Source code for bridge.pipelines.gh2bt_for_meta.map_funcs.publication

"""
Mapping functions for publication metadata.

This module reconciles GitHub CITATION.cff references with bio.tools
publication entries by converting CITATION.cff data into bio.tools
PublicationItem instances and merging them with existing entries.
Duplicates are removed, prioritizing CITATION.cff entries.
"""

from typing import Any

from bridge.core.biotools import PublicationItem, TypeEnum2 as PublicationType
from bridge.logging import get_user_logger
from bridge.pipelines.shared.publications import deduplicate_references, extract_cff_references

logger = get_user_logger()


def _cff_ref_to_biotools(
    ref: dict[str, Any], pub_type: list[PublicationType] | PublicationType | None = None
) -> PublicationItem | None:
    """
    Convert a CITATION.cff reference dictionary to a bio.tools PublicationItem.

    Parameters
    ----------
    ref : dict[str, Any]
        A single reference entry from CITATION.cff.

    Returns
    -------
    PublicationItem | None
        The corresponding bio.tools PublicationItem instance, or ``None`` if no
        valid identifiers were found in the reference.
    """
    doi = ref.get("doi")
    pmid = ref.get("pmid")
    pmcid = ref.get("pmcid")

    if not doi and not pmid and not pmcid:
        return None

    pub_type_bt: list[PublicationType] | None = (
        pub_type if isinstance(pub_type, list) else [pub_type] if pub_type else None
    )

    return PublicationItem(
        doi=doi,
        pmid=pmid,
        pmcid=pmcid,
        type=pub_type_bt,
        note=None,
        version=None,
    )




def map_publication(
    gh_citation_cff: dict[str, Any], bt_publications: list[PublicationItem] | None
) -> list[PublicationItem] | None:
    """
    Map and reconcile GitHub CITATION.cff metadata and bio.tools publication entries.

    Policy:
    - If no CITATION.cff data is present, the existing bio.tools publication
      entries are unchanged.
    - If CITATION.cff data is present, its references are converted to
      bio.tools PublicationItem instances and merged with existing bio.tools
      entries. Duplicates are removed, prioritizing CITATION.cff entries.

    Parameters
    ----------
    gh_citation_cff : dict[str, Any]
        Parsed content of an existing CITATION.cff file from the GitHub
        repository.
    bt_publications : list[PublicationItem] | None
        Existing bio.tools publication entries, or ``None`` if none are defined.

    Returns
    -------
    list[PublicationItem] | None
        Updated list of bio.tools publication entries after reconciliation,
        or ``None`` if no publications are defined.
    """
    if not gh_citation_cff:
        logger.unchanged("No CITATION.cff data found in GitHub repository, nothing to map.")
        return bt_publications

    cff_references, cff_preferred = extract_cff_references(gh_citation_cff)

    gh_publications: list[PublicationItem] = []
    if cff_preferred:
        gh_publications.append(_cff_ref_to_biotools(cff_preferred, pub_type=PublicationType.Primary))
    gh_publications.extend([_cff_ref_to_biotools(ref) for ref in cff_references])
    gh_publications = [pub for pub in gh_publications if pub is not None]

    if not gh_publications:
        logger.unchanged("CITATION.cff exists but contains no references. Using only bio.tools metadata.")
        return bt_publications

    logger.added(f"{len(gh_publications)} reference(s) to merge with bio.tools metadata.")

    all_publications = gh_publications + (bt_publications or [])
    all_publications = deduplicate_references(all_publications)

    return all_publications