feat: Azbatch executor #1953

jakevc · 2022-11-04T05:23:06Z

Description

Finish remaining issues with the original implementation of the Azure Batch Executor originally tackled by @andreas-wilm in #533.

simplified command line options
batch configuration as a class with sensible defaults, or environment variable overrides.
made use of existing AzBlob helper where possible.
updates dockerfile with necessary deps
container jakevc/snakemake:latest contains these changes for testing

Toyed with the idea of having more configuration from command line options, but this litters the codebase with redundant code (each command line option needs to be repeated a few times in init.py, scheduler.py, workflow.py, azure_batch.py). Env Variables seem appropriate with sensible defaults.

QC

The PR contains a test case for the changes or the changes are already covered by an existing test case.
The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

Example

Example invocation:

export AZ_BLOB_ACCOUNT_URL=*********
export AZ_BATCH_ACCOUNT_KEY=*********

snakemake \
    --jobs 3 \
    -rpf --verbose --default-remote-prefix snaketest \
    --use-conda \
    --default-remote-provider AzBlob \
    --envvars AZ_BLOB_ACCOUNT_URL \
    --az-batch \
    --container-image jakevc/snakemake \
    --az-batch-account-url **********

…akemake/pull/533/files#diff-a4bcd796d9ae03f8be3597dd3f85b5ac873f52efc71b3d0790cfb566d9725330

…ious parameter, code or software env changes

### Description  ### QC  * [ ] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [ ] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

…nakemake#1921) ### Description This just removes a single period in the documentation section about the multiext function, so that this, with a redundant period: ``` expand("some/plot.{ext}", ext=[".pdf", ".svg", ".png"]) ``` becomes this, matching the expected output: ``` expand("some/plot{ext}", ext=[".pdf", ".svg", ".png"]) ``` Fixes snakemake#1012. ### QC  * [X] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [X] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

🤖 I have created a release *beep* *boop* --- ## [7.16.2](snakemake/snakemake@v7.16.1...v7.16.2) (2022-10-26) ### Bug Fixes * fix false rerun triggering downstream of checkpoints due to spurious parameter, code or software env changes ([638ea86](snakemake@638ea86)) * remove redundant dot in expand call in multiext documentation ([snakemake#1921](snakemake#1921)) ([278beaa](snakemake@278beaa)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

…e software envs from the caching hash value, which can be handy e.g. for download rules where the software version does not affect the result) (snakemake#1933) ### Description  ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

### Description The value of `os.pathconf(self._incomplete_path, "PC_NAME_MAX")` is cached in an attribute `Persistence._max_len` -- this avoids repeatedly querying the operating system for the same configuration information every time `marked_incomplete()` is called on a file/job output. (Note: this will dramatically speed up Snakemake DAG building on compute clusters where `os.pathconf()` is slow to return and the number of files checked for incompleteness is very large.) ### QC  * [X] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [X] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

🤖 I have created a release *beep* *boop* --- ## [7.17.0](snakemake/snakemake@v7.16.2...v7.17.0) (2022-10-27) ### Features * allow to define the cache mode per rule (this enables to exclude software envs from the caching hash value, which can be handy e.g. for download rules where the software version does not affect the result) ([snakemake#1933](snakemake#1933)) ([715e618](snakemake@715e618)) ### Performance Improvements * cached os.pathconf() call in _record_path() ([snakemake#1920](snakemake#1920)) ([551badb](snakemake@551badb)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

… structure, such that imports from e.g. scripts also work with remote modules (if specified as additional input files with workflow.source_path) (snakemake#1936) ### Description  ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

🤖 I have created a release *beep* *boop* --- ## [7.17.1](snakemake/snakemake@v7.17.0...v7.17.1) (2022-10-28) ### Bug Fixes * change source cache entries to keep the original name and folder structure, such that imports from e.g. scripts also work with remote modules (if specified as additional input files with workflow.source_path) ([snakemake#1936](snakemake#1936)) ([c34f3f6](snakemake@c34f3f6)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

…s. This allows to import from Python modules next to scripts while deploying the workflow as a snakemake module, even from remote locations. (snakemake#1940) ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

🤖 I have created a release *beep* *boop* --- ## [7.17.2](snakemake/snakemake@v7.17.1...v7.17.2) (2022-10-28) ### Bug Fixes * Consider source cache when setting search path for python scripts. This allows to import from Python modules next to scripts while deploying the workflow as a snakemake module, even from remote locations. ([snakemake#1940](snakemake#1940)) ([27be1d4](snakemake@27be1d4)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

@descostesn

…sting wildcard values from the consuming job. This can dramatically reduce ambiuity problems. Thanks to @descostesn! (snakemake#1939) Only fall back to generic regex based matching if the wildcard based approach does not work. This is inspired by a chat with @descostesn.  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

@descostesn

🤖 I have created a release *beep* *boop* --- ## [7.18.0](snakemake/snakemake@v7.17.2...v7.18.0) (2022-10-31) ### Features * first try to match output files against input files while persisting wildcard values from the consuming job. This can dramatically reduce ambiuity problems. Thanks to [@descostesn](https://github.com/descostesn)! ([snakemake#1939](snakemake#1939)) ([d093907](snakemake@d093907)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

…o 2.3.0 (snakemake#1945) Bumps [marocchino/sticky-pull-request-comment](https://github.com/marocchino/sticky-pull-request-comment) from 2.2.1 to 2.3.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/marocchino/sticky-pull-request-comment/releases">marocchino/sticky-pull-request-comment's releases</a>.</em></p> <blockquote> <h2>v2.3.0</h2> <ul> <li>Support glob path</li> <li>Add <code>follow_symbolic_links</code> for path</li> <li>Add <code>ignore_empty</code> for skip empty body</li> <li>Update README for new output syntax</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/adca94abcaf73c10466a71cc83ae561fd66d1a56"><code>adca94a</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/799">#799</a> from marocchino/dependabot/npm_and_yarn/octokit/graph...</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/af76947473de144ee8fd8a8a2a0e5b2f392f5626"><code>af76947</code></a> build(deps): Bump <code>@octokit/graphql-schema</code> from 12.11.0 to 12.21.0</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/e5883ea53c71dc8e52b346fd5c883eb1ea63ece7"><code>e5883ea</code></a> 🔀 Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/782">#782</a> from marocchino/dependabot/npm_and_yarn/eslint-plug...</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/2520dca5b1f09dab5376fc18715ff64dab2ceebb"><code>2520dca</code></a> 🔀 Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/790">#790</a> from marocchino/dependabot/npm_and_yarn/typescript-...</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/f4ae94070a1b2cc47b7a126d9271c48c3dd7e803"><code>f4ae940</code></a> 🔀 Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/793">#793</a> from marocchino/dependabot/npm_and_yarn/jest-circus...</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/97e16fd48982b5a81b0ef88b530b54e8995e27c4"><code>97e16fd</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/792">#792</a> from samkio/feature/glob</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/da2f89048f71a00bda8f6df93622691adf401be3"><code>da2f890</code></a> build(deps-dev): Bump eslint-plugin-jest from 27.1.2 to 27.1.3</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/ba82cbc35c1c35bab4a3bca541920a5d9e4d6f60"><code>ba82cbc</code></a> build(deps-dev): Bump <code>@typescript-eslint/parser</code> from 5.40.1 to 5.41.0</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/b8644f1ac559a999648c96168f58c769bb1af49a"><code>b8644f1</code></a> 🔀 Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/789">#789</a> from marocchino/dependabot/npm_and_yarn/eslint-8.26.0</li> <li><a href="https://github.com/marocchino/sticky-pull-request-comment/commit/95c224a6ab058ad5a70e45bb6d16f8b221078bfb"><code>95c224a</code></a> 🔀 Merge pull request <a href="https://github-redirect.dependabot.com/marocchino/sticky-pull-request-comment/issues/797">#797</a> from marocchino/dependabot/npm_and_yarn/types/node-...</li> <li>Additional commits viewable in <a href="https://github.com/marocchino/sticky-pull-request-comment/compare/v2.2.1...v2.3.0">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=marocchino/sticky-pull-request-comment&package-manager=github_actions&previous-version=2.2.1&new-version=2.3.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. 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…akemake/pull/533/files#diff-a4bcd796d9ae03f8be3597dd3f85b5ac873f52efc71b3d0790cfb566d9725330

jakevc · 2023-04-27T00:41:48Z

This is the format of the secrets I am using when I run the test locally and it passes:

AZ_BLOB_PREFIX=snaketest
AZ_BLOB_ACCOUNT_URL=https://***********.blob.core.windows.net/
AZ_BATCH_ACCOUNT_URL=https://**********.westus2.batch.azure.com
AZ_BLOB_CREDENTIAL=$SAS
AZ_BATCH_ACCOUNT_KEY=$KEY

johanneskoester · 2023-04-28T12:13:08Z

No clue, I just checked it again. The URL for the storage account seems follow the same pattern as you suggest.

johanneskoester · 2023-04-28T12:14:04Z

Maybe you can add some parsing of those env vars to the remote provider and the executor, which gives a proper error message if something is invalid (without printing any secrets of course).

vsmalladi · 2023-04-28T15:07:00Z

I wonder if there is some special characters that aren't escaped correctly.

@jakevc can you try dummy variables and print those to stdout and see if there is something odd with the variables.

vsmalladi · 2023-04-28T15:42:26Z

@jakevc can you do this

      AZ_BLOB_PREFIX: '$${{ secrets.AZ_BLOB_PREFIX }}'
      AZ_BLOB_ACCOUNT_URL: '${{ secrets.AZ_STORAGE_ACCOUNT_URL }}'
      AZ_BLOB_CREDENTIAL: '${{ secrets.AZ_STORAGE_KEY }}'
      AZ_BATCH_ACCOUNT_URL: '${{ secrets.AZ_BATCH_ACCOUNT_URL }}'
      AZ_BATCH_ACCOUNT_KEY: '${{ secrets.AZ_BATCH_KEY }}'

jakevc · 2023-04-28T17:01:18Z

Face palm: of course this is the issue. The funny thing is on my development environment zsh doesn't even let me set the blob credential without quoting it.

jakevc · 2023-04-28T18:40:37Z

or not...

Still failing with the same error from the BlobServiceClient initialization:
ValueError: Invalid URL: https://

To me that looks like thee AZ_BLOB_ACCOUNT_URL is empty. I just tested that I get the same error when I specify an empty value for the AZ_BLOB_ACCOUNT_URL locally.

@johanneskoester is it correct that this is the name of the secrets? At one point it was, maybe you changed them at some point to match the environment variable names?

secrets.AZ_BLOB_PREFIX
secrets.AZ_STORAGE_ACCOUNT_URL
secrets.AZ_STORAGE_KEY
secrets.AZ_BATCH_ACCOUNT_URL
secrets.AZ_BATCH_KEY

jakevc · 2023-05-01T16:10:08Z

Okay I'm not crazy.. I slightly more specific error and now we are failing with:

raise ValueError("Blob Account URL is None or empty string")
[220](https://github.com/snakemake/snakemake/actions/runs/4848828641/jobs/8640274478#step:20:221)
ValueError: Blob Account URL is None or empty string

sonarcloud · 2023-05-03T14:06:56Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

No Coverage information
1.1% Duplication

johanneskoester · 2023-05-04T18:45:34Z

Understood the problem now! The issue is that as the PR comes from a fork, it does not have access to secrets.

johanneskoester · 2023-05-04T18:48:14Z

I've merged your changes in a snakemake-owned branch and created a PR for merging into main here: #2246
Let us go on from there. As you are anyway already part of the Snakemake org, you should in the future work directly in our repo in order to ensure that your PRs always have the secrets.

vsmalladi · 2023-05-13T13:27:42Z

snakemake/remote/AzBlob.py

+        bool: True if the environment variable is a valid Azure Storage Account URL, False otherwise.
+        """
+        url_pattern = re.compile(
+            r"^https:\/\/[a-z0-9]+(\.[a-z0-9]+)*\.blob\.core\.windows\.net\/?$"


@jakevc this url pattern fails when the sas token is added should be

r"^https:\/\/[a-z0-9]+(\.[a-z0-9]+)*\.blob\.core\.windows\.net\/(\?.+)?$"

@andreas-wilm

### Description Finish remaining issues with the original implementation of the Azure Batch Executor originally tackled by @andreas-wilm in #533. - simplified command line options - batch configuration as a class with sensible defaults, or environment variable overrides. - made use of existing AzBlob helper where possible. - updates dockerfile with necessary deps - container jakevc/snakemake:latest contains these changes for testing Toyed with the idea of having more configuration from command line options, but this litters the codebase with redundant code (each command line option needs to be repeated a few times in __init__.py, scheduler.py, workflow.py, azure_batch.py). Env Variables seem appropriate with sensible defaults. ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). ### Example Example invocation: ```bash export AZ_BLOB_ACCOUNT_URL=********* export AZ_BATCH_ACCOUNT_KEY=********* snakemake \ --jobs 3 \ -rpf --verbose --default-remote-prefix snaketest \ --use-conda \ --default-remote-provider AzBlob \ --envvars AZ_BLOB_ACCOUNT_URL \ --az-batch \ --container-image jakevc/snakemake \ --az-batch-account-url ********** ``` --------- ### Description  ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jake VanCampen <jake.vancampen7@gmail.com> Co-authored-by: Emmanouil "Manolis" Maragkakis <em.maragkakis@gmail.com> Co-authored-by: Jesse Connell <jesse08@gmail.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: roshnipatel <roshnipatel@berkeley.edu> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mike Taves <mwtoews@gmail.com> Co-authored-by: Rich Abdill <rabdill@users.noreply.github.com> Co-authored-by: Koen van Greevenbroek <74298901+koen-vg@users.noreply.github.com> Co-authored-by: Chang Y <yech1990@gmail.com>

🤖 I have created a release *beep* *boop* --- ## [7.28.0](v7.27.0...v7.28.0) (2023-06-11) ### Features * Added native support for execution via Azure Batch ([#1953](#1953)) ([#2246](#2246)) ([0f9c49f](0f9c49f)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

jakevc and others added 28 commits October 21, 2022 19:02

init azbatch implementation based on, https://github.com/snakemake/sn…

75f24cb

…akemake/pull/533/files#diff-a4bcd796d9ae03f8be3597dd3f85b5ac873f52efc71b3d0790cfb566d9725330

refactor, config, working

8371a17

refactor, docker image seems to be failing

021845d

update dockerfile

fc9c994

respect keep_remote_local

7cb8d1c

fix: fix false rerun triggering downstream of checkpoints due to spur…

49b3ad6

…ious parameter, code or software env changes

refactor: fmt

d395166

use v1 release of publish to pypi github action

02fe2d0

init azbatch implementation based on, https://github.com/snakemake/sn…

5b5761c

…akemake/pull/533/files#diff-a4bcd796d9ae03f8be3597dd3f85b5ac873f52efc71b3d0790cfb566d9725330

refactor, config, working

8af24b6

Merge branch 'main' into azbatch-executor

ac42624

cleanup

bb0b1d0

use config class

cb0f706

cleanup upload, logging

3e02bbe

Merge branch 'main' into azbatch-executor

c7fd264

jakevc requested a review from johanneskoester as a code owner November 4, 2022 05:23

jakevc changed the title ~~Azbatch executor~~ feat: Azbatch executor Nov 4, 2022

jakevc added 2 commits April 26, 2023 07:38

better syntax for env variables in action

73a1082

oops forgot that one

1b56033

jakevc added 2 commits April 28, 2023 08:58

check SAS first

4f38a7d

update docs, quote all for good measure

346163d

Merge branch 'main' into azbatch-executor

96f71c6

jakevc added 7 commits April 28, 2023 11:56

test different secret name hypothesis

0bfd261

back to old way

b1035b9

double quotes and quick check to see if it's actually none

e4d8e90

black

a7e66d5

okay what is the value

bdfe82e

testing az blob account url

346164f

just url

f4f96c8

debugging

4081a30

johanneskoester changed the base branch from main to azbatch-test May 4, 2023 18:44

johanneskoester merged commit a7f2124 into snakemake:azbatch-test May 4, 2023
8 of 9 checks passed

vsmalladi reviewed May 13, 2023

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github-actions bot mentioned this pull request Jun 11, 2023

chore(main): release 7.28.0 #2293

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feat: Azbatch executor #1953

feat: Azbatch executor #1953

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feat: Azbatch executor #1953

feat: Azbatch executor #1953

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