Web documentation update

sureshhewabi commented 1 week ago

User description

Crosslinking documentation
PRIDE reference update to the latest

PR Type

documentation, enhancement

Description

Updated multiple citations across the project to reference the latest PRIDE database publication for 2025.
Enhanced the crosslinking dataset submission instructions with new guidelines and validation steps.
Added a new tool, Kojak, to the list of supported tools for crosslinking data analysis.

Changes walkthrough 📝

Relevant files

Documentation

Spectra.vue `Update PRIDE database citation in Spectra view` src/views/archive/Spectra.vue - Updated the citation for the PRIDE database to the 2025 version.	+1/-1
content.md `Update PRIDE database citation in citation page` public/markdown/citationpage/content.md Updated general citation for the PRIDE database to the 2025 version.	+2/-2
content.md `Add dataset validation steps and new tool support` public/markdown/crosslinking/content.md Added a new section for dataset validation. Included steps and requirements for dataset validation. Added Kojak as a supported tool for crosslinking data analysis.	+26/-0
content.md `Update PRIDE database citation in introduction` public/markdown/intropride/content.md - Updated citation for the PRIDE database to the 2025 version.	+1/-1
content.md `Update PRIDE database citation in USI content` public/markdown/usi/content.md - Updated citation for the PRIDE database to the 2025 version.	+1/-1

Enhancement

Xiview.vue

Enhance crosslinking dataset submission instructions

src/views/archive/Xiview.vue

Added instructions for submitting crosslinking datasets.

Updated existing text for clarity and completeness.

+2/-1

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⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

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⚡ Recommended focus areas for review

Code Clarity
The Python command examples should include error handling guidance and expected output format to help users troubleshoot validation issues

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Enhancement	Add troubleshooting guidance to help users resolve validation failures ___ Add error handling guidance and troubleshooting steps for when validation fails. This would help users resolve common validation issues independently. [public/markdown/crosslinking/content.md [31-32]](https://github.com/PRIDE-Archive/pride-web/pull/370/files#diff-ea176224e95fb2220bd6bbd7e2e563b6cdd14ea177e525fa72b8be6abcd02462R31-R32) ```diff STEP 3: Run the validation and check for any errors in the console In order to run the validation, run the following command: `process_dataset -v "/absolute/file/path/to/the/folder/here"` +If validation fails, check: +- File paths contain no special characters or spaces +- All referenced peak files exist in the specified location +- XML syntax is valid in mzIdentML files +- All required fields are populated + ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 7 Why: Adding troubleshooting guidance would significantly improve user experience by helping them resolve common validation issues independently, reducing support requests and submission delays.	7
Best practice	Specify complete dependency requirements to ensure successful tool installation ___ Include version requirements for the validation tool and specify any dependencies needed beyond Python 3.10. [public/markdown/crosslinking/content.md [23-27]](https://github.com/PRIDE-Archive/pride-web/pull/370/files#diff-ea176224e95fb2220bd6bbd7e2e563b6cdd14ea177e525fa72b8be6abcd02462R23-R27) ```diff -STEP 2: Secondly, make sure you have `python > 3.10` and `pip` installed in your machine. Pip installation guide can be found here . -Then please install a python library in order to validate your dataset. +STEP 2: Secondly, make sure you have `python > 3.10` and `pip` installed in your machine. Pip installation guide can be found here. +Then install the validation library and its dependencies: +```bash +# Install required packages +pip install wheel setuptools +pip install xi-mzidentml-converter>=1.0.0 +``` + ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 6 Why: Providing specific version requirements and complete dependency information helps ensure successful installation and prevents compatibility issues.	6
Typo	Fix a spelling error in user support text ___ Fix the typo in 'contract us' which should be 'contact us' in the support text. [src/views/archive/Xiview.vue [86]](https://github.com/PRIDE-Archive/pride-web/pull/370/files#diff-dbf5ac6fb683e0011caf86fd79dd4a7d40af07abd11cff40dd8c72ae5e259410R86-R86) ```diff - You can add your crosslinking dataset to this newly developed resource by providing a COMPLETE submission with valid mzIdentML 1.2.0 files. Please read the complete guideline first and feel free to contract us if further support needed. + You can add your crosslinking dataset to this newly developed resource by providing a COMPLETE submission with valid mzIdentML 1.2.0 files. Please read the complete guideline first and feel free to contact us if further support needed. ``` - [ ] Apply this suggestion Suggestion importance[1-10]: 5 Why: Fixing the typo from 'contract us' to 'contact us' improves text clarity and professionalism, though it's a minor correction.	5

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PRIDE-Archive / pride-web