Fastapi integration

.github/scripts/convert_airtable_to_json.py

@@ -6,35 +6,50 @@
 import requests
 
 AIRTABLE_MODEL_HUB_BASE_ID = "appgxpCzCDNyGjWc8"
-AIRTABLE_TABLE_ID = 'tblZGe2a2XeBxrEHP'
+AIRTABLE_TABLE_ID = "tblZGe2a2XeBxrEHP"
 AWS_ACCOUNT_REGION = "eu-central-1"
-ERSILIA_MODEL_HUB_S3_BUCKET= 'ersilia-model-hub'
+ERSILIA_MODEL_HUB_S3_BUCKET = "ersilia-model-hub"
 
-def convert_airtable_to_json(airtable_api_key, aws_access_key_id, aws_secret_access_key):
-
-    headers = {'Authorization': f'Bearer {airtable_api_key}'}
-    response= requests.get(f'https://api.airtable.com/v0/{AIRTABLE_MODEL_HUB_BASE_ID}/{AIRTABLE_TABLE_ID}', headers=headers)
 
-    data=response.json()
-    records_models= [record['fields'] for record in data['records']]
-    models_json=json.dumps(records_models, indent=4)
+def convert_airtable_to_json(
+    airtable_api_key, aws_access_key_id, aws_secret_access_key
+):
+    headers = {"Authorization": f"Bearer {airtable_api_key}"}
+    response = requests.get(
+        f"https://api.airtable.com/v0/{AIRTABLE_MODEL_HUB_BASE_ID}/{AIRTABLE_TABLE_ID}",
+        headers=headers,
+    )
 
-    #Load JSON in AWS S3 bucket
-    s3 = boto3.client('s3',aws_access_key_id=aws_access_key_id,aws_secret_access_key=aws_secret_access_key,region_name=AWS_ACCOUNT_REGION)
+    data = response.json()
+    records_models = [record["fields"] for record in data["records"]]
+    models_json = json.dumps(records_models, indent=4)
+
+    # Load JSON in AWS S3 bucket
+    s3 = boto3.client(
+        "s3",
+        aws_access_key_id=aws_access_key_id,
+        aws_secret_access_key=aws_secret_access_key,
+        region_name=AWS_ACCOUNT_REGION,
+    )
     try:
-        s3.put_object(Body=models_json, Bucket=ERSILIA_MODEL_HUB_S3_BUCKET, Key='models.json', ACL='public-read')
+        s3.put_object(
+            Body=models_json,
+            Bucket=ERSILIA_MODEL_HUB_S3_BUCKET,
+            Key="models.json",
+            ACL="public-read",
+        )
         print("file models.json uploaded")
     except NoCredentialsError:
         logging.error("Unable to upload tracking data to AWS: Credentials not found")
     except ClientError as e:
         logging.error(e)
-
-if __name__ == "__main__":
 
+
+if __name__ == "__main__":
     print("Getting environmental variables")
-    airtable_api_key = os.environ.get('AIRTABLE_API_KEY')
-    aws_access_key_id = os.environ.get('AWS_ACCESS_KEY_ID')
-    aws_secret_access_key = os.environ.get('AWS_SECRET_ACCESS_KEY')
+    airtable_api_key = os.environ.get("AIRTABLE_API_KEY")
+    aws_access_key_id = os.environ.get("AWS_ACCESS_KEY_ID")
+    aws_secret_access_key = os.environ.get("AWS_SECRET_ACCESS_KEY")
 
     print("Converting AirTable base to JSON file")
     convert_airtable_to_json(airtable_api_key, aws_access_key_id, aws_secret_access_key)

.github/scripts/place_a_dockerfile_in_current_eos_repo.py

@@ -25,4 +25,4 @@ def download_file(url, filename):
 text = text.replace("eos_identifier", model_id)
 
 with open("Dockerfile", "w") as f:
-    f.write(text)
+    f.write(text)

.github/scripts/update_metadata.py

@@ -106,10 +106,12 @@ def populate_metadata(self):
             # Check if model_description is a list
             if isinstance(self.json_input["model_description"], list):
                 # Join the list elements into a single string separated by commas
-                self.metadata["Description"] = ", ".join(self.json_input["model_description"])
+                self.metadata["Description"] = ", ".join(
+                    self.json_input["model_description"]
+                )
             else:
                 # If it's already a string, just assign it directly
-                self.metadata["Description"] = self.json_input["model_description"] 
+                self.metadata["Description"] = self.json_input["model_description"]
         if self.metadata["Publication"] == "":
             self.metadata["Publication"] = self.json_input["publication"]
         if self.metadata["Source Code"] == "":

ersilia/_version.py

@@ -33,11 +33,13 @@ def get_latest_semver_tag():
                     return tag
     return None
 
+
 def increment_patch_version(version):
     version = version.split(".")
     version[2] = str(int(version[2]) + 1)
     return ".".join(version)
 
+
 def get_version_for_setup():
     # version = get_latest_semver_tag()
     version = increment_patch_version(get_version_from_static())

ersilia/auth/auth.py

@@ -2,6 +2,7 @@
 Deal with privileges in Ersilia.
 Base on GitHub login.
 """
+
 from pathlib import Path
 import os
 import yaml

ersilia/cli/commands/close.py

@@ -4,7 +4,7 @@
 from .. import echo
 from ... import ErsiliaModel
 from ...core.session import Session
-from ...core.tracking import check_file_exists,  close_persistent_file
+from ...core.tracking import check_file_exists, close_persistent_file
 
 
 def close_cmd():
@@ -23,4 +23,4 @@ def close():
 
         # Close our persistent tracking file
         if check_file_exists(model_id):
-           close_persistent_file(mdl.model_id)
+            close_persistent_file(mdl.model_id)

ersilia/cli/commands/example.py

@@ -20,7 +20,7 @@ def example_cmd():
     @click.option("--n_samples", "-n", default=5, type=click.INT)
     @click.option("--file_name", "-f", default=None, type=click.STRING)
     @click.option("--simple/--complete", "-s/-c", default=True)
-    @click.option("--predefined/--random", "-p/-r", default=False)
+    @click.option("--predefined/--random", "-p/-r", default=True)
     def example(model, n_samples, file_name, simple, predefined):
         if model is not None:
             model_id = ModelBase(model).model_id

ersilia/cli/commands/fetch.py

@@ -31,7 +31,7 @@ def _fetch(mf, model_id):
         "--from_dir",
         default=None,
         type=click.STRING,
-        help="Local path where the model is stored"
+        help="Local path where the model is stored",
     )
     @click.option(
         "--from_github",
@@ -60,6 +60,18 @@ def _fetch(mf, model_id):
         default=None,
         help="Fetch a model based on a URL. This only creates a basic folder structure for the model, the model is not actually downloaded.",
     )
+    @click.option(
+        "--with_bentoml",
+        is_flag=True,
+        default=False,
+        help="Force fetch using BentoML",
+    )
+    @click.option(
+        "--with_fastapi",
+        is_flag=True,
+        default=False,
+        help="Force fetch using FastAPI",
+    )
     def fetch(
         model,
         repo_path,
@@ -72,7 +84,11 @@ def fetch(
         from_s3,
         from_hosted,
         from_url,
+        with_bentoml,
+        with_fastapi,
     ):
+        if with_bentoml and with_fastapi:
+            raise Exception("Cannot use both BentoML and FastAPI")
         if repo_path is not None:
             mdl = ModelBase(repo_path=repo_path)
         elif from_dir is not None:
@@ -94,6 +110,8 @@ def fetch(
             force_from_s3=from_s3,
             force_from_dockerhub=from_dockerhub,
             force_from_hosted=from_hosted,
+            force_with_bentoml=with_bentoml,
+            force_with_fastapi=with_fastapi,
             hosted_url=from_url,
         )
         _fetch(mf, model_id)

ersilia/cli/commands/run.py

@@ -41,7 +41,7 @@ def run(input, output, batch_size, standard):
                 fg="red",
             )
             return
-        
+
         mdl = ErsiliaModel(
             model_id,
             service_class=service_class,
@@ -64,17 +64,11 @@ def run(input, output, batch_size, standard):
                     echo("Something went wrong", fg="red")
         else:
             echo(result)
-            
+
         if track_runs:
             """
-            Retrieve the time taken to run the model and update the total. 
+            Retrieve the time taken to run the model and update the total.
             """
-            time_tracker = RunTracker(
-            model_id=model_id,
-            config_json=None
-            )
-
-            time_tracker.update_total_time(
-            model_id=model_id,
-            start_time=start_time
-            )      
+            time_tracker = RunTracker(model_id=model_id, config_json=None)
+
+            time_tracker.update_total_time(model_id=model_id, start_time=start_time)

ersilia/cli/commands/serve.py

@@ -47,8 +47,7 @@ def serve(model, lake, docker, port, track):
         )
         if not mdl.is_valid():
             ModelNotFound(mdl).echo()
-
-
+
         mdl.serve()
         if mdl.url is None:
             echo("No URL found. Service unsuccessful.", fg="red")
@@ -73,7 +72,7 @@ def serve(model, lake, docker, port, track):
         echo("")
         echo(":person_tipping_hand: Information:", fg="blue")
         echo("   - info", fg="blue")
-        
+
         if track:
             """
             Retrieve the time taken in seconds to serve the Model.

ersilia/core/base.py

@@ -2,6 +2,7 @@
 import subprocess
 from pathlib import Path
 from ..utils.config import Config, Credentials
+from ..utils.paths import resolve_pack_method
 from ..default import EOS
 from .. import logger
 
@@ -89,8 +90,10 @@ def _get_bundle_location(self, model_id):
         else:
             return path
 
-    @staticmethod
-    def _get_bento_location(model_id):
+    def _get_bento_location(self, model_id):
+        bundle_path = self._get_bundle_location(model_id)
+        if resolve_pack_method(bundle_path) != "bentoml":
+            return None
         cmd = ["bentoml", "get", "%s:latest" % model_id, "--print-location", "--quiet"]
         result = subprocess.run(cmd, stdout=subprocess.PIPE)
         result = result.stdout.decode("utf-8").rstrip()

ersilia/core/model.py

@@ -445,7 +445,6 @@ def get_apis(self):
     def _run(
         self, input=None, output=None, batch_size=DEFAULT_BATCH_SIZE, track_run=False
     ):
-
         api_name = self.get_apis()[0]
         result = self.api(
             api_name=api_name, input=input, output=output, batch_size=batch_size
@@ -498,9 +497,7 @@ def run(
             )
         # Start tracking model run if track flag is used in serve
         if self._run_tracker is not None and track_run:
-            self._run_tracker.track(
-                input=input, result=result, meta=self._model_info
-            )
+            self._run_tracker.track(input=input, result=result, meta=self._model_info)
             self._run_tracker.log(result=result, meta=self._model_info)
         return result