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

Linked issues: #5918

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1 when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

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Shorthand for review comments

  • L line is too long
  • W line wrapping is wrong
  • Q bad quotes
  • F other formatting problem

@dsotirho-ucsc dsotirho-ucsc added the API API change affecting callers label Mar 26, 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: 85.439% (-0.02%) from 85.46%
when pulling 6d3c890 on issues/dsotirho-ucsc/5918-manifest-post
into 57627b3 on develop.

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codecov bot commented Mar 27, 2024

Codecov Report

❌ Patch coverage is 70.00000% with 18 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.20%. Comparing base (57627b3) to head (6d3c890).

Files with missing lines Patch % Lines
test/integration_test.py 0.00% 13 Missing ⚠️
src/azul/service/manifest_controller.py 71.42% 4 Missing ⚠️
src/azul/service/app_controller.py 83.33% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #6099      +/-   ##
===========================================
- Coverage    85.22%   85.20%   -0.03%     
===========================================
  Files          156      156              
  Lines        22408    22451      +43     
===========================================
+ Hits         19098    19130      +32     
- Misses        3310     3321      +11     

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@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


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'}


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.

@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from 600eb8b to 81a4905 Compare April 1, 2024 19:22
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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
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6099_IT_2024-08-22.txt

@hannes-ucsc hannes-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from ec5f5cc to cb02ca7 Compare September 4, 2024 00:47
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.

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Moved change to commit Fix rounding of /repository/file retry-after value

Comment on lines -1060 to +830
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.

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Moved change to commit Refine parameter hoisting note

@hannes-ucsc hannes-ucsc removed their assignment Sep 4, 2024
@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

@hannes-ucsc hannes-ucsc removed their assignment Dec 13, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from 0d778e1 to 16f80de Compare May 15, 2025 18:18
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch from 16f80de to c923904 Compare May 15, 2025 18:28
@hannes-ucsc hannes-ucsc linked an issue Sep 11, 2025 that may be closed by this pull request
14 tasks
@hannes-ucsc hannes-ucsc removed the orange label Oct 2, 2025
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/5918-manifest-post branch 2 times, most recently from e050a15 to e69f45a Compare October 9, 2025 18:30
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 e69f45a to 6d3c890 Compare October 9, 2025 21:06
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Can't use curl to download a single manifest in one invocation

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