carrot-transform 0.7.1__tar.gz

carrot_transform-0.7.1/.gitignore

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+data
+.ipynb_checkpoints
+*_pycache_*
+*.whl
+*.spec
+*egg-info
+dist
+.DS_store
+build
+*.env
+temp
+.python-version
+
+*.orig
+.mypy_cache/
+.venv/*

carrot_transform-0.7.1/LICENSE

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+MIT License
+
+Copyright (c) [2024] [Philip Duncan Appleby]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

carrot_transform-0.7.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: carrot_transform
+Version: 0.7.1
+Author-email: anwarfg <913028+anwarfg@users.noreply.github.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: awscli>=1.42.74
+Requires-Dist: boto3>=1.40.74
+Requires-Dist: case-insensitive-dictionary>=0.2.1
+Requires-Dist: click<9,>=8.1.7
+Requires-Dist: minio>=7.2.20
+Requires-Dist: psycopg2-binary>=2.9.10
+Requires-Dist: sqlalchemy>=2.0.42
+Requires-Dist: trino>=0.335.0
+Description-Content-Type: text/markdown
+
+
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-dark.png">
+    <img alt="Carrot Logo" src="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+
+
+<p align="center">
+
+<a href="https://github.com/Health-Informatics-UoN/carrot-transform/releases">
+  <img src="https://img.shields.io/github/v/release/Health-Informatics-UoN/carrot-transform" alt="Release">
+</a>
+<a href="https://opensource.org/license/mit">
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License">
+</a>
+</p>
+
+
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Transformation to OMOP</h2><br />
+<a href="https://carrot.ac.uk/">Carrot Transform</a> automates data transformation processes and facilitates the standardisation of datasets to the OMOP vocabulary, simplifying the integration of diverse data sources.
+  <br />
+  </strong>
+</div>
+
+<p align="center">
+  <br />
+  <a href="https://carrot.ac.uk/transform" rel="dofollow"><strong>Explore the docs »</strong></a>
+  <br />
+<br />  
+
+<a href="https://carrot.ac.uk/">Carrot Mapper</a> is a webapp which allows the user to use the metadata (as output by [WhiteRabbit](https://github.com/OHDSI/WhiteRabbit)) from a dataset to produce mapping rules to the OMOP standard, in the JSON format. These can be ingested by [Carrot Transform](https://carrot.ac.uk/transform/quickstart) to perform the mapping of the contents of the dataset to OMOP.
+
+Carrot Transform transforms input data into tab separated variable files of standard OMOP tables, with  concepts mapped according to the provided rules (generated from Carrot Mapper).
+
+## Quick Start
+
+To have the project up and running, please follow the [Quick Start Guide](https://carrot.ac.uk/transform/quickstart).
+
+If you need to perform development, [there's a brief guide here](https://carrot.ac.uk/transform/development) to get the tool up and running.
+
+## Formatting and Linting
+
+This project is using [ruff](https://docs.astral.sh/ruff/) to check formatting and linting. 
+The only dependency is the [`uv` command line tool.](https://docs.astral.sh/uv/)
+The `.vscode/tasks.json` file contains a task to run this tool for the currently open file. 
+The commands can be run on thier own (in the root folder) like this ...
+
+```bash
+# reformat all the files in `./`
+λ uv run ruff format .
+
+# run linting checks all the files in `./` 
+λ uv run ruff check .
+
+# check and fix all the files in `./`
+λ uv run ruff check --fix .
+
+# check and fix all the files in `./` but do so so more eggrsively
+λ uv run ruff check --fix --unsafe-fixes .
+```
+
+## SQLAlchemy Workflow
+
+Carrot-Transform can read input tables from [SQLAlchemy](https://www.sqlalchemy.org/).
+This is experimental, and requires [specifying a connection-string](https://docs.sqlalchemy.org/en/20/tutorial/engine.html) as `--input-db-url` instead of an input dir folder.
+The person-file parameter and carrot-mapper workflow should still be used, as if working with .csv files, but carrot-transform can read from an SQLAlchemy database.
+
+1. Extract/export some rows from the various tables
+    - something like `SELECT column_name(s) FROM patients LIMIT 1000;` is written to `patients.csv`
+2. the usual [scan reports](https://carrot.ac.uk/mapper/user_guide/projects_datasets_scanreports) are performed on these subsets
+3. [when carrot-transform is invoked](https://carrot.ac.uk/transform/quickstart) instead of `--input-dir` one specifies `--input-db-url` with a database connection string
+    - the `--person-file` parameter should still point to the equivalent of `person_tablename.csv`
+    - the `--rules-file` parameter needs to refer to a file on the disk as usual
+4. carrot transform will still write data to `--output-dir` and otherwise operate as normal
+    - The following parameters have undefined behaviour with this functionality
+      - `--write-mode`
+      - `--saved-person-id-file`
+      - `--use-input-person-ids`
+      - `--last-used-ids-file`
+
+## Release Procedure 
+
+To release a new version of `carrot-transform` [follow the steps outlined on the documentation website.](https://carrot.ac.uk/transform/development#release) 
+
+## License
+
+This repository's source code is available under the [MIT license](LICENSE).

carrot_transform-0.7.1/README.md

@@ -0,0 +1,93 @@
+
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-dark.png">
+    <img alt="Carrot Logo" src="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+
+
+<p align="center">
+
+<a href="https://github.com/Health-Informatics-UoN/carrot-transform/releases">
+  <img src="https://img.shields.io/github/v/release/Health-Informatics-UoN/carrot-transform" alt="Release">
+</a>
+<a href="https://opensource.org/license/mit">
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License">
+</a>
+</p>
+
+
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Transformation to OMOP</h2><br />
+<a href="https://carrot.ac.uk/">Carrot Transform</a> automates data transformation processes and facilitates the standardisation of datasets to the OMOP vocabulary, simplifying the integration of diverse data sources.
+  <br />
+  </strong>
+</div>
+
+<p align="center">
+  <br />
+  <a href="https://carrot.ac.uk/transform" rel="dofollow"><strong>Explore the docs »</strong></a>
+  <br />
+<br />  
+
+<a href="https://carrot.ac.uk/">Carrot Mapper</a> is a webapp which allows the user to use the metadata (as output by [WhiteRabbit](https://github.com/OHDSI/WhiteRabbit)) from a dataset to produce mapping rules to the OMOP standard, in the JSON format. These can be ingested by [Carrot Transform](https://carrot.ac.uk/transform/quickstart) to perform the mapping of the contents of the dataset to OMOP.
+
+Carrot Transform transforms input data into tab separated variable files of standard OMOP tables, with  concepts mapped according to the provided rules (generated from Carrot Mapper).
+
+## Quick Start
+
+To have the project up and running, please follow the [Quick Start Guide](https://carrot.ac.uk/transform/quickstart).
+
+If you need to perform development, [there's a brief guide here](https://carrot.ac.uk/transform/development) to get the tool up and running.
+
+## Formatting and Linting
+
+This project is using [ruff](https://docs.astral.sh/ruff/) to check formatting and linting. 
+The only dependency is the [`uv` command line tool.](https://docs.astral.sh/uv/)
+The `.vscode/tasks.json` file contains a task to run this tool for the currently open file. 
+The commands can be run on thier own (in the root folder) like this ...
+
+```bash
+# reformat all the files in `./`
+λ uv run ruff format .
+
+# run linting checks all the files in `./` 
+λ uv run ruff check .
+
+# check and fix all the files in `./`
+λ uv run ruff check --fix .
+
+# check and fix all the files in `./` but do so so more eggrsively
+λ uv run ruff check --fix --unsafe-fixes .
+```
+
+## SQLAlchemy Workflow
+
+Carrot-Transform can read input tables from [SQLAlchemy](https://www.sqlalchemy.org/).
+This is experimental, and requires [specifying a connection-string](https://docs.sqlalchemy.org/en/20/tutorial/engine.html) as `--input-db-url` instead of an input dir folder.
+The person-file parameter and carrot-mapper workflow should still be used, as if working with .csv files, but carrot-transform can read from an SQLAlchemy database.
+
+1. Extract/export some rows from the various tables
+    - something like `SELECT column_name(s) FROM patients LIMIT 1000;` is written to `patients.csv`
+2. the usual [scan reports](https://carrot.ac.uk/mapper/user_guide/projects_datasets_scanreports) are performed on these subsets
+3. [when carrot-transform is invoked](https://carrot.ac.uk/transform/quickstart) instead of `--input-dir` one specifies `--input-db-url` with a database connection string
+    - the `--person-file` parameter should still point to the equivalent of `person_tablename.csv`
+    - the `--rules-file` parameter needs to refer to a file on the disk as usual
+4. carrot transform will still write data to `--output-dir` and otherwise operate as normal
+    - The following parameters have undefined behaviour with this functionality
+      - `--write-mode`
+      - `--saved-person-id-file`
+      - `--use-input-person-ids`
+      - `--last-used-ids-file`
+
+## Release Procedure 
+
+To release a new version of `carrot-transform` [follow the steps outlined on the documentation website.](https://carrot.ac.uk/transform/development#release) 
+
+## License
+
+This repository's source code is available under the [MIT license](LICENSE).

carrot_transform-0.7.1/carrottransform/__init__.py

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+from ._version import __version__
+
+params = {
+    "version": __version__,
+}
+
+
+def require(con: bool, msg: str = ""):
+    """this is a run-time check for various things that are needed, but, don't feel "worth" more elabourate checks"""
+
+    # if the condition passes; return
+    if con:
+        return
+
+    # prepare the message for output
+    if msg == "":
+        pass  # if there's no message; leave it as a short string
+    else:
+        # if there is a message;
+        msg = "\n\t" + msg
+
+    import inspect
+
+    # Get the calling frame and its code context
+    currentframe = inspect.currentframe()
+
+    # most of the complexity here is because of mypy checks
+    frame = currentframe.f_back if currentframe is not None else None
+    frame_info = inspect.getframeinfo(frame) if frame is not None else None
+    context = frame_info.code_context if frame_info is not None else None
+
+    prefix: str
+    if context and frame_info:
+        call_line: str = context[0].strip()
+        prefix = f"failed {frame_info.filename}:{frame_info.lineno}: {call_line}"
+    elif frame_info is not None:
+        prefix = f"failed {frame_info.filename}:{frame_info.lineno}"
+    else:
+        prefix = "failed requirement"
+
+    raise AssertionError(prefix + msg)

carrot_transform-0.7.1/carrottransform/_version.py

@@ -0,0 +1,6 @@
+from importlib.metadata import version
+
+try:
+    __version__ = version("carrot_transform")  # Defined in the pyproject.toml
+except Exception:
+    __version__ = "unknown"

carrot_transform-0.7.1/carrottransform/cli/command.py

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+# Package entry point - sets up the "run" subcommand
+import click
+
+import carrottransform as c
+
+from .subcommands.run import run
+
+
+@click.group(invoke_without_command=True)
+@click.option("--version", "-v", is_flag=True)
+@click.pass_context
+def transform(ctx, version):
+    if ctx.invoked_subcommand is None:
+        if version:
+            click.echo(c.__version__)
+        else:
+            click.echo(ctx.get_help())
+        return
+
+
+transform.add_command(run, "run")
+
+if __name__ == "__main__":
+    transform()