store results to S3 and firebase

cellpack/autopack/AWSHandler.py

@@ -0,0 +1,42 @@
+import logging
+import boto3
+from botocore.exceptions import ClientError
+import os
+
+class AWSHandler(object):
+    """
+    Handles all the AWS S3 operations
+    """
+
+    def __init__(self, bucket_name, aws_access_key_id=None, aws_secret_access_key=None, region_name=None):
+        self.bucket_name = bucket_name
+        self.s3_client = boto3.client(
+            's3',
+            aws_access_key_id=aws_access_key_id,
+            aws_secret_access_key=aws_secret_access_key, # TODO: check how do we want to handle credentials?
+            region_name=region_name
+        )
+
+
+    def upload_file(self, file_name, folder_name=None, object_name=None):
+        """Upload a file to an S3 bucket
+
+        :param file_name: File to upload
+        :param bucket: Bucket to upload to
+        :param object_name: S3 object name. If not specified then file_name is used
+        :return: True if file was uploaded, else False
+        """
+
+        # If S3 object_name was not specified, use file_name
+        if object_name is None:
+            object_name = folder_name + os.path.basename(file_name)
+        else:
+            object_name = folder_name + object_name
+
+        # Upload the file
+        try:
+            response = self.s3_client.upload_file(file_name, self.bucket_name, object_name)
+        except ClientError as e:
+            logging.error(e)
+            return False
+        return True

cellpack/autopack/FirebaseHandler.py

@@ -42,6 +42,14 @@ def get_creds():
         if creds is None or "firebase" not in creds:
             creds = FirebaseHandler.write_creds_path()
         return creds["firebase"]
+
+    @staticmethod
+    def get_username():
+        creds = read_json_file("./.creds")
+        try:
+            return creds["username"]
+        except KeyError:
+            raise ValueError("No username found in .creds file")
 
     def db_name(self):
         return self.name
@@ -53,6 +61,10 @@ def doc_id(doc):
     @staticmethod
     def create_path(collection, doc_id):
         return f"firebase:{collection}/{doc_id}"
+
+    @staticmethod
+    def create_timestamp():
+        return firestore.SERVER_TIMESTAMP
 
     @staticmethod
     def get_path_from_ref(doc):

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -17,13 +17,12 @@
 )
 from simulariumio.cellpack import CellpackConverter, HAND_TYPE
 from simulariumio.constants import DISPLAY_TYPE, VIZ_TYPE
+from cellpack.autopack.FirebaseHandler import FirebaseHandler
 
 from cellpack.autopack.upy import hostHelper
+from cellpack.autopack.AWSHandler import AWSHandler
 import collada
 
-import boto3
-import logging
-
 
 class Instance:
     def __init__(self, name, instance_id, unique_id, radius, viz_type, mesh=None):
@@ -1334,8 +1333,11 @@ def writeToFile(self, file_name, bb, recipe_name, version):
             time_units=UnitData("ns"),  # nanoseconds
             spatial_units=UnitData("nm"),  # nanometers
         )
-        print("simularium helper---", vars(converted_data))
         TrajectoryConverter(converted_data).save(file_name, False)
+        print("file--", file_name)
+        simularium_file = file_name + ".simularium"
+        print("sim_file", simularium_file)
+        # simulariumHelper.store_results_to_s3(simularium_file,folder_name="simularium/")
 
     def raycast(self, **kw):
         intersect = False
@@ -1350,15 +1352,28 @@ def raycast(self, **kw):
     def raycast_test(self, obj, start, end, length, **kw):
         return
 
-    # def store_results_in_s3(bucket_name, file_name, object_name=None):
-    #     if object_name is None:
-    #         object_name = file_name
-
-    #     s3_client = boto3.client("3s")
-    #     try:
-    #         response = s3_client.upload_file(file_name, bucket_name, object_name)
-    #     except ClientError as e:
-    #         logging.error(e)
-    #         return False
-    #     return True
+    @staticmethod
+    def store_results_to_s3(file_name, folder_name=None, object_name=None):
+        handler = AWSHandler(
+            bucket_name="cellpack-results",
+            aws_access_key_id=os.environ.get("AWS_ACCESS_KEY_ID"),
+            aws_secret_access_key=os.environ.get("AWS_SECRET_ACCESS_KEY"),
+            region_name="us-west-2",
+        )
+        print(handler.upload_file(file_name,folder_name,object_name))
+
+    def upload_metadata_to_firebase(result_name, aws_url):
+        db = FirebaseHandler()
+        username = db.get_username()
+        timestamp = db.create_timestamp()
+        db.set_doc(
+            "results", 
+            result_name,
+            {
+            "user": username,
+            "created": timestamp,
+            "aws_url": aws_url
+            }
+        )
+    upload_metadata_to_firebase("testing result2", "testing_url2")