fix: add assets and use local file links to allow offline reports by fs82 · Pull Request #2904 · snakemake/snakemake

fs82 · 2024-05-31T13:38:01Z

This PR solves the issue with the offline reports. Several files are downloaded on the fly while generating the report(js, css and licenses). They are now added to the package as assets.

I used the test_report test case to verify that the generated report is the same and works as expected. One minor change in the report appears, as I thought it is more logical to use major.minor version numbering for the react package as well.

To my opinion a update of the documentation is not necessary.

Closes #282

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).

Summary by CodeRabbit

New Features
- Improved installation process with the addition of setuptools-download for enhanced dependency management.
- New section added to manage the downloading of essential resources during installation.
Bug Fixes
- Enhanced file path handling to support both absolute and relative paths, ensuring better file accessibility.
Chores
- Reaffirmed inclusion of the LICENSE.md file in the package distribution for compliance.
Refactor
- Updated package resource management to utilize local paths, improving reliability and portability.
- Streamlined HTML template for loading JavaScript resources, enhancing performance and maintainability.

fs82 · 2024-05-31T13:46:27Z

@johanneskoester The checks are failing on the new files added to the repository as assets for the reports. To my opinion they should not be checked by the ci of snakemake, as they are obtained from other projects. However, my knowledge about Github and its CI is limited. Would be good if you can comment on how to work around this.

fs82 · 2024-05-31T13:53:39Z

The only other way I see is to compress the files and extract the on the fly?

johanneskoester · 2024-06-04T09:16:02Z

I think the files can simply be excluded via adding a sonar-project.properties file to the repo: https://docs.sonarsource.com/sonarcloud/advanced-setup/analysis-scope/#file-exclusion-and-inclusion

fs82 · 2024-06-04T09:18:02Z

I think the files can simply be excluded via adding a sonar-project.properties file to the repo: https://docs.sonarsource.com/sonarcloud/advanced-setup/analysis-scope/#file-exclusion-and-inclusion

Ok, sounds good. I will have a look asap.

sonarqubecloud · 2024-06-04T14:37:01Z

Quality Gate failed

Failed conditions
5 Security Hotspots
C Reliability Rating on New Code (required ≥ A)
D Security Rating on New Code (required ≥ A)

See analysis details on SonarCloud

Catch issues before they fail your Quality Gate with our IDE extension SonarLint

fs82 · 2024-06-04T14:43:09Z

I think the files can simply be excluded via adding a sonar-project.properties file to the repo: https://docs.sonarsource.com/sonarcloud/advanced-setup/analysis-scope/#file-exclusion-and-inclusion

I give up, is there a way to see somehow the log output of the sonar cloud? I tried several ways to ignore the assets folder, but it does not seem to be that the sonar cloud respects the settings in sonar-project.properties. It is honestly not my field of knowledge 😄

daaaaande · 2024-06-12T08:37:18Z

would be happy to see that feature. using snakemake on a cluster that is offline, and the reports could help. is there maybe a workaround for this issue?

rahedges · 2024-06-18T18:43:59Z

I would also make use of this feature, offline reports are necessary for my snakemake analysis.

fs82 · 2024-06-19T15:41:22Z

I think the files can simply be excluded via adding a sonar-project.properties file to the repo: https://docs.sonarsource.com/sonarcloud/advanced-setup/analysis-scope/#file-exclusion-and-inclusion

I give up, is there a way to see somehow the log output of the sonar cloud? I tried several ways to ignore the assets folder, but it does not seem to be that the sonar cloud respects the settings in sonar-project.properties. It is honestly not my field of knowledge 😄

Ok from cross reading the sonar cloud manual, it looks like there are automatic analysis enabled for snakemake repository, due to the presence of the .sonarcloud.properties file. This seems to conflict with the sonar-project.properties file, which is only for ci-based analysis. I honestly dont get the difference, but the manual states, this is conflicting. I move the exclude settings now to the .sonarcloud.properties, lets see what happens

https://docs.sonarsource.com/sonarcloud/advanced-setup/automatic-analysis/#presence-of-a-properties-file

johanneskoester · 2024-06-20T10:32:03Z

Actually, I think we can solve the issue in a way that fixes two problems at a time.
It is in general not so desirable to have copies of foreign code within the repo.
So why don't we make their download part of the package building process, e.g. via setuptools-download? This way, they won't be checked by any linter, and the source tree and git history remains clean of foreign code. Further, an update is just doable by changing the URLs in the setup.cfg. Alternatively, if more complex logic is needed, one can also put some download code using requests into the setup.py.

fs82 · 2024-06-21T13:30:46Z

Actually, I think we can solve the issue in a way that fixes two problems at a time. It is in general not so desirable to have copies of foreign code within the repo. So why don't we make their download part of the package building process, e.g. via setuptools-download? This way, they won't be checked by any linter, and the source tree and git history remains clean of foreign code. Further, an update is just doable by changing the URLs in the setup.cfg. Alternatively, if more complex logic is needed, one can also put some download code using requests into the setup.py.

Ok, the latest commit tries to apply your suggestion. I tried to make the get_resource_as_a_string function backward compatible. The download during package build seems to work for all License, css and js files, except for tailwindcss. The content delivery network (CDN) of tailwindcss does not allow access via urllib.request (used by setuptools-download). The reason is probably a wrong header, but this can only be solved in setuptools-download to my understanding. Anyhow, when flying over the tailwindcss website, this it seems to be not a good idea to use in production the Play CDN. They strongly recommend to build a css file for the project locally and supply it.

@johanneskoester Sorry to say, but this is all I can do. I have no clue what tailwind does, how it is used and in particular not how it is integrated in snakemake.

coderabbitai · 2024-08-16T13:58:35Z

Caution

Review failed

The pull request is closed.

Walkthrough

The recent changes primarily enhance the Snakemake report generation process for offline environments by improving the handling of local resources. Key modifications include the addition of local paths for license files and assets, ensuring that the reports do not rely on external CDNs. This enhances usability for users operating without internet access, aligning with the objective of generating reports solely from local resources.

Changes

File Path	Change Summary
`MANIFEST.in`	Reasserted inclusion of `LICENSE.md`, added newline.
`setup.cfg`	Added `setup_requires` for `setuptools-download` and new section for managing local resource downloads.
`snakemake/report/html_reporter/common.py`	Updated `get_resource_as_string` to handle both absolute and relative paths.
`snakemake/report/html_reporter/data/packages.py`	Modified `get_packages` to use local paths for licensing information instead of hardcoded URLs.
`snakemake/report/html_reporter/template/index.html.jinja2`	Changed JavaScript resource references to use local paths directly.

Assessment against linked issues

Objective	Addressed	Explanation
Allow offline report generation by using local resources instead of CDN (##282)	✅
Enable passing custom CSS paths to the report command (##282)	❌	Custom CSS paths functionality not implemented.

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Actionable comments posted: 1

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Commits

Files that changed from the base of the PR and between 6bd67d7 and 025a0c6.

Files selected for processing (4)

MANIFEST.in (1 hunks)
setup.cfg (2 hunks)
snakemake/report/html_reporter/common.py (1 hunks)
snakemake/report/html_reporter/data/packages.py (2 hunks)

Additional context used

Path-based instructions (2)

snakemake/report/html_reporter/common.py (1)

Pattern **/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.

snakemake/report/html_reporter/data/packages.py (1)

Pattern **/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.

Ruff

snakemake/report/html_reporter/common.py

17-17: Use context handler for opening files

(SIM115)

snakemake/report/html_reporter/data/packages.py

29-29: Trailing comma missing

Add trailing comma

(COM812)

Additional comments not posted (5)

MANIFEST.in (1)

3-3: Reaffirmed inclusion of LICENSE.md.

The inclusion of LICENSE.md in the manifest file ensures that the license is part of the distribution, which is essential for compliance and transparency.

snakemake/report/html_reporter/data/packages.py (1)

Line range hint 5-53: Enhanced portability with local paths.

The use of sys.prefix to construct local paths for package resources improves portability and robustness across different environments, aligning with the PR's objectives to support offline report generation.

Tools

Ruff

29-29: Trailing comma missing

Add trailing comma

(COM812)

55-55: Trailing comma missing

Add trailing comma

(COM812)

setup.cfg (3)

53-53: Addition of smart-open dependency looks good.

The addition of smart-open >=4.0,<8.0 is consistent with the versioning strategy used for other dependencies.

66-66: Inclusion of setuptools-download is appropriate.

The addition of setuptools-download >= 1.1.0 ensures that necessary tools for downloading data files are available during the setup process.

68-117: New [setuptools_download] section is well-structured.

The section provides a systematic approach to managing external resources with URLs and SHA256 checksums for integrity verification.

To ensure correctness, verify that all URLs are accessible and checksums match the files.

snakemake/report/html_reporter/common.py

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snakemake/report/html_reporter/common.py (1)

Pattern **/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.

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snakemake/report/html_reporter/common.py (1)
13-18: Use a context manager for file operations.

To ensure proper resource management and avoid potential file handle leaks, use a context manager when opening files. This was flagged in previous reviews.
-        with open(fpath) as file:
-            return file.read()
+        with open(fpath) as file:
+            return file.read()

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snakemake/report/html_reporter/data/packages.py (2 hunks)

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snakemake/report/html_reporter/data/packages.py (1)

Pattern **/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.

Additional comments not posted (2)

snakemake/report/html_reporter/data/packages.py (2)

5-6: Imports are appropriate.

The addition of sys and os imports is necessary for constructing local paths for resources.

21-53: Local path construction is correct.

The use of os.path.join(sys.prefix, ...) to construct local paths for package resources is a robust solution for offline environments.

Ensure that the local paths used here exist and are correctly set up during installation or packaging.

…/fs82/2904

sonarqubecloud · 2024-08-16T15:50:08Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

johanneskoester · 2024-08-16T15:56:43Z

Oh, that is clearly a bug with automerge. It merged before all the tests were done, and some even failed!!

johanneskoester · 2024-08-16T15:57:08Z

I will check the main branch and see if I can fix it in a quick follow-up.

…orts (#2904)" This reverts commit 9cd94f7.

🤖 I have created a release *beep* *boop* --- ## [8.18.1](v8.18.0...v8.18.1) (2024-08-19) ### Bug Fixes * add assets and use local file links to allow offline reports ([#2904](#2904)) ([9cd94f7](9cd94f7)) * use query from storage object in order to be able to reflect possible modifications (via StorageProvider.postprocess_query()) ([#3031](#3031)) ([3ddae58](3ddae58)) ### Documentation * clarify config file location ([6bd67d7](6bd67d7)) --- 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>

@fs82

…me possible offline (cont. of #2904) (#3026) The original PR has been reverted in main because it does not seem to work will with developer installation mode (assets are not installed in the right place in that case). cc @fs82 ### 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).  ## Summary by CodeRabbit ## Summary by CodeRabbit - **New Features** - Introduced structured asset management within the Snakemake framework, allowing for better handling and deployment of external resources. - **Improvements** - Enhanced package metadata handling for improved maintainability and accessibility of license and source files. - Enabled the inclusion of additional package data during installation, ensuring necessary files are available. - **Bug Fixes** - Improved reliability by transitioning to local paths for resource referencing, enhancing accessibility and reducing dependency on external URLs.  --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

🤖 I have created a release *beep* *boop* --- ## [8.19.0](v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([#3050](#3050)) ([666cf62](666cf62)) * print host name when executing workflow ([#3048](#3048)) ([b0ff787](b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([#3040](#3040)) ([7530794](7530794)) * avoid error accessing superclass in ioutils ([#3056](#3056)) ([a66a5f5](a66a5f5)) * disable execute after print compilation ([#3041](#3041)) ([86ed3cd](86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [#2904](#2904)) ([#3026](#3026)) ([e8dad4b](e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([#3045](#3045)) ([9a4006d](9a4006d)) * Fix typo (seesee to see) ([#3037](#3037)) ([de201fb](de201fb)) * various documentation fixes ([#3052](#3052)) ([b11460c](b11460c)) --- 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>

@fs82

…me possible offline (cont. of snakemake#2904) (snakemake#3026) The original PR has been reverted in main because it does not seem to work will with developer installation mode (assets are not installed in the right place in that case). cc @fs82 ### 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).  ## Summary by CodeRabbit ## Summary by CodeRabbit - **New Features** - Introduced structured asset management within the Snakemake framework, allowing for better handling and deployment of external resources. - **Improvements** - Enhanced package metadata handling for improved maintainability and accessibility of license and source files. - Enabled the inclusion of additional package data during installation, ensuring necessary files are available. - **Bug Fixes** - Improved reliability by transitioning to local paths for resource referencing, enhancing accessibility and reducing dependency on external URLs.  --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

🤖 I have created a release *beep* *boop* --- ## [8.19.0](snakemake/snakemake@v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([snakemake#3050](snakemake#3050)) ([666cf62](snakemake@666cf62)) * print host name when executing workflow ([snakemake#3048](snakemake#3048)) ([b0ff787](snakemake@b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([snakemake#3040](snakemake#3040)) ([7530794](snakemake@7530794)) * avoid error accessing superclass in ioutils ([snakemake#3056](snakemake#3056)) ([a66a5f5](snakemake@a66a5f5)) * disable execute after print compilation ([snakemake#3041](snakemake#3041)) ([86ed3cd](snakemake@86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [snakemake#2904](snakemake#2904)) ([snakemake#3026](snakemake#3026)) ([e8dad4b](snakemake@e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([snakemake#3045](snakemake#3045)) ([9a4006d](snakemake@9a4006d)) * Fix typo (seesee to see) ([snakemake#3037](snakemake#3037)) ([de201fb](snakemake@de201fb)) * various documentation fixes ([snakemake#3052](snakemake#3052)) ([b11460c](snakemake@b11460c)) --- 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>

Add assets and use local file links

291baa8

fs82 requested a review from johanneskoester as a code owner May 31, 2024 13:38

fs82 changed the title ~~Add assets and use local file links~~ fix: add assets and use local file links to allow offline reports May 31, 2024

Remove a leftover asset

7e3ccab

fs82 added 9 commits June 4, 2024 16:05

Exclude assets from tests in sonar cloud

ca12a4a

Fix copy and paste mistake for sonar cloud properties key

8bb0ce1

Fix path to assets

cdeb921

Try and error to figure out the settings for sonar cloud

bb07483

Next try to figure out settings for sonar cloud

17f87ab

Next try to figure out settings for sonar cloud

3b332b2

One more try to figure out sonar cloud settings

2c23d52

One more try

f8334b2

Another try ... is getting boring

732e5f5

fs82 and others added 4 commits June 18, 2024 21:21

Remove space, check if it helps

0495df8

Merge branch 'main' into offline-reporting

8820533

One more test

ba57a02

Remove sonar-project.properties

a4a7a32

Download files during package building

0ef58f8

Fix formating with black

34d7336

fs82 and others added 2 commits July 12, 2024 23:13

Merge branch 'main' into offline-reporting

797bc81

Merge branch 'main' into offline-reporting

025a0c6

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johanneskoester added 2 commits August 16, 2024 17:47

remove some redundancy, install assets under share/snakemake/assets

4419aa9

Merge branch 'offline-reporting' of github.com:fs82/snakemake into pr…

560a4d5

…/fs82/2904

johanneskoester enabled auto-merge (squash) August 16, 2024 15:49

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chore(main): release 8.18.1 #3017

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Revert "fix: add assets and use local file links to allow offline rep…

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…orts (#2904)" This reverts commit 9cd94f7.

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chore(main): release 8.19.0 #3051

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chore: For assets bundled at a particular version, reference the version’s license #3098

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docs: addition of interction/visualization/reporting tutorial #3159

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