add upload_results as a config option

README.md

@@ -71,6 +71,21 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the
    each set of changes to `main` atomic and as a side effect naturally encourages small
    well defined PR's.
 
+## Introduction to Remote Databases 
+### AWS S3
+1. Pre-requisites
+   * Obtain an AWS account for AICS. Please contact the IT team or the code owner. 
+   * Generate an `aws_access_key_id` and `aws_secret_access_key` in your AWS account.
+
+2. Step-by-step Guide
+   * Download and install the [AWS CLI](https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html)
+   * Configure AWS CLI by running `aws configure`, then enter your credentials as prompted.
+   * Ensure that Boto3, the AWS SDK for Python is installed and included in the requirements section of `setup.py`. 
+
+### Firebase Firestore
+1. Step-by-step Guide
+   * Create a Firebase project in test mode with your google account, select `firebase_admin` as the SDK. [Firebase Firestore tutorial](https://firebase.google.com/docs/firestore)
+   * Generate a new private key by navigating to "Project settings">"Service account" in the project's dashboard.
 
 **MIT license**
 

cellpack/autopack/AWSHandler.py

@@ -0,0 +1,85 @@
+import logging
+from pathlib import Path
+
+import boto3
+from botocore.exceptions import ClientError
+
+
+class AWSHandler(object):
+    """
+    Handles all the AWS S3 operations
+    """
+
+    def __init__(
+        self,
+        bucket_name,
+        sub_folder_name=None,
+        region_name=None,
+    ):
+        self.bucket_name = bucket_name
+        self.folder_name = sub_folder_name
+        session = boto3.Session()
+        self.s3_client = session.client(
+            "s3",
+            endpoint_url=f"https://s3.{region_name}.amazonaws.com",
+            region_name=region_name,
+        )
+
+    def get_aws_object_key(self, object_name):
+        if self.folder_name is not None:
+            object_name = self.folder_name + object_name
+        else:
+            object_name = object_name
+        return object_name
+
+    def upload_file(self, file_path):
+        """Upload a file to an S3 bucket
+        :param file_path: File to upload
+        :param bucket: Bucket to upload to
+        :param object_name: S3 object name. If not specified then file_path is used
+        :return: True if file was uploaded, else False
+        """
+
+        file_name = Path(file_path).name
+
+        object_name = self.get_aws_object_key(file_name)
+        # Upload the file
+        try:
+            self.s3_client.upload_file(file_path, self.bucket_name, object_name)
+            self.s3_client.put_object_acl(
+                ACL="public-read", Bucket=self.bucket_name, Key=object_name
+            )
+
+        except ClientError as e:
+            logging.error(e)
+            return False
+        return file_name
+
+    def create_presigned_url(self, object_name, expiration=3600):
+        """Generate a presigned URL to share an S3 object
+        :param object_name: string
+        :param expiration: Time in seconds for the presigned URL to remain valid
+        :return: Presigned URL as string. If error, returns None.
+        """
+        object_name = self.get_aws_object_key(object_name)
+        # Generate a presigned URL for the S3 object
+        try:
+            url = self.s3_client.generate_presigned_url(
+                "get_object",
+                Params={"Bucket": self.bucket_name, "Key": object_name},
+                ExpiresIn=expiration,
+            )
+        except ClientError as e:
+            logging.error(e)
+            return None
+        # The response contains the presigned URL
+        # https://{self.bucket_name}.s3.{region}.amazonaws.com/{object_key}
+        return url
+
+    def save_file(self, file_path):
+        """
+        Uploads a file to S3 and returns the presigned url
+        """
+        file_name = self.upload_file(file_path)
+        if file_name:
+            return self.create_presigned_url(file_name)

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -1,9 +1,13 @@
 # -*- coding: utf-8 -*-
 # standardmodule
 import os
+import webbrowser
+from pathlib import Path
+
 import matplotlib
 import numpy as np
 import trimesh
+from botocore.exceptions import NoCredentialsError
 
 from simulariumio import (
     TrajectoryConverter,
@@ -19,6 +23,7 @@
 from simulariumio.constants import DISPLAY_TYPE, VIZ_TYPE
 
 from cellpack.autopack.upy import hostHelper
+from cellpack.autopack.AWSHandler import AWSHandler
 import collada
 
 
@@ -1335,6 +1340,7 @@ def writeToFile(self, file_name, bb, recipe_name, version):
             spatial_units=UnitData("nm"),  # nanometers
         )
         TrajectoryConverter(converted_data).save(file_name, False)
+        return file_name
 
     def raycast(self, **kw):
         intersect = False
@@ -1348,3 +1354,37 @@ def raycast(self, **kw):
 
     def raycast_test(self, obj, start, end, length, **kw):
         return
+
+    def post_and_open_file(self, file_name):
+        simularium_file = Path(f"{file_name}.simularium")
+        url = None
+        try:
+            url = simulariumHelper.store_results_to_s3(simularium_file)
+        except Exception as e:
+            aws_readme_url = "https://github.com/mesoscope/cellpack/blob/feature/main/README.md#aws-s3"
+            if isinstance(e, NoCredentialsError):
+                print(
+                    f"need to configure your aws account, find instructions here: {aws_readme_url}"
+                )
+            else:
+                print(
+                    f"An error occurred while storing the file {simularium_file} to S3: {e}"
+                )
+        if url is not None:
+            simulariumHelper.open_in_simularium(url)
+
+    @staticmethod
+    def store_results_to_s3(file_path):
+        handler = AWSHandler(
+            bucket_name="cellpack-results",
+            sub_folder_name="simularium/",
+            region_name="us-west-2",
+        )
+        url = handler.save_file(file_path)
+        return url
+
+    @staticmethod
+    def open_in_simularium(aws_url):
+        webbrowser.open_new_tab(
+            f"https://simularium.allencell.org/viewer?trajUrl={aws_url}"
+        )

cellpack/autopack/writers/__init__.py

@@ -172,7 +172,13 @@ def save_as_simularium(self, env, all_ingr_as_array, compartments):
                 env.helper.add_grid_data_to_scene(
                     f"{gradient.name}-weights", grid_positions, gradient.weight
                 )
-        env.helper.writeToFile(env.result_file, env.boundingBox, env.name, env.version)
+        file_name = env.helper.writeToFile(
+            env.result_file, env.boundingBox, env.name, env.version
+        )
+        if env.config_data is None or env.config_data.get(
+            "upload_results", env.config_data.get("number_of_packings", 1) <= 1
+        ):
+            autopack.helper.post_and_open_file(file_name)
 
     def save_Mixed_asJson(
         self,

cellpack/tests/packing-configs/test_parallel_config.json

@@ -14,5 +14,6 @@
     "number_of_packings": 5,
     "spacing":  null,
     "use_periodicity": false,
-    "show_sphere_trees": true
+    "show_sphere_trees": true,
+    "upload_results": false
 }

cellpack/tests/packing-configs/test_variable_count_config.json

@@ -13,5 +13,6 @@
     "spacing": null,
     "parallel": false,
     "use_periodicity": false,
-    "show_sphere_trees": true
+    "show_sphere_trees": true,
+    "upload_results": false
 }

examples/packing-configs/pcna_parallel_packing_config.json

@@ -16,5 +16,6 @@
     "show_progress_bar": true,
     "spacing": 2.5,
     "use_periodicity": false,
-    "show_sphere_trees": false
+    "show_sphere_trees": false,
+    "upload_results": false
 }

examples/packing-configs/peroxisome_packing_config.json

@@ -14,5 +14,6 @@
     "spacing": 2.5,
     "use_periodicity": false,
     "show_sphere_trees": false,
-    "load_from_grid_file": true
+    "load_from_grid_file": true,
+    "upload_results": false
 }

examples/packing-configs/peroxisome_parallel_packing_config.json

@@ -18,7 +18,8 @@
     "show_sphere_trees": false,
     "image_export_options": {
         "hollow": false,
-        "voxel_size": [1,1,1],
+        "voxel_size": [1, 1, 1],
         "projection_axis": "z"
-    }
+    },
+    "upload_results": false
 }

examples/packing-configs/run.json

@@ -13,5 +13,6 @@
     "use_periodicity": false,
     "show_sphere_trees": false,
     "load_from_grid_file": false,
-    "save_converted_recipe": true
+    "save_converted_recipe": true,
+    "upload_results": true
 }

setup.py

@@ -46,6 +46,7 @@
 ]
 
 requirements = [
+    "boto3>=1.28.3",
     "fire>=0.4.0",
     "firebase_admin>=6.0.1",
     "matplotlib>=3.3.4",