add auto check for updates to prebuilt UShER tree

README.md

@@ -91,3 +91,5 @@ The Nextstrain Auspice JSON files are placed in [./auspice/](auspice), where the
 ## Re-running the pipeline as data are updated
 As the [pre-built UShER tree](https://hgdownload.gi.ucsc.edu/hubs/GCF/000/864/105/GCF_000864105.1/UShER_NC_007362.1/) is updated, you will want to re-run the pipeline.
 To do that, just remove the contents of the [./results/](results), [./docs/](docs), and [./auspice](auspice) subidirectories and then just re-run the pipeline.
+
+The script [check_for_prebuilt_usher_update.py](check_for_prebuilt_usher_update.py) can be set up to run using `crontab -e` to check for such updates.

check_for_prebuilt_usher_update.py

@@ -0,0 +1,55 @@
+"""Check if UShER pre-built tree has been updated.
+
+This script is designed to be run as a cron job to indicate if the
+UShER pre-built tree has been updated, which means the repo should
+be re-run.
+
+Note it reads the Slack webhook from a file not tracked in this repo.
+
+After creating that webhook file and giving it a valid Slack webhook,
+add a line like the following via ``crontab -e``:
+
+    0 5 * * * python3 <full_path>/check_for_prebuilt_usher_update.py
+
+"""
+
+
+import json
+import os
+import urllib.request
+
+
+currdir = os.path.dirname(__file__)
+
+
+with open(os.path.join(currdir, "results/usher_prebuilt/version_info.txt")) as f:
+    existing_version = f.read()
+
+response = urllib.request.urlopen("https://hgdownload.gi.ucsc.edu/hubs/GCF/000/864/105/GCF_000864105.1/UShER_NC_007362.1/fluA.GCF_000864105.1.NC_007362.1.latest.version.txt")
+new_version = response.read().decode("utf-8")
+
+if existing_version == new_version:
+    msg = "UShER H5N1 version unchanged"
+else:
+    msg = f"UShER H5N1 version has **changed**"
+
+msg += "\n\nnew_version=" + new_version + "\nexisting_version=" + existing_version + "\n"
+
+print(msg)
+
+with open(os.path.join(currdir, "_Slack_webhook_url.txt")) as f:
+    webhook_url = f.read()
+
+payload = {"text": msg}
+data = json.dumps(payload).encode("utf-8")
+req = urllib.request.Request(
+    webhook_url,
+    data=data,
+    headers={'Content-Type': 'application/json'}
+)
+
+with urllib.request.urlopen(req) as response:
+    if response.status == 200:
+        print("Message sent successfully.")
+    else:
+        raise ValueError(f"Failed to send message. Status code: {response.status}")