user-facing bridge process diagrams (for GitHub ⇄ bio.tools)

user-facing bridge process diagrams (for GitHub ⇄ bio.tools)#

The sequence diagram below shows how the bridge is invoked via the

  • command-line interface (CLI),

  • REST API, or

  • Python package

to synchronize metadata between a GitHub repository and a bio.tools record.

In the GitHub → bio.tools direction, repository metadata is retrieved from GitHub, optionally combined with existing bio.tools metadata, and processed by an internal pipeline to produce a bio.tools–compliant metadata record.

In the reverse bio.tools → GitHub direction, metadata is fetched from bio.tools and used to determine repository updates, resulting in a GitHub pull request and, optionally, issues creation.

Internal pipeline components are abstracted to emphasize the user-level interaction and high-level data flow.

        ---
config:
  theme: base
  look: neo
  themeVariables:
    darkMode: true
    background: "#121212"
    sequenceNumberColor: "#005a7a"
    actorBkg: "#005a7a"
    actorBorder: "#005a7a"
    actorLineColor: "#005a7a"
    activationBkgColor: "#1099c9"
    activationBorderColor: "#1099c9"
    labelBoxBorderColor: "#5DD3FC"
    loopTextColor: "#5DD3FC"
    labelTextColor: "#5DD3FC"
    noteBkgColor: "#F47D22"
    noteBorderColor: "#F47D22"
    noteTextColor: "#fff"
---
sequenceDiagram
  autonumber
  actor User
  participant Bridge as Bridge
  participant GitHub
  participant BioTools as bio.tools
  participant Pipeline

  alt GitHub → bio.tools (CLI)
    User->>Bridge: bridge cli<br/>github-to-biotools extract<br/>--owner O --repo R [--biotools-id ID]
  else GitHub → bio.tools (API)
    User-)Bridge: POST<br/>/github-to-biotools<br/>{owner, repo, biotools_id?}
  else GitHub → bio.tools (Python)
    User-)Bridge: import bridge<br/>await bridge.extract_meta_from_repo<br/>(schema="biotools", repo_type="github", owner=O, repo=R, identifier=ID?)
  else bio.tools → GitHub (CLI)
    User->>Bridge: bridge cli<br/>biotools-to-github update<br/>--biotools-id ID --owner O --repo R [--allow-issues]
  else bio.tools → GitHub (API)
    User-)Bridge: POST<br/>/biotools-to-github<br/>{biotools_id, owner, repo, allow_issues?}
  else bio.tools → GitHub (Python)
    User-)Bridge: import bridge<br/>await bridge.create_pr_issues_from_meta<br/>(schema="biotools", repo_type="github", identifier=ID, owner=O, repo=R, allow_issues=?)
  end

  alt GitHub → bio.tools
    Bridge-)GitHub: Fetch repo metadata
    opt If bio.tools ID provided
      Bridge-)BioTools: Fetch existing tool metadata
    end
    Bridge-)Pipeline: Create/update tool record fields
    Pipeline-->>Bridge: bio.tools tool metadata
    Bridge-->>User: bio.tools metadata JSON
  else bio.tools → GitHub
    Bridge-)GitHub: Fetch repo metadata
    Bridge-)BioTools: Fetch tool metadata
    Bridge-)Pipeline: Determine PR + (optional) issues
    Pipeline-->>Bridge: File changes for PR + issues list
    Bridge-)GitHub: Open PR with file changes
    opt If issues enabled
      Bridge-)GitHub: Create issues for missing info
    end
    GitHub-->>Bridge: PR (and issues) info
    Bridge-->>User: PR (and issues) info
  end

TBD#

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