Proactively update Prefix.cc (#1056)

References
OBOFoundry/OBOFoundry.github.io#1038

.github/workflows/update_prefix_cc.yml

@@ -0,0 +1,22 @@
+name: Send data to Prefix.cc
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "5 4 * * *"  # run at 4:05 in the morning (cron format is minute hour day month day, check https://crontab.guru)
+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 fail to push refs to dest repo
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        run: pip install tox tox-uv
+
+      - name: Send a prefix to Prefix.cc
+        run: tox -e send-prefixcc

src/bioregistry/export/prefixcc.py

@@ -0,0 +1,56 @@
+"""Update Prefix.cc to reflect the content of the Bioregistry.
+
+.. seealso:: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1038
+"""
+
+import random
+
+import click
+import requests
+
+import bioregistry
+
+
+def create(curie_prefix: str, uri_prefix: str) -> requests.Response:
+    """Send a CURIE prefix/URI prefix to the Prefix.cc "create" endpoint."""
+    return requests.post(
+        f"https://prefix.cc/{curie_prefix}",
+        data={"create": uri_prefix},
+    )
+
+
+def main():
+    """Add an OBO Foundry prefix to Prefix.cc."""
+    prefix_cc_map = requests.get("https://prefix.cc/context").json()["@context"]
+    records = []
+    for record in bioregistry.resources():
+        if not record.get_obofoundry_prefix():
+            continue
+        uri_prefix = record.get_uri_prefix()
+        if not uri_prefix:
+            continue
+        if uri_prefix == prefix_cc_map.get(record.prefix):
+            # No need to re-create something that's already
+            # both available and correct wrt Bioregistry/OBO
+            continue
+        records.append(record)
+
+    if not records:
+        click.echo("No records left to submit to Prefix.cc, good job!")
+        return
+
+    click.echo(f"{len(records):,} records remain to submit to Prefix.cc")
+
+    # shuffle records to make sure that if there's an error, it doesn't
+    # lock the update permenantly
+    random.shuffle(records)
+
+    # Pick only the first record, since we can only make one update per day
+    record = records[0]
+    click.echo(f"Attempting to create a record for {record.prefix} {uri_prefix}")
+    res = create(record.prefix, uri_prefix)
+    click.echo(res.text)
+
+
+if __name__ == "__main__":
+    main()

tox.ini

@@ -121,6 +121,10 @@ description = Lint the Bioregistry data
 deps =
     mypy
     pydantic
+    types-PyYAML
+    types-Markdown
+    types-tabulate
+    types-requests
 skip_install = true
 commands = mypy --install-types --non-interactive --ignore-missing-imports src/bioregistry/
 description = Run the mypy tool to check static typing on the project.
@@ -197,6 +201,12 @@ commands =
     erdantic bioregistry.Registry bioregistry.Resource -o docs/img/datamodel_umls.svg
     erdantic bioregistry.Registry bioregistry.Resource -o docs/img/datamodel_umls.png
 
+[testenv:send-prefixcc]
+usedevelop = true
+commands =
+    python -m bioregistry.export.prefixcc
+description = Send a Bioregistry CURIE prefix/URI prefix pair to Prefix.cc via its "create" API endpoint. Note that only one request to this endpoint can be sent per day.
+
 ####################
 # Deployment tools #
 ####################