refactor

.github/workflows/main.yml

@@ -13,14 +13,14 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.10'  # Ensure this matches your project's requirements
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install duckdb  # Install the duckdb package
+        pip install duckdb==1.0.0
 
     - name: Run MotherDuck Test
       env:
         MOTHERDUCK_TOKEN: ${{ secrets.MOTHERDUCK_TOKEN }}
-      run: python ./tests/motherduck_test.py
+      run: python ./hestia/tests/motherduck_test.py

.gitignore

@@ -1,8 +1,7 @@
+notebooks/
+data/*
 
 .ruff_cache
-.old
-.vscode
-
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

CHANGELOG.md

@@ -0,0 +1,40 @@
+# Changelog
+
+## [0.2.0](https://github.com/OHDSI/Hestia/compare/v0.1.0...v0.2.0) (2024-03-05)
+
+
+### Features
+
+* added dev container ([3ddcc41](https://github.com/OHDSI/Hestia/commit/3ddcc4104b618c622a9f8e13f0b98d4810bb89f0))
+* added dev container ([3934c53](https://github.com/OHDSI/Hestia/commit/3934c5373e806430402851f067537a45f535590c))
+
+
+### Bug Fixes
+
+* release-please set to push for main ([5682581](https://github.com/OHDSI/Hestia/commit/568258197dd56a08b451f267a46e83a100e7657e))
+
+
+### Documentation
+
+* added CONTRIBUTING.md ([54d393c](https://github.com/OHDSI/Hestia/commit/54d393c5131504d95391de3b0e2087d61b10a06a))
+* organization ([9efe22f](https://github.com/OHDSI/Hestia/commit/9efe22f9c83e70e5b1caed9e20c58dc810296d81))
+* typo ([e32f838](https://github.com/OHDSI/Hestia/commit/e32f83821de303ad17f96b1aba0bce7d6ba4d1c6))
+* update readme ([fc8f48a](https://github.com/OHDSI/Hestia/commit/fc8f48a17319725e2bcd06067b30b459f48c6297))
+* updated contrib ([2f2ead3](https://github.com/OHDSI/Hestia/commit/2f2ead3f73cd487022b13e1337f8c92770a0353f))
+* updated readme ([aaae4da](https://github.com/OHDSI/Hestia/commit/aaae4dae9e26113186b08920032dce200994201c))
+* updated README ([2919cec](https://github.com/OHDSI/Hestia/commit/2919cec4cafdc67b572405900620fd50f449b2bf))
+* updated security.md ([6272ebc](https://github.com/OHDSI/Hestia/commit/6272ebcb57ce65d7b600e8d8253f35430e3a3dd0))
+* updates ([b6c6be3](https://github.com/OHDSI/Hestia/commit/b6c6be3502c44e79892eb3872b97ed1b055cad2d))
+
+## 0.1.0 (2024-02-16)
+
+
+### Features
+
+* added setup.cfg ([7aff036](https://github.com/OHDSI/Hestia/commit/7aff036b5b1e437220c725532d063eccddb97a8c))
+
+
+### Documentation
+
+* added code owner ([887b7df](https://github.com/OHDSI/Hestia/commit/887b7dfa3e494c21e84d548df19e1ddc5e09eaf0))
+* added templates and file structure ([3d33b3d](https://github.com/OHDSI/Hestia/commit/3d33b3d399144224116690ef1ddc215f229f3413))

README.md

@@ -17,6 +17,21 @@ Hestia is an implementation of the OpenAPI standard to the OMOP CDM and OHDSI to
 ## Design
 
 
+## Technology
+
+| Name | Licence |
+|------|---------|
+| [FastAPI](https://fastapi.tiangolo.com/) | MIT |
+| [Ibis](https://ibis-project.org/) | Apache License 2.0 |
+| [Pydantic](https://docs.pydantic.dev/latest/) | MIT |
+| [Duckdb](https://github.com/duckdb/duckdb) | MIT |
+| [Pytest](https://github.com/pytest-dev/pytest) | MIT |
+| [Ruff](https://github.com/astral-sh/ruff) | MIT |
+| [Docker Engine](https://docs.docker.com/engine/) | Apache License 2.0 |
+| [FastUI](https://github.com/pydantic/FastUI) | MIT|
+
+
+
 ## Installation
 
 ```bash
@@ -49,7 +64,11 @@ Pre-alpha
 
 - Please read our [CONTRIBUTING.md](.github/CONTRIBUTING.md) document.
 
-- We use [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0-beta.2/) to assist with change log automation, please use this style as much as possible.
+
+## References
+
+- [zhanymkanov/fastapi-best-practices](https://github.com/zhanymkanov/fastapi-best-practices?tab=readme-ov-file#project-structure)
+- [tiangolo/full-stack-fastapi-template](https://github.com/tiangolo/full-stack-fastapi-template)
 
 ## License
 Hestia is licensed under [Apache License 2.0](./LICENSE)

hestia/.dockerignore

@@ -0,0 +1,8 @@
+# Python
+__pycache__
+app.egg-info
+*.pyc
+.mypy_cache
+.coverage
+htmlcov
+.venv

hestia/.gitignore

@@ -0,0 +1,8 @@
+__pycache__
+app.egg-info
+*.pyc
+.mypy_cache
+.coverage
+htmlcov
+.cache
+.venv

hestia/app/api/endpoints/endpoint_concept.py

@@ -0,0 +1,15 @@
+# app/api/endpoints/endpoint_concept.py
+
+from fastapi import APIRouter, Depends, HTTPException
+from sqlalchemy.orm import Session
+from app.crud import crud_concept
+from app.db.session import get_db  # Assuming you have a function to get the DB session
+
+router = APIRouter()
+
+@router.get("/concept/{concept_id}")
+def read_concept(concept_id: int, db: Session = Depends(get_db)):
+    db_concept = crud_concept.get_concept(db, concept_id=concept_id)
+    if db_concept is None:
+        raise HTTPException(status_code=404, detail="Concept not found")
+    return db_concept

hestia/app/db/queries.py

@@ -0,0 +1,161 @@
+
+### CARE SITE ###
+
+
+
+### CONDITION ###
+
+### CONDITION ERA ###
+
+### CONDITION OCCURRENCE COMBINATIONS ###
+
+
+
+
+### DRUG ###
+
+### DRUG COST ###
+
+### DRUG ERA ###
+
+### DRUG EXPOSURE ###
+
+### OBSERVATION PERIOD ###
+
+### OBSERVATION ###
+
+### PAYER PLAN ###
+
+### PROCEDURE ###
+
+### PERSON ###
+
+
+
+
+### GENERAL ###
+
+
+
+# G01: Find concept by concept ID
+def find_concept_by_concept_id(concept_id, connection):
+    """
+    This is the most generic look-up for obtaining concept details associated with a concept identifier. The query is intended as a tool for quick reference for the name, class, level and source vocabulary details associated with a concept identifier.
+    
+    Parameters:
+        concept_id (int): The ID of the concept to retrieve.
+        connection: An ibis backend connection object to the OMOP CDM database using the ibis framework.
+
+    Returns:
+        DataFrame: The result of the query is an Ibis DataFrame.
+    """
+
+    query = (
+        connection.table('concept').sql(f"""
+                        SELECT
+                        c.concept_id,
+                        c.concept_name,
+                        c.concept_code,
+                        c.concept_class_id,
+                        c.standard_concept,
+                        c.vocabulary_id
+                        FROM concept AS c
+                        WHERE concept_id = {concept_id}
+                        ;
+                        """)
+    )
+
+    return query
+
+
+# G02: Find a concept by code from a source vocabulary
+def find_concept_by_code_form_a_source_vocabulary(concept_id, vocabulary_id, connection):
+    """
+    This query obtains the concept details associated with a concept code, such as name, class, level and source vocabulary.
+
+    Only concepts from the Standard Vocabularies can be searched using this query. If you want to translate codes from other Source Vocabularies to Standard Vocabularies use G06 query.
+    
+    Parameters:
+        concept_id (int): The ID of the concept to retrieve.
+        vocabulary_id (str): The source vocabulary ID of the concept to retrieve.
+        connection: An ibis backend connection object to the OMOP CDM database using the ibis framework.
+
+    Returns:
+        DataFrame: The result of the query is an Ibis DataFrame.
+    """
+
+    query = (
+        connection.table('concept').sql(f"""
+            SELECT
+            c.concept_id,
+            c.concept_name,
+            c.concept_code,
+            c.concept_class_id,
+            c.vocabulary_id
+            FROM concept AS c
+            WHERE 
+            c.concept_code = {concept_id} AND
+            c.vocabulary_id = {vocabulary_id} AND
+            c.invalid_reason IS NULL
+            ;
+            """)
+        )
+
+    return query
+
+
+# G04: Find synonyms for a given concept
+def find_synonyms_for_a_given_concept():
+
+
+# G05: Translate a code from a source to a standard vocabulary.
+def translate_a_code_from_a_source_to_a_standard_vocabulary():
+
+
+# G06: Find concepts and their descendants that are covered by a given source code
+def find_concepts_and_their_descendants_that_are_covered_by_a_given_source_code():
+
+
+# G07: Find concepts that have a relationship with a given concept
+def find_concepts_that_have_a_relationship_with_a_given_concept():
+
+
+# G08: Find ancestors for a given concept
+def find_ancestors_for_a_given_concept():
+
+
+# G09: Find descendants for a given concept
+def find_descendants_for_a_given_concept():
+
+
+# G10: Find parents for a given concept
+def find_parents_for_a_given_concept():
+
+
+# G11: Find children for a given concept
+def find_children_for_a_given_concept():
+
+
+# G12: List current vocabulary release number
+def list_current_vocabulary_release_number():
+
+
+# G13: List available vocabularies
+def list_available_vocabularies():
+
+
+# G14: Statistics about relationships between concepts
+def statistics_about_relationships_between_concepts():
+
+
+# G15: Statistic about Concepts, Vocabularies, Classes and Levels
+def statistic_about_concepts_vocabularies_classes_and_levels():
+
+
+# G16: Statistics about Condition Mapping of Source Vocabularies
+def statistics_about_condition_mapping_of_source_vocabularies():
+
+
+# G17: Statistics about Drugs Mapping of Source Vocabularies
+def statistics_about_drugs_mapping_of_source_vocabularies():
+