Source code for bridge.pipelines.gh2bt_for_meta.main

"""
Implements the GitHub→bio.tools metadata pipeline:
derives a BiotoolsToolModel from a GitHubRepoModel.
"""

import base64
import logging
import urllib

from bridge.config import settings
from bridge.core import BiotoolsToolModel, GitHubRepoModel
from bridge.pipelines.protocols import PipelineArgs

from .map import MapGitHub2BioTools

logger = logging.getLogger(__name__)




class GitHubToBiotoolsForMetaPipelineArgs(PipelineArgs):
    """
    Pipeline argument model for the GitHub to bio.tools for metadata pipeline.

    Parameters
    ----------
    repo_model : GitHubRepoModel
        The source GitHub repository model.
    repo_path : str
        The local path to the cloned GitHub repository.
    existing_metadata : BiotoolsToolModel | None
        Existing bio.tools metadata model, if available. Default is None.
    """

    repo_model: GitHubRepoModel
    repo_path: str
    existing_metadata: BiotoolsToolModel | None = None





async def run(args: GitHubToBiotoolsForMetaPipelineArgs) -> BiotoolsToolModel:
    """
    Run the pipeline to extract bio.tools metadata from a GitHub repository.

    Parameters
    ----------
    args : GitHubToBiotoolsForMetaPipelineArgs
        The pipeline arguments containing the GitHub repository model and existing bio.tools metadata.

    Returns
    -------
    BiotoolsToolModel
        The extracted or updated bio.tools metadata model.
    """
    logger.info(f"Running GitHub → bio.tools metadata pipeline for repo {args.repo_model.repo.name}")

    github_repo = args.repo_model

    mapper = MapGitHub2BioTools(
        repo=github_repo,
        metadata=args.existing_metadata,
        repo_path=args.repo_path,
    )

    biotools_metadata = BiotoolsToolModel(
        biotoolsID=await mapper.map["biotools_id"].run(),
        name=await mapper.map["name"].run(),
        description=((await mapper.map["description"].run()) or "***Please change this description***"),
        homepage=await mapper.map["homepage"].run(),
        maturity=await mapper.map["maturity"].run(),
        language=await mapper.map["language"].run(),
        license=await mapper.map["license"].run(),
        version=await mapper.map["version"].run(),
        documentation=await mapper.map["documentation"].run(),
        publication=await mapper.map["publication"].run(),
    )

    biotools_url = settings.biotools_url
    logger.info(args.existing_metadata)
    logger.info(f"Extracted bio.tools metadata for repo {github_repo.repo.name}")

    json_bytes = biotools_metadata.model_dump_json().encode("utf-8")
    b64 = base64.b64encode(json_bytes).decode("ascii")
    encoded_json = urllib.parse.quote(b64)

    if args.existing_metadata is not None:
        logger.info(
            f"\n\n*** 🛠  Want to update the bio.tools entry for this repo? "
            f"(You must have edit permissions on this tool in bio.tools) ***\n"
            f"🚀 (1) Log in to {biotools_url}\n"
            f"✨ (2) click the following link:\n\n"
            f"{biotools_url}/{args.existing_metadata.name}/edit?json={encoded_json}\n"
        )
    else:
        logger.info(
            f"\n\n*** 🛠  Want to create a bio.tools entry for this repo? ***\n"
            f"🚀 (1) Log in to {biotools_url}\n"
            f"✨ (2) click the following link:\n\n"
            f"{biotools_url}/register?json={encoded_json}\n"
        )

    return biotools_metadata