Server should Accept Recipe JSON

cellpack/autopack/__init__.py

@@ -411,8 +411,17 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
 
 
 def load_file(
-    filename, destination="", cache="geometries", force=None, use_docker=False
+    filename,
+    destination="",
+    cache="geometries",
+    force=None,
+    use_docker=False,
+    json_recipe=None,
 ):
+    if json_recipe is not None:
+        composition = DBRecipeLoader.remove_empty(json_recipe.get("composition", {}))
+        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

@@ -30,14 +30,21 @@ 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):
+    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.json_recipe = json_recipe
 
         # set CURRENT_RECIPE_PATH appropriately for remote(firebase) vs local recipes
         if autopack.is_remote_path(self.file_path):
@@ -169,7 +176,10 @@ 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
+            self.file_path,
+            cache="recipes",
+            use_docker=use_docker,
+            json_recipe=self.json_recipe,
         )
         if database_name == "firebase":
             if is_unnested_firebase:

cellpack/bin/pack.py

@@ -25,7 +25,12 @@
 
 
 def pack(
-    recipe, config_path=None, analysis_config_path=None, docker=False, validate=True
+    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 +45,7 @@ def pack(
     packing_config_data = ConfigLoader(config_path, docker).config
 
     recipe_loader = RecipeLoader(
-        recipe, packing_config_data["save_converted_recipe"], docker
+        recipe, packing_config_data["save_converted_recipe"], docker, json_recipe
     )
     recipe_data = recipe_loader.recipe_data
     analysis_config_data = {}

docker/Dockerfile.ecs

@@ -4,7 +4,7 @@ WORKDIR /cellpack
 COPY . /cellpack
 
 RUN python -m pip install --upgrade pip --root-user-action=ignore
-RUN python -m pip install . -r requirements/linux/requirements.txt --root-user-action=ignore
+RUN python -m pip install . --root-user-action=ignore
 
 EXPOSE 80
 

docker/server.py

@@ -12,11 +12,11 @@ class CellpackServer:
     def __init__(self):
         self.packing_tasks = set()
 
-    async def run_packing(self, recipe, config, job_id):
+    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)
+            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))
 
@@ -37,16 +37,20 @@ async def health_check(self, request: web.Request) -> web.Response:
         return web.Response()
 
     async def pack_handler(self, request: web.Request) -> web.Response:
-        recipe = request.rel_url.query.get("recipe")
-        if recipe is None:
+        recipe = request.rel_url.query.get("recipe") or ""
+        if request.can_read_body:
+            body = await request.json()
+        else:
+            body = None
+        if not recipe and not body:
             raise web.HTTPBadRequest(
                 "Pack requests must include recipe as a query param"
             )
         config = request.rel_url.query.get("config")
         job_id = str(uuid.uuid4())
 
         # Initiate packing task to run in background
-        packing_task = asyncio.create_task(self.run_packing(recipe, config, job_id))
+        packing_task = asyncio.create_task(self.run_packing(recipe, config, job_id, body))
 
         # Keep track of task references to prevent them from being garbage
         # collected, then discard after task completion

docs/DOCKER.md

@@ -13,6 +13,6 @@
 ## AWS ECS Docker Image
 1. Build image, running `docker build -f docker/Dockerfile.ecs -t [CONTAINER-NAME] .`
 2. Run packings in the container, running: `docker run -v ~/.aws:/root/.aws -p 80:80 [CONTAINER-NAME]`
-3. Try hitting the test endpoint on the server, by navigating to `http://0.0.0.0:8443/hello` in your browser.
-4. Try running a packing on the server, by hitting the `http://0.0.0.0:80/pack?recipe=firebase:recipes/one_sphere_v_1.0.0` in your browser.
+3. Try hitting the test endpoint on the server, by navigating to `http://0.0.0.0:80/hello` in your browser.
+4. Try running a packing on the server, by hitting the `http://0.0.0.0:80/start-packing?recipe=firebase:recipes/one_sphere_v_1.0.0` in your browser.
 5. Verify that the packing result path was uploaded to the firebase results table, with the job id specified in the response from the request in step 4.The result simularium file can be found at the s3 path specified there.