Feature/client upload script

cellpack/autopack/DBRecipeHandler.py

@@ -515,6 +515,7 @@ def upload_recipe(self, recipe_meta_data, recipe_data):
         recipe_to_save = self.upload_collections(recipe_meta_data, recipe_data)
         recipe_to_save["recipe_path"] = self.db.create_path("recipes", recipe_id)
         self.upload_data("recipes", recipe_to_save, recipe_id)
+        return recipe_id
 
     def upload_config(self, config_data, source_path):
         """
@@ -526,7 +527,7 @@ def upload_config(self, config_data, source_path):
         # update the config data with the firebase doc path
         config_data["config_path"] = doc_path
         self.db.update_doc("configs", id, config_data)
-        return
+        return id
 
     def upload_result_metadata(self, file_name, url, job_id=None):
         """

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -1394,21 +1394,23 @@ def post_and_open_file(self, file_name, open_results_in_browser=True):
                 simulariumHelper.open_in_simularium(url)
 
     @staticmethod
-    def store_result_file(file_path, storage=None, batch_job_id=None):
+    def store_result_file(
+        file_path, storage=None, batch_job_id=None, sub_folder="simularium"
+    ):
         if storage == "aws":
             handler = DATABASE_IDS.handlers().get(storage)
             # if batch_job_id is not None, then we are in a batch job and should use the temp bucket
             # TODO: use cellpack-results bucket for batch jobs once we have the correct permissions
             if batch_job_id:
                 initialized_handler = handler(
                     bucket_name="cellpack-demo",
-                    sub_folder_name="simularium",
+                    sub_folder_name=sub_folder,
                     region_name="us-west-2",
                 )
             else:
                 initialized_handler = handler(
                     bucket_name="cellpack-results",
-                    sub_folder_name="simularium",
+                    sub_folder_name=sub_folder,
                     region_name="us-west-2",
                 )
             file_name, url = initialized_handler.save_file_and_get_url(file_path)

cellpack/bin/upload.py

@@ -1,9 +1,10 @@
 import sys
 import fire
+import json
 
 from cellpack.autopack.FirebaseHandler import FirebaseHandler
 from cellpack.autopack.DBRecipeHandler import DBUploader, DBMaintenance
-
+from cellpack.autopack.upy.simularium.simularium_helper import simulariumHelper
 from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS
 from cellpack.autopack.loaders.config_loader import ConfigLoader
 from cellpack.autopack.loaders.recipe_loader import RecipeLoader
@@ -32,12 +33,40 @@ def upload(
     recipe_path=None,
     config_path=None,
     db_id=DATABASE_IDS.FIREBASE,
+    studio: bool = False,
+    fields: str = None,
+    name: str = None,
+    output_file: str = None,
 ):
     """
     Uploads a recipe to the database
 
+    :param recipe: string argument
+    path to local recipe file to upload to firebase
+    :param config: string argument
+    path to local config file to upload to firebase
+    :param db_id: string argument
+    database ID to use for the upload
+    :param studio: boolean argument
+    upload for use in cellPACK studio if True
+    :param fields: string argument
+    path to local editable fields file to upload to firebase
+    :param name: string argument
+    display name for recipe in studio selection menu
+    :param output_file: string argument
+    path to local simularium output file to upload
+
     :return: void
     """
+    if studio and (not name or not recipe_path or not fields):
+        sys.exit(
+            "To upload a recipe for cellPACK studio, please provide --name, --recipe_path, and --fields arguments."
+        )
+
+    recipe_id = ""
+    config_id = ""
+    result_url = ""
+    editable_fields_ids = []
     if db_id == DATABASE_IDS.FIREBASE:
         # fetch the service key json file
         db_handler = FirebaseHandler()
@@ -47,10 +76,29 @@ def upload(
                 recipe_loader = RecipeLoader(recipe_path)
                 recipe_full_data = recipe_loader._read(resolve_inheritance=False)
                 recipe_meta_data = get_recipe_metadata(recipe_loader)
-                db_handler.upload_recipe(recipe_meta_data, recipe_full_data)
+                recipe_id = db_handler.upload_recipe(recipe_meta_data, recipe_full_data)
             if config_path:
                 config_data = ConfigLoader(config_path).config
-                db_handler.upload_config(config_data, config_path)
+                config_id = db_handler.upload_config(config_data, config_path)
+            if fields:
+                editable_fields_data = json.load(open(fields, "r"))
+                for field in editable_fields_data.get("editable_fields", []):
+                    id, _ = db_handler.upload_data("editable_fields", field)
+                    editable_fields_ids.append(id)
+            if output_file:
+                _, result_url = simulariumHelper.store_result_file(
+                    output_file, storage="aws", sub_folder="client"
+                )
+            if studio:
+                recipe_metadata = {
+                    "name": name,
+                    "recipe": recipe_id,
+                    "config": config_id,
+                    "editable_fields": editable_fields_ids,
+                    "result_path": result_url,
+                }
+                # Upload the combined recipe metadata to example_packings collection for studio
+                db_handler.upload_data("example_packings", recipe_metadata)
 
         else:
             db_maintainer = DBMaintenance(db_handler)

docs/STUDIO_SITE.md

@@ -0,0 +1,14 @@
+# cellPACK Studio Site
+
+cellPACK studio allows users to edit example recipes, run packings, and visualize results in the browser.
+
+* Production site: https://cellpack.allencell.org/
+* GitHub repository: https://github.com/AllenCell/cellpack-client
+
+### Publishing Recipes to cellPACK Studio
+To add new example recipes to the client site, the recipe and its associated metadata must be uploaded to Firebase.
+
+1. Set up access to the staging Firebase account, following [these instructions](https://github.com/mesoscope/cellpack/blob/main/docs/REMOTE_DATABASES.md#firebase-firestore)
+2. Determine which recipe fields should be editable in the client, and create a JSON file specifying these editable fields following the schema outlined in [this example](https://github.com/mesoscope/cellpack/blob/0f140859824086d73edab008ff381b5e5717db8b/examples/client-data/example_editable_fields.json)
+3. Follow cellPACK installation requirements [in README](https://github.com/mesoscope/cellpack?tab=readme-ov-file#installation)
+4. Run the following script to upload necessary files to Firebase: `upload -s -r <path_to_recipe_file> -c <path_to_config_file> -f <path_to_editable_fields_file> -n "Name of Recipe" -o <local_path_to_simularium_result_file>`

examples/client-data/example_editable_fields.json

@@ -0,0 +1,70 @@
+{
+  "editable_fields": [
+    {
+        "name": "Display Name",
+        "description": "Description text",
+        "path": "path.to.field.in.recipe.json",
+        "data_type": "integer/float/string",
+        "input_type": "slider/dropdown/gradient"
+    },
+    {
+        "name": "Endosome Count",
+        "description": "Number of spheres to be packed",
+        "path": "composition.membrane.regions.interior.1.count",
+        "data_type": "integer",
+        "input_type": "slider",
+        "min": 0,
+        "max": 300
+    },
+    {
+        "name": "Endosome Radius",
+        "description": "Radius of spheres",
+        "path": "objects.endosome.radius",
+        "data_type": "float",
+        "input_type": "slider",
+        "min": 0,
+        "max": 10,
+        "unit": "µm",
+        "conversion_factor": 0.108
+    },
+    {
+        "name": "Spatial Distribution Rule",
+        "description": "Choose from one of the listed gradient types",
+        "path": "objects.endosome.gradient",
+        "data_type": "gradient",
+        "input_type": "gradient",
+        "gradient_options": [
+            {
+                "display_name": "Nuclear Bias",
+                "value": "nucleus_gradient",
+                "path": "objects.endosome.gradient",
+                "packing_mode": "gradient",
+                "packing_mode_path": "objects.endosome.packing_mode",
+                "strength_path": "gradients.nucleus_gradient.weight_mode_settings.decay_length",
+                "strength_display_name": "Decay Length",
+                "strength_description": "Smaller decay length indicates stronger bias",
+                "strength_min": 0,
+                "strength_max": 1
+            },
+            {
+                "display_name": "Membrane Bias",
+                "value": "membrane_gradient",
+                "path": "objects.endosome.gradient",
+                "packing_mode": "gradient",
+                "packing_mode_path": "objects.endosome.packing_mode",
+                "strength_path": "gradients.membrane_gradient.weight_mode_settings.decay_length",
+                "strength_display_name": "Decay Length",
+                "strength_description": "Smaller decay length indicates stronger bias",
+                "strength_min": 0,
+                "strength_max": 1
+            },
+            {
+                "display_name": "Unbiased",
+                "value": "random",
+                "path": "objects.endosome.packing_mode",
+                "packing_mode": "random"
+            }
+        ]
+    }
+  ]
+}