Feature/pass recipe to docker

.dockerignore

@@ -0,0 +1,37 @@
+# Distribution / packaging
+build/
+develop-eggs/
+eggs/
+.eggs/
+*.egg-info/
+.installed.cfg
+*.egg
+__pycache__
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+*.cover
+cellpack/tests/
+cellpack/bin/tests/
+
+# Documentation
+docs/
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Generated data
+out/
+*.simularium
+**/converted/*
+data/
+results/
+
+# git
+.github/

cellpack/autopack/__init__.py

@@ -392,13 +392,13 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
     return sphere_data
 
 
-def load_file(filename, destination="", cache="geometries", force=None):
+def load_file(filename, destination="", cache="geometries", force=None, use_docker=False):
     if is_remote_path(filename):
         database_name, file_path = convert_db_shortname_to_url(filename)
         # command example: `pack -r firebase:recipes/[FIREBASE-RECIPE-ID] -c [CONFIG-FILE-PATH]`
         if database_name == "firebase":
             db = DATABASE_IDS.handlers().get(database_name)
-            initialize_db = db()
+            initialize_db = db(default_db="staging") if use_docker else db()
             if not initialize_db._initialized:
                 readme_url = "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases"
                 sys.exit(

cellpack/autopack/loaders/recipe_loader.py

@@ -27,7 +27,7 @@ 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):
+    def __init__(self, input_file_path, save_converted_recipe=False, use_docker=False):
         _, file_extension = os.path.splitext(input_file_path)
         self.current_version = CURRENT_VERSION
         self.file_path = input_file_path
@@ -36,7 +36,7 @@ def __init__(self, input_file_path, save_converted_recipe=False):
         self.compartment_list = []
         self.save_converted_recipe = save_converted_recipe
         autopack.CURRENT_RECIPE_PATH = os.path.dirname(self.file_path)
-        self.recipe_data = self._read()
+        self.recipe_data = self._read(use_docker=use_docker)
 
     @staticmethod
     def _resolve_object(key, objects):
@@ -156,8 +156,8 @@ def _migrate_version(self, old_recipe):
                 f"{old_recipe['format_version']} is not a format version we support"
             )
 
-    def _read(self, resolve_inheritance=True):
-        new_values, database_name = autopack.load_file(self.file_path, cache="recipes")
+    def _read(self, resolve_inheritance=True, use_docker=False):
+        new_values, database_name = autopack.load_file(self.file_path, cache="recipes", use_docker=use_docker)
         if database_name == "firebase":
             objects, gradients, composition = DBRecipeLoader.collect_and_sort_data(
                 new_values["composition"]

cellpack/bin/pack.py

@@ -20,18 +20,19 @@
 ###############################################################################
 
 
-def pack(recipe, config_path=None, analysis_config_path=None):
+def pack(recipe, config_path=None, analysis_config_path=None, docker=False):
     """
     Initializes an autopack packing from the command line
     :param recipe: string argument, path to recipe
     :param config_path: string argument, path to packing config file
     :param analysis_config_path: string argument, path to analysis config file
+    :param docker: boolean argument, are we using docker
 
     :return: void
     """
     packing_config_data = ConfigLoader(config_path).config
     recipe_data = RecipeLoader(
-        recipe, packing_config_data["save_converted_recipe"]
+        recipe, packing_config_data["save_converted_recipe"], docker
     ).recipe_data
     analysis_config_data = {}
     if analysis_config_path is not None:

docker-entrypoint.sh

@@ -1,15 +1,20 @@
 #!/bin/bash -e
 
-# if [ -z "$recipe" ]; then
-#     echo "Required recipe parameter is missing, please include recipe in Docker run script, ie: -e r=path/to/recipe"
-#     exit 
-# fi
-
-# if [ -z "$config" ]; then
-#     echo "Required config parameter is missing, please include packing config in Docker run script, ie: -e c=path/to/config"
-#     exit 
-# fi
+if [ -z "$recipe" ]; then
+    echo "Required recipe parameter is missing, please include recipe in Docker run script, ie: -e recipe=path/to/recipe"
+    exit;
+else
+    echo "recipe passed in: '$recipe'"
+fi
 
 cd /cellpack
-# pack -r ${recipe} -c ${config}
-pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json
+
+if [ -z "$config" ]; then
+    echo "Config parameter not included, using default value"
+    pack -r $recipe -d
+    exit;
+else
+    echo "config passed in: '$config'"
+fi
+
+pack -r $recipe -c $config -d