bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation module

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bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation module#

Generate a CITATION.cff file from bio.tools publication metadata.

This module retrieves publications from a bio.tools entry, resolves them via the Europe PMC REST API, and converts the resulting bibliographic information into the Citation File Format (CFF).

If a CITATION.cff already exists in the GitHub repository, its non-publication metadata is preserved where present, and its publication list is merged with publications discovered via bio.tools / Europe PMC. References are deduplicated, and a preferred citation is chosen with a clear precedence: existing preferred-citation (if any) > bio.tools primary publications > other publications.

async bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation.map_citation(gh_citation_cff, bt_params)[source]#

Generate or update a CITATION.cff file based on bio.tools and Europe PMC metadata.

Steps performed: 1. Reads publication metadata from a bio.tools tool entry. 2. Resolves each publication via the Europe PMC API to obtain

bibliographic metadata.

  1. Optionally parses an existing CITATION.cff (if provided) and extracts existing references and a preferred-citation.

  2. Merges existing references and new references, deduplicating based on DOI/PMID/PMCID/title.

  3. Chooses a preferred citation following the configured precedence rules.

  4. Merges top-level metadata from the existing CFF and bio.tools.

  5. Returns a dictionary mapping “CITATION.cff” to the YAML-serialized CFF content.

Parameters:

  • gh_citation_cff (dict[str, Any]) – Parsed content of an existing CITATION.cff file from the GitHub repository.

  • bt_params (dict[str, Any]) – The bio.tools tool metadata as a dictionary. Expected keys include: - ‘publication’ : list of publication items from bio.tools metadata. - ‘name’ : name of the tool. - ‘biotoolsID’ : bio.tools identifier. - ‘homepage’ : homepage or repository URL. - ‘license’ : license identifier. - ‘topic’ : list of topics. - ‘description’ : description of the tool.

Returns:

A dictionary with the filename “CITATION.cff” as key, and the YAML-formatted CFF content as value.

Return type:

dict[str, str]

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