response type.
	Add a retry-after header to the response based on its type.

	response.headers.setdefault('Location', location.url)
	response.headers.setdefault('Location', str(location))

	# When a client's request fails due to an internal request to TDR
	# When a client's request fails due to an internal request to Terra

Fix: Frequent timeouts from TDR (#7452) #7623

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Fix: Frequent timeouts from TDR (#7452) #7623

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dsotirho-ucsc commented Dec 11, 2025

Before adding the drop! commit

After adding the drop! commit

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dsotirho-ucsc commented Dec 8, 2025 •

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Before adding the `drop!` commit

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