carrot-transform 0.3__tar.gz

carrot_transform-0.3/.github/workflows/pypi.publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+name: Upload Python Package
+
+# on:
+#   release:
+#     types: [published]
+on: push
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish Python distribution to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/carrot-transform
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

carrot_transform-0.3/.gitignore

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

carrot_transform-0.3/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-0.3/MANIFEST.in

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+include carrottransform/config/*.sql
+include carrottransform/config/*.json

carrot_transform-0.3/PKG-INFO

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+Metadata-Version: 2.1
+Name: carrot-transform
+Version: 0.3
+Summary: Carrot somple transformer, input rules and data csvs, output OMOP
+Author-email: PD Appleby <pdappleby@gmail.com>
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# carrot-transform
+
+TODO: 
+* Document carrot-transform 
+* Add more comments in-code
+* Handle capture of ddl and json config via the command-line as optional args
+
+Reduction in complexity over the original CaRROT-CDM version for the Transform part of *ETL* - In practice *Extract* is always 
+performed by Data Partners, *Load* by database bulk-load software.
+
+Statistics
+
+External libraries imported (approximate)
+
+carrot-cdm      61
+carrot-transform 12

carrot_transform-0.3/README.md

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+# carrot-transform
+
+TODO: 
+* Document carrot-transform 
+* Add more comments in-code
+* Handle capture of ddl and json config via the command-line as optional args
+
+Reduction in complexity over the original CaRROT-CDM version for the Transform part of *ETL* - In practice *Extract* is always 
+performed by Data Partners, *Load* by database bulk-load software.
+
+Statistics
+
+External libraries imported (approximate)
+
+carrot-cdm      61
+carrot-transform 12

carrot_transform-0.3/carrot_transform.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: carrot-transform
+Version: 0.3
+Summary: Carrot somple transformer, input rules and data csvs, output OMOP
+Author-email: PD Appleby <pdappleby@gmail.com>
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# carrot-transform
+
+TODO: 
+* Document carrot-transform 
+* Add more comments in-code
+* Handle capture of ddl and json config via the command-line as optional args
+
+Reduction in complexity over the original CaRROT-CDM version for the Transform part of *ETL* - In practice *Extract* is always 
+performed by Data Partners, *Load* by database bulk-load software.
+
+Statistics
+
+External libraries imported (approximate)
+
+carrot-cdm      61
+carrot-transform 12

carrot_transform-0.3/carrot_transform.egg-info/SOURCES.txt

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+.gitignore
+LICENSE
+MANIFEST.in
+README.md
+carrot_transform.py
+pyproject.toml
+.github/workflows/pypi.publish.yml
+carrot_transform.egg-info/PKG-INFO
+carrot_transform.egg-info/SOURCES.txt
+carrot_transform.egg-info/dependency_links.txt
+carrot_transform.egg-info/entry_points.txt
+carrot_transform.egg-info/top_level.txt
+carrottransform/__init__.py
+carrottransform/_version.py
+carrottransform/cli/__init__.py
+carrottransform/cli/command.py
+carrottransform/cli/subcommands/__init__.py
+carrottransform/cli/subcommands/run.py
+carrottransform/config/OMOPCDM_postgresql_5.3_ddl.sql
+carrottransform/config/omop.json
+carrottransform/tools/__init__.py
+carrottransform/tools/file_helpers.py
+carrottransform/tools/mappingrules.py
+carrottransform/tools/metrics.py
+carrottransform/tools/omopcdm.py

carrot_transform-0.3/carrot_transform.egg-info/dependency_links.txt

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+

carrot_transform-0.3/carrot_transform.egg-info/entry_points.txt

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+[console_scripts]
+carrot-transform = carrottransform.cli.command:transform

carrot_transform-0.3/carrot_transform.egg-info/top_level.txt

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+carrottransform

carrot_transform-0.3/carrot_transform.py

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+# Provides an entry point for the built executable
+from carrottransform.cli.command import transform
+if __name__ == '__main__':
+  transform()

carrot_transform-0.3/carrottransform/__init__.py

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+from ._version import __version__
+
+params = {
+  'version':__version__,
+}

carrot_transform-0.3/carrottransform/_version.py

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+# TODO - pick this up automatically when building
+__version__ = '0.3'

carrot_transform-0.3/carrottransform/cli/command.py

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