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Adding grid_file_path to recipe metadata for uploads #268

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merged 2 commits into from
Jul 1, 2024
Merged

Adding grid_file_path to recipe metadata for uploads #268

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b8ad296
get metadata in upload.py instead
rugeli Jun 20, 2024
35e2dfc
update docstring
rugeli Jun 24, 2024
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10 changes: 0 additions & 10 deletions cellpack/autopack/loaders/recipe_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,16 +132,6 @@ def _sanitize_format_version(recipe_data):
format_version = recipe_data["format_version"]
return format_version

def get_only_recipe_metadata(self):
recipe_meta_data = {
"format_version": self.recipe_data["format_version"],
"version": self.recipe_data["version"],
"name": self.recipe_data["name"],
"bounding_box": self.recipe_data["bounding_box"],
"composition": {},
}
return recipe_meta_data

def _migrate_version(self, old_recipe):
converted = False
if old_recipe["format_version"] == "1.0":
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21 changes: 20 additions & 1 deletion cellpack/bin/upload.py
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Expand Up @@ -8,6 +8,25 @@
from cellpack.autopack.loaders.recipe_loader import RecipeLoader


def get_recipe_metadata(loader):
"""
Extracts and returns essential metadata from a recipe for uploading
"""
try:
recipe_meta_data = {
"format_version": loader.recipe_data["format_version"],
"version": loader.recipe_data["version"],
"name": loader.recipe_data["name"],
"bounding_box": loader.recipe_data["bounding_box"],
"composition": {},
}
if "grid_file_path" in loader.recipe_data:
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Q: should we check for all keys in loader.recipe_data and add them to the recipe_meta_data (except composition)? This way we won't have to do a special check for grid_file_path or any new keys we add to the recipe down the line.

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@rugeli rugeli Jun 26, 2024 •
edited
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Thank you for asking! I was thinking the same approach: iterating over recipe data and recording every key except for objects, representations, etc., to make the uploading more programmatic. However I went with specified keys(for now) so we get to fully control which keys are displayed and needed in the metadata. Helping to prevent errors during data handling.

And you're right, if there will be more new top-layer keys, we should think about a more dynamic way to manage it.

recipe_meta_data["grid_file_path"] = loader.recipe_data["grid_file_path"]
return recipe_meta_data
except KeyError as e:
sys.exit(f"Recipe metadata is missing. {e}")


def upload(
recipe_path,
db_id=DATABASE_IDS.FIREBASE,
Expand All @@ -23,7 +42,7 @@ def upload(
if FirebaseHandler._initialized:
recipe_loader = RecipeLoader(recipe_path)
recipe_full_data = recipe_loader._read(resolve_inheritance=False)
recipe_meta_data = recipe_loader.get_only_recipe_metadata()
recipe_meta_data = get_recipe_metadata(recipe_loader)
recipe_db_handler = DBUploader(db_handler)
recipe_db_handler.upload_recipe(recipe_meta_data, recipe_full_data)
else:
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