ignore case in original extension #183

daichengxin · 2024-10-27T02:07:16Z

PR Type

enhancement, documentation

Description

Enhanced the _removesuffix function to handle suffixes in a case-insensitive manner.
Updated the logic for file extension conversion to be case-insensitive.
Revised the help text in parse_sdrf.py to reflect the case-insensitive nature of extension conversion.
Bumped the version from 0.0.31 to 0.0.32.

Changes walkthrough 📝

Relevant files

Configuration changes

__init__.py `Bump version to 0.0.32` sdrf_pipelines/init.py Updated the version from 0.0.31 to 0.0.32.	+1/-1

Enhancement

openms.py `Implement case-insensitive extension handling` sdrf_pipelines/openms/openms.py Modified `_removesuffix` function to ignore case when checking suffix. Updated logic to handle case-insensitive extension conversion.	+4/-3

Documentation

parse_sdrf.py `Update documentation for case-insensitive extension conversion` sdrf_pipelines/parse_sdrf.py Updated help text to indicate case-insensitive extension conversion.	+1/-1

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Dev

coderabbitai · 2024-10-27T02:07:23Z

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codiumai-pr-agent-pro · 2024-10-27T02:07:39Z

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PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪
🧪 No relevant tests
🔒 No security concerns identified
⚡ Recommended focus areas for review Performance Concern The new implementation of `_removesuffix` uses regex, which might be less efficient than the previous string slicing approach. Consider benchmarking to ensure no significant performance impact. Potential Bug The case-insensitive comparison is implemented inconsistently. While `endswith` is made case-insensitive, the `_removesuffix` function still uses case-sensitive regex replacement. This might lead to unexpected behavior.

codiumai-pr-agent-pro · 2024-10-27T02:07:55Z

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Enhancement	Use a more robust method for case-insensitive string comparison Consider using the `casefold()` method instead of `lower()` for more robust case-insensitive string comparison, especially for Unicode strings. sdrf_pipelines/openms/openms.py [45-47] -if suffix and x.lower().endswith(suffix.lower()): +if suffix and x.casefold().endswith(suffix.casefold()): res = re.sub(suffix + "$", "", x, flags=re.I) return res Apply this suggestion Suggestion importance[1-10]: 7 Why: The suggestion to use `casefold()` instead of `lower()` provides a more robust solution for case-insensitive comparisons, especially with Unicode strings. This enhances the reliability of the code without altering its logic.	7
Enhancement	Use a more concise and efficient method to create a dictionary from a list of strings Consider using a dictionary comprehension to create `extension_convert_dict` for improved readability and potentially better performance. sdrf_pipelines/openms/openms.py [56-59] -extension_convert_dict = {} -for extension_convert in extension_convert_list: - current_extension, new_extension = extension_convert.split(":") - extension_convert_dict[current_extension] = new_extension +extension_convert_dict = {current_ext: new_ext for current_ext, new_ext in + (ext.split(":") for ext in extension_convert_list)} Apply this suggestion Suggestion importance[1-10]: 6 Why: The suggestion to use a dictionary comprehension improves code readability and conciseness. While it may not significantly impact performance, it simplifies the code structure, making it easier to understand and maintain.	6

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jpfeuffer · 2024-10-27T09:06:24Z

sdrf_pipelines/openms/openms.py

@@ -59,7 +60,7 @@ def _removesuffix(x: str, suffix: str, /) -> str:

    raw_bkp = raw
    for current_extension, target_extension in extension_convert_dict.items():
-        if raw.endswith(current_extension):
+        if raw.lower().endswith(current_extension.lower()):
            raw = _removesuffix(raw, current_extension)
            raw += target_extension
            if not any(raw.endswith(x) for x in possible_extension):


I think you will need to change this,too in case the user uses RAW and does no conversion of it.

Here I assume that the final openms experimental design file has the same suffix. Is that right? For example
Example 1: raw:mzML:
1.raw -> 1.mzML
2.Raw -> 2.mzML
3.RAW -> 3.mzML

Example 2: raw:RAW:
1.raw -> 1.RAW
2.Raw -> 2.RAW
3. RAW -> 3.RAW

And also we assumed only suppoted four format in the ending file: "raw", "mzML", "mzml", "d"

sdrf-pipelines/sdrf_pipelines/openms/openms.py

Lines 66 to 67 in d87d22c

if not any(raw.endswith(x) for x in possible_extension):

raise RuntimeError(

If I am not mistaken your example raw:RAW will fail.
If you only allow ".raw" as possible extension you have to add RAW:raw or raw:raw as a default conversion to the pipeline which is a bit weird.

Why not allow the possible extensions case-insensitive then? (i.e. "raw", "mzml", "d" in any possible casing)
Would solve a lot of problems.

It depends a bit on if downstream tools allow different cases. (e.g. does DIANN allow .D?)
Is this conversion to openms experimental design even used in the DIA branch of the pipeline?

Good ideas. I need to test it. Wait a while. Also is ProteomicsLFQ allowed different cases? For example input .mzML file, but in the experimental design file it's mzml

ProteomicLFQ expects exact matches of the full filename of the files that you pass as -in and what is written in the experimental design (including extension, excluding paths).

DIA-NN don't support .D format. So I suggest the possible extensions is case-sensitive. What do you think?

Is this conversion to openms experimental design even used in the DIA branch of the pipeline?

Yes. It also used in DIA branch https://github.com/bigbio/quantms/blob/b7c9b6a416723c4210effd3889dadce3d9032938/workflows/quantms.nf#L55

jpfeuffer · 2024-10-27T10:28:23Z

@ypriverol I think this was too quick

daichengxin · 2024-10-27T13:11:08Z

Another related question: Do we need to support this format ? bigbio/quantms#430

ypriverol · 2024-10-27T13:32:25Z

@daichengxin I have asked how the .dia is obtained. Let's see what they say.

daichengxin added 3 commits July 29, 2024 18:37

Merge pull request #17 from bigbio/dev

42ea2d7

Dev

Merge pull request #18 from bigbio/dev

b4a74d3

Dev

ignore case in original extension

ee099f8

codiumai-pr-agent-pro bot added the Review effort [1-5]: 2 label Oct 27, 2024

daichengxin requested review from ypriverol and jpfeuffer October 27, 2024 02:08

ypriverol approved these changes Oct 27, 2024

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ypriverol merged commit d87d22c into bigbio:dev Oct 27, 2024
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jpfeuffer requested changes Oct 27, 2024

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ignore case in original extension #183

ignore case in original extension #183

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ypriverol commented Oct 27, 2024

	if not any(raw.endswith(x) for x in possible_extension):
	raise RuntimeError(

ignore case in original extension #183

ignore case in original extension #183

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daichengxin commented Oct 27, 2024 • edited by codiumai-pr-agent-pro bot Loading

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