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Fix: Can't use curl to download a single manifest in one invocation (#5918) #6099

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@dsotirho-ucsc dsotirho-ucsc commented Mar 26, 2024

Connected issues: #5918

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@dsotirho-ucsc dsotirho-ucsc added the API API change affecting callers label Mar 26, 2024
@github-actions github-actions bot added the orange [process] Done by the Azul team label Mar 27, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch 2 times, most recently from 8b62dbc to 830a1e4 Compare March 27, 2024 00:33
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coveralls commented Mar 27, 2024

Coverage Status

coverage: 85.396% (-0.003%) from 85.399%
when pulling 0d778e1 on issues/dsotirho-ucsc/5918-manifest-post
into c1d8633 on develop.

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codecov bot commented Mar 27, 2024

Codecov Report

Attention: Patch coverage is 71.42857% with 16 lines in your changes missing coverage. Please review.

Project coverage is 85.36%. Comparing base (c1d8633) to head (0d778e1).

Files with missing lines Patch % Lines
test/integration_test.py 0.00% 12 Missing ⚠️
src/azul/service/manifest_controller.py 71.42% 4 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #6099      +/-   ##
===========================================
- Coverage    85.38%   85.36%   -0.02%     
===========================================
  Files          155      155              
  Lines        20735    20773      +38     
===========================================
+ Hits         17704    17733      +29     
- Misses        3031     3040       +9     

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

@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch 2 times, most recently from da860a5 to b81d052 Compare March 27, 2024 16:07
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch 5 times, most recently from 9fb4dbb to 391cedb Compare March 28, 2024 23:50
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Successful use of curl to download a manifest in one invocation:

(Unabridged version: 6099_manifest_invocation_unabridged.txt)

daniel@Crispin ~ $ curl --verbose --data '' --location 'https://service.daniel.dev.singlecell.gi.ucsc.edu/manifest/files?catalog=dcp3&filters=%7B%22cellCount%22%3A%7B%22within%22%3A%5B%5B1%2C2222222222%5D%5D%7D%7D&format=curl'

> POST /manifest/files?catalog=dcp3&filters=%7B%22cellCount%22%3A%7B%22within%22%3A%5B%5B1%2C2222222222%5D%5D%7D%7D&format=curl HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.4.0
> Accept: */*
> Content-Length: 0
> Content-Type: application/x-www-form-urlencoded

< HTTP/2 301
< content-type: application/json
< content-length: 4
< location: https://service.daniel.dev.singlecell.gi.ucsc.edu/manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kAAQ==

> GET /manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kAAQ== HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.4.0
> Accept: */*

< HTTP/2 301
< content-type: application/json
< content-length: 4
< location: https://service.daniel.dev.singlecell.gi.ucsc.edu/manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kBAQ==

> GET /manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kBAQ== HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.4.0
> Accept: */*

…

< HTTP/2 301
< content-type: application/json
< content-length: 4
< location: https://service.daniel.dev.singlecell.gi.ucsc.edu/manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kgCg==

> GET /manifest/files/k8Qgp9pWcfTS0-CkTvX1MrLsApTFGithYhAvFgORT-E-D0kgCg== HTTP/2
> Host: service.daniel.dev.singlecell.gi.ucsc.edu
> User-Agent: curl/8.4.0
> Accept: */*

< HTTP/2 302
< content-type: text/plain
< content-length: 3215
< location: https://s3.amazonaws.com/edu-ucsc-gi-platform-hca-dev-storage-daniel.us-east-1/manifests/39e58996-f70d-55ec-8250-98d0f6c92456.ad14b32b-dea0-555e-b745-8ebe5bb0958d.curlrc?response-content-disposition=attachment%3Bfilename%3D%22hca-manifest-39e58996-f70d-55ec-8250-98d0f6c92456.ad14b32b-dea0-555e-b745-8ebe5bb0958d.curlrc%22&AWSAccessKeyId=ASIARZFZ7W77QFHNZFUL&Signature=2QnTDdkuUII9wZKFrAL7rXZ3L0I%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEMn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJGMEQCIDYEjKDSa5U5%2Fa6nN2P1%2BSWvzJPwv0J5xXrumvTOvzXdAiBMTBy0vvDg2R%2BsaCSHByX%2BFHsVd7xnNnRsP6fBNUEWciqWAwjh%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAQaDDEyMjc5NjYxOTc3NSIMSx7PsxpRaWQWQZsKKuoCpfE0yyl5h24d%2F%2FxFh8qjwBgJ%2FKIUNPGadCRETM1rZS7%2BvpcUd0a1FtxAiaWePMy6yme4ZquN7rBrup2vmFzUocOT%2FPmEc0wdKAJ45E97cNt4MUzH7aGY9qi49dnWWDtnYL65r%2FLSz%2BtSyV8Ly6Bb%2Btp9shZaEaKzAKuR5Ha7Wz0uEQkyi%2BK8qbqEW9IyHw%2BZZ19utq0fewqpv5mnrffRkvKbegzu%2B2G9iATr7ywaNuYFoC10itubY95rS0ILajMWQdGR9Lpe5bZfmIrpVgIgzinue9UR%2BhLHx%2Fve3ry%2BEF5iiDXsoJeWY%2Fg%2Bnr0TpDTW33RIyp%2BstZVnX40JDEV7F9yehXX3GwAC9Zwu%2BuSYEYPs4avFDIogATVLjVQvRhFmXW8EcknDZ3ngOz5bU32FKUkn1BITDSkEQEe5j46a%2FJTpWOieLSUy0e35DZdtwomu6TGVdfOyTwefiuGinAPyE4t8zdm67q6hcwQwgo2YsAY6ngEQCkNB3UFolbnF%2BqzZCgbImeJmbZWbEr3zMZbzQM7w5KYUSHANYD%2BzDQYDq7UsKu9fvX2uPX0%2BXmICHXCiNX30S8AymOSowXaLsxP7FlY7Sx9EA7we4YjU0%2BIIHm6sd2jnrTk5Jq7kv3yniCGfgxYKH1ucbOFns6GmhnKpVIQMgQ6q8KaSyjRpXI51JwHChMbakT9yTpPA2wwlmIQvTA%3D%3D&Expires=1711674521

> GET /edu-ucsc-gi-platform-hca-dev-storage-daniel.us-east-1/manifests/39e58996-f70d-55ec-8250-98d0f6c92456.ad14b32b-dea0-555e-b745-8ebe5bb0958d.curlrc?response-content-disposition=attachment%3Bfilename%3D%22hca-manifest-39e58996-f70d-55ec-8250-98d0f6c92456.ad14b32b-dea0-555e-b745-8ebe5bb0958d.curlrc%22&AWSAccessKeyId=ASIARZFZ7W77QFHNZFUL&Signature=2QnTDdkuUII9wZKFrAL7rXZ3L0I%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEMn%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJGMEQCIDYEjKDSa5U5%2Fa6nN2P1%2BSWvzJPwv0J5xXrumvTOvzXdAiBMTBy0vvDg2R%2BsaCSHByX%2BFHsVd7xnNnRsP6fBNUEWciqWAwjh%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAQaDDEyMjc5NjYxOTc3NSIMSx7PsxpRaWQWQZsKKuoCpfE0yyl5h24d%2F%2FxFh8qjwBgJ%2FKIUNPGadCRETM1rZS7%2BvpcUd0a1FtxAiaWePMy6yme4ZquN7rBrup2vmFzUocOT%2FPmEc0wdKAJ45E97cNt4MUzH7aGY9qi49dnWWDtnYL65r%2FLSz%2BtSyV8Ly6Bb%2Btp9shZaEaKzAKuR5Ha7Wz0uEQkyi%2BK8qbqEW9IyHw%2BZZ19utq0fewqpv5mnrffRkvKbegzu%2B2G9iATr7ywaNuYFoC10itubY95rS0ILajMWQdGR9Lpe5bZfmIrpVgIgzinue9UR%2BhLHx%2Fve3ry%2BEF5iiDXsoJeWY%2Fg%2Bnr0TpDTW33RIyp%2BstZVnX40JDEV7F9yehXX3GwAC9Zwu%2BuSYEYPs4avFDIogATVLjVQvRhFmXW8EcknDZ3ngOz5bU32FKUkn1BITDSkEQEe5j46a%2FJTpWOieLSUy0e35DZdtwomu6TGVdfOyTwefiuGinAPyE4t8zdm67q6hcwQwgo2YsAY6ngEQCkNB3UFolbnF%2BqzZCgbImeJmbZWbEr3zMZbzQM7w5KYUSHANYD%2BzDQYDq7UsKu9fvX2uPX0%2BXmICHXCiNX30S8AymOSowXaLsxP7FlY7Sx9EA7we4YjU0%2BIIHm6sd2jnrTk5Jq7kv3yniCGfgxYKH1ucbOFns6GmhnKpVIQMgQ6q8KaSyjRpXI51JwHChMbakT9yTpPA2wwlmIQvTA%3D%3D&Expires=1711674521 HTTP/1.1
> Host: s3.amazonaws.com
> User-Agent: curl/8.4.0
> Accept: */*

< HTTP/1.1 200 OK
< Content-Disposition: attachment;filename="hca-manifest-39e58996-f70d-55ec-8250-98d0f6c92456.ad14b32b-dea0-555e-b745-8ebe5bb0958d.curlrc"
< Accept-Ranges: bytes
< Content-Type: binary/octet-stream
< Content-Length: 494554
<
--create-dirs

--compressed

--location

--globoff

--fail

--write-out "Downloading to: %{filename_effective}\n\n"

url="https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/files/7113cb1e-7289-4fe2-ba15-bbe0620bd808?catalog=dcp3&version=2021-06-28T14%3A21%3A17.533000Z"
output="39fdb0ae-9a00-4829-a581-e7cb59798f02/mouse_cortex_S2_L003_I1_001.fastq"

url="https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/files/9a6e412e-a4bd-4b34-a8f7-38aef94432a2?catalog=dcp3&version=2021-03-15T23%3A40%3A56.660000Z"
output="0fd2d069-f144-443b-9ece-aec641a959e1/SRR9004342_2.fastq.gz"

url="https://service.daniel.dev.singlecell.gi.ucsc.edu/repository/files/50d634ef-77b0-4339-a9c3-9a83bd9e5ab6?catalog=dcp3&version=2022-02-04T12%3A37%3A12.966000Z"
output="da317018-1b0b-4e4f-b508-2c1c7d049507/experiment2_mouse_pbs_scp_barcodes.tsv"

…

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6090_IT_2024-03-28.txt

@@ -1273,14 +1273,16 @@ def get_summary():
authentication=request.authentication)


def manifest_route(*, fetch: bool, initiate: bool):
def manifest_route(*, fetch: bool, method: str):
initiate = method in ['PUT', 'POST']
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Suggested change
initiate = method in ['PUT', 'POST']
initiate = method in {'PUT', 'POST'}

test/integration_test.py Outdated Show resolved Hide resolved
def fetch_file_manifest_with_token(token: str):
return _file_manifest(fetch=True, token_or_key=token)


def _file_manifest(fetch: bool, token_or_key: Optional[str] = None):
request = app.current_request
require(request.method != 'POST' or request.raw_body.decode() == '',
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This is the same as

Suggested change
require(request.method != 'POST' or request.raw_body.decode() == '',
require(request.method != 'POST' or request.raw_body == b'',

Right?

@nadove-ucsc nadove-ucsc removed their assignment Apr 1, 2024
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Added #6003 as a blocker due to overlapping changes to the IT _test_manifest method.

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Looks good but needs rebase

@nadove-ucsc nadove-ucsc removed their assignment Apr 4, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from 81a4905 to ff39020 Compare April 4, 2024 00:57
@hannes-ucsc hannes-ucsc removed their assignment Aug 20, 2024
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6099_IT_2024-08-20.txt

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Please push the commits individually.

@@ -617,3 +618,25 @@ def lambda_context(self) -> LambdaContext:
@property
def current_request(self) -> AzulRequest:
return self.app.current_request

def server_side_sleep(self, max_seconds: int | float) -> float:
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Suggested change
def server_side_sleep(self, max_seconds: int | float) -> float:
def server_side_sleep(self, max_seconds: float) -> float:

Time in Python is always a float. Supporting int may seem like a convenience but just leads to sloppy use of this function.


:return: The actual amount of time slept in seconds
"""
remaining_time = self.lambda_context.get_remaining_time_in_millis() / 1000
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Add validation of type and range of the argument.

retry_after = body.get('Retry-After')
if retry_after is not None:
time_slept = self.server_side_sleep(retry_after)
body['Retry-After'] = round(retry_after - time_slept)
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Suggested change
body['Retry-After'] = round(retry_after - time_slept)
body['Retry-After'] = ceil(retry_after - time_slept)

Comment on lines 363 to 364
if wait is None:
azul_url.args['wait'] = '0'
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This indicates that Azul now yields a URL with wait set to the default. I'd prefer not to do that.

@hannes-ucsc hannes-ucsc removed their assignment Aug 21, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch 2 times, most recently from de14d18 to db304df Compare August 22, 2024 17:23
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6099_IT_2024-08-22.txt

@@ -263,7 +266,7 @@ def download_file(self,
pass
elif wait == '1':
time_slept = self.server_side_sleep(float(retry_after))
retry_after = round(retry_after - time_slept)
retry_after = ceil(retry_after - time_slept)
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The change from round to ceil is currently in a commit labeled "Add a default value for the /repository/files wait parameter". Please explain why going from round to ceil is related to adding a default or isolate that change in its own commit.

Comment on lines -1060 to +1070
as a property of a JSON object in the body of the request. This can be
useful in case the value of the `filters` query parameter causes the URL
to exceed the maximum length of 8192 characters, resulting in a 413
Request Entity Too Large response.
as a property of a JSON object in the body of the request. This is
referred to as *parameter hoisting* and can be useful in case the value
of the `filters` query parameter causes the URL to exceed the maximum
length of 8192 characters, resulting in a 413 Request Entity Too Large
response.

The request `%s %s?filters={…}`, for example, is equivalent to `%s %s`
with the body `{"filters": "{…}"}` in which any double quotes or
backslash characters inside `…` are escaped with another backslash. That
escaping is the requisite procedure for embedding one JSON structure
inside another.
with a `Content-Type` header of `application/json` and the body
`{"filters": "{…}"}` in which any double quotes or backslash characters
inside `…` are escaped with another backslash. That escaping is the
requisite procedure for embedding one JSON structure inside another.
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Correct me if I am wrong but it seems like these two hunks are unrelated documentation improvement that I requested at some point, but that have nothing to do with "Add[ing] support for POST requests to the manifest endpoint", as is the title of the commit the hunks are part of.

@hannes-ucsc hannes-ucsc removed their assignment Sep 4, 2024
Fixes regression from fb58b01. The problem manifested as an error with the
`app` property in an AppController subclass, and this wasn't noticed until
now due to the `app` property not being accessed in a controller that had
this problem, namely ManifestController.
…vocation (#5918)

Add support for POST requests to the manifest endpoint
…vocation (#5918)

Add a wait parameter option to the manifest endpoint
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from cb02ca7 to f1a03b6 Compare September 4, 2024 18:53
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6099_IT_2024-09-04.txt

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