Fix: Eliminate uses of requests library (#7633) by achave11-ucsc · Pull Request #7745 · DataBiosphere/azul

achave11-ucsc · 2026-02-04T20:06:15Z

Linked issues: #7633

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L line is too long
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coveralls · 2026-02-04T20:21:11Z

coverage: 85.123% (+0.04%) from 85.08% — issues/achave11-ucsc/7633-eliminate-requests-usages into develop

codecov · 2026-02-05T19:00:57Z

Codecov Report

❌ Patch coverage is 90.12739% with 31 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.97%. Comparing base (ef177e1) to head (6e3644f).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	28 Missing ⚠️
src/azul/plugins/repository/dss/__init__.py	80.00%	1 Missing ⚠️
src/azul/service/drs_controller.py	93.75%	1 Missing ⚠️
test/service/test_repository_files.py	88.88%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7745      +/-   ##
===========================================
+ Coverage    84.93%   84.97%   +0.04%     
===========================================
  Files          161      162       +1     
  Lines        23130    23182      +52     
===========================================
+ Hits         19646    19700      +54     
+ Misses        3484     3482       -2

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

🚀 New features to boost your workflow:

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…#7633)

….py (#7633)

…ng.py (#7633)

…s.py (#7633)

…l.py (#7633)

…ation.py (#7633)

…7633)

#7633)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…/__init__.py (#7633) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…a/helpers/schema_validation.py (#7633)

nadove-ucsc

The commit "Eliminate uses of requests library in test/app_test_case.py (#7633)" touches many files besides the one references in the file. I think those changes were meant to go in other commits.

Many overly long lines. Some should probably be fixed in a separate commit since they predate your changes.

$ git diff develop | longlines
src/azul/service/drs_controller.py:261     def _dss_get_file(self, file_uuid, replica, **kwargs) -> urllib3.BaseHTTPResponse:
test/app_test_case.py:144         return self._http_client.urlopen('GET', str(self.base_url.set(path='/health/basic')),
test/health_check_test_case.py:91         response = self._http_client.urlopen('GET', str(self.base_url.set(path='/health/basic')),
test/health_check_test_case.py:98             response = self._http_client.urlopen('GET', str(self.base_url.set(path=('health', path))),
test/service/test_drs.py:199     def _mock_responses(self, helper: Urllib3Mock, redirects, file_uuid, file_version=None):
test/service/test_drs.py:202             self._dss_response(helper, file_uuid, file_version, 'aws', initial=True, _301=False)
test/service/test_drs.py:203             self._dss_response(helper, file_uuid, file_version, 'gcp', initial=True, _301=False)
test/service/test_drs.py:206             self._dss_response(helper, file_uuid, file_version, 'aws', initial=True, _301=True)
test/service/test_drs.py:207             self._dss_response(helper, file_uuid, file_version, 'gcp', initial=True, _301=True)
test/service/test_drs.py:211                 self._dss_response(helper, file_uuid, file_version, 'aws', initial=False, _301=True)
test/service/test_drs.py:212                 self._dss_response(helper, file_uuid, file_version, 'gcp', initial=False, _301=True)
test/service/test_drs.py:213             self._dss_response(helper, file_uuid, file_version, 'aws', initial=False, _301=False)
test/service/test_drs.py:214             self._dss_response(helper, file_uuid, file_version, 'gcp', initial=False, _301=False)
test/service/test_request_validation.py:61     def assertResponseStatus(self, url: furl, status: int) -> urllib3.BaseHTTPResponse:
test/service/test_response.py:1041                 response = self._http_client.urlopen('GET', str(self.base_url.set(path=('index', entity_type),
test/service/test_response.py:3709         response = self._http_client.urlopen('GET', str(self.base_url.set(path='/index/catalogs')))

nadove-ucsc · 2026-04-10T06:55:39Z

src/azul/http.py

    return StatusRetryHttpClient(client)


+def raise_on_status(response: urllib3.BaseHTTPResponse) -> None:


Is there a reason to deviate from the name used by the requests library?

Suggested change

def raise_on_status(response: urllib3.BaseHTTPResponse) -> None:

def raise_for_status(response: urllib3.BaseHTTPResponse) -> None:

nadove-ucsc · 2026-04-10T06:55:53Z

src/azul/http.py


+def raise_on_status(response: urllib3.BaseHTTPResponse) -> None:
+    if not 200 <= response.status <= 399:
+        msg = f"{response.reason} for url: {response.url}"


nadove-ucsc · 2026-04-10T06:56:47Z

src/azul/service/drs_controller.py

+                    'retry-after':
+                        response.headers['retry-after']


nadove-ucsc · 2026-04-10T06:56:55Z

src/azul/service/drs_controller.py

        }
        url = self.dss_file_url(file_uuid)
-        return requests.api.get(str(url), params=dss_params, allow_redirects=False)
+        return self._http_client.request('GET', str(url),


nadove-ucsc · 2026-04-10T06:59:08Z

test/health_check_test_case.py

+    no_retries: Retry = Retry(status=0,
+                              status_forcelist={500},
+                              raise_on_status=False)


Consolidate with the identical definition in TestAppLogging, either in a superclass or as a standalone global in the http module.

nadove-ucsc · 2026-04-10T07:00:31Z

test/health_check_test_case.py

+            url = str(config.lambda_endpoint(lambda_name).set(path='/health/basic',
+                                                              args={'catalog': self.catalog}))
+            helper.add('GET',
+                       url,


Suggested change

url = str(config.lambda_endpoint(lambda_name).set(path='/health/basic',

args={'catalog': self.catalog}))

helper.add('GET',

url,

url = config.lambda_endpoint(lambda_name).set(path='/health/basic',

args={'catalog': self.catalog})

helper.add('GET',

str(url),

nadove-ucsc · 2026-04-10T07:00:59Z

test/test_app_logging.py

                        with self.assertLogs(app.log, level=log_level) as app_log:
                            with self.assertLogs(azul.log, level=log_level) as azul_log:
-                                response = requests.get(f'http://{host}:{port}{path}')
+                                response = self._http_client.urlopen('GET', f'http://{host}:{port}{path}',


nadove-ucsc · 2026-04-10T07:02:48Z

test/urllib3_mock.py

+
+
+def _normalize_url(url: str) -> str:
+    f = furl(url).copy()


Suggested change

f = furl(url).copy()

f = furl(url)

nadove-ucsc · 2026-04-10T07:03:18Z

.mypy.ini

+    urllib3_mock,



Suggested change

urllib3_mock,

urllib3_mock,

nadove-ucsc · 2026-04-10T07:10:53Z

test/urllib3_mock.py

+            body: bytes | str = b'',
+            json_body: dict | None = None,
+            reason: str | None = None,
+            ) -> None:
+        if json_body is not None:
+            body = json.dumps(json_body).encode()
+            headers = {'Content-Type': 'application/json', **(headers or {})}
+        elif isinstance(body, str):
+            body = body.encode()
+        response = urllib3.HTTPResponse(
+            body=body,
+            headers=headers or {},


Suggested change

body: bytes | str = b'',

json_body: dict | None = None,

reason: str | None = None,

) -> None:

if json_body is not None:

body = json.dumps(json_body).encode()

headers = {'Content-Type': 'application/json', **(headers or {})}

elif isinstance(body, str):

body = body.encode()

response = urllib3.HTTPResponse(

body=body,

headers=headers or {},

body: bytes | str | JSON = b'',

reason: str | None = None,

) -> None:

if headers is None:

headers = {}

if isinstance(body, dict):

body = json.dumps(body)

headers['Content-Type'] = 'application/json'

if isinstance(body, str):

body = body.encode()

response = urllib3.HTTPResponse(

body=body,

headers=headers,

achave11-ucsc self-assigned this Feb 4, 2026

achave11-ucsc requested a review from hannes-ucsc as a code owner February 4, 2026 20:06

achave11-ucsc marked this pull request as draft February 4, 2026 20:06

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch from feb9b32 to b9bc81d Compare February 4, 2026 20:12

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch 3 times, most recently from dadf91d to aa2bfcf Compare February 5, 2026 18:47

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch 6 times, most recently from eafd283 to 032ef7c Compare February 12, 2026 17:35

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch 15 times, most recently from e5f9720 to e0a85ba Compare February 20, 2026 18:52

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch 8 times, most recently from 6c3d09e to 0dafbb8 Compare April 10, 2026 02:24

achave11-ucsc and others added 6 commits April 9, 2026 19:41

Add HasCachedHttpClient mixin to AzulUnitTestCase

4a45e1b

Add raise_on_status functionality to the http module

716e2f7

Add urllib3 mock HTTP client for tests (#7633)

7b7a108

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Eliminate uses of requests library in test/service/test_pagination.py (…

01f2675

…#7633)

Eliminate uses of requests library in test/service/test_index_samples…

4b3f218

….py (#7633)

Eliminate uses of requests library in test/service/test_cache_poisoni…

9d29fe8

…ng.py (#7633)

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch from 7d6d8e8 to 4a45e1b Compare April 10, 2026 02:57

achave11-ucsc added 5 commits April 9, 2026 20:10

Eliminate uses of requests library in test/service/test_index_project…

9c11aaf

…s.py (#7633)

Eliminate uses of requests library in test/service/test_response_anvi…

ebb8262

…l.py (#7633)

Eliminate uses of requests library in test/service/test_request_valid…

2dd6d8c

…ation.py (#7633)

Eliminate uses of requests library in test/app_test_case.py (#7633)

e157ee7

Eliminate uses of requests library in test/service/test_response.py (#…

375aad8

…7633)

achave11-ucsc force-pushed the issues/achave11-ucsc/7633-eliminate-requests-usages branch from 5a24366 to 905b31f Compare April 10, 2026 03:49

achave11-ucsc and others added 8 commits April 9, 2026 21:38

Eliminate uses of requests library in test/service/test_app_logging.py (

aacd4bd

#7633)

Eliminate uses of requests library in test/test_app_logging.py (#7633)

8eda257

Eliminate uses of requests library in test/integration_test.py (#7633)

e38fa3c

Eliminate uses of requests library in scripts/request_flooder.py (#7633)

133eae4

Eliminate uses of requests library in drs_controller.py (#7633)

47150dc

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Eliminate uses of requests library in src/azul/health.py (#7633)

5816490

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Eliminate uses of requests library in src/azul/plugins/repository/dss…

1668379

…/__init__.py (#7633) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Eliminate uses of requests library in src/humancellatlas/data/metadat…

6e3644f

…a/helpers/schema_validation.py (#7633)

nadove-ucsc requested changes Apr 10, 2026

View reviewed changes

		return StatusRetryHttpClient(client)


		def raise_on_status(response: urllib3.BaseHTTPResponse) -> None:

	def raise_on_status(response: urllib3.BaseHTTPResponse) -> None:
	def raise_for_status(response: urllib3.BaseHTTPResponse) -> None:

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achave11-ucsc commented Feb 4, 2026 •

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