feat: Add configurable protocol support to ensembl reference download #2649

pettyalex · 2024-02-15T22:12:22Z

This PR adds support for configurable protocol, ftp, http, or https to ensembl reference data download and vep cache download.

I was evaluating snakemake-wrapper and widely used workflows as a tool for my group to potentially use, and immediately ran into our firewall rules. By default we're able to make outgoing HTTP and HTTPS requests, but not FTP. I can request a change to our firewall, but it also would be helpful if these rules that download reference files were able to download them over HTTP, as ftp.ensembl.org has has been available over HTTP for a very long time.

If you'd prefer, I can create an issue to track this. I also intend to update test cases on these wrappers, and if you are happy with this pattern I could apply it across all wrappers in this repository that are currently hard-coded to make ftp requests.

QC

I confirm that:

For all wrappers added by this PR,

there is a test case which covers any introduced changes,
input: and output: file paths in the resulting rule can be changed arbitrarily,
either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
all environment.yaml specifications follow the respective best practices,
the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
the meta.yaml contains a link to the documentation of the respective tool or command,
Snakefiles pass the linting (snakemake --lint),
Snakefiles are formatted with snakefmt,
Python wrapper scripts are formatted with black.
Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

Summary by CodeRabbit

New Features
- Enhanced data retrieval workflows now support dynamic protocol selection, enabling secure downloads (HTTPS/HTTP) for annotation, genome, variation, and cache data.
- Added a workflow step for processing multiple chromosomes in a single operation.
Tests
- Expanded the test suite to validate and ensure reliability of the new secure protocol-based workflows.

…embl reference data download and vep cache download.

fgvieira · 2024-02-16T07:06:34Z

Thanks for your contribution.
Can you add a test case for (e.g.) HTTP and HTTPS?

pettyalex · 2024-02-19T20:33:40Z

I've run snakefmt, black and the linter over these changes. I believe this to be ready to merge.

fgvieira · 2024-02-20T18:38:49Z

@pettyalex can you fix the fail test?
And you need to add the tests to test.py.

…n. Add each new test case to test.py.

pettyalex · 2024-02-22T16:12:20Z

@fgvieira I fixed all the tests, and now see that what I had previously done introduced multiple ways to generate the desired output files.

I also unintentionally ran black over test.py, which it seems like is not being done? Should I revert running black over test.py, or should we have it running through black as well?

fgvieira · 2024-02-23T22:11:22Z

test.py

+def test_vep_cache_https_protocol():
+    run(
+        "bio/vep/cache",
+        ["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F"],


Suggested change

["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F"],

["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F", "-s", "vep_cache_https.smk"],

fgvieira · 2024-02-23T22:11:36Z

test.py

+            "-s",
+            "vep_cache_https.smk",


Suggested change

"-s",

"vep_cache_https.smk",

fgvieira · 2024-02-23T22:16:36Z

test.py

@@ -5428,17 +5461,26 @@ def test_ensembl_variation_with_contig_lengths():


 @skip_if_not_modified
-def test_ega_fetch():
+def test_ensembl_variation_old_release():


Suggested change

def test_ensembl_variation_old_release():

def test_ensembl_variation_old_release_https_protocol():

johanneskoester

Fantastic, thanks! Can you please also add the respective protocol lines to each Snakefile in the test folder? Those are used to generate the wrapper docs, from which people can copy paste into their workflows.

Allow for custom URLs (fix issues #366 and #2649). ### QC  * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

fgvieira · 2024-05-28T12:09:25Z

PR #2928 allowed for custom URLs when downloading from VEP cache. Maybe something similar can be done here for ensembl annotation/variation/sequence?

Allow for custom URLs (fix issues snakemake#366 and snakemake#2649). ### QC  * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

fgvieira · 2024-08-23T11:13:50Z

Can you fix the conflicts?

github-actions · 2025-03-01T01:31:09Z

This PR was marked as stale because it has been open for 6 months with no activity.

coderabbitai · 2025-03-01T01:31:16Z

📝 Walkthrough

Walkthrough

The changes introduce several new Snakemake rules that support HTTPS (and HTTP) protocols for downloading Ensembl resources, including annotation, sequence, variation, and VEP cache data. Wrapper scripts are updated to use a dynamic protocol parameter (defaulting to "ftp") for URL construction. Additionally, a new rule for processing multiple chromosomes is added, and several existing Snakemake files receive trailing comma adjustments for formatting consistency. New test functions have been added and existing tests updated to reflect the new HTTPS-based workflows.

Changes

File(s)	Change Summary
`bio/.../ensembl_annotation_https.smk`, `bio/.../ensembl_sequence_https.smk`, `bio/.../ensembl_variation_https.smk`, `bio/.../vep_cache_https.smk`, `bio/.../Snakefile` (multi-chromosome rule)	Added new Snakemake rules specifying outputs, parameters (including protocol), logging, and caching for HTTPS/HTTP downloads and multi-chromosome processing.
`bio/.../ensembl-annotation/wrapper.py`, `bio/.../ensembl-sequence/wrapper.py`, `bio/.../ensembl-variation/wrapper.py`, `bio/.../vep/cache/wrapper.py`	Introduced a new `protocol` parameter (default `"ftp"`) to dynamically construct URL strings instead of using a hardcoded protocol.
`bio/.../chrom_wise.smk`, `bio/.../grch37.smk`, `bio/.../old_release.smk`, `bio/.../with_fai.smk`	Added trailing commas in rule sections (input, output, params, log) for standardized formatting.
`test.py`	Added new test functions (`test_ensembl_sequence_https`, `test_ensembl_annotation_gtf_https_gz`) and modified the `test_ensembl_variation_old_release` to reference the updated HTTPS Snakefile; reordering tests as necessary.

Sequence Diagram(s)

sequenceDiagram
    participant S as Snakemake Rule
    participant W as Wrapper Script
    participant D as Download Service

    S->>W: Invoke rule with parameters (including protocol)
    W->>W: Retrieve protocol (default "ftp" or overridden to "https"/"http")
    W->>D: Construct URL and request download using dynamic protocol
    D-->>W: Return downloaded data
    W-->>S: Output file and log execution

Suggested Reviewers

fgvieira

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9797636 and 1a84082.

📒 Files selected for processing (14)

bio/reference/ensembl-annotation/test/ensembl_annotation_https.smk (1 hunks)
bio/reference/ensembl-annotation/wrapper.py (3 hunks)
bio/reference/ensembl-sequence/test/Snakefile (1 hunks)
bio/reference/ensembl-sequence/test/ensembl_sequence_https.smk (1 hunks)
bio/reference/ensembl-sequence/wrapper.py (2 hunks)
bio/reference/ensembl-variation/test/chrom_wise.smk (1 hunks)
bio/reference/ensembl-variation/test/ensembl_variation_https.smk (1 hunks)
bio/reference/ensembl-variation/test/grch37.smk (1 hunks)
bio/reference/ensembl-variation/test/old_release.smk (1 hunks)
bio/reference/ensembl-variation/test/with_fai.smk (1 hunks)
bio/reference/ensembl-variation/wrapper.py (2 hunks)
bio/vep/cache/test/vep_cache_https.smk (1 hunks)
bio/vep/cache/wrapper.py (2 hunks)
test.py (4 hunks)

✅ Files skipped from review due to trivial changes (4)

bio/reference/ensembl-variation/test/with_fai.smk
bio/reference/ensembl-variation/test/grch37.smk
bio/reference/ensembl-variation/test/chrom_wise.smk
bio/reference/ensembl-variation/test/old_release.smk

🧰 Additional context used

📓 Path-based instructions (2)

`**/*.py`: Do not try to improve formatting. Do not suggest ...

**/*.py: Do not try to improve formatting.
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.
Do not suggest return type annotation if a function or method does not contain a return statement.

bio/vep/cache/wrapper.py
bio/reference/ensembl-annotation/wrapper.py
bio/reference/ensembl-variation/wrapper.py
bio/reference/ensembl-sequence/wrapper.py
test.py

`**/wrapper.py`: Do not complain about use of undefined vari...

**/wrapper.py: Do not complain about use of undefined variable called snakemake.

bio/vep/cache/wrapper.py
bio/reference/ensembl-annotation/wrapper.py
bio/reference/ensembl-variation/wrapper.py
bio/reference/ensembl-sequence/wrapper.py

🪛 Ruff (0.8.2)

bio/vep/cache/wrapper.py

12-12: Undefined name snakemake

(F821)

bio/reference/ensembl-annotation/wrapper.py

22-22: Undefined name snakemake

(F821)

bio/reference/ensembl-variation/wrapper.py

18-18: Undefined name snakemake

(F821)

bio/reference/ensembl-sequence/wrapper.py

14-14: Undefined name snakemake

(F821)

test.py

5464-5464: Redefinition of unused test_ensembl_variation_old_release from line 5423

(F811)

🔇 Additional comments (17)

bio/reference/ensembl-sequence/test/Snakefile (1)

33-47: New rule for multiple chromosomes looks good.

The new get_multiple_chromosome rule is well-structured and consistent with the existing rules. It appropriately demonstrates how to retrieve multiple chromosomes (I and II) in a single workflow step.

While the PR objective mentions adding configurable protocol support, I don't see a direct protocol parameter in this rule. This parameter might be implemented in the wrapper script itself. If not already handled by the wrapper, consider adding a protocol parameter here to demonstrate the new functionality.

bio/vep/cache/wrapper.py (2)

12-12: Parameter added to allow for configurable protocol.

The new protocol parameter allows users to specify an alternative protocol (HTTP or HTTPS) when facing firewall restrictions, aligning well with the PR objective. The default "ftp" maintains backward compatibility.

🧰 Tools

🪛 Ruff (0.8.2)

12-12: Undefined name snakemake

(F821)

28-28: URL pattern updated to use the configurable protocol.

The hardcoded "ftp" protocol has been replaced with the dynamically determined {protocol}, enabling the wrapper to use alternative protocols as specified in the parameters.

bio/reference/ensembl-annotation/test/ensembl_annotation_https.smk (1)

1-14: New test rule for HTTPS protocol download looks good.

This test rule correctly verifies the new functionality by explicitly setting the protocol parameter to "https". The rule structure is appropriate and follows the standard pattern for Snakemake rules.

bio/reference/ensembl-sequence/test/ensembl_sequence_https.smk (1)

1-14: New test rule for HTTP protocol download looks good.

The rule properly tests the HTTP protocol functionality. Note that despite the filename including "https", this test is using the "http" protocol, which is acceptable since the PR aims to support both HTTP and HTTPS protocols.

bio/reference/ensembl-variation/test/ensembl_variation_https.smk (1)

1-14: New test rule for HTTPS protocol download looks good.

This test rule correctly verifies the variation data download functionality with the HTTPS protocol. The rule structure follows the established pattern and includes all necessary parameters.

bio/vep/cache/test/vep_cache_https.smk (1)

1-15: Rule looks good - correctly exercises HTTPS protocol support.

This new test rule correctly defines a test case for the HTTPS protocol functionality, with appropriate parameters and output specifications. The rule structure follows Snakemake conventions and properly exercises the new protocol parameter.

bio/reference/ensembl-variation/wrapper.py (2)

18-18: Good implementation of the protocol parameter.

Adding the protocol parameter with a default value of "ftp" maintains backward compatibility while enabling the new functionality.

🧰 Tools

🪛 Ruff (0.8.2)

18-18: Undefined name snakemake

(F821)

67-74: URL construction correctly incorporates the protocol parameter.

The URL formatting has been updated to use the protocol parameter rather than hardcoding "ftp", which successfully implements the configurable protocol feature.

bio/reference/ensembl-annotation/wrapper.py (2)

22-22: Good implementation of the protocol parameter.

Adding the protocol parameter with a default value of "ftp" maintains backward compatibility while enabling the new functionality.

🧰 Tools

🪛 Ruff (0.8.2)

22-22: Undefined name snakemake

(F821)

52-63: URL construction correctly incorporates the protocol parameter.

The URL formatting has been updated to use the protocol parameter rather than hardcoding "ftp", which successfully implements the configurable protocol feature.

bio/reference/ensembl-sequence/wrapper.py (2)

14-14: Good implementation of the protocol parameter.

Adding the protocol parameter with a default value of "ftp" maintains backward compatibility while enabling the new functionality.

🧰 Tools

🪛 Ruff (0.8.2)

14-14: Undefined name snakemake

(F821)

55-55: URL construction correctly incorporates the protocol parameter.

The f-string URL construction has been updated to use the protocol parameter rather than hardcoding "ftp", which successfully implements the configurable protocol feature.

test.py (4)

5333-5346: LGTM! Added test function for HTTPS protocol support.

This new test function aligns perfectly with the PR objective to add support for configurable protocols (HTTP, HTTPS) for Ensembl reference data.

5398-5412: LGTM! Added test function for HTTPS protocol annotation downloads.

The test function correctly tests Ensembl GTF annotation downloads via HTTPS protocol, aligned with the PR's objectives.

5847-5852: LGTM! Added test function for VEP cache downloads via HTTPS.

This new test function appropriately extends the HTTPS protocol support to VEP cache downloads.

5858-5867: LGTM! Updated to use HTTPS-enabled Snakefile.

The modification correctly updates the test to use the HTTPS-compatible Snakefile for VEP plugins.

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Add the support for configurable protocol, ftp, http, or https to ens…

16e9da4

…embl reference data download and vep cache download.

pettyalex added 2 commits February 19, 2024 14:21

Add tests for getting reference data over http

d82fa78

Run snakefmt over reference download tools.

94cdbfd

Split off https into different snakemake files to avoid name collisio…

17d4d28

…n. Add each new test case to test.py.

Fix tests for annotation and make https protocol output gzipped.

1a84082

fgvieira reviewed Feb 23, 2024

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test.py

Comment on lines +5865 to +5866

"-s",

"vep_cache_https.smk",

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Suggested change

"-s",

"vep_cache_https.smk",

fgvieira reviewed Feb 23, 2024

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johanneskoester requested changes Feb 27, 2024

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fgvieira mentioned this pull request May 13, 2024

fix: issue #366 and #2649 #2928

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	["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F"],
	["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F", "-s", "vep_cache_https.smk"],

	def test_ensembl_variation_old_release():
	def test_ensembl_variation_old_release_https_protocol():

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