compressedfhir 0.0.1__tar.gz

compressedfhir-0.0.1/LICENSE

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compressedfhir-0.0.1/MANIFEST.in

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+include README.md
+include requirements.txt
+include requirements-test.txt
+include VERSION
+include Makefile
+include compressedfhir/py.typed

compressedfhir-0.0.1/Makefile

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+LANG=en_US.utf-8
+
+export LANG
+
+.PHONY: Pipfile.lock
+Pipfile.lock:
+	docker compose --progress=plain build --no-cache --build-arg RUN_PIPENV_LOCK=true dev && \
+	docker compose --progress=plain run --rm dev sh -c "cp -f /tmp/Pipfile.lock /usr/src/compressedfhir/Pipfile.lock"
+
+.PHONY:devdocker
+devdocker: ## Builds the docker for dev
+	docker compose build
+
+.PHONY:init
+init: Pipfile.lock devdocker up setup-pre-commit  ## Initializes the local developer environment
+
+.PHONY: up
+up:
+	docker compose up --build -d --remove-orphans
+
+.PHONY: down
+down:
+	docker compose down
+
+.PHONY:clean-pre-commit
+clean-pre-commit: ## removes pre-commit hook
+	rm -f .git/hooks/pre-commit
+
+.PHONY:setup-pre-commit
+setup-pre-commit:
+	cp ./pre-commit-hook ./.git/hooks/pre-commit && \
+	chmod +x ./.git/hooks/pre-commit
+
+.PHONY:run-pre-commit
+run-pre-commit: setup-pre-commit
+	./.git/hooks/pre-commit
+
+.PHONY:update
+update: down Pipfile.lock setup-pre-commit  ## Updates all the packages using Pipfile
+	make devdocker && \
+	make pipenv-setup
+
+.PHONY:tests
+tests: up
+	docker compose run --rm --name compressedfhir dev pytest tests compressedfhir
+
+.PHONY:shell
+shell:devdocker ## Brings up the bash shell in dev docker
+	docker compose run --rm --name compressedfhir dev sh
+
+.PHONY:build
+build:
+	docker compose run --rm --name compressedfhir dev rm -rf dist/
+	docker compose run --rm --name compressedfhir dev python3 setup.py sdist bdist_wheel
+
+.PHONY:testpackage
+testpackage:build
+	docker compose run --rm --name compressedfhir dev python3 -m twine upload -u __token__ --repository testpypi dist/*
+# password can be set in TWINE_PASSWORD. https://twine.readthedocs.io/en/latest/
+
+.PHONY:package
+package:build
+	docker compose run --rm --name compressedfhir dev python3 -m twine upload -u __token__ --repository pypi dist/*
+# password can be set in TWINE_PASSWORD. https://twine.readthedocs.io/en/latest/ (note this is the token not your password)
+
+.DEFAULT_GOAL := help
+.PHONY: help
+help: ## Show this help.
+	# from https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+
+.PHONY:pipenv-setup
+pipenv-setup:devdocker ## Run pipenv-setup to update setup.py with latest dependencies
+	docker compose run --rm dev sh -c "pipenv run pipenv install --skip-lock --categories \"pipenvsetup\" && pipenv run pipenv-setup sync --pipfile" && \
+	make run-pre-commit

compressedfhir-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: compressedfhir
+Version: 0.0.1
+Summary: Stores FHIR JSON resources in compressed form in memory
+Home-page: https://github.com/icanbwell/compressed-fhir
+Author: Imran Qureshi
+Author-email: imran.qureshi@icanbwell.com
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: msgpack>=1.0.0
+Requires-Dist: orjson>=3.10.16
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# compressedfhir

compressedfhir-0.0.1/README.md

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+# compressedfhir

compressedfhir-0.0.1/VERSION

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+0.0.1

compressedfhir-0.0.1/compressedfhir/fhir/base_resource_list.py

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+import copy
+import json
+from contextlib import contextmanager
+from typing import (
+    Deque,
+    List,
+    AsyncGenerator,
+    Optional,
+    Any,
+    Dict,
+    Iterator,
+    override,
+    Iterable,
+    Generator,
+)
+
+from compressedfhir.utilities.compressed_dict.v1.compressed_dict import (
+    CompressedDict,
+)
+from compressedfhir.utilities.fhir_json_encoder import FhirJSONEncoder
+
+
+class BaseResourceList[T: CompressedDict[str, Any]](Deque[T]):
+    """
+    Represents a list of FHIR resources.
+    """
+
+    __slots__: List[str] = []
+
+    def __init__(
+        self,
+        iterable: Iterable[T] | None = None,
+        maxlen: Optional[int] = None,
+    ) -> None:
+        # if iterable is not None:
+        # assert all([isinstance(r, CompressedDict) for r in iterable]), f"type {type(next(iter(iterable)))}"
+        super().__init__(iterable, maxlen=maxlen) if iterable else super().__init__()
+
+    @override
+    def append(self, x: T, /) -> None:
+        super().append(x)
+        # assert isinstance(x, CompressedDict), f"{type(x)} is not a CompressedDict"
+
+    def json(self) -> str:
+        """
+        Convert the list of FhirResource objects to a JSON string.
+
+        :return: JSON string representation of the list.
+        """
+        return json.dumps([r.dict() for r in self], cls=FhirJSONEncoder)
+
+    def get_resources(self) -> "BaseResourceList[T]":
+        """
+        Get all resources in the list.
+
+        :return: A list of FhirResource objects.
+        """
+        # this is here to keep compatibility with FhirResourceMap
+        return self
+
+    async def consume_resource_batch_async(
+        self,
+        *,
+        batch_size: Optional[int],
+    ) -> AsyncGenerator["BaseResourceList[T]", None]:
+        """
+        Consume resources in batches asynchronously.
+
+        :param batch_size: The size of each batch.
+        :return: An async generator yielding batches of FhirResourceList.
+        """
+        batch: BaseResourceList[T]
+        if batch_size is None:
+            batch = BaseResourceList[T]()
+            while self:
+                batch.append(self.popleft())
+            yield batch
+        elif batch_size <= 0:
+            raise ValueError("Batch size must be greater than 0.")
+        else:
+            while self:
+                batch = BaseResourceList[T]()
+                for _ in range(min(batch_size, len(self))):
+                    batch.append(self.popleft())
+                yield batch
+
+    def consume_resource_batch(
+        self,
+        *,
+        batch_size: Optional[int],
+    ) -> Generator["BaseResourceList[T]", None, None]:
+        """
+        Consume resources in batches asynchronously.
+
+        :param batch_size: The size of each batch.
+        :return: An async generator yielding batches of FhirResourceList.
+        """
+        batch: BaseResourceList[T]
+        if batch_size is None:
+            batch = BaseResourceList[T]()
+            while self:
+                batch.append(self.popleft())
+            yield batch
+        elif batch_size <= 0:
+            raise ValueError("Batch size must be greater than 0.")
+        else:
+            while self:
+                batch = BaseResourceList[T]()
+                for _ in range(min(batch_size, len(self))):
+                    batch.append(self.popleft())
+                yield batch
+
+    def __deepcopy__(self, memo: Dict[int, Any]) -> "BaseResourceList[T]":
+        """
+        Create a copy of the FhirResourceList.
+
+        :return: A new FhirResourceList object with the same resources.
+        """
+        return BaseResourceList[T]([copy.deepcopy(r) for r in self])
+
+    def __repr__(self) -> str:
+        """
+        Return a string representation of the FhirResourceList.
+
+        :return: A string representation of the FhirResourceList.
+        """
+        return f"FhirResourceList(resources: {len(self)})"
+
+    @contextmanager
+    def transaction(self) -> Iterator["BaseResourceList[T]"]:
+        """
+        Opens a transaction for all resources in the list.
+
+        Deserializes the dictionary before entering the context
+        Serializes the dictionary after exiting the context
+
+        Raises:
+            CompressedDictAccessError: If methods are called outside the context
+
+        """
+        try:
+            self.start_transaction()
+
+            yield self
+
+        finally:
+            self.end_transaction()
+
+    def start_transaction(self) -> "BaseResourceList[T]":
+        """
+        Starts a transaction for each resource in the list.  Use transaction() for a contextmanager for simpler usage.
+        """
+
+        for resource in self:
+            resource.start_transaction()
+        return self
+
+    def end_transaction(self) -> "BaseResourceList[T]":
+        """
+        Ends a transaction.  Use transaction() for a context_manager for simpler usage.
+
+        """
+        for resource in self:
+            resource.end_transaction()
+        return self