feat: ✨ Align Citation generation based off latest citation schema (1.3.0)

[slugb0t]

Summary by Sourcery

Align citation generation and metadata handling with the updated citation schema by normalizing DOI values and avoiding redundant DOI URL storage.

New Features:

• Normalize and extract bare DOI values from various identifier formats when generating citation metadata.

Bug Fixes:

• Ensure DOI values in generated citation files are consistently stored as canonical DOI strings rather than resolver URLs or arbitrary identifiers.

Enhancements:

• Avoid redundant DOI information in citation metadata by using the dedicated doi field instead of identifiers arrays where appropriate.

[fairdataihub-bot]

Thank you for submitting this pull request! We appreciate your contribution to the project. Before we can merge it, we need to review the changes you've made to ensure they align with our code standards and meet the requirements of the project. We'll get back to you as soon as we can with feedback. Thanks again!

[sourcery-ai]

Reviewer's Guide

Aligns DOI handling and citation.cff generation with citation schema 1.3.0 by extracting clean DOI values from various identifier formats and using them consistently in both the API code-metadata handler and the metadata compliance bot.

File-Level Changes

Change	Details	Files
Normalize and extract a canonical DOI value from uniqueIdentifier for citation.cff generation in the code-metadata API handler.	Introduce a DOI extraction regex and helper logic to parse different DOI/URL formats from uniqueIdentifier. Prefer extracting the bare DOI from resolver URLs (doi.org/dx.doi.org) and fall back to the raw uniqueIdentifier when no pattern matches. Stop constructing full https://doi.org URLs for the doi field and instead set it only when a parsed DOI value is available. Disable the identifiers block to avoid redundancy with the dedicated doi field.	ui/server/api/[owner]/[repo]/code-metadata/index.post.ts
Update metadata compliance-check DOI normalization to store a cleaned DOI value instead of a full resolver URL.	Add shared-style DOI regex and parsing logic to normalize identifier into a bare DOI where possible. Handle resolver URLs (https://doi.org/...) by extracting and validating the DOI portion, otherwise attempt direct DOI matching or fallback to the original identifier string. Assign the normalized DOI value to citationFile.doi instead of always generating a https://doi.org URL, while still keeping the original identifier in codeMetaFile.identifier.	bot/compliance-checks/metadata/index.js

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[fairdataihub-bot]

Thanks for making updates to your pull request. Our team will take a look and provide feedback as soon as possible. Please wait for any GitHub Actions to complete before editing your pull request. If you have any additional questions or concerns, feel free to let us know. Thank you for your contributions!

[what-the-diff]

PR Summary

• Improvement in DOI Handling in index.js File:

  • Utilized a formula to validate the correctness of DOI formats.
  • Developed a robust system to manage the cases of DOI resolver URLs and direct DOI identifiers.
  • Enhanced clarity by renaming the variable from doiUrl to doiValue and modifying the assignment pattern to the citationFile.doi.

• Advanced DOI Extraction Process in index.post.ts File:

  • Incorporated a new method to obtain DOIs from within the codeMetadataRecord.
  • The same formula is used for validating DOIs in this process.
  • Designed to retain the raw identifier value if no matches are found to preserve the old practice for unmatched identifiers.
  • Tweaked the method for including DOIs in the citationCFF object to prevent repetition and supports the new extraction method.

[fairdataihub-bot]

Thanks for closing this pull request! If you have any further questions, please feel free to open a new issue. We are always happy to help!

[sourcery-ai]

Hey there - I've reviewed your changes - here's some feedback:

• The DOI extraction logic and DOI_REGEX are duplicated in both the API handler and the compliance-checks script; consider extracting a shared utility to keep the behavior and pattern consistent and easier to maintain.
• In code-metadata/index.post.ts, the comment above the (disabled) identifiers block now mixes a JSDoc opening /** with a line comment // Note: ...; converting this to a single coherent block comment or a plain line comment would improve readability.
• In updateMetadataIdentifier, when identifierString is empty citationFile.doi is set to an empty string; if the intention is to omit the DOI in that case, consider leaving citationFile.doi undefined instead of assigning an empty value.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The DOI extraction logic and `DOI_REGEX` are duplicated in both the API handler and the compliance-checks script; consider extracting a shared utility to keep the behavior and pattern consistent and easier to maintain.
- In `code-metadata/index.post.ts`, the comment above the (disabled) `identifiers` block now mixes a JSDoc opening `/**` with a line comment `// Note: ...`; converting this to a single coherent block comment or a plain line comment would improve readability.
- In `updateMetadataIdentifier`, when `identifierString` is empty `citationFile.doi` is set to an empty string; if the intention is to omit the DOI in that case, consider leaving `citationFile.doi` undefined instead of assigning an empty value.

## Individual Comments

### Comment 1
<location> `bot/compliance-checks/metadata/index.js:678-680` </location>
<code_context>
+      }
     }
-    citationFile.doi = doiUrl;
+    citationFile.doi = doiValue;
     citationFile["date-released"] = updated_date;
     citationFile.version = zenodoMetadata?.zenodo_metadata?.version;
</code_context>

<issue_to_address>
**suggestion (bug_risk):** Avoid assigning an empty string to `citationFile.doi` when no identifier is provided.

With the current logic, a falsy `identifier` leaves `doiValue` as `""`, so `citationFile.doi` is explicitly set to an empty string. Instead, consider only setting the field when `doiValue` is truthy, e.g.:

```js
if (doiValue) {
  citationFile.doi = doiValue;
}
```

This prevents persisting an empty DOI and keeps the field’s presence meaningful.

```suggestion
    }
    if (doiValue) {
      citationFile.doi = doiValue;
    }
    citationFile["date-released"] = updated_date;
```
</issue_to_address>

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