search

snakemake / snakemake-storage-plugin-gcs

A Snakemake storage plugin for Google Cloud Storage
MIT License
4 stars 5 forks source link

fix: fixing the directory() issue due to uploading the local_prefix instead of GCS prefix. #41

Closed jjjermiah closed 1 month ago

jjjermiah commented 5 months ago

first contribution here. Think I found the error.

This works for my test Snakefile: 

rule all:
    input:
        "data/done.txt",
        "data2/done.txt"

rule get_directories:
    input:
        expand(
            "data/{directory}",
            directory = ["a", "b", "c"]
        ),
    output:
        touch("data/done.txt")

rule make_a_directory:
    output:
        directory("data/{directory}")
    shell:
        """
        mkdir -p {output}
        touch {output}/test.txt
        """

rule get_files:
    input:
        expand(
            "data2/{directory}.txt",
            directory = ["a", "b", "c"]
        )
    output:
        touch("data2/done.txt")

rule make_a_file:
    output:
        "data2/{directory}.txt"
    shell:
        """
        mkdir -p $(dirname {output})
        touch {output}
        """

I also tried to add another test case which seems to work. I see that the test suites in the storage plugins use testClasses. Would adding actual snakefiles and a script to run them also help or does that not follow the plugin standards?

Summary by CodeRabbit

vsoch commented 5 months ago

Thansk @jjjermiah ! You probably want to remove the __pycache__ stuff.

jjjermiah commented 5 months ago

thanks for pointing that out @vsoch I also tried formatting and fixing the test suite

coderabbitai[bot] commented 1 month ago

Walkthrough

This update enhances the GitHub Actions workflow for testing, improves handling of Google Cloud Storage in the snakemake_storage_plugin_gcs module with new methods, and refines test cases for better clarity and functionality. Key changes include increased verbosity in test outputs, a new .gitignore file to exclude unnecessary files, and adjustments to ensure comprehensive testing of both files and directories.

Changes

Files Change Summary
.github/workflows/ci.yml Updated pytest command to include more verbosity and display print outputs during tests.
.gitignore New file created to prevent tracking of autogenerated files such as .coverage and __pycache__.
snakemake_storage_plugin_gcs/__init__.py Added ensure_bucket_exists and upload_directory methods; refactored store_object and remove methods for improved functionality and clarity.
tests/tests.py Updated TestStorage class to prioritize file operations, added tests for non-empty directories, and improved debug output and cleanup.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant CI
    participant GCS
    participant StoragePlugin

    User->>CI: Trigger Test Workflow
    CI->>StoragePlugin: execute tests
    StoragePlugin->>GCS: ensure_bucket_exists()
    GCS-->>StoragePlugin: bucket status
    StoragePlugin->>StoragePlugin: upload_directory()
    StoragePlugin->>GCS: upload files
    GCS-->>StoragePlugin: confirm upload
    StoragePlugin->>CI: return test results
    CI->>User: display results

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share - [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)
Tips ### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai generate interesting stats about this repository and render them as a table.` - `@coderabbitai show all the console.log statements in this repository.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (invoked as PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. Additionally, you can add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.
johanneskoester commented 1 month ago

Thanks a lot for the fixes!

johanneskoester commented 1 month ago

and sorry for the slow reply. This somehow slipped my attention. Feel free to contact me via discord or email if something like that happens again in the future.