bridge.pipelines package

Public Interface

This section documents user-facing interface of the bridge.pipelines package (as defined in its __init__.py file).

Functions

run_bt2gh_pipeline_for_pr_issues(args)	Run the pipeline to generate repository file changes based on bio.tools metadata.
run_gh2bt_pipeline_for_meta(args)	Run the pipeline to extract bio.tools metadata from a GitHub repository.

Classes

PipelineGoal(*values)	Enumeration of possible pipeline goals.
BiotoolsToGitHubForPRPipelineArgs(**data)	Pipeline argument model for the bio.tools to GitHub for PR pipeline.
GitHubToBiotoolsForMetaPipelineArgs(**data)	Pipeline argument model for the GitHub to bio.tools for metadata pipeline.

End-to-end pipelines that implement the bridge’s directional workflows. Exposes run functions for the pipelines and argument models.

class bridge.pipelines.BiotoolsToGitHubForPRPipelineArgs(**data)

Bases: PipelineArgs

Pipeline argument model for the bio.tools to GitHub for PR pipeline.

Parameters:

• repo_path (str) – Path to the cloned GitHub repository to make changes in.

• metadata_model (BiotoolsToolModel) – The source bio.tools metadata model.

• existing_repo_model (GitHubRepoModel)

existing_repo_model: GitHubRepoModel

metadata_model: ToolModel

repo_path: str

class bridge.pipelines.GitHubToBiotoolsForMetaPipelineArgs(**data)

Bases: 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.

existing_metadata: ToolModel | None

repo_model: GitHubRepoModel

repo_path: str

class bridge.pipelines.PipelineGoal(*values)

Bases: str, Enum

Enumeration of possible pipeline goals.

CREATE_PR_ISSUES

Goal to create a pull request and issues in a repository based on source metadata.

Type:

str

EXTRACT_METADATA

Goal to extract metadata from a repository.

Type:

str

async bridge.pipelines.run_bt2gh_pipeline_for_pr_issues(args)

Run the pipeline to generate repository file changes based on bio.tools metadata.

Parameters:

args (BiotoolsToGitHubForPRPipelineArgs) – The pipeline arguments containing a path to the cloned GitHub repository and metadata model.

Returns:

A dictionary mapping file paths to their new content, and a dictionary mapping issue titles to their bodies.

Return type:

tuple[dict, dict]

async bridge.pipelines.run_gh2bt_pipeline_for_meta(args)

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:

The extracted or updated bio.tools metadata model.

Return type:

BiotoolsToolModel

Subpackages

bt2gh_for_pr_issues	Pipeline package for generating repository changes (PR-ready for GitHub) from bio.tools metadata.
gh2bt_for_meta	Pipeline package for extracting (or updating) bio.tools metadata from a GitHub repository.
policies	Generic reconciliation policies.
protocols	Protocol and base classes for pipeline argument models consumed by pipeline run functions.
shared	Shared components for mapping functions across pipelines.
utils	Utilities for pipelines.

Submodules

goals

Enumeration of supported pipeline goals used to bind handlers to pipeline implementations.

Dependencies diagram

Each architecture diagram below visualizes the internal dependency structure of the bridge.pipelines package. It shows how modules and subpackages within the package depend on each other, based on direct Python imports.

• Packages are shown as purple rectangles

• Modules are shown as pink rectangles

• Arrows (A → B) indicate that A directly imports B

Each subpackage’s diagram focuses only on its own internal structure, it does not include imports to or from higher-level packages (those appear in the parent package’s diagram).