PyPI - carrot-transform - Versions diffs - 0.3.2__tar.gz → 0.3.3__tar.gz - Mend

carrot-transform 0.3.2tar.gz → 0.3.3tar.gz

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carrot_transform-0.3.3/PKG-INFO ADDED Viewed

@@ -0,0 +1,48 @@
+Metadata-Version: 2.3
+Name: carrot_transform
+Version: 0.3.3
+Summary:
+Author: anwarfg
+Author-email: 913028+anwarfg@users.noreply.github.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: click (>=8.1.7,<9.0.0)
+Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
+Requires-Dist: pandas (>=2.2.3,<3.0.0)
+Description-Content-Type: text/markdown
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="/images/logo-dark.png">
+    <img alt="Carrot Logo" src="/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Mapping to OMOP</h2>
+  <a href="https://carrot.ac.uk/">Carrot Tranform</a> executes the conversion of the data to the OMOP CDM.<br />
+  </strong>
+</div>
+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-0.3.3/README.md ADDED Viewed

@@ -0,0 +1,30 @@
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="/images/logo-dark.png">
+    <img alt="Carrot Logo" src="/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Mapping to OMOP</h2>
+  <a href="https://carrot.ac.uk/">Carrot Tranform</a> executes the conversion of the data to the OMOP CDM.<br />
+  </strong>
+</div>
+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-0.3.2 → carrot_transform-0.3.3}/carrottransform/config/omop.json RENAMED Viewed

@@ -26,6 +26,10 @@
     "visit_occurrence": {
 	    "visit_start_datetime": "visit_start_date",
 	    "visit_end_datetime": "visit_end_date"
+    },
+    "device_exposure": {
+	    "device_exposure_start_datetime": "device_exposure_start_date",
+	    "device_exposure_end_datetime": "device_exposure_end_date"
     }
   },
   "date_field_components": {
@@ -46,6 +50,7 @@
     "person": "person_id",
     "procedure_occurrence": "person_id",
     "specimen": "person_id",
+    "device_exposure": "person_id",
     "visit_occurrence": "person_id"
   },
   "auto_number_field": {
@@ -56,6 +61,7 @@
     "observation": "observation_id",
     "procedure_occurrence": "procedure_occurrence_id",
     "specimen": "specimen_id",
+    "device_exposure": "device_exposure_id",
     "visit_occurrence": "visit_occurrence_id"
   }
 }

carrot_transform-0.3.3/pyproject.toml ADDED Viewed

@@ -0,0 +1,20 @@
+[tool.poetry]
+name = "carrot_transform"
+version = "0.3.3"
+description = ""
+authors = ["anwarfg <913028+anwarfg@users.noreply.github.com>"]
+readme = "README.md"
+packages = [
+    { include = "carrottransform" }
+]
+[tool.poetry.dependencies]
+python = "^3.10"
+click = "^8.1.7"
+pandas = "^2.2.3"
+jinja2 = "^3.1.4"
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

carrot_transform-0.3.2/.github/workflows/pypi.publish.yml DELETED Viewed

@@ -1,55 +0,0 @@
-# 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-0.3.2/.gitignore DELETED Viewed

@@ -1,12 +0,0 @@
-data
-.ipynb_checkpoints
-*_pycache_*
-*.whl
-*.spec
-*egg-info
-dist
-.DS_store
-build
-*.env
-temp
-.python-version

carrot_transform-0.3.2/MANIFEST.in DELETED Viewed

	@@ -1,2 +0,0 @@
1	- include carrottransform/config/*.sql
2	- include carrottransform/config/*.json

carrot_transform-0.3.2/PKG-INFO DELETED Viewed

@@ -1,28 +0,0 @@
-Metadata-Version: 2.1
-Name: carrot-transform
-Version: 0.3.2
-Summary: Carrot simple transformer, input rules and data csv's, 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-0.3.2/README.md DELETED Viewed

@@ -1,16 +0,0 @@
-# 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-0.3.2/carrot_transform.egg-info/PKG-INFO DELETED Viewed

@@ -1,28 +0,0 @@
-Metadata-Version: 2.1
-Name: carrot-transform
-Version: 0.3.2
-Summary: Carrot simple transformer, input rules and data csv's, 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-0.3.2/carrot_transform.egg-info/SOURCES.txt DELETED Viewed

@@ -1,25 +0,0 @@
-.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-0.3.2/carrot_transform.egg-info/dependency_links.txt DELETED Viewed

	@@ -1 +0,0 @@
1	-

carrot_transform-0.3.2/carrot_transform.egg-info/entry_points.txt DELETED Viewed

	@@ -1,2 +0,0 @@
1	- [console_scripts]
2	- carrot-transform = carrottransform.cli.command:transform

carrot_transform-0.3.2/carrot_transform.egg-info/top_level.txt DELETED Viewed

	@@ -1 +0,0 @@
1	- carrottransform

carrot_transform-0.3.2/carrot_transform.py DELETED Viewed

@@ -1,5 +0,0 @@
-# Provides an entry point for the built executable
-# Build with "pyinstaller --onefile carrot_transform.py"
-from carrottransform.cli.command import transform
-if __name__ == '__main__':
-  transform()

carrot_transform-0.3.2/pyproject.toml DELETED Viewed

@@ -1,20 +0,0 @@
-[build-system]
-requires = ["setuptools", "setuptools-scm"]
-build-backend = "setuptools.build_meta"
-[project]
-name = "carrot-transform"
-version = "0.3.2"
-authors = [
-  { name="PD Appleby", email="pdappleby@gmail.com" },
-]
-description = "Carrot simple transformer, input rules and data csv's, output OMOP"
-readme = "README.md"
-requires-python = ">=3.9"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
-]
-[project.scripts]
-carrot-transform="carrottransform.cli.command:transform"