dzdomop 0.3.1__tar.gz

dzdomop-0.3.1/PKG-INFO

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+Metadata-Version: 2.2
+Name: dzdomop
+Version: 0.3.1
+Summary: A Python ORM/data classes representation of the OMOP Common Data Model in different flavors powered by sqlacodegen
+Author-email: Tim Bleimehl <bleimehl@helmholtz-munich.de>
+License: MIT
+Project-URL: Source, https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
+Project-URL: Issues, https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models/issues
+Keywords: DZD,OMOP
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: sqlmodel
+Requires-Dist: sqlalchemy
+Requires-Dist: tqdm
+Requires-Dist: pg8000
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: deepdiff; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Requires-Dist: mkdocs-autorefs; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+
+# DZD - OMOP CDM Python ORM/Data Classes Representation
+A Python ORM/data classes representation of the [Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)](https://www.ohdsi.org/data-standardization/) in different flavors powered by [sqlacodegen](https://github.com/agronholm/sqlacodegen)
+
+Author/Maintainer: Tim Bleimehl  
+
+For more background how this sausage is made have a look at the github repo at https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
+
+This Readme is a "work in process". Come back later for a more complete manual.
+
+# Install
+
+Just install the python module from pypi.org
+
+`python -m pip install --upgrade dzdomop`
+
+# How to use
+
+
+
+This tiny script demostrates how this module can help you to
+* Create a local dev database with the complete omop datamodel
+* insert some data based on our classes with some basic guardrails like type validation, typo prevention, ...
+
+```python
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+from omopmodel import OMOP_5_3_declarative as omop
+
+# Create a local SQLite database with all OMOP CDM tables+properties
+engine = create_engine("sqlite:///cdm_source.db", echo=True)
+omop.Base.metadata.create_all(engine)
+
+# Create a some basic OMOP objects
+care_site = omop.CareSite(care_site_id=5678, care_site_name="St. Local")
+person = omop.Person(
+    person_id=1234,
+    year_of_birth=1985,
+    care_site=care_site,
+    gender_concept_id=1,
+    race_concept_id=1,
+    ethnicity_concept_id=1,
+)
+
+# Write the Object to the database
+with Session(engine) as session:
+    session.add(care_site)
+    session.add(person)
+    session.commit()
+```
+

dzdomop-0.3.1/README.md

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+# DZD - OMOP CDM Python ORM/Data Classes Representation
+A Python ORM/data classes representation of the [Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)](https://www.ohdsi.org/data-standardization/) in different flavors powered by [sqlacodegen](https://github.com/agronholm/sqlacodegen)
+
+Author/Maintainer: Tim Bleimehl  
+
+For more background how this sausage is made have a look at the github repo at https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
+
+This Readme is a "work in process". Come back later for a more complete manual.
+
+# Install
+
+Just install the python module from pypi.org
+
+`python -m pip install --upgrade dzdomop`
+
+# How to use
+
+
+
+This tiny script demostrates how this module can help you to
+* Create a local dev database with the complete omop datamodel
+* insert some data based on our classes with some basic guardrails like type validation, typo prevention, ...
+
+```python
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+from omopmodel import OMOP_5_3_declarative as omop
+
+# Create a local SQLite database with all OMOP CDM tables+properties
+engine = create_engine("sqlite:///cdm_source.db", echo=True)
+omop.Base.metadata.create_all(engine)
+
+# Create a some basic OMOP objects
+care_site = omop.CareSite(care_site_id=5678, care_site_name="St. Local")
+person = omop.Person(
+    person_id=1234,
+    year_of_birth=1985,
+    care_site=care_site,
+    gender_concept_id=1,
+    race_concept_id=1,
+    ethnicity_concept_id=1,
+)
+
+# Write the Object to the database
+with Session(engine) as session:
+    session.add(care_site)
+    session.add(person)
+    session.commit()
+```
+

dzdomop-0.3.1/dzdomop.egg-info/PKG-INFO

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+Metadata-Version: 2.2
+Name: dzdomop
+Version: 0.3.1
+Summary: A Python ORM/data classes representation of the OMOP Common Data Model in different flavors powered by sqlacodegen
+Author-email: Tim Bleimehl <bleimehl@helmholtz-munich.de>
+License: MIT
+Project-URL: Source, https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
+Project-URL: Issues, https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models/issues
+Keywords: DZD,OMOP
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: sqlmodel
+Requires-Dist: sqlalchemy
+Requires-Dist: tqdm
+Requires-Dist: pg8000
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: deepdiff; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Requires-Dist: mkdocs-autorefs; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+
+# DZD - OMOP CDM Python ORM/Data Classes Representation
+A Python ORM/data classes representation of the [Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)](https://www.ohdsi.org/data-standardization/) in different flavors powered by [sqlacodegen](https://github.com/agronholm/sqlacodegen)
+
+Author/Maintainer: Tim Bleimehl  
+
+For more background how this sausage is made have a look at the github repo at https://github.com/DZD-eV-Diabetes-Research/dzd-omop-cdm-python-models
+
+This Readme is a "work in process". Come back later for a more complete manual.
+
+# Install
+
+Just install the python module from pypi.org
+
+`python -m pip install --upgrade dzdomop`
+
+# How to use
+
+
+
+This tiny script demostrates how this module can help you to
+* Create a local dev database with the complete omop datamodel
+* insert some data based on our classes with some basic guardrails like type validation, typo prevention, ...
+
+```python
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+from omopmodel import OMOP_5_3_declarative as omop
+
+# Create a local SQLite database with all OMOP CDM tables+properties
+engine = create_engine("sqlite:///cdm_source.db", echo=True)
+omop.Base.metadata.create_all(engine)
+
+# Create a some basic OMOP objects
+care_site = omop.CareSite(care_site_id=5678, care_site_name="St. Local")
+person = omop.Person(
+    person_id=1234,
+    year_of_birth=1985,
+    care_site=care_site,
+    gender_concept_id=1,
+    race_concept_id=1,
+    ethnicity_concept_id=1,
+)
+
+# Write the Object to the database
+with Session(engine) as session:
+    session.add(care_site)
+    session.add(person)
+    session.commit()
+```
+

dzdomop-0.3.1/dzdomop.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+dzdomop.egg-info/PKG-INFO
+dzdomop.egg-info/SOURCES.txt
+dzdomop.egg-info/dependency_links.txt
+dzdomop.egg-info/requires.txt
+dzdomop.egg-info/top_level.txt
+examples/postgresql_create_omop_schema_and_load_vocab.py
+examples/sqlite_create_omop_schema_and_load_vocab.py
+examples/sqlite_insert_person.py
+examples/sqlite_insert_person_sqlmodel_wip.py
+omopmodel/OMOP_5_3_dataclasses.py
+omopmodel/OMOP_5_3_declarative.py
+omopmodel/OMOP_5_3_sqlmodels.py
+omopmodel/OMOP_5_3_tables.py
+omopmodel/OMOP_5_4_dataclasses.py
+omopmodel/OMOP_5_4_declarative.py
+omopmodel/OMOP_5_4_sqlmodels.py
+omopmodel/OMOP_5_4_tables.py
+omopmodel/__init__.py
+omopmodel/vocabularies_loader.py

dzdomop-0.3.1/dzdomop.egg-info/dependency_links.txt

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+

dzdomop-0.3.1/dzdomop.egg-info/requires.txt

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+sqlmodel
+sqlalchemy
+tqdm
+pg8000
+
+[docs]
+mkdocs
+mkdocstrings[python]
+mkdocs-autorefs
+mkdocs-material
+
+[test]
+pytest
+deepdiff

dzdomop-0.3.1/dzdomop.egg-info/top_level.txt

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+omopmodel

dzdomop-0.3.1/examples/postgresql_create_omop_schema_and_load_vocab.py

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+from sqlalchemy import create_engine
+from omopmodel import OMOP_5_4_declarative as omop54
+from omopmodel import VocabulariesLoader
+
+# Define the connection to our running postgresql database
+engine = create_engine("postgresql+pg8000://ps:ps@localhost/ps")
+
+# Define the directory where our athena vocabularies csv files are stored.
+authena_export_directory = "/home/me/Downloads/AthenaUnzipped"
+
+# Create the OMOP Schema on our database
+omop54.Base.metadata.create_all(engine)
+
+# Initialize the vocabulary loader.
+v = VocabulariesLoader(
+    authena_export_directory,
+    database_engine=engine,
+    omop_module=omop54,  # <- This is optional. default is OMOP CDM V5.4
+)
+# Load the vocaablary from the CSV files into the database.
+# This will take some time, you will see some progress bars.
+# Take your time make a coffe
+v.load_all()

dzdomop-0.3.1/examples/sqlite_create_omop_schema_and_load_vocab.py

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+from sqlalchemy import create_engine
+from omopmodel import OMOP_5_4_declarative as omop54
+from omopmodel import VocabulariesLoader
+
+# Define the connection to our sqlite database.
+# if it does not exists, it will created on the fly
+engine = create_engine("sqlite:///cdm_source.db", echo=False)
+
+# Define the directory where our athena vocabularies csv files are stored.
+authena_export_directory = "/home/tim/Downloads/tmp/athenalars"
+
+# Create the OMOP Schema on our database
+omop54.Base.metadata.create_all(engine)
+
+# Initialize the vocabulary loader.
+v = VocabulariesLoader(
+    authena_export_directory,
+    database_engine=engine,
+    omop_module=omop54,  # <- This is optional. default is OMOP CDM V5.4
+)
+# Load the vocabulary from the CSV files into the database.
+# HINT: If you are using a sqlite database this can take unbearably long
+# sqlite is for testing and tinkering but will have a hard time storing larger vocabulary exports
+# Use postgresql instead
+v.load_all()

dzdomop-0.3.1/examples/sqlite_insert_person.py

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+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+from omopmodel import OMOP_5_3_declarative as omop53
+
+# Create a SQLite database and deploy the omop schema (tables,constraints, indices and primary keys)
+
+engine = create_engine("sqlite:///cdm_source.db", echo=False)
+
+# Create the schema if not done
+omop53.Base.metadata.create_all(engine)
+
+# Define a caresite and a person. Connect these two
+care_site = omop53.CareSite(care_site_id=5678, care_site_name="St. Local")
+person = omop53.Person(
+    person_id=1234,
+    year_of_birth=1985,
+    care_site=care_site,
+    gender_concept_id=0,
+    race_concept_id=0,
+    ethnicity_concept_id=0,
+)
+
+# Open a session and write these object/rows to the database
+with Session(engine) as session:
+    session.add(care_site)
+    session.add(person)
+    session.commit()

dzdomop-0.3.1/examples/sqlite_insert_person_sqlmodel_wip.py

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+from sqlmodel import SQLModel, Session, create_engine
+
+
+from omopmodel import OMOP_5_4_sqlmodels as omop54
+
+
+# Create a SQLite database and deploy the omop schema (tables,constraints, indices and primary keys)
+
+engine = create_engine("sqlite:///cdm_source.db", echo=False)
+
+# Create the schema if not done
+SQLModel.metadata.create_all(engine)
+
+# Define a caresite and a person. Connect these two
+care_site = omop54.CareSite(care_site_id=5678, care_site_name="St. Local")
+person = omop54.Person(
+    person_id=1234,
+    year_of_birth=1985,
+    care_site=care_site,
+    gender_concept_id=0,
+    race_concept_id=0,
+    ethnicity_concept_id=0,
+)
+
+# Open a session and write these object/rows to the database
+with Session(engine) as session:
+    session.add(care_site)
+    session.add(person)
+    session.commit()