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2 changes: 1 addition & 1 deletion .buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: cac6a737651ef2763a249709de69e78f
config: ef34b1f20bd8e0d5c05be275f911de02
tags: 645f666f9bcd5a90fca523b33c5a78b7
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6 changes: 3 additions & 3 deletions _sources/contributing.rst.txt
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Contributing to cyclops-query
=============================
Contributing to cycquery
========================

Thanks for your interest in contributing to the cyclops-query tool!
Thanks for your interest in contributing to the cycquery tool!

To submit PRs, please fill out the PR template along with the PR. If the
PR fixes an issue, don’t forget to link the PR to the issue!
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4 changes: 2 additions & 2 deletions _sources/index.rst.txt
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Welcome to cyclops-query's documentation!
=========================================
Welcome to cycquery's documentation!
====================================


.. toctree::
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76 changes: 22 additions & 54 deletions _sources/intro.rst.txt
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cyclops-query
=============
cycquery
========

|PyPI| |PyPI - Python Version| |code checks| |integration tests| |docs|
|codecov| |license|
|PyPI| |PyPI - Python Version| |code checks| |integration tests| |docs| |codecov| |license|

``cyclops-query`` is a tool for querying relational databases using a
simple Python API. It is specifically developed to query Electronic
Health Record (EHR) databases. The tool is a wrapper around
`SQLAlchemy <https://www.sqlalchemy.org/>`__ and can be used to write
SQL-like queries in Python, including joins, conditions, groupby
aggregation and many more.
``cycquery`` is a tool for querying relational databases using a simple Python API. It is specifically developed to query Electronic Health Record (EHR) databases. The tool is a wrapper around `SQLAlchemy <https://www.sqlalchemy.org/>`__ and can be used to write SQL-like queries in Python, including joins, conditions, groupby aggregation and many more.

🐣 Getting Started
==================

Installing cyclops-query using pip
----------------------------------
Installing cycquery using pip
-----------------------------

.. code:: bash
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Using poetry
------------

The development environment can be set up using
`poetry <https://python-poetry.org/docs/#installation>`__. Hence, make
sure it is installed and then run:
The development environment can be set up using `poetry <https://python-poetry.org/docs/#installation>`__. Hence, make sure it is installed and then run:

.. code:: bash
python3 -m poetry install
source $(poetry env info --path)/bin/activate
In order to install dependencies for testing (codestyle, unit tests,
integration tests), run:
In order to install dependencies for testing (codestyle, unit tests, integration tests), run:

.. code:: bash
python3 -m poetry install --with test
API documentation is built using
`Sphinx <https://www.sphinx-doc.org/en/master/>`__ and can be locally
built by:
API documentation is built using `Sphinx <https://www.sphinx-doc.org/en/master/>`__ and can be locally built by:

.. code:: bash
Expand All @@ -93,42 +82,21 @@ built by:
Contributing
------------

Contributing to ``cyclops-query`` is welcomed. See
`Contributing <https://vectorinstitute.github.io/cyclops-query/api/contributing.html>`__
for guidelines.
Contributing to ``cycquery`` is welcomed. See `Contributing <https://vectorinstitute.github.io/cycquery/api/contributing.html>`__ for guidelines.

📚 `Documentation <https://vectorinstitute.github.io/cyclops-query/>`__
=======================================================================

🎓 Citation
===========

Reference to cite when you use ``cyclops-query`` in a project or a
research paper:

::

@article {Krishnan2022.12.02.22283021,
author = {Krishnan, Amrit and Subasri, Vallijah and McKeen, Kaden and Kore, Ali and Ogidi, Franklin and Alinoori, Mahshid and Lalani, Nadim and Dhalla, Azra and Verma, Amol and Razak, Fahad and Pandya, Deval and Dolatabadi, Elham},
title = {CyclOps: Cyclical development towards operationalizing ML models for health},
elocation-id = {2022.12.02.22283021},
year = {2022},
doi = {10.1101/2022.12.02.22283021},
publisher = {Cold Spring Harbor Laboratory Press},
URL = {https://www.medrxiv.org/content/early/2022/12/08/2022.12.02.22283021},
journal = {medRxiv}
}
📚 `Documentation <https://vectorinstitute.github.io/cycquery/>`__
==================================================================

.. |PyPI| image:: https://img.shields.io/pypi/v/cycquery
:target: https://pypi.org/project/cycquery
.. |PyPI - Python Version| image:: https://img.shields.io/pypi/pyversions/cycquery
.. |code checks| image:: https://github.com/VectorInstitute/cyclops-query/actions/workflows/code_checks.yml/badge.svg
:target: https://github.com/VectorInstitute/cyclops-query/actions/workflows/code_checks.yml
.. |integration tests| image:: https://github.com/VectorInstitute/cyclops-query/actions/workflows/integration_tests.yml/badge.svg
:target: https://github.com/VectorInstitute/cyclops-query/actions/workflows/integration_tests.yml
.. |docs| image:: https://github.com/VectorInstitute/cyclops-query/actions/workflows/docs_deploy.yml/badge.svg
:target: https://github.com/VectorInstitute/cyclops-query/actions/workflows/docs_deploy.yml
.. |codecov| image:: https://codecov.io/gh/VectorInstitute/cyclops-query/branch/main/graph/badge.svg
:target: https://codecov.io/gh/VectorInstitute/cyclops-query
.. |license| image:: https://img.shields.io/github/license/VectorInstitute/cyclops-query.svg
:target: https://github.com/VectorInstitute/cyclops-query/blob/main/LICENSE
.. |code checks| image:: https://github.com/VectorInstitute/cycquery/actions/workflows/code_checks.yml/badge.svg
:target: https://github.com/VectorInstitute/cycquery/actions/workflows/code_checks.yml
.. |integration tests| image:: https://github.com/VectorInstitute/cycquery/actions/workflows/integration_tests.yml/badge.svg
:target: https://github.com/VectorInstitute/cycquery/actions/workflows/integration_tests.yml
.. |docs| image:: https://github.com/VectorInstitute/cycquery/actions/workflows/docs_deploy.yml/badge.svg
:target: https://github.com/VectorInstitute/cycquery/actions/workflows/docs_deploy.yml
.. |codecov| image:: https://codecov.io/gh/VectorInstitute/cycquery/branch/main/graph/badge.svg
:target: https://codecov.io/gh/VectorInstitute/cycquery
.. |license| image:: https://img.shields.io/github/license/VectorInstitute/cycquery.svg
:target: https://github.com/VectorInstitute/cycquery/blob/main/LICENSE
2 changes: 1 addition & 1 deletion _sources/tutorials.rst.txt
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Tutorials
=========

The cyclops-query tool allows you to query EHR databases. It is a Python API that
The cycquery tool allows you to query EHR databases. It is a Python API that
that communicates with postgresql databases. It is a wrapper around the
SQLAlchemy ORM and uses SQLAlchemy query objects and functions to build
queries.
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"id": "74b155b9-9ba6-455c-b987-4c261c339364",
"metadata": {},
"source": [
"This notebook shows examples of how to use the cyclops-query tool on [eicu-CRD](https://eicu-crd.mit.edu/).\n",
"This notebook shows examples of how to use the cycquery tool on [eicu-CRD](https://eicu-crd.mit.edu/).\n",
"\n",
"Each query is limit to 100 rows (for quick results).\n",
"\n",
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"id": "57e3214e-f1d5-46cb-bb2a-514a48e0269d",
"metadata": {},
"source": [
"This notebook shows examples of how to use the cyclops-query tool on [GEMINI](https://www.geminimedicine.ca/)."
"This notebook shows examples of how to use the cycquery tool on [GEMINI](https://www.geminimedicine.ca/)."
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"2023-09-21 09:17:45,449 \u001b[1;37mINFO\u001b[0m cyclops.query.orm - Database setup, ready to run queries!\n"
"2023-09-21 09:17:45,449 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"2023-09-21 09:17:51,902 \u001b[1;37mINFO\u001b[0m cyclops.query.orm - Query returned successfully!\n",
"2023-09-21 09:17:51,903 \u001b[1;37mINFO\u001b[0m cyclops.utils.profile - Finished executing function run_query in 6.093352 s\n"
"2023-09-21 09:17:51,902 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n",
"2023-09-21 09:17:51,903 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 6.093352 s\n"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"2023-09-21 09:17:52,591 \u001b[1;37mINFO\u001b[0m cyclops.query.orm - Query returned successfully!\n",
"2023-09-21 09:17:52,592 \u001b[1;37mINFO\u001b[0m cyclops.utils.profile - Finished executing function run_query in 0.675141 s\n"
"2023-09-21 09:17:52,591 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n",
"2023-09-21 09:17:52,592 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.675141 s\n"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"2023-09-21 09:17:52,856 \u001b[1;37mINFO\u001b[0m cyclops.query.orm - Query returned successfully!\n",
"2023-09-21 09:17:52,857 \u001b[1;37mINFO\u001b[0m cyclops.utils.profile - Finished executing function run_query in 0.145693 s\n"
"2023-09-21 09:17:52,856 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n",
"2023-09-21 09:17:52,857 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.145693 s\n"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"2023-09-21 09:26:19,814 \u001b[1;37mINFO\u001b[0m cyclops.query.orm - Query returned successfully!\n",
"2023-09-21 09:26:19,815 \u001b[1;37mINFO\u001b[0m cyclops.utils.profile - Finished executing function run_query in 506.939296 s\n"
"2023-09-21 09:26:19,814 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n",
"2023-09-21 09:26:19,815 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 506.939296 s\n"
]
},
{
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"id": "74b155b9-9ba6-455c-b987-4c261c339364",
"metadata": {},
"source": [
"This notebook shows examples of how to use the cyclops-query tool on [MIMIC-III v1.4](https://physionet.org/content/mimiciii/1.4/).\n",
"This notebook shows examples of how to use the cycquery tool on [MIMIC-III v1.4](https://physionet.org/content/mimiciii/1.4/).\n",
"\n",
"Each query is limit to 100 rows (for quick results).\n",
"\n",
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"id": "1efffc64",
"metadata": {},
"source": [
"This notebook shows examples of how to use the cyclops-query tool on [MIMIC-IV v2.0](https://physionet.org/content/mimiciv/2.0/).\n",
"This notebook shows examples of how to use the cycquery tool on [MIMIC-IV v2.0](https://physionet.org/content/mimiciv/2.0/).\n",
"\n",
"Each query is limit to 100 rows (for quick results).\n",
"\n",
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"id": "e2baea54",
"metadata": {},
"source": [
"## Example 3. Advanced - uses `ConditionRegexMatch` from `cyclops.query.ops`. Get all patient encounters with diagnoses (ICD-9 long title contains `schizophrenia` and `chronic` ), in the year 2015."
"## Example 3. Advanced - uses `ConditionRegexMatch` from `cycquery.ops`. Get all patient encounters with diagnoses (ICD-9 long title contains `schizophrenia` and `chronic` ), in the year 2015."
]
},
{
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"id": "1efffc64",
"metadata": {},
"source": [
"This notebook shows examples of how to use the cyclops-query tool to query EHR databases that follow the OMOP common data model. Each query is limit to 100 rows (for quick results).\n",
"This notebook shows examples of how to use the cycquery tool to query EHR databases that follow the OMOP common data model. Each query is limit to 100 rows (for quick results).\n",
"\n",
"We showcase the examples on:\n",
"\n",
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*
* Sphinx stylesheet -- basic theme.
*
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
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