* adding username to .creds

* formatting

cellpack/autopack/DBRecipeHandler.py

@@ -58,7 +58,9 @@ def as_dict(self):
 
     @staticmethod
     def get_gradient_reference(downloaded_data, db):
-        if "gradient" in downloaded_data and db.is_reference(downloaded_data["gradient"]):
+        if "gradient" in downloaded_data and db.is_reference(
+            downloaded_data["gradient"]
+        ):
             gradient_key = downloaded_data["gradient"]
             downloaded_data["gradient"], _ = db.get_doc_by_ref(gradient_key)
 
@@ -151,12 +153,8 @@ def resolve_local_regions(self, local_data, recipe_data, db):
                             "object"
                         ] = prep_recipe_data["objects"][obj_item["name"]]
                     # replace gradient reference with gradient data
-                    obj_data = local_data["regions"][region_name][index][
-                            "object"
-                        ]
-                    if "gradient" in obj_data and isinstance(
-                        obj_data["gradient"], str
-                    ):
+                    obj_data = local_data["regions"][region_name][index]["object"]
+                    if "gradient" in obj_data and isinstance(obj_data["gradient"], str):
                         local_data["regions"][region_name][index]["object"][
                             "gradient"
                         ] = prep_recipe_data["gradients"][obj_data["gradient"]]

cellpack/autopack/FirebaseHandler.py

@@ -3,6 +3,7 @@
 from firebase_admin import credentials, firestore
 from cellpack.autopack.loaders.utils import read_json_file, write_json_file
 
+
 class FirebaseHandler(object):
     """
     Retrieve data and perform common tasks when working with firebase.
@@ -18,25 +19,27 @@ def __init__(self):
     @staticmethod
     def doc_to_dict(doc):
         return doc.to_dict()
-    
+
     @staticmethod
     def write_creds_path():
         path = ast.literal_eval(input("provide path to firebase credentials: "))
         print(path)
         data = read_json_file(path)
         if data is None:
             raise ValueError("The path to your credentials doesn't exist")
-        firebase_cred = {
-            "firebase": data
-        }
-        write_json_file("./.creds", firebase_cred)
+        firebase_cred = {"firebase": data}
+        creds = read_json_file("./.creds")
+        if creds is None:
+            write_json_file("./.creds", firebase_cred)
+        else:
+            creds["firebase"] = data
+            write_json_file("./.creds", creds)
         return firebase_cred
-
 
     @staticmethod
     def get_creds():
         creds = read_json_file("./.creds")
-        if creds is None:
+        if creds is None or "firebase" not in creds:
             creds = FirebaseHandler.write_creds_path()
         return creds["firebase"]
 

cellpack/autopack/__init__.py

@@ -41,6 +41,7 @@
 import re
 import shutil
 from os import path, environ
+import pwd
 from pathlib import Path
 import urllib.request as urllib
 from collections import OrderedDict
@@ -50,6 +51,7 @@
 from cellpack.autopack.interface_objects.meta_enum import MetaEnum
 from cellpack.autopack.FirebaseHandler import FirebaseHandler
 from cellpack.autopack.DBRecipeHandler import DBRecipeHandler
+from cellpack.autopack.loaders.utils import read_json_file, write_json_file
 
 
 packageContainsVFCommands = 1
@@ -539,6 +541,15 @@ def clearCaches(*args):
             print("problem cleaning ", cache_dir[k])
 
 
+def write_username_to_creds():
+    username = pwd.getpwuid(os.getuid())[0]
+    creds = read_json_file("./.creds")
+    if creds is None or "username" not in creds:
+        creds = {}
+        creds["username"] = username
+        write_json_file("./.creds", creds)
+
+
 # we should read a file to fill the RECIPE Dictionary
 # so we can add some and write/save setup
 # afdir  or user_pref
@@ -547,6 +558,7 @@ def clearCaches(*args):
     checkPath()
     updatePathJSON()
     checkRecipeAvailable()
+    write_username_to_creds()
     log.info("path are updated ")
 
 log.info(f"currently number recipes is {len(RECIPES)}")

cellpack/autopack/loaders/migrate_v1_to_v2.py

@@ -145,7 +145,7 @@ def convert(old_recipe):
     new_recipe["name"] = old_recipe["recipe"]["name"]
     new_recipe["bounding_box"] = old_recipe["options"]["boundingBox"]
     objects_dict = {}
-    #TODO: check if composition structure is correct
+    # TODO: check if composition structure is correct
     composition = {"space": {"regions": {}}}
     if "cytoplasme" in old_recipe:
         outer_most_region_array = []

cellpack/autopack/loaders/recipe_loader.py

@@ -180,7 +180,7 @@ def _get_gradient_data(obj_data, obj_dict, grad_dict):
 
     @staticmethod
     def _is_obj(comp_or_obj):
-        # if the top level of a downloaded comp doesn't have the key `name`, it's an obj 
+        # if the top level of a downloaded comp doesn't have the key `name`, it's an obj
         return not comp_or_obj.get("name") and "object" in comp_or_obj
 
     def _collect_and_sort_data(self, comp_data):
@@ -208,14 +208,16 @@ def _collect_and_sort_data(self, comp_data):
                 # RecipeLoader._remove_name_key(object_copy)
             if "regions" in comp_value and comp_value["regions"] is not None:
                 for region_name in comp_value["regions"]:
-                    composition[comp_name]["regions"]={}
-                    composition[comp_name].setdefault("regions",{})[region_name]=[]
+                    composition[comp_name]["regions"] = {}
+                    composition[comp_name].setdefault("regions", {})[region_name] = []
                     for region_item in comp_value["regions"][region_name]:
-                        if RecipeLoader._is_obj(region_item):  
-                            composition[comp_name]["regions"][region_name].append({
-                                "object": region_item["object"].get("name"),
-                                "count": region_item.get("count")
-                            })
+                        if RecipeLoader._is_obj(region_item):
+                            composition[comp_name]["regions"][region_name].append(
+                                {
+                                    "object": region_item["object"].get("name"),
+                                    "count": region_item.get("count"),
+                                }
+                            )
                             object_copy = copy.deepcopy(region_item["object"])
                             objects[object_copy["name"]] = object_copy
                             if "gradient" in object_copy and isinstance(
@@ -225,12 +227,15 @@ def _collect_and_sort_data(self, comp_data):
                                     object_copy, objects, gradients
                                 )
                         # RecipeLoader._remove_name_key(object_copy)
-                        else: 
-                            composition[comp_name]["regions"][region_name].append(region_item["name"])
+                        else:
+                            composition[comp_name]["regions"][region_name].append(
+                                region_item["name"]
+                            )
         return objects, gradients, composition
 
-
-    def _compile_recipe_from_firebase(self, db_recipe_data, obj_dict, grad_dict, comp_dict):
+    def _compile_recipe_from_firebase(
+        self, db_recipe_data, obj_dict, grad_dict, comp_dict
+    ):
         """
         Compile recipe data from firebase recipe data into a ready-to-pack structure
         """
@@ -241,17 +246,19 @@ def _compile_recipe_from_firebase(self, db_recipe_data, obj_dict, grad_dict, com
         recipe_data["bounding_box"] = db_recipe_data["bounding_box"]
         recipe_data["objects"] = obj_dict
         if grad_dict:
-            recipe_data["gradients"] = [
-                {**v} for v in grad_dict.values()
-            ]
+            recipe_data["gradients"] = [{**v} for v in grad_dict.values()]
         recipe_data["composition"] = comp_dict
         return recipe_data
 
     def _read(self):
         new_values, database_name = autopack.load_file(self.file_path, cache="recipes")
         if database_name == "firebase":
-            objects, gradients, composition = self._collect_and_sort_data(new_values["composition"])
-            new_values = self._compile_recipe_from_firebase(new_values, objects, gradients, composition)
+            objects, gradients, composition = self._collect_and_sort_data(
+                new_values["composition"]
+            )
+            new_values = self._compile_recipe_from_firebase(
+                new_values, objects, gradients, composition
+            )
         recipe_data = RecipeLoader.default_values.copy()
         recipe_data = deep_merge(recipe_data, new_values)
         recipe_data["format_version"] = RecipeLoader._sanitize_format_version(

cellpack/autopack/loaders/utils.py

@@ -23,14 +23,15 @@ def create_output_dir(out_base_folder, recipe_name, sub_dir=None):
     os.makedirs(output_folder, exist_ok=True)
     return output_folder
 
+
 def read_json_file(path):
     if not Path(path).exists():
         return None
     with open(path, "r") as file_name:
         return json.load(file_name)
 
+
 def write_json_file(path, data):
     Path(path).parent.mkdir(exist_ok=True, parents=True)
     with open(path, "w") as file_name:
         json.dump(data, file_name)
-