rename param json_recipe

Author: ascibisz

cellpack/autopack/__init__.py

@@ -411,14 +411,14 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
 
 
 def load_file(
-    filename, destination="", cache="geometries", force=None, use_docker=False, recipe_obj=None
+    filename, destination="", cache="geometries", force=None, use_docker=False, json_recipe=None
 ):
-    if recipe_obj is not None:
+    if json_recipe is not None:
         composition = DBRecipeLoader.remove_empty(
-            recipe_obj.get("composition", {})
+            json_recipe.get("composition", {})
         )
-        recipe_obj["composition"] = composition
-        return recipe_obj, None, False
+        json_recipe["composition"] = composition
+        return json_recipe, None, False
     if is_remote_path(filename):
         database_name, file_path = convert_db_shortname_to_url(filename)
         if database_name == DATABASE_IDS.GITHUB:

cellpack/autopack/loaders/recipe_loader.py

@@ -30,15 +30,15 @@ class RecipeLoader(object):
     # TODO: add all default values here
     default_values = default_recipe_values.copy()
 
-    def __init__(self, input_file_path, save_converted_recipe=False, use_docker=False, recipe_obj=None):
+    def __init__(self, input_file_path, save_converted_recipe=False, use_docker=False, json_recipe=None):
         _, file_extension = os.path.splitext(input_file_path)
         self.current_version = CURRENT_VERSION
         self.file_path = input_file_path
         self.file_extension = file_extension
         self.ingredient_list = []
         self.compartment_list = []
         self.save_converted_recipe = save_converted_recipe
-        self.recipe_obj = recipe_obj
+        self.json_recipe = json_recipe
 
         # set CURRENT_RECIPE_PATH appropriately for remote(firebase) vs local recipes
         if autopack.is_remote_path(self.file_path):
@@ -170,7 +170,7 @@ def _migrate_version(self, old_recipe):
 
     def _read(self, resolve_inheritance=True, use_docker=False):
         new_values, database_name, is_unnested_firebase = autopack.load_file(
-            self.file_path, cache="recipes", use_docker=use_docker, recipe_obj=self.recipe_obj
+            self.file_path, cache="recipes", use_docker=use_docker, json_recipe=self.json_recipe
         )
         if database_name == "firebase":
             if is_unnested_firebase:

cellpack/bin/data-manifest.json

@@ -0,0 +1,10 @@
+{
+    "assay-dev": {
+        "data_source": "https://s3-us-west-2.amazonaws.com/file-download-service.allencell.org/assay-dev_2018-10-03.csv?versionId=XVdmE.6g1kk77c7jYA2Ge54eehTjY_AP",
+        "static_files": []
+    },
+    "test": {
+        "data_source": "https://cellpack-demo.s3.us-west-2.amazonaws.com/alli-test/test-manifest.csv",
+        "static_files": []
+    }
+}

cellpack/bin/pack.py

@@ -25,7 +25,7 @@
 
 
 def pack(
-    recipe, config_path=None, analysis_config_path=None, docker=False, validate=True, recipe_str=None
+    recipe, config_path=None, analysis_config_path=None, docker=False, validate=True, json_recipe=None
 ):
     """
     Initializes an autopack packing from the command line
@@ -40,7 +40,7 @@ def pack(
     packing_config_data = ConfigLoader(config_path, docker).config
 
     recipe_loader = RecipeLoader(
-        recipe, packing_config_data["save_converted_recipe"], docker, recipe_str
+        recipe, packing_config_data["save_converted_recipe"], docker, json_recipe
     )
     recipe_data = recipe_loader.recipe_data
     analysis_config_data = {}

docker/server.py

@@ -16,7 +16,7 @@ async def run_packing(self, recipe, config, job_id, body=None):
         os.environ["AWS_BATCH_JOB_ID"] = job_id
         self.update_job_status(job_id, "RUNNING")
         try:
-            pack(recipe=recipe, config_path=config, docker=True, recipe_str=body)
+            pack(recipe=recipe, config_path=config, docker=True, json_recipe=body)
         except Exception as e:
             self.update_job_status(job_id, "FAILED", error_message=str(e))