use GH cli to get list of neuron simulator models

Author: alexsavulescu

.github/workflows/nrn-modeldb-ci.yaml

@@ -130,6 +130,8 @@ jobs:
       id: install-deps
       run: |
         set
+        # Install GH cli
+        sudo apt-get install gh
         # Set up Xvfb
         sudo apt-get install xvfb
         sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem &  # run in bg

README.md

@@ -66,8 +66,6 @@ The following commands are now available:
   | MODELDB_RUN_FILE        | yaml file containing run instructions for models (required for `runmodels`) |
   | MODELDB_METADATA_FILE   | yaml file containing model info for those downloaded with `getmodels`       |
   | MODELS_ZIP_DIR          | location of cache folder for models populated via `getmodels`               |
-  | MDB_NEURON_MODELS_URL   | url used to get list of all NEURON model ids (necessary for `getmodels`)    |
-  | MDB_MODEL_DOWNLOAD_URL  | url template used for model downloading (cf `{model_id}`)                   |
 
 ## Model Run
 

modeldb/commands.py

@@ -142,7 +142,7 @@ def modeldb_config(args=None):
 
     Examples
         modeldb-config
-        modeldb-config --item=MDB_NEURON_MODELS_URL
+        modeldb-config --item=MODELS_ZIP_DIR
     """
     options = docopt(modeldb_config.__doc__, args)
     item = options.pop("--item", None)

modeldb/config.py

@@ -2,10 +2,6 @@
 
 import os
 
-MDB_NEURON_MODELS_URL = (
-    "http://modeldb.science/api/v1/models?modeling_application=NEURON"
-)
-
 ROOT_DIR = os.path.abspath(__file__ + "/../../")
 
 MODELS_ZIP_DIR = "%s/cache" % ROOT_DIR

modeldb/modeldb.py

@@ -11,6 +11,7 @@
 import traceback
 from pprint import pformat
 
+
 def download_model(arg_tuple):
     model_id, model_run_info = arg_tuple
     try:
@@ -60,11 +61,23 @@ def __init__(self):
         except Exception as e:
             raise e
 
+    def _gh_cli_get_neuron_simulator_repositories(self):
+        import subprocess
+
+        # Run the gh command to fetch the repository list and capture the output
+        command = ['gh', 'repo', 'list', 'modeldbrepository', '--topic', 'neuron-simulator', '--json', 'name', '-L', '2000']
+        output = subprocess.check_output(command, text=True)
+
+        # Parse the json output to get the repository names
+        import json
+        repositories = json.loads(output)
+        return [int(repository['name']) for repository in repositories]
+        
     def _download_models(self, model_list=None):
         if not os.path.isdir(MODELS_ZIP_DIR):
             logging.info("Creating cache directory: {}".format(MODELS_ZIP_DIR))
             os.mkdir(MODELS_ZIP_DIR)
-        models = requests.get(MDB_NEURON_MODELS_URL).json() if model_list is None else model_list
+        models = self._gh_cli_get_neuron_simulator_repositories() if model_list is None else model_list
         pool = multiprocessing.Pool()
         processed_models = pool.imap_unordered(
             download_model,