Opentrons / junk-drawer

junk-drawer

Simple JSON data storage on the filesystem

junk_drawer is a Python module to place JSON-serializable objects in a key-value store, backed by JSON-on-the-filesystem in a simple directory structure. The library allows you to create a store that will accept items of the same shape, similarly to a database table.

Work in progress - Not yet available

install

pip install junk-drawer

Usage

Create a store

from junk_drawer import Store
from pydantic import BaseModel

class MyModel(BaseModel):
    name: str

async def main():
    store = Store.create("path/to/store", schema=MyModel)

A store can be used to save and retrieve multiple items conforming to the same schema. Use Pydantic to define your model shape. When this store is created, it will create the directory ${cwd}/path/to/store if it doesn't already exist.

Note: If you use a string to create your store's directory, the string will always be interpreted as a POSIX path, using / as directory separators.

Read only store

If you have a set of items in your filesystem that you'd like to have a read-only interface to, you may create a ReadStore. A ReadStore has the same interface as a full Store, excepting any methods that add, update, or remove items in the store.

from junk_drawer import ReadStore
from pydantic import BaseModel

class MyModel(BaseModel):
    name: str

async def main():
    store = ReadStore.create("path/to/store", schema=MyModel)

Get an item from the store

async def main():
    store = Store.create("path/to/store", schema=MyModel)
    item = await store.get("some-key")

The store has the following methods for getting items and keys from the store.

• store.get(key)
  • Gets an item by key from the store, if that key exists and item passes validation
• store.exists(key)
  • Checks whether a given key exists in the store (does not read or check the item itself)
• store.get_all_items()
  • Returns all items in the store
• store.get_all_keys()
  • Returns all items in the store
• store.get_all_entries()
  • Returns all items in the store zipped in tuples with their keys

Note: A key may contain forward slashes (/). The store will interpret forward slashes in a key as additional directories in the path to the item.

Put an item in the store

async def main():
    item = MyModel(name="fizzbuzz")
    store = Store.create("path/to/store", schema=MyModel)
    item_key = await store.put(item, "some-key")

The store has the following methods that may add an item at a specific key. The key will be used as the name of the JSON file and should not begin with a dot.

• store.put(item, key)
  • Put an item in the store or update an existing item if the key already exists
• store.ensure(default_item, key)
  • Get an item by key, inserting a default value if the key doesn't exist
  • Basically a shortcut for get followed by put if get returns None

The snippet above will create the following directory and file:

Directory: {cwd}/path/to/store

• File: some-key.json
  • Contents: { "name": "fizzbuzz" }

Put an item using key from model

class KeyedModel(BaseModel):
    uid: UUID
    name: str

async def main():
    item = ModelWithKey(uid=uuid4(), name="fizzbuzz")
    store = Store.create("store", schema=KeyedModel, primary_key="uid")
    item_key = await store.put(item)

If you specify the primary_key option when creating the store, put and ensure will use the value of primary_key from the item to determine the key. The value of primary_key will be converted to a str before use and should not begin with a dot.

Remove an item from the store

async def main():
    item = MyModel(name="fizzbuzz")
    store = Store.create("path/to/store", schema=MyModel)

    removed_key = await store.delete("some-key")

Migrate schemas

class MyModel(BaseModel):
    # present the first time store was used (schema v0)
    name: str
    # added in schema v1
    new_field: str
    # added in schema v2
    another_new_field: int

def migration_v1(prev: Dict[str, Any]) -> Dict[str, Any]:
    next_model = prev
    next_model["new_field"] = "default_value"
    return next_model

def migration_v2(prev: Dict[str, Any]) -> Dict[str, Any]:
    next_model = prev
    next_model["another_new_field"] = 42
    return next_model

async def main():
    store = Store.create(
        "./data/existing_store",
        schema=MyModel,
        migrations=(migration_v1, migration_v2)
    )

If you need to change the schema of items in an already existing store, you need to add a migration. A migration is a function that takes the previous version of the item as a plain-old-Python-dict and returns the new version of the item as a dict.

The store can be initialized with a list of migration functions, where each function represents one version of the schema. The migration functions will be called as a waterfall, and the last function in the chain must output a dict in the correct format. Pydantic will raise an error if the dict cannot be used to successfully initialize a model instance.

Once a Store has a migration function in its migrations list, that function can never be removed. When adding a migration function, you should write unit tests to ensure the correct fields are added / modified in the dict.

Migrations happen lazily on read whenever a given item is accessed. If an item exists on disk at a previous schema version and is never written to, the on-disk representation will remain at the previous version.

Synchronous vs Asynchronous Usage

All "default" methods of the store are asynchronous, and run their file I/O, parsing, and encoding operations in an asyncio thread pool. In general, using these asynchronous methods is good because you can avoid blocking your main application thread(s). However, in some instances, synchronous, blocking behavior is preferred.

All Store methods have a _sync counterpart that allows interacting with the store synchronously. Always carefully consider whether you really need to use the store synchronously, as certain actions (e.g. retrieving all items in a large store, parsing complex models) may block for a while, preventing your application from responding to other requests.

from junk_drawer import Store
from pydantic import BaseModel

class MyModel(BaseModel):
    name: str

def main():
    store = Store.create_sync("path/to/store", schema=MyModel)
    item_key = store.put_sync(MyModel(name="fizzbuzz"), "some-key")
    item = store.get_sync(item_key)

Reference

Besides Store.create, all methods of Store listed below are async and should be awaited. To use synchronously, append _sync to a given method's name.

Store.create(directory, schema, primary_key = None, ignore_errors = False, migrations=()) -> Store

argument	type	required	description
directory	str	Yes	Store root directory, in POSIX format
schema	Type[BaseModel]	Yes	Document schema
primary_key	str	No	Primary key field in schema, if applicable
ignore_errors	bool	No	Return None instead of raising read/parse/write/encode errors
migrations	Sequence[Migration]	No	Sequence of schema migration functions

from junk_drawer import Store
from pydantic import BaseModel

class MyModel(BaseModel):
    name: str

async def main():
    store = Store.create("path/to/store", schema=MyModel)

Creates a Store instance to store items in a given directory relative to the current working directory. Do not configure multiple stores for the same directory.

store.get(key: str) -> Optional[BaseModel]

argument	type	required	description
key	str	No	Key to retrieve

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    scissors = await store.get("my-scissors")

Get an item by key from the store. Returns None if no item with that key exists.

store.get_all_items() -> List[BaseModel]

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    all_scissors = await store.get_all_items()

Returns a list of all items in the store. If items are not using a primary_key, use get_all_entries to get items and their associated keys. The order of the entries may be arbitrary (it depends on Path.glob).

store.get_all_keys() -> List[str]

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    all_scissor_keys = await store.get_all_keys()

Returns a list of all keys in the store. May return more keys than actual valid documents if there are invalid JSON files in the store directory. The order of the entries may be arbitrary (it depends on Path.glob).

store.get_all_entries() -> List[Tuple[str, BaseModel]]

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    all_scissor_entries = await store.get_all_entries()

Returns a zipped list of all key/item pairs in the store. Useful if you're not using primary_key but you still need to get all items and their associated keys. The order of the entries may be arbitrary (it depends on Path.glob).

store.put(item: BaseModel, key: Optional[str] = None) -> Optional[str]

argument	type	required	description
item	BaseModel	Yes	Item to serialize and store
key	str	No	Key, optional if using primary_key from item

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    scissors = Scissors(left_handed=true)
    scissors_key = await store.put(scissors, "my-scissors")

Add an item into the store, serializing item to JSON and placing it in ${store_name}/${key}.json. Will replace the item with key if it already exists.

Note: This method is not present in ReadStore.

store.ensure(default_item: BaseModel, key: Optional[str] = None) -> BaseModel

argument	type	required	description
default_item	BaseModel	Yes	Item to insert if key is missing
key	str	No	Key, optional if using primary_key from item

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    default_scissors = Scissors(left_handed=true)
    store = Store.create("scissors", schema=Scissors)
    scissors = await store.ensure(default_scissors, "my-scissors")

Get an item by key from the store. If no item with that key exists, adds default_item to the store before returning the item. Effectively a shortcut for a get followed by a put if the get returns None.

Note: This method is not present in ReadStore.

store.delete(key: str) -> Optional[str]

argument	type	required	description
key	str	Yes	Document ID to delete

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    scissors_key = await store.put(Scissors(left_handed=true), "key")
    await store.delete(scissors_key)

Removes the document with key key from the store. Returns the key of the item it removed or None if no item at that key was found.

Note: This method is not present in ReadStore.

store.delete_store() -> None

from junk_drawer import Store
from pydantic import BaseModel

class Scissors(BaseModel):
  left_handed: bool

async def main():
    store = Store.create("scissors", schema=Scissors)
    await store.delete_store()

Deletes the backing directory and all files for the store.

Note: This method is not present in ReadStore.

Migration

A Migration is a function that takes a Dict[str, Any] and returns a Dict[str, Any]. See Migrate schemas section for usage details.

Migration = Callable[[Dict[str, Any]], Dict[str, Any]]