Add script to automatically remove accepted ontologies

.github/workflows/purge.yml

@@ -0,0 +1,37 @@
+name: Remove Accepted Ontologies
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * *"  # once per day
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install --upgrade setuptools wheel
+          pip install tox
+      - name: Update
+        run: |
+          tox -e purge
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add --all
+          git commit -m "Automatically remove accepted ontologies" -a
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

README.md

@@ -1,9 +1,21 @@
-# Repo to manage the OBO Foundry Dashboard for New Ontology Requests
+# Repo to manage the OBO Foundry Dashboard for New Ontology Requests (NORs)
 
 Page deployed at: https://obofoundry.github.io/obo-nor.github.io/
 
-To update:
+## Update
 
 1. change `dashboard-config.yml`
 2. run `sh run-dash.sh`
 
+## Remove accepted ontologies
+
+After ontologies have been accepted into the OBO Foundry, they will be displayed on the
+main [OBO Dashboard](https://dashboard.obofoundry.org/) and can be safely removed from the NOR dashboard. This is
+automated with the following code:
+
+```shell
+pip install tox
+tox -e purge
+```
+
+This is also automatically run nightly via GitHub Actions. [![Remove Accepted Ontologies](https://github.com/OBOFoundry/obo-nor.github.io/actions/workflows/purge.yml/badge.svg)](https://github.com/OBOFoundry/obo-nor.github.io/actions/workflows/purge.yml)

scripts/purge.py

@@ -0,0 +1,44 @@
+"""Purge accepted ontologies from NOR Dashboard."""
+
+from pathlib import Path
+
+import click
+import requests
+import yaml
+
+HERE = Path(__file__).parent.resolve()
+ROOT = HERE.parent.resolve()
+DASHBOARD_DIRECTORY = ROOT.joinpath("dashboard")
+DASHBOARD_CONFIG_PATH = ROOT.joinpath("dashboard-config.yml")
+
+URL = "https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml"
+
+
+@click.command()
+def main():
+    """Purge accepted ontologies from NOR Dashboard."""
+    #: A set of prefixes for active ontologies in the OBO Foundry
+    prefixes = {
+        record["id"]
+        for record in yaml.safe_load(requests.get(URL).content)["ontologies"]
+        if record["activity_status"] in {"active"}
+    }
+
+    # Remove folders corresponding to active ontologies
+    for directory in DASHBOARD_DIRECTORY.iterdir():
+        if directory.is_dir() and directory.name in prefixes:
+            for path in directory.iterdir():
+                click.echo(f"removing file: {path}")
+                path.unlink()
+            click.echo(f"removing directory: {directory}")
+            directory.rmdir()
+
+    # Remove configuration corresponding to active ontologies
+    config = yaml.safe_load(DASHBOARD_CONFIG_PATH.read_text())
+    config["ontologies"]["custom"] = [
+        row for row in config["ontologies"]["custom"] if row["id"] not in prefixes
+    ]
+
+
+if __name__ == "__main__":
+    main()

tox.ini

@@ -0,0 +1,22 @@
+[tox]
+envlist =
+    lint
+    purge
+
+[testenv:purge]
+skip_install = true
+deps =
+    click
+    requests
+    pyyaml
+commands =
+    python scripts/purge.py
+
+[testenv:lint]
+skip_install = true
+deps =
+    black
+    isort
+commands =
+    isort --profile=black .
+    black .