cumulus-etl 2.1.0__tar.gz

cumulus_etl-2.1.0/LICENSE

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cumulus_etl-2.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: cumulus-etl
+Version: 2.1.0
+Summary: Turns FHIR data into de-identified & aggregated records
+Author-email: "Andy McMurry, PhD" <andrew.mcmurry@childrens.harvard.edu>, Michael Terry <michael.terry@childrens.harvard.edu>
+Requires-Python: >= 3.10
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+License-File: LICENSE
+Requires-Dist: ctakesclient >= 5.1, < 6
+Requires-Dist: cumulus-fhir-support >= 1.2, < 2
+Requires-Dist: delta-spark >= 3.2.1, < 4
+Requires-Dist: httpx < 1
+Requires-Dist: inscriptis < 3
+Requires-Dist: jwcrypto < 2
+Requires-Dist: label-studio-sdk < 2
+Requires-Dist: nltk >= 3.9, < 4
+Requires-Dist: openai < 2
+Requires-Dist: oracledb < 4
+Requires-Dist: philter-lite < 1
+Requires-Dist: pyarrow < 20
+Requires-Dist: rich < 14
+Requires-Dist: s3fs
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: ruff < 0.10 ; extra == "dev"
+Requires-Dist: coverage ; extra == "tests"
+Requires-Dist: ddt ; extra == "tests"
+Requires-Dist: moto[server, s3] >= 5.0 ; extra == "tests"
+Requires-Dist: pytest ; extra == "tests"
+Requires-Dist: pytest-cov ; extra == "tests"
+Requires-Dist: respx ; extra == "tests"
+Requires-Dist: time-machine ; extra == "tests"
+Project-URL: Homepage, https://github.com/smart-on-fhir/cumulus-etl
+Provides-Extra: dev
+Provides-Extra: tests
+
+# Cumulus ETL
+
+[Cumulus](https://docs.smarthealthit.org/cumulus/)
+is an entire healthcare pipeline for population-scale clinical investigations.
+
+Cumulus ETL is the first critical piece of that pipeline.
+- It **extracts** bulk patient data from your EHR.
+- It **transforms** that data by anonymizing it and running NLP on clinical notes
+- It **loads** that data onto the cloud to be queried by
+  [Cumulus Library](https://github.com/smart-on-fhir/cumulus-library) SQL
+
+## Documentation
+
+For guides on installing & using Cumulus ETL,
+[read our documentation](https://docs.smarthealthit.org/cumulus/etl/).
+
+## Example
+
+A simple run of Cumulus ETL might look something like:
+```shell
+docker compose run \
+  cumulus-etl \
+  s3://my-input-bucket/bulk-export/ \
+  s3://my-output-bucket/delta-lakes/ \
+  s3://my-phi-bucket/build-and-phi-artifacts/
+```
+
+This line would read ndjson files from the input bucket,
+drop the result as [Delta Lakes](https://delta.io/) into the output bucket,
+and save some bookkeeping configuration to a build/phi bucket.
+
+## Contributing
+
+We love 💖 contributions!
+
+If you have a good suggestion 💡 or found a bug 🐛,
+[read our brief contributors guide](CONTRIBUTING.md)
+for pointers to filing issues and what to expect.
+
+If you're a programmer ⌨ and are looking for a starting place to help, we keep a
+[list of good bite-size issues](https://github.com/smart-on-fhir/cumulus-etl/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)
+for first-time contributions.
+

cumulus_etl-2.1.0/README.md

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+# Cumulus ETL
+
+[Cumulus](https://docs.smarthealthit.org/cumulus/)
+is an entire healthcare pipeline for population-scale clinical investigations.
+
+Cumulus ETL is the first critical piece of that pipeline.
+- It **extracts** bulk patient data from your EHR.
+- It **transforms** that data by anonymizing it and running NLP on clinical notes
+- It **loads** that data onto the cloud to be queried by
+  [Cumulus Library](https://github.com/smart-on-fhir/cumulus-library) SQL
+
+## Documentation
+
+For guides on installing & using Cumulus ETL,
+[read our documentation](https://docs.smarthealthit.org/cumulus/etl/).
+
+## Example
+
+A simple run of Cumulus ETL might look something like:
+```shell
+docker compose run \
+  cumulus-etl \
+  s3://my-input-bucket/bulk-export/ \
+  s3://my-output-bucket/delta-lakes/ \
+  s3://my-phi-bucket/build-and-phi-artifacts/
+```
+
+This line would read ndjson files from the input bucket,
+drop the result as [Delta Lakes](https://delta.io/) into the output bucket,
+and save some bookkeeping configuration to a build/phi bucket.
+
+## Contributing
+
+We love 💖 contributions!
+
+If you have a good suggestion 💡 or found a bug 🐛,
+[read our brief contributors guide](CONTRIBUTING.md)
+for pointers to filing issues and what to expect.
+
+If you're a programmer ⌨ and are looking for a starting place to help, we keep a
+[list of good bite-size issues](https://github.com/smart-on-fhir/cumulus-etl/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)
+for first-time contributions.

cumulus_etl-2.1.0/cumulus_etl/__init__.py

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+"""Turns FHIR data into de-identified & aggregated records"""
+
+__version__ = "2.1.0"

cumulus_etl-2.1.0/cumulus_etl/batching.py

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+"""Iteration utilities to support batching values."""
+
+from collections.abc import AsyncIterable, AsyncIterator, Iterable
+from typing import TypeVar
+
+Item = TypeVar("Item")
+Atom = Item | list[Item] | None  # one single item (or group of items that can't be broken up)
+AtomStreams = Atom | tuple[Atom, ...]  # separated streams of atoms (which should be kept separated)
+ItemBatch = list[Item]
+ItemBatchStreams = tuple[ItemBatch, ...]  # separated lists of items
+
+
+async def _batch_slice(iterable: AsyncIterable[AtomStreams], n: int) -> ItemBatchStreams | None:
+    """
+    Returns the first n elements of iterable, flattening lists.
+
+    But include an entire list if we would end in middle.
+    For example, list(_batch_slice([1, [2.1, 2.1], 3], 2)) returns [1, 2.1, 2.2]
+
+    Note that this will only flatten elements that are actual Python lists (isinstance list is True)
+    """
+    count = 0
+    slices = None
+
+    async for atom_streams in iterable:
+        if not isinstance(atom_streams, tuple):
+            atom_streams = (atom_streams,)  # ensure that we are always dealing with a streams tuple
+
+        if slices is None:  # Create a tuple of empty lists that we will fill with slice data
+            slices = tuple([] for _ in range(len(atom_streams)))
+
+        for index, atom in enumerate(atom_streams):
+            if isinstance(atom, list):
+                slices[index].extend(atom)
+                count += len(atom)
+            elif atom is not None:
+                slices[index].append(atom)
+                count += 1
+
+        if count >= n:
+            break
+
+    return slices
+
+
+async def _force_aiter(iterable: AsyncIterable[Item] | Iterable[Item]) -> AsyncIterator[Item]:
+    """A version of aiter() that also promotes sync iterables into async iterables"""
+    if hasattr(iterable, "__aiter__"):
+        async for item in iterable:
+            yield item
+    else:
+        for item in iterable:
+            yield item
+
+
+async def batch_iterate_streams(
+    iterable: AsyncIterable[AtomStreams] | Iterable[AtomStreams], size: int
+) -> AsyncIterator[ItemBatchStreams]:
+    """
+    Yields batches of items, each roughly {size} elements from iterable.
+
+    This is similar to itertools.batched() from Python 3.12, with a few major changes:
+    - this is fully async, accepting async (or sync) iteratables, and returning an async iterable
+    - lists are returned, rather than tuples
+    - batches might be larger than the batch size, if a list is encountered inside the source
+      iterable. In that case, all elements of the list are included in the same sub-iterator batch,
+      which might put us over size. See the comments for the EtlTask.group_field class attribute
+      for why we support this.
+    - this accepts an iterator of tuples, where all the items in the tuple count against the batch
+      size and lists inside the tuple get expanded like above. This allows batching parallel streams
+      of data, like we do in ETL tasks that generate multiple output tables (see MedicationRequest).
+      All elements in a tuple will be in the same batch. The return value is always given in tuple
+      form, even if the input was not tupled.
+
+    The whole iterable is never fully loaded into memory. Rather we load only one element at a time.
+
+    Example of sub-lists:
+        async for batch in _batch_iterate_streams([1, [2.1, 2.2], 3, 4, 5], 2):
+            print(batch)
+        # ([1, 2.1, 2.2],)
+        # ([3, 4],)
+        # ([5],)
+
+    Example of multiple streams, tupled together:
+        items = [(1, "a"), ([2.1, 2.2], "b"), (None, ["c", "d"])]
+        async for batch in _batch_iterate_streams(items, 3):
+            print(batch)
+        # ([1, 2.1, 2.2], ["a", "b"]),
+        # ([], ["c", "d"]),
+    """
+    if size < 1:
+        raise ValueError("Must iterate by at least a batch of 1")
+
+    # get a real once-through iterable (we want to iterate only once)
+    true_iterable = _force_aiter(iterable)
+    while batches := await _batch_slice(true_iterable, size):
+        yield batches
+
+
+async def batch_iterate(
+    iterable: AsyncIterable[Atom] | Iterable[Atom], size: int
+) -> AsyncIterator[ItemBatch]:
+    """
+    A version of batch_iterate_streams that simplifies the common "one stream" case.
+
+    That is, this does not support accepting an iterator of tuples.
+
+    Read its documentation for the full explanation.
+
+    Example of sub-lists:
+        async for batch in _batch_iterate([1, [2.1, 2.2], 3, 4, 5], 2):
+            print(batch)
+        # [1, 2.1, 2.2]
+        # [3, 4]
+        # [5]
+    """
+    async for batch in batch_iterate_streams(iterable, size):
+        yield batch[0]

cumulus_etl-2.1.0/cumulus_etl/cli.py

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+"""The command line interface to cumulus-etl"""
+
+import argparse
+import asyncio
+import enum
+import logging
+import sys
+import tempfile
+
+import rich.logging
+
+from cumulus_etl import common, etl, export, inliner, upload_notes
+from cumulus_etl.etl import convert, init
+
+
+class Command(enum.Enum):
+    """Subcommand strings"""
+
+    CONVERT = "convert"
+    ETL = "etl"
+    EXPORT = "export"
+    INIT = "init"
+    INLINE = "inline"
+    UPLOAD_NOTES = "upload-notes"
+
+    # Why isn't this part of Enum directly...?
+    @classmethod
+    def values(cls):
+        return [e.value for e in cls]
+
+
+def get_subcommand(argv: list[str]) -> str | None:
+    """
+    Determines which subcommand was requested by the given command line.
+
+    Python's argparse has no good way of setting a default sub-parser.
+    (i.e. one that parses the command line if no sub parser subcommand is specified)
+    So instead, this method inspects the first positional argument.
+    If it's a recognized command, we return it. Else None.
+    """
+    for i, arg in enumerate(argv):
+        if arg in Command.values():
+            return argv.pop(i)  # remove it to make later parsers' jobs easier
+        elif not arg.startswith("-"):
+            # first positional arg did not match a known command, assume default command
+            return None
+
+
+async def main(argv: list[str]) -> None:
+    # Use RichHandler for logging because it works better when interacting with other rich components
+    # (e.g. I've seen the default logger lose the last warning emitted when progress bars are also active).
+    # But also turn off all the complex bits - we just want the message.
+    logging.basicConfig(
+        format="%(message)s",
+        handlers=[rich.logging.RichHandler(show_time=False, show_level=False, show_path=False)],
+    )
+
+    subcommand = get_subcommand(argv)
+
+    prog = "cumulus-etl"
+    if subcommand:
+        prog += f" {subcommand}"  # to make --help look nicer
+    parser = argparse.ArgumentParser(prog=prog)
+
+    if subcommand == Command.UPLOAD_NOTES.value:
+        run_method = upload_notes.run_upload_notes
+    elif subcommand == Command.CONVERT.value:
+        run_method = convert.run_convert
+    elif subcommand == Command.EXPORT.value:
+        run_method = export.run_export
+    elif subcommand == Command.INIT.value:
+        run_method = init.run_init
+    elif subcommand == Command.INLINE.value:
+        run_method = inliner.run_inline
+    else:
+        parser.description = "Extract, transform, and load FHIR data."
+        if not subcommand:
+            # Add a note about other subcommands we offer, and tell argparse not to wrap our formatting
+            parser.formatter_class = argparse.RawDescriptionHelpFormatter
+            parser.description += "\n\nother commands available:\n"
+            parser.description += "  convert\n  export\n  init\n  inline\n  upload-notes"
+        run_method = etl.run_etl
+
+    with tempfile.TemporaryDirectory() as tempdir:
+        common.set_global_temp_dir(tempdir)
+        await run_method(parser, argv)
+
+
+def main_cli():
+    asyncio.run(main(sys.argv[1:]))  # pragma: no cover
+
+
+if __name__ == "__main__":
+    main_cli()  # pragma: no cover