Fix: Eliminate uses of requests library (#7633)#7745
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achave11-ucsc wants to merge 21 commits intodevelopfrom
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Fix: Eliminate uses of requests library (#7633)#7745achave11-ucsc wants to merge 21 commits intodevelopfrom
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## develop #7745 +/- ##
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+ Coverage 85.03% 85.08% +0.04%
===========================================
Files 162 163 +1
Lines 23306 23359 +53
===========================================
+ Hits 19819 19874 +55
+ Misses 3487 3485 -2 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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nadove-ucsc
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Apr 10, 2026
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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')))
| return StatusRetryHttpClient(client) | ||
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| def raise_on_status(response: urllib3.BaseHTTPResponse) -> None: |
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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: |
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Yes, raise_on_status (https://urllib3.readthedocs.io/en/stable/reference/urllib3.util.html) is more apt to urllib3, than introducing a different name (albeit familiar).
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| def raise_on_status(response: urllib3.BaseHTTPResponse) -> None: | ||
| if not 200 <= response.status <= 399: | ||
| msg = f"{response.reason} for url: {response.url}" |
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| 'retry-after': | ||
| response.headers['retry-after'] |
| } | ||
| 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), |
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| no_retries: Retry = Retry(status=0, | ||
| status_forcelist={500}, | ||
| raise_on_status=False) |
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Consolidate with the identical definition in TestAppLogging, either in a superclass or as a standalone global in the http module.
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| url = str(config.lambda_endpoint(lambda_name).set(path='/health/basic', | ||
| args={'catalog': self.catalog})) | ||
| helper.add('GET', | ||
| url, |
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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), |
| 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}', |
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| def _normalize_url(url: str) -> str: | ||
| f = furl(url).copy() |
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Suggested change
| f = furl(url).copy() | |
| f = furl(url) |
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Only .copy returns a mutable instance of furl. Otherwise mypy complains, unless a new URL is instantiated. The .copy pattern seems to already be in employed elsewhere in the codebase, hence the usage here.
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| urllib3_mock, | ||
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Suggested change
| urllib3_mock, | |
| urllib3_mock, | |
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| 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 {}, |
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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, |
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Assigning @dsotirho-ucsc for review since @nadove-ucsc is focused on other high priority work. |
dsotirho-ucsc
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Apr 16, 2026
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This should be a partial PR.
Regarding the changes to request_flooder.py:
- The script manually logs lines such as
Making GET request...andGOT 200 response..., so now that the HTTP client is also logging these there is duplicate output. - The
--log-headersoption is now redundant since the these are always being included in the output now. - (For the purpose of this script) the (
… with/without a request/response body) lines are unnecessary and ideally would be omitted if possible.
I think 1 and 2 should be fixed in this PR. I suspect we'll just have to live with 3.
old output
❯ python scripts/request_flooder.py --method GET --url https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary --rate 5 --per 30
2026-04-15 17:13:28,232 INFO MainThread __main__: Starting requests at a rate of 5 requests per 30 seconds for 300 seconds
2026-04-15 17:13:34,238 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:13:35,326 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 1.088s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
2026-04-15 17:13:40,243 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:13:41,627 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 1.383s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
2026-04-15 17:13:46,247 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:13:47,246 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 0.998s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
new output
❯ python scripts/request_flooder.py --method GET --url https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary --rate 5 --per 30
2026-04-15 17:15:10,458 INFO MainThread __main__: Starting requests at a rate of 5 requests per 30 seconds for 300 seconds
2026-04-15 17:15:16,464 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:15:16,464 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:15:16,464 INFO ThreadPoolExecutor-0_0 __main__: … without a request body
2026-04-15 17:15:16,475 INFO ThreadPoolExecutor-0_0 __main__: … without request headers
2026-04-15 17:15:17,693 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 1.228s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
2026-04-15 17:15:17,693 INFO ThreadPoolExecutor-0_0 __main__: … with response headers HTTPHeaderDict({'Content-Type': 'application/json', 'Content-Length': '7808', 'Connection': 'keep-alive', 'Date': 'Thu, 16 Apr 2026 00:15:17 GMT', 'X-Amzn-Trace-Id': 'Root=1-69e02a14-1df05f260381a0f0103add9e;Parent=06e7b1b4225fd9bc;Sampled=0;Lineage=1:18704a40:0', 'x-amzn-RequestId': 'd1f3e699-5606-475f-9c3f-a7b0b90fbd18', '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': 'b4uDUGeaoAMEtUw=', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'X-Cache': 'Miss from cloudfront', 'Via': '1.1 3289feb7922c3bed2dd498f7353add3e.cloudfront.net (CloudFront)', 'X-Amz-Cf-Pop': 'IAD55-P5', 'X-Amz-Cf-Id': 'qihUI0blBmucscBWMmYXElCIRreehJAFeh-CjSjG_wvx9yH4DXnYxg=='})
2026-04-15 17:15:17,693 INFO ThreadPoolExecutor-0_0 __main__: … with a response body of length 7808 starting in b'{"projectCount":111,"specimenCount":1279,"speciesCount":2,"fileCount":5411,"totalFileSize":13444490554440.0,"donorCount":796,"labCount":241,"organTypes":["blood","brain","skin of body","kidney","lung","large intestine","wall of lateral ventricle","pancreas","gonad","hematopoietic system","ovary","central nervous system","endometrium","skeletal muscle organ","small intestine","heart","tumor","hindlimb","muscle","lymph node","embryo","eye","placenta","decidua","tonsil","umbilical cord","colon","digestive system","thymus","adipose tissue","liver","retina",null,"Molar tooth","adrenal gland","arterial blood vessel","blastocyst","muscle organ","nose","testis","whole embryos","bone marrow","calcareous tooth","cerebral cortex","immune system","stem cell","tail","uterus","abdomen","immune organ","mouse kidney","oral cavity","skin","trachea"],"fileTypeSummaries":[{"count":4655,"totalSize":9988470899450.0,"matrixCellCount":0.0,"format":"fastq.gz"},{"count":195,"totalSize":224837175327.0,"matrixCellCount":0.0,"format"...'
2026-04-15 17:15:17,693 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 1.230s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
2026-04-15 17:15:22,467 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:15:22,467 INFO ThreadPoolExecutor-0_0 __main__: Making GET request to 'https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary'
2026-04-15 17:15:22,467 INFO ThreadPoolExecutor-0_0 __main__: … without a request body
2026-04-15 17:15:22,468 INFO ThreadPoolExecutor-0_0 __main__: … without request headers
2026-04-15 17:15:23,248 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 0.781s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
2026-04-15 17:15:23,248 INFO ThreadPoolExecutor-0_0 __main__: … with response headers HTTPHeaderDict({'Content-Type': 'application/json', 'Content-Length': '7808', 'Connection': 'keep-alive', 'Date': 'Thu, 16 Apr 2026 00:15:23 GMT', 'X-Amzn-Trace-Id': 'Root=1-69e02a1a-3b325fb232f7db1328e31abe;Parent=02f86c560bc72374;Sampled=0;Lineage=1:18704a40:0', 'x-amzn-RequestId': 'ef191851-bb3c-4ada-afd4-dc262c90f599', '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': 'b4uENG3PoAMEo5Q=', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'X-Cache': 'Miss from cloudfront', 'Via': '1.1 3289feb7922c3bed2dd498f7353add3e.cloudfront.net (CloudFront)', 'X-Amz-Cf-Pop': 'IAD55-P5', 'X-Amz-Cf-Id': 'l5oYqA1JjQjO8Vby_-MX0co9T8G6LlkNp1hptvUxz0Y1kxrL34xL8g=='})
2026-04-15 17:15:23,249 INFO ThreadPoolExecutor-0_0 __main__: … with a response body of length 7808 starting in b'{"projectCount":111,"specimenCount":1279,"speciesCount":2,"fileCount":5411,"totalFileSize":13444490554440.0,"donorCount":796,"labCount":241,"organTypes":["blood","brain","skin of body","kidney","lung","large intestine","wall of lateral ventricle","pancreas","gonad","hematopoietic system","ovary","central nervous system","endometrium","skeletal muscle organ","small intestine","heart","tumor","hindlimb","muscle","lymph node","embryo","eye","placenta","decidua","tonsil","umbilical cord","colon","digestive system","thymus","adipose tissue","liver","retina",null,"Molar tooth","adrenal gland","arterial blood vessel","blastocyst","muscle organ","nose","testis","whole embryos","bone marrow","calcareous tooth","cerebral cortex","immune system","stem cell","tail","uterus","abdomen","immune organ","mouse kidney","oral cavity","skin","trachea"],"fileTypeSummaries":[{"count":4655,"totalSize":9988470899450.0,"matrixCellCount":0.0,"format":"fastq.gz"},{"count":195,"totalSize":224837175327.0,"matrixCellCount":0.0,"format"...'
2026-04-15 17:15:23,249 INFO ThreadPoolExecutor-0_0 __main__: Got 200 response after 0.782s from GET to https://service.daniel.dev.singlecell.gi.ucsc.edu/index/summary
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| if isinstance(body, str): | ||
| body = body.encode() | ||
| assert isinstance(body, (bytes, str)), type(body) |
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body would never be str in the assert, since right above that it is converted to bytes
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| def filter_body(organ: str) -> JSON: | ||
| return {'filters': json.dumps({'organ': {'is': [organ]}})} | ||
| return {"filters": json.dumps({'organ': {'is': [organ]}})} |
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Suggested change
| return {"filters": json.dumps({'organ': {'is': [organ]}})} | |
| return {'filters': json.dumps({'organ': {'is': [organ]}})} |
| url.set(path='/') | ||
| response = requests.get(str(url)) | ||
| self.assertEqual(response.status_code, 200) | ||
| response = self._http_client.urlopen('GET', str(url)) |
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Suggested change
| response = self._http_client.urlopen('GET', str(url)) | |
| response = self._http_client.urlopen(GET, str(url)) |
integration_test.py has variables for the method types.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…/dss/__init__.py (#7633) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…adata/helpers/schema_validation.py (#7633)
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Linked issues: #7633
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pif the PR is also labeledpartialOperator (main build)
devanvildevdevdevanvildevanvildev_select dev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shared_select anvildev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shareddevanvildevOperator (reindex)
devor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevdevor this PR does not require reindexingdevdeploy_browserjob in the GitLab pipeline for this PR indevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdeploy_browserjob in the GitLab pipeline for this PR inanvildevor this PR does not require reindexinganvildevOperator (mirroring)
devor this PR does not require mirroringdevanvildevor this PR does not require mirroringanvildevdevor this PR does not require mirroringdevanvildevor this PR does not require mirroringanvildevdevor this PR does not require mirroringdevanvildevor this PR does not require mirroringanvildevOperator
deploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels to the next promotion PRs or this PR carries none of these labelsdeploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels, from the description of this PR to that of the next promotion PRs or this PR carries none of these labelsShorthand for review comments
Lline is too longWline wrapping is wrongQbad quotesFother formatting problem