diff --git a/.buildinfo b/.buildinfo index 0c209b3..c38ab4b 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # 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 diff --git a/_modules/cycquery/base.html b/_modules/cycquery/base.html index c403a15..88bdfb8 100644 --- a/_modules/cycquery/base.html +++ b/_modules/cycquery/base.html @@ -1,169 +1,300 @@ + + + + + + + + cycquery.base - cycquery documentation + + + + + + + - - - - - - - - - - cycquery.base — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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Source code for cycquery.base

 """Base querier class."""
 
 import logging
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Source code for cycquery.base
             setattr(self, schema_name, schema)
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Source code for cycquery.eicu

 """EICU-CRD query module.
 
 Supports querying of eICU.
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Source code for cycquery.eicu
     """EICU dataset querier."""
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Source code for cycquery.gemini

 """GEMINI query module."""
 
 import logging
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Source code for cycquery.gemini
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Source code for cycquery.interface

 """A query interface class to wrap database objects and queries."""
 
 import logging
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Source code for cycquery.interface
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Source code for cycquery.mimiciii

 """MIMIC-III query module.
 
 Supports querying of MIMIC-III.
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Source code for cycquery.mimiciii
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Source code for cycquery.mimiciv

 """MIMIC-IV query module.
 
 Supports querying of MIMICIV-2.0.
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Source code for cycquery.mimiciv
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Source code for cycquery.omop

 """OMOP query API."""
 
 import logging
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Source code for cycquery.ops

 """Query operations."""
 
 from __future__ import annotations
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Source code for cycquery.ops
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+ - - - + + + + + + + + + + \ No newline at end of file diff --git a/_sources/contributing.rst.txt b/_sources/contributing.rst.txt index 07f23a2..265ee9c 100644 --- a/_sources/contributing.rst.txt +++ b/_sources/contributing.rst.txt @@ -1,7 +1,7 @@ -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! diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt index adb9b40..5099527 100644 --- a/_sources/index.rst.txt +++ b/_sources/index.rst.txt @@ -1,5 +1,5 @@ -Welcome to cyclops-query's documentation! -========================================= +Welcome to cycquery's documentation! +==================================== .. toctree:: diff --git a/_sources/intro.rst.txt b/_sources/intro.rst.txt index e5a6c67..cc7fbb4 100644 --- a/_sources/intro.rst.txt +++ b/_sources/intro.rst.txt @@ -1,21 +1,15 @@ -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 `__ 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 `__ 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 @@ -64,25 +58,20 @@ Query postgresql database Using poetry ------------ -The development environment can be set up using -`poetry `__. Hence, make -sure it is installed and then run: +The development environment can be set up using `poetry `__. 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 `__ and can be locally -built by: +API documentation is built using `Sphinx `__ and can be locally built by: .. code:: bash @@ -93,42 +82,21 @@ built by: Contributing ------------ -Contributing to ``cyclops-query`` is welcomed. See -`Contributing `__ -for guidelines. +Contributing to ``cycquery`` is welcomed. See `Contributing `__ for guidelines. -📚 `Documentation `__ -======================================================================= - -🎓 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 `__ +================================================================== .. |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 diff --git a/_sources/tutorials.rst.txt b/_sources/tutorials.rst.txt index aa91cba..d83f4d8 100644 --- a/_sources/tutorials.rst.txt +++ b/_sources/tutorials.rst.txt @@ -1,7 +1,7 @@ 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. diff --git a/_sources/tutorials/eicu.ipynb.txt b/_sources/tutorials/eicu.ipynb.txt index e0874e7..fd52836 100644 --- a/_sources/tutorials/eicu.ipynb.txt +++ b/_sources/tutorials/eicu.ipynb.txt @@ -13,7 +13,7 @@ "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", diff --git a/_sources/tutorials/gemini.ipynb.txt b/_sources/tutorials/gemini.ipynb.txt index 53797d6..759a3fc 100644 --- a/_sources/tutorials/gemini.ipynb.txt +++ b/_sources/tutorials/gemini.ipynb.txt @@ -13,7 +13,7 @@ "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/)." ] }, { @@ -34,7 +34,7 @@ "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" ] }, { @@ -116,8 +116,8 @@ "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" ] }, { @@ -159,8 +159,8 @@ "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" ] }, { @@ -201,8 +201,8 @@ "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" ] }, { @@ -237,8 +237,8 @@ "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" ] }, { diff --git a/_sources/tutorials/mimiciii.ipynb.txt b/_sources/tutorials/mimiciii.ipynb.txt index b935b26..1f10751 100644 --- a/_sources/tutorials/mimiciii.ipynb.txt +++ b/_sources/tutorials/mimiciii.ipynb.txt @@ -13,7 +13,7 @@ "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", diff --git a/_sources/tutorials/mimiciv.ipynb.txt b/_sources/tutorials/mimiciv.ipynb.txt index a05874c..7b27081 100644 --- a/_sources/tutorials/mimiciv.ipynb.txt +++ b/_sources/tutorials/mimiciv.ipynb.txt @@ -13,7 +13,7 @@ "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", @@ -125,7 +125,7 @@ "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." ] }, { diff --git a/_sources/tutorials/omop.ipynb.txt b/_sources/tutorials/omop.ipynb.txt index 16b7928..a651f18 100644 --- a/_sources/tutorials/omop.ipynb.txt +++ b/_sources/tutorials/omop.ipynb.txt @@ -13,7 +13,7 @@ "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", diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 8141580..0000000 --- a/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} diff --git a/_static/basic.css b/_static/basic.css index 30fee9d..f316efc 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * 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. * */ diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css deleted file mode 100644 index c718cee..0000000 --- a/_static/css/badge_only.css +++ /dev/null @@ -1 +0,0 @@ -.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before,.icon-book:before{content:"\f02d"}.fa-caret-down:before,.icon-caret-down:before{content:"\f0d7"}.fa-caret-up:before,.icon-caret-up:before{content:"\f0d8"}.fa-caret-left:before,.icon-caret-left:before{content:"\f0d9"}.fa-caret-right:before,.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60}.rst-versions .rst-current-version:after{clear:both;content:"";display:block}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}} \ No newline at end of file diff --git a/_static/css/cyclops.css b/_static/css/cyclops.css index 45fbc6f..56b1c69 100644 --- a/_static/css/cyclops.css +++ b/_static/css/cyclops.css @@ -1,43 +1,3 @@ -@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,100;0,300;0,400;0,700;0,900;1,100;1,300;1,400;1,700;1,900&display=swap'); -@import url('https://fonts.googleapis.com/css2?family=IBM+Plex+Mono:ital,wght@0,400;0,700;1,400;1,700&display=swap'); -@import "theme.css"; /* From sphinx_rtd_theme */ - -html { - --text-color: #24292e; - --heading-color: #404040; - --link-color: #5097ba; - --sidebar-background-color: #2e76d49d; - --content-background-color: #ffffff; -} - -body { - font-family: 'Roboto', sans-serif; - font-weight: 400; - color: var(--text-color); - line-height: 1.5; -} - -.wy-menu-vertical a { color: #98a8f5;; } - -h1, h2, h3, h4, h5, h6, legend, .rst-content .toctree-wrapper p.caption, .rst-content .sidebar .sidebar-title { - font-family: Lato, 'Helvetica Neue', sans-serif; - font-weight: 600; - color: var(--heading-color); -} - -p { - line-height: inherit; -} - -a { - color: var(--link-color); -} -/* underlign lins on hover */ -a:hover { - text-decoration: underline; -} - -/* Monospace typography */ footer span.commit code, .rst-content pre.literal-block, .rst-content div[class^='highlight'] pre, @@ -50,218 +10,9 @@ footer span.commit code, font-family: 'IBM Plex Mono', monospace; font-size: 0.8rem; } - -/* Inline (backticks) code inspired by docusaurus (which Auspice used previously) */ -.rst-content code.literal, -.rst-content tt.literal { - background-color: rgba(27,31,35,.05); - border-radius: 3px; - border: 0; - color: inherit; - margin: 0; - padding: 3.2px 6.4px; -} - -/* Sidebar */ -.wy-nav-side { - background: var(--sidebar-background-color); -} - -/* main content section */ -.wy-nav-content { - background: var(--content-background-color); -} - -/* don't change the background for the area on the RHS of the main content */ -.wy-nav-content-wrap { - background: inherit; -} - -/* Pin the Nextstrain logo, project name, version, and search box to the top of - * the sidebar when the sidebar scrolls. - */ -.wy-side-nav-search { - position: sticky; - top: 0; -} - -/* Sub-project name, version (optional) and link back to the main docs */ -.wy-side-nav-search > div.subproject { - margin-top: -1rem; - margin-bottom: 1.2rem; -} -.wy-side-nav-search > div.subproject > a { /* subproject name */ - font-size: 1.5rem; 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However, tables also remain - * horizontally scrollable as necessary to accommodate overflow. This - * provides two means for seeing overflowing table content (scrolling or - * expanding the viewport). - * - * For reference in the calculation below: - * - * 100vw = width of the viewport - * 300px = width of .wy-nav-side and corresponding margin-left of .wy-nav-content-wrap - * 3.236em = padding-left of .wy-nav-content - * - * -trs, 16 March 2022 - */ -/* width: max(100%, calc(100vw - 300px - 3.236em)); - - /* override earlier max-width: 100% */ -/* max-width: none; -}*/ - -/* Mobile nav (top bar heading + flyout menu icon) - */ - -.wy-nav-top a, .wy-nav-top i { - color: var(--heading-color); -} - - -/* Footer styles. Largely chosen to mimic the previous rendering of the docs. 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false,\n nestedClass: \"active\",\n\n // Offset & reflow\n offset: 0,\n reflow: false,\n\n // Event support\n events: true,\n };\n\n //\n // Methods\n //\n\n /**\n * Merge two or more objects together.\n * @param {Object} objects The objects to merge together\n * @returns {Object} Merged values of defaults and options\n */\n var extend = function () {\n var merged = {};\n Array.prototype.forEach.call(arguments, function (obj) {\n for (var key in obj) {\n if (!obj.hasOwnProperty(key)) return;\n merged[key] = obj[key];\n }\n });\n return merged;\n };\n\n /**\n * Emit a custom event\n * @param {String} type The event type\n * @param {Node} elem The element to attach the event to\n * @param {Object} detail Any details to pass along with the event\n */\n var emitEvent = function (type, elem, detail) {\n // Make sure events are enabled\n if (!detail.settings.events) return;\n\n // Create a new event\n var event = new CustomEvent(type, {\n bubbles: true,\n cancelable: true,\n detail: detail,\n });\n\n // Dispatch the event\n elem.dispatchEvent(event);\n };\n\n /**\n * Get an element's distance from the top of the Document.\n * @param {Node} elem The element\n * @return {Number} Distance from the top in pixels\n */\n var getOffsetTop = function (elem) {\n var location = 0;\n if (elem.offsetParent) {\n while (elem) {\n location += elem.offsetTop;\n elem = elem.offsetParent;\n }\n }\n return location >= 0 ? location : 0;\n };\n\n /**\n * Sort content from first to last in the DOM\n * @param {Array} contents The content areas\n */\n var sortContents = function (contents) {\n if (contents) {\n contents.sort(function (item1, item2) {\n var offset1 = getOffsetTop(item1.content);\n var offset2 = getOffsetTop(item2.content);\n if (offset1 < offset2) return -1;\n return 1;\n });\n }\n };\n\n /**\n * Get the offset to use for calculating position\n * @param {Object} settings The settings for this instantiation\n * @return {Float} The number of pixels to offset the 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content areas\n * @param {Object} settings The settings for this instantiation\n * @return {Object} The content area and matching navigation link\n */\n var getActive = function (contents, settings) {\n var last = contents[contents.length - 1];\n if (useLastItem(last, settings)) return last;\n for (var i = contents.length - 1; i >= 0; i--) {\n if (isInView(contents[i].content, settings)) return contents[i];\n }\n };\n\n /**\n * Deactivate parent navs in a nested navigation\n * @param {Node} nav The starting navigation element\n * @param {Object} settings The settings for this instantiation\n */\n var deactivateNested = function (nav, settings) {\n // If nesting isn't activated, bail\n if (!settings.nested || !nav.parentNode) return;\n\n // Get the parent navigation\n var li = nav.parentNode.closest(\"li\");\n if (!li) return;\n\n // Remove the active class\n li.classList.remove(settings.nestedClass);\n\n // Apply recursively to any parent navigation elements\n deactivateNested(li, settings);\n };\n\n /**\n * Deactivate a nav and content area\n * @param {Object} items The nav item and content to deactivate\n * @param {Object} settings The settings for this instantiation\n */\n var deactivate = function (items, settings) {\n // Make sure there are items to deactivate\n if (!items) return;\n\n // Get the parent list item\n var li = items.nav.closest(\"li\");\n if (!li) return;\n\n // Remove the active class from the nav and content\n li.classList.remove(settings.navClass);\n items.content.classList.remove(settings.contentClass);\n\n // Deactivate any parent navs in a nested navigation\n deactivateNested(li, settings);\n\n // Emit a custom event\n emitEvent(\"gumshoeDeactivate\", li, {\n link: items.nav,\n content: items.content,\n settings: settings,\n });\n };\n\n /**\n * Activate parent navs in a nested navigation\n * @param {Node} nav The starting navigation element\n * @param {Object} settings The settings for this instantiation\n */\n var activateNested = function (nav, settings) {\n // If nesting isn't activated, bail\n if (!settings.nested) return;\n\n // Get the parent navigation\n var li = nav.parentNode.closest(\"li\");\n if (!li) return;\n\n // Add the active class\n li.classList.add(settings.nestedClass);\n\n // Apply recursively to any parent navigation elements\n activateNested(li, settings);\n };\n\n /**\n * Activate a nav and content area\n * @param {Object} items The nav item and content to activate\n * @param {Object} settings The settings for this instantiation\n */\n var activate = function (items, settings) {\n // Make sure there are items to activate\n if (!items) return;\n\n // Get the parent list item\n var li = items.nav.closest(\"li\");\n if (!li) return;\n\n // Add the active class to the nav and content\n li.classList.add(settings.navClass);\n items.content.classList.add(settings.contentClass);\n\n // Activate any parent navs in a nested navigation\n activateNested(li, settings);\n\n // Emit a custom event\n emitEvent(\"gumshoeActivate\", li, {\n link: items.nav,\n content: items.content,\n settings: settings,\n });\n };\n\n /**\n * Create the Constructor object\n * @param {String} selector The selector to use for navigation items\n * @param {Object} options User options and settings\n */\n var Constructor = function (selector, options) {\n //\n // Variables\n //\n\n var publicAPIs = {};\n var navItems, contents, current, timeout, settings;\n\n //\n // Methods\n //\n\n /**\n * Set variables from DOM elements\n */\n publicAPIs.setup = function () {\n // Get all nav items\n navItems = document.querySelectorAll(selector);\n\n // Create contents array\n contents = [];\n\n // Loop through each item, get it's matching content, and push to the array\n Array.prototype.forEach.call(navItems, function (item) {\n // Get the content for the nav item\n var content = document.getElementById(\n decodeURIComponent(item.hash.substr(1)),\n );\n if (!content) return;\n\n // Push to the contents array\n 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window.cancelAnimationFrame(timeout);\n }\n\n // Setup debounce callback\n timeout = window.requestAnimationFrame(publicAPIs.detect);\n };\n\n /**\n * Update content sorting on resize\n * Debounced for performance\n */\n var resizeHandler = function (event) {\n // If there's a timer, cancel it\n if (timeout) {\n window.cancelAnimationFrame(timeout);\n }\n\n // Setup debounce callback\n timeout = window.requestAnimationFrame(function () {\n sortContents(contents);\n publicAPIs.detect();\n });\n };\n\n /**\n * Destroy the current instantiation\n */\n publicAPIs.destroy = function () {\n // Undo DOM changes\n if (current) {\n deactivate(current, settings);\n }\n\n // Remove event listeners\n window.removeEventListener(\"scroll\", scrollHandler, false);\n if (settings.reflow) {\n window.removeEventListener(\"resize\", resizeHandler, false);\n }\n\n // Reset variables\n contents = null;\n navItems = null;\n current = null;\n timeout = null;\n settings = null;\n };\n\n /**\n * Initialize the 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__webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId].call(module.exports, module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n","// getDefaultExport function for compatibility with non-harmony modules\n__webpack_require__.n = (module) => {\n\tvar getter = module && module.__esModule ?\n\t\t() => (module['default']) :\n\t\t() => (module);\n\t__webpack_require__.d(getter, { a: getter });\n\treturn getter;\n};","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.g = (function() {\n\tif (typeof globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","import Gumshoe from \"./gumshoe-patched.js\";\n\n////////////////////////////////////////////////////////////////////////////////\n// Scroll Handling\n////////////////////////////////////////////////////////////////////////////////\nvar tocScroll = null;\nvar header = null;\nvar lastScrollTop = window.pageYOffset || document.documentElement.scrollTop;\nconst GO_TO_TOP_OFFSET = 64;\n\nfunction scrollHandlerForHeader() {\n if (Math.floor(header.getBoundingClientRect().top) == 0) {\n header.classList.add(\"scrolled\");\n } else {\n header.classList.remove(\"scrolled\");\n }\n}\n\nfunction scrollHandlerForBackToTop(positionY) {\n if (positionY < GO_TO_TOP_OFFSET) {\n document.documentElement.classList.remove(\"show-back-to-top\");\n } else {\n if (positionY < lastScrollTop) {\n document.documentElement.classList.add(\"show-back-to-top\");\n } else if (positionY > lastScrollTop) {\n document.documentElement.classList.remove(\"show-back-to-top\");\n }\n }\n lastScrollTop = positionY;\n}\n\nfunction scrollHandlerForTOC(positionY) {\n if (tocScroll === null) {\n return;\n }\n\n // top of page.\n if (positionY == 0) {\n tocScroll.scrollTo(0, 0);\n } else if (\n // bottom of page.\n Math.ceil(positionY) >=\n Math.floor(document.documentElement.scrollHeight - window.innerHeight)\n ) {\n tocScroll.scrollTo(0, tocScroll.scrollHeight);\n } else {\n // somewhere in the middle.\n const current = document.querySelector(\".scroll-current\");\n if (current == null) {\n return;\n }\n\n // https://github.com/pypa/pip/issues/9159 This breaks scroll behaviours.\n // // scroll the currently \"active\" heading in toc, into view.\n // const rect = current.getBoundingClientRect();\n // if (0 > rect.top) {\n // current.scrollIntoView(true); // the argument is \"alignTop\"\n // } else if (rect.bottom > window.innerHeight) {\n // current.scrollIntoView(false);\n // }\n }\n}\n\nfunction scrollHandler(positionY) {\n scrollHandlerForHeader();\n scrollHandlerForBackToTop(positionY);\n scrollHandlerForTOC(positionY);\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Theme Toggle\n////////////////////////////////////////////////////////////////////////////////\nfunction setTheme(mode) {\n if (mode !== \"light\" && mode !== \"dark\" && mode !== \"auto\") {\n console.error(`Got invalid theme mode: ${mode}. Resetting to auto.`);\n mode = \"auto\";\n }\n\n document.body.dataset.theme = mode;\n localStorage.setItem(\"theme\", mode);\n console.log(`Changed to ${mode} mode.`);\n}\n\nfunction cycleThemeOnce() {\n const currentTheme = localStorage.getItem(\"theme\") || \"auto\";\n const prefersDark = window.matchMedia(\"(prefers-color-scheme: dark)\").matches;\n\n if (prefersDark) {\n // Auto (dark) -> Light -> Dark\n if (currentTheme === \"auto\") {\n setTheme(\"light\");\n } else if (currentTheme == \"light\") {\n setTheme(\"dark\");\n } else {\n setTheme(\"auto\");\n }\n } else {\n // Auto (light) -> Dark -> Light\n if (currentTheme === \"auto\") {\n setTheme(\"dark\");\n } else if (currentTheme == \"dark\") {\n setTheme(\"light\");\n } else {\n setTheme(\"auto\");\n }\n }\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Setup\n////////////////////////////////////////////////////////////////////////////////\nfunction setupScrollHandler() {\n // Taken from https://developer.mozilla.org/en-US/docs/Web/API/Document/scroll_event\n let last_known_scroll_position = 0;\n let ticking = false;\n\n window.addEventListener(\"scroll\", function (e) {\n last_known_scroll_position = window.scrollY;\n\n if (!ticking) {\n window.requestAnimationFrame(function () {\n scrollHandler(last_known_scroll_position);\n ticking = false;\n });\n\n ticking = true;\n }\n });\n window.scroll();\n}\n\nfunction setupScrollSpy() {\n if (tocScroll === null) {\n return;\n }\n\n // Scrollspy -- highlight table on contents, based on scroll\n new Gumshoe(\".toc-tree a\", {\n reflow: true,\n recursive: true,\n navClass: \"scroll-current\",\n offset: () => {\n let rem = parseFloat(getComputedStyle(document.documentElement).fontSize);\n return header.getBoundingClientRect().height + 0.5 * rem + 1;\n },\n });\n}\n\nfunction setupTheme() {\n // Attach event handlers for toggling themes\n const buttons = document.getElementsByClassName(\"theme-toggle\");\n Array.from(buttons).forEach((btn) => {\n btn.addEventListener(\"click\", cycleThemeOnce);\n });\n}\n\nfunction setup() {\n setupTheme();\n setupScrollHandler();\n setupScrollSpy();\n}\n\n////////////////////////////////////////////////////////////////////////////////\n// Main entrypoint\n////////////////////////////////////////////////////////////////////////////////\nfunction main() {\n document.body.parentNode.classList.remove(\"no-js\");\n\n header = document.querySelector(\"header\");\n tocScroll = document.querySelector(\".toc-scroll\");\n\n setup();\n}\n\ndocument.addEventListener(\"DOMContentLoaded\", main);\n"],"names":["root","g","window","this","defaults","navClass","contentClass","nested","nestedClass","offset","reflow","events","emitEvent","type","elem","detail","settings","event","CustomEvent","bubbles","cancelable","dispatchEvent","getOffsetTop","location","offsetParent","offsetTop","sortContents","contents","sort","item1","item2","content","isInView","bottom","bounds","getBoundingClientRect","parseFloat","getOffset","parseInt","innerHeight","document","documentElement","clientHeight","top","isAtBottom","Math","ceil","pageYOffset","max","body","scrollHeight","offsetHeight","getActive","last","length","item","useLastItem","i","deactivateNested","nav","parentNode","li","closest","classList","remove","deactivate","items","link","activateNested","add","selector","options","navItems","current","timeout","publicAPIs","querySelectorAll","Array","prototype","forEach","call","getElementById","decodeURIComponent","hash","substr","push","active","activate","scrollHandler","cancelAnimationFrame","requestAnimationFrame","detect","resizeHandler","destroy","removeEventListener","merged","arguments","obj","key","hasOwnProperty","extend","setup","addEventListener","factory","__webpack_module_cache__","__webpack_require__","moduleId","cachedModule","undefined","exports","module","__webpack_modules__","n","getter","__esModule","d","a","definition","o","Object","defineProperty","enumerable","get","globalThis","Function","e","prop","tocScroll","header","lastScrollTop","scrollTop","GO_TO_TOP_OFFSET","cycleThemeOnce","currentTheme","localStorage","getItem","mode","matchMedia","matches","console","error","dataset","theme","setItem","log","buttons","getElementsByClassName","from","btn","setupTheme","last_known_scroll_position","ticking","scrollY","positionY","floor","scrollHandlerForBackToTop","scrollTo","querySelector","scrollHandlerForTOC","scroll","setupScrollHandler","recursive","rem","getComputedStyle","fontSize","height"],"sourceRoot":""} \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js index 7918c3f..92da3f8 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :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. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/_static/skeleton.css b/_static/skeleton.css new file mode 100644 index 0000000..467c878 --- /dev/null +++ b/_static/skeleton.css @@ -0,0 +1,296 @@ +/* Some sane resets. */ +html { + height: 100%; +} + +body { + margin: 0; + min-height: 100%; +} + +/* All the flexbox magic! */ +body, +.sb-announcement, +.sb-content, +.sb-main, +.sb-container, +.sb-container__inner, +.sb-article-container, +.sb-footer-content, +.sb-header, +.sb-header-secondary, +.sb-footer { + display: flex; +} + +/* These order things vertically */ +body, +.sb-main, +.sb-article-container { + flex-direction: column; +} + +/* Put elements in the center */ +.sb-header, +.sb-header-secondary, +.sb-container, +.sb-content, +.sb-footer, +.sb-footer-content { + justify-content: center; +} +/* Put elements at the ends */ +.sb-article-container { + justify-content: space-between; +} + +/* These elements grow. */ +.sb-main, +.sb-content, +.sb-container, +article { + flex-grow: 1; +} + +/* Because padding making this wider is not fun */ +article { + box-sizing: border-box; +} + +/* The announcements element should never be wider than the page. */ +.sb-announcement { + max-width: 100%; +} + +.sb-sidebar-primary, +.sb-sidebar-secondary { + flex-shrink: 0; + width: 17rem; +} + +.sb-announcement__inner { + justify-content: center; + + box-sizing: border-box; + height: 3rem; + + overflow-x: auto; + white-space: nowrap; +} + +/* Sidebars, with checkbox-based toggle */ +.sb-sidebar-primary, +.sb-sidebar-secondary { + position: fixed; + height: 100%; + top: 0; +} + +.sb-sidebar-primary { + left: -17rem; + transition: left 250ms ease-in-out; +} +.sb-sidebar-secondary { + right: -17rem; + transition: right 250ms ease-in-out; +} + +.sb-sidebar-toggle { + display: none; +} +.sb-sidebar-overlay { + position: fixed; + top: 0; + width: 0; + height: 0; + + transition: width 0ms ease 250ms, height 0ms ease 250ms, opacity 250ms ease; + + opacity: 0; + background-color: rgba(0, 0, 0, 0.54); +} + +#sb-sidebar-toggle--primary:checked + ~ .sb-sidebar-overlay[for="sb-sidebar-toggle--primary"], +#sb-sidebar-toggle--secondary:checked + ~ .sb-sidebar-overlay[for="sb-sidebar-toggle--secondary"] { + width: 100%; + height: 100%; + opacity: 1; + transition: width 0ms ease, height 0ms ease, opacity 250ms ease; +} + +#sb-sidebar-toggle--primary:checked ~ .sb-container .sb-sidebar-primary { + left: 0; +} +#sb-sidebar-toggle--secondary:checked ~ .sb-container .sb-sidebar-secondary { + right: 0; +} + +/* Full-width mode */ +.drop-secondary-sidebar-for-full-width-content + .hide-when-secondary-sidebar-shown { + display: none !important; +} +.drop-secondary-sidebar-for-full-width-content .sb-sidebar-secondary { + display: none !important; +} + +/* Mobile views */ +.sb-page-width { + width: 100%; +} + +.sb-article-container, +.sb-footer-content__inner, +.drop-secondary-sidebar-for-full-width-content .sb-article, +.drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 100vw; +} + +.sb-article, +.match-content-width { + padding: 0 1rem; + box-sizing: border-box; +} + +@media (min-width: 32rem) { + .sb-article, + .match-content-width { + padding: 0 2rem; + } +} + +/* Tablet views */ +@media (min-width: 42rem) { + .sb-article-container { + width: auto; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 42rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} +@media (min-width: 46rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 46rem; + } + .sb-article, + .match-content-width { + width: 46rem; + } +} +@media (min-width: 50rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 50rem; + } + .sb-article, + .match-content-width { + width: 50rem; + } +} + +/* Tablet views */ +@media (min-width: 59rem) { + .sb-sidebar-secondary { + position: static; + } + .hide-when-secondary-sidebar-shown { + display: none !important; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 59rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} +@media (min-width: 63rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 63rem; + } + .sb-article, + .match-content-width { + width: 46rem; + } +} +@media (min-width: 67rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } + .sb-article, + .match-content-width { + width: 50rem; + } +} + +/* Desktop views */ +@media (min-width: 76rem) { + .sb-sidebar-primary { + position: static; + } + .hide-when-primary-sidebar-shown { + display: none !important; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 59rem; + } + .sb-article, + .match-content-width { + width: 42rem; + } +} + +/* Full desktop views */ +@media (min-width: 80rem) { + .sb-article, + .match-content-width { + width: 46rem; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 63rem; + } +} + +@media (min-width: 84rem) { + .sb-article, + .match-content-width { + width: 50rem; + } + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } +} + +@media (min-width: 88rem) { + .sb-footer-content__inner, + .drop-secondary-sidebar-for-full-width-content .sb-article, + .drop-secondary-sidebar-for-full-width-content .match-content-width { + width: 67rem; + } + .sb-page-width { + width: 88rem; + } +} diff --git a/_static/styles/furo-extensions.css b/_static/styles/furo-extensions.css new file mode 100644 index 0000000..bc447f2 --- /dev/null +++ b/_static/styles/furo-extensions.css @@ -0,0 +1,2 @@ +#furo-sidebar-ad-placement{padding:var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)}#furo-sidebar-ad-placement .ethical-sidebar{background:var(--color-background-secondary);border:none;box-shadow:none}#furo-sidebar-ad-placement .ethical-sidebar:hover{background:var(--color-background-hover)}#furo-sidebar-ad-placement .ethical-sidebar 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Remove the inheritance of text transform in Firefox.\n */\n\nbutton,\nselect { /* 1 */\n text-transform: none;\n}\n\n/**\n * Correct the inability to style clickable types in iOS and Safari.\n */\n\nbutton,\n[type=\"button\"],\n[type=\"reset\"],\n[type=\"submit\"] {\n -webkit-appearance: button;\n}\n\n/**\n * Remove the inner border and padding in Firefox.\n */\n\nbutton::-moz-focus-inner,\n[type=\"button\"]::-moz-focus-inner,\n[type=\"reset\"]::-moz-focus-inner,\n[type=\"submit\"]::-moz-focus-inner {\n border-style: none;\n padding: 0;\n}\n\n/**\n * Restore the focus styles unset by the previous rule.\n */\n\nbutton:-moz-focusring,\n[type=\"button\"]:-moz-focusring,\n[type=\"reset\"]:-moz-focusring,\n[type=\"submit\"]:-moz-focusring {\n outline: 1px dotted ButtonText;\n}\n\n/**\n * Correct the padding in Firefox.\n */\n\nfieldset {\n padding: 0.35em 0.75em 0.625em;\n}\n\n/**\n * 1. Correct the text wrapping in Edge and IE.\n * 2. Correct the color inheritance from `fieldset` elements in IE.\n * 3. Remove the padding so developers are not caught out when they zero out\n * `fieldset` elements in all browsers.\n */\n\nlegend {\n box-sizing: border-box; /* 1 */\n color: inherit; /* 2 */\n display: table; /* 1 */\n max-width: 100%; /* 1 */\n padding: 0; /* 3 */\n white-space: normal; /* 1 */\n}\n\n/**\n * Add the correct vertical alignment in Chrome, Firefox, and Opera.\n */\n\nprogress {\n vertical-align: baseline;\n}\n\n/**\n * Remove the default vertical scrollbar in IE 10+.\n */\n\ntextarea {\n overflow: auto;\n}\n\n/**\n * 1. Add the correct box sizing in IE 10.\n * 2. Remove the padding in IE 10.\n */\n\n[type=\"checkbox\"],\n[type=\"radio\"] {\n box-sizing: border-box; /* 1 */\n padding: 0; /* 2 */\n}\n\n/**\n * Correct the cursor style of increment and decrement buttons in Chrome.\n */\n\n[type=\"number\"]::-webkit-inner-spin-button,\n[type=\"number\"]::-webkit-outer-spin-button {\n height: auto;\n}\n\n/**\n * 1. Correct the odd appearance in Chrome and Safari.\n * 2. Correct the outline style in Safari.\n */\n\n[type=\"search\"] {\n -webkit-appearance: textfield; /* 1 */\n outline-offset: -2px; /* 2 */\n}\n\n/**\n * Remove the inner padding in Chrome and Safari on macOS.\n */\n\n[type=\"search\"]::-webkit-search-decoration {\n -webkit-appearance: none;\n}\n\n/**\n * 1. Correct the inability to style clickable types in iOS and Safari.\n * 2. Change font properties to `inherit` in Safari.\n */\n\n::-webkit-file-upload-button {\n -webkit-appearance: button; /* 1 */\n font: inherit; /* 2 */\n}\n\n/* Interactive\n ========================================================================== */\n\n/*\n * Add the correct display in Edge, IE 10+, and Firefox.\n */\n\ndetails {\n display: block;\n}\n\n/*\n * Add the correct display in all browsers.\n */\n\nsummary {\n display: list-item;\n}\n\n/* Misc\n ========================================================================== */\n\n/**\n * Add the correct display in IE 10+.\n */\n\ntemplate {\n display: none;\n}\n\n/**\n * Add the correct display in IE 10.\n */\n\n[hidden] {\n display: none;\n}\n","// This file contains styles for managing print media.\n\n////////////////////////////////////////////////////////////////////////////////\n// Hide elements not relevant to print media.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n // Hide icon container.\n .content-icon-container\n display: none !important\n\n // Hide showing header links if hovering over when printing.\n .headerlink\n display: none !important\n\n // Hide mobile header.\n .mobile-header\n display: none !important\n\n // Hide navigation links.\n .related-pages\n display: none !important\n\n////////////////////////////////////////////////////////////////////////////////\n// Tweaks related to decolorization.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n // Apply a border around code which no longer have a color background.\n .highlight\n border: 0.1pt solid var(--color-foreground-border)\n\n////////////////////////////////////////////////////////////////////////////////\n// Avoid page break in some relevant cases.\n////////////////////////////////////////////////////////////////////////////////\n@media print\n ul, ol, dl, a, table, pre, blockquote\n page-break-inside: avoid\n\n h1, h2, h3, h4, h5, h6, img, figure, caption\n page-break-inside: avoid\n page-break-after: avoid\n\n ul, ol, dl\n page-break-before: avoid\n",".visually-hidden\n position: absolute !important\n width: 1px !important\n height: 1px !important\n padding: 0 !important\n margin: -1px !important\n overflow: hidden !important\n clip: rect(0,0,0,0) !important\n white-space: nowrap !important\n border: 0 !important\n\n:-moz-focusring\n outline: auto\n","// This file serves as the \"skeleton\" of the theming logic.\n//\n// This contains the bulk of the logic for handling dark mode, color scheme\n// toggling and the handling of color-scheme-specific hiding of elements.\n\nbody\n @include fonts\n @include spacing\n @include icons\n @include admonitions\n @include default-admonition(#651fff, \"abstract\")\n @include default-topic(#14B8A6, \"pencil\")\n\n @include colors\n\n.only-light\n display: block !important\nhtml body .only-dark\n display: none !important\n\n// Ignore dark-mode hints if print media.\n@media not print\n // Enable dark-mode, if requested.\n body[data-theme=\"dark\"]\n @include colors-dark\n\n html & .only-light\n display: none !important\n .only-dark\n display: block !important\n\n // Enable dark mode, unless explicitly told to avoid.\n @media (prefers-color-scheme: dark)\n body:not([data-theme=\"light\"])\n @include colors-dark\n\n html & .only-light\n display: none !important\n .only-dark\n display: block !important\n\n//\n// Theme toggle presentation\n//\nbody[data-theme=\"auto\"]\n .theme-toggle svg.theme-icon-when-auto\n display: block\n\nbody[data-theme=\"dark\"]\n .theme-toggle svg.theme-icon-when-dark\n display: block\n\nbody[data-theme=\"light\"]\n .theme-toggle svg.theme-icon-when-light\n display: block\n","// Fonts used by this theme.\n//\n// There are basically two things here -- using the system font stack and\n// defining sizes for various elements in %ages. We could have also used `em`\n// but %age is easier to reason about for me.\n\n@mixin fonts {\n // These are adapted from https://systemfontstack.com/\n --font-stack: -apple-system, BlinkMacSystemFont, Segoe UI, Helvetica, Arial,\n sans-serif, Apple Color Emoji, Segoe UI Emoji;\n --font-stack--monospace: \"SFMono-Regular\", Menlo, Consolas, Monaco,\n Liberation Mono, Lucida Console, monospace;\n\n --font-size--normal: 100%;\n --font-size--small: 87.5%;\n --font-size--small--2: 81.25%;\n --font-size--small--3: 75%;\n --font-size--small--4: 62.5%;\n\n // Sidebar\n --sidebar-caption-font-size: var(--font-size--small--2);\n --sidebar-item-font-size: var(--font-size--small);\n --sidebar-search-input-font-size: var(--font-size--small);\n\n // Table of Contents\n --toc-font-size: var(--font-size--small--3);\n --toc-font-size--mobile: var(--font-size--normal);\n --toc-title-font-size: var(--font-size--small--4);\n\n // Admonitions\n //\n // These aren't defined in terms of %ages, since nesting these is permitted.\n --admonition-font-size: 0.8125rem;\n --admonition-title-font-size: 0.8125rem;\n\n // Code\n --code-font-size: var(--font-size--small--2);\n\n // API\n --api-font-size: var(--font-size--small);\n}\n","// Spacing for various elements on the page\n//\n// If the user wants to tweak things in a certain way, they are permitted to.\n// They also have to deal with the consequences though!\n\n@mixin spacing {\n // Header!\n --header-height: calc(\n var(--sidebar-item-line-height) + 4 * #{var(--sidebar-item-spacing-vertical)}\n );\n --header-padding: 0.5rem;\n\n // Sidebar\n --sidebar-tree-space-above: 1.5rem;\n --sidebar-caption-space-above: 1rem;\n\n --sidebar-item-line-height: 1rem;\n --sidebar-item-spacing-vertical: 0.5rem;\n --sidebar-item-spacing-horizontal: 1rem;\n --sidebar-item-height: calc(\n var(--sidebar-item-line-height) + 2 *#{var(--sidebar-item-spacing-vertical)}\n );\n\n --sidebar-expander-width: var(--sidebar-item-height); // be square\n\n --sidebar-search-space-above: 0.5rem;\n --sidebar-search-input-spacing-vertical: 0.5rem;\n --sidebar-search-input-spacing-horizontal: 0.5rem;\n --sidebar-search-input-height: 1rem;\n --sidebar-search-icon-size: var(--sidebar-search-input-height);\n\n // Table of Contents\n --toc-title-padding: 0.25rem 0;\n --toc-spacing-vertical: 1.5rem;\n --toc-spacing-horizontal: 1.5rem;\n --toc-item-spacing-vertical: 0.4rem;\n --toc-item-spacing-horizontal: 1rem;\n}\n","// Expose theme icons as CSS variables.\n\n$icons: (\n // Adapted from tabler-icons\n // url: https://tablericons.com/\n \"search\":\n url('data:image/svg+xml;charset=utf-8,'),\n // Factored out from mkdocs-material on 24-Aug-2020.\n // url: https://squidfunk.github.io/mkdocs-material/reference/admonitions/\n \"pencil\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"abstract\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"info\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"flame\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"question\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"warning\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"failure\":\n url('data:image/svg+xml;charset=utf-8,'),\n \"spark\":\n url('data:image/svg+xml;charset=utf-8,')\n);\n\n@mixin icons {\n @each $name, $glyph in $icons {\n --icon-#{$name}: #{$glyph};\n }\n}\n","// Admonitions\n\n// Structure of these is:\n// admonition-class: color \"icon-name\";\n//\n// The colors are translated into CSS variables below. The icons are\n// used directly in the main declarations to set the `mask-image` in\n// the title.\n\n// prettier-ignore\n$admonitions: (\n // Each of these has an reST directives for it.\n \"caution\": #ff9100 \"spark\",\n \"warning\": #ff9100 \"warning\",\n \"danger\": #ff5252 \"spark\",\n \"attention\": #ff5252 \"warning\",\n \"error\": #ff5252 \"failure\",\n \"hint\": #00c852 \"question\",\n \"tip\": #00c852 \"info\",\n \"important\": #00bfa5 \"flame\",\n \"note\": #00b0ff \"pencil\",\n \"seealso\": #448aff \"info\",\n \"admonition-todo\": #808080 \"pencil\"\n);\n\n@mixin default-admonition($color, $icon-name) {\n --color-admonition-title: #{$color};\n --color-admonition-title-background: #{rgba($color, 0.2)};\n\n --icon-admonition-default: var(--icon-#{$icon-name});\n}\n\n@mixin default-topic($color, $icon-name) {\n --color-topic-title: #{$color};\n --color-topic-title-background: #{rgba($color, 0.2)};\n\n --icon-topic-default: var(--icon-#{$icon-name});\n}\n\n@mixin admonitions {\n @each $name, $values in $admonitions {\n --color-admonition-title--#{$name}: #{nth($values, 1)};\n --color-admonition-title-background--#{$name}: #{rgba(\n nth($values, 1),\n 0.2\n )};\n }\n}\n","// Colors used throughout this theme.\n//\n// The aim is to give the user more control. Thus, instead of hard-coding colors\n// in various parts of the stylesheet, the approach taken is to define all\n// colors as CSS variables and reusing them in all the places.\n//\n// `colors-dark` depends on `colors` being included at a lower specificity.\n\n@mixin colors {\n --color-problematic: #b30000;\n\n // Base Colors\n --color-foreground-primary: black; // for main text and headings\n --color-foreground-secondary: #5a5c63; // for secondary text\n --color-foreground-muted: #646776; // for muted text\n --color-foreground-border: #878787; // for content borders\n\n --color-background-primary: white; // for content\n --color-background-secondary: #f8f9fb; // for navigation + ToC\n --color-background-hover: #efeff4ff; // for navigation-item hover\n --color-background-hover--transparent: #efeff400;\n --color-background-border: #eeebee; // for UI borders\n --color-background-item: #ccc; // for \"background\" items (eg: copybutton)\n\n // Announcements\n --color-announcement-background: #000000dd;\n --color-announcement-text: #eeebee;\n\n // Brand colors\n --color-brand-primary: #2962ff;\n --color-brand-content: #2a5adf;\n\n // API documentation\n --color-api-background: var(--color-background-hover--transparent);\n --color-api-background-hover: var(--color-background-hover);\n --color-api-overall: var(--color-foreground-secondary);\n --color-api-name: var(--color-problematic);\n --color-api-pre-name: var(--color-problematic);\n --color-api-paren: var(--color-foreground-secondary);\n --color-api-keyword: var(--color-foreground-primary);\n --color-highlight-on-target: #ffffcc;\n\n // Inline code background\n --color-inline-code-background: var(--color-background-secondary);\n\n // Highlighted text (search)\n --color-highlighted-background: #ddeeff;\n --color-highlighted-text: var(--color-foreground-primary);\n\n // GUI Labels\n --color-guilabel-background: #ddeeff80;\n --color-guilabel-border: #bedaf580;\n --color-guilabel-text: var(--color-foreground-primary);\n\n // Admonitions!\n --color-admonition-background: transparent;\n\n //////////////////////////////////////////////////////////////////////////////\n // Everything below this should be one of:\n // - var(...)\n // - *-gradient(...)\n // - special literal values (eg: transparent, none)\n //////////////////////////////////////////////////////////////////////////////\n\n // Tables\n --color-table-header-background: var(--color-background-secondary);\n --color-table-border: var(--color-background-border);\n\n // Cards\n --color-card-border: var(--color-background-secondary);\n --color-card-background: transparent;\n --color-card-marginals-background: var(--color-background-secondary);\n\n // Header\n --color-header-background: var(--color-background-primary);\n --color-header-border: var(--color-background-border);\n --color-header-text: var(--color-foreground-primary);\n\n // Sidebar (left)\n --color-sidebar-background: var(--color-background-secondary);\n --color-sidebar-background-border: var(--color-background-border);\n\n --color-sidebar-brand-text: var(--color-foreground-primary);\n --color-sidebar-caption-text: var(--color-foreground-muted);\n --color-sidebar-link-text: var(--color-foreground-secondary);\n --color-sidebar-link-text--top-level: var(--color-brand-primary);\n\n --color-sidebar-item-background: var(--color-sidebar-background);\n --color-sidebar-item-background--current: var(\n --color-sidebar-item-background\n );\n --color-sidebar-item-background--hover: linear-gradient(\n 90deg,\n var(--color-background-hover--transparent) 0%,\n var(--color-background-hover) var(--sidebar-item-spacing-horizontal),\n var(--color-background-hover) 100%\n );\n\n --color-sidebar-item-expander-background: transparent;\n --color-sidebar-item-expander-background--hover: var(\n --color-background-hover\n );\n\n --color-sidebar-search-text: var(--color-foreground-primary);\n --color-sidebar-search-background: var(--color-background-secondary);\n --color-sidebar-search-background--focus: var(--color-background-primary);\n --color-sidebar-search-border: var(--color-background-border);\n --color-sidebar-search-icon: var(--color-foreground-muted);\n\n // Table of Contents (right)\n --color-toc-background: var(--color-background-primary);\n --color-toc-title-text: var(--color-foreground-muted);\n --color-toc-item-text: var(--color-foreground-secondary);\n --color-toc-item-text--hover: var(--color-foreground-primary);\n --color-toc-item-text--active: var(--color-brand-primary);\n\n // Actual page contents\n --color-content-foreground: var(--color-foreground-primary);\n --color-content-background: transparent;\n\n // Links\n --color-link: var(--color-brand-content);\n --color-link--hover: var(--color-brand-content);\n --color-link-underline: var(--color-background-border);\n --color-link-underline--hover: var(--color-foreground-border);\n}\n\n@mixin colors-dark {\n --color-problematic: #ee5151;\n\n // Base Colors\n --color-foreground-primary: #ffffffcc; // for main text and headings\n --color-foreground-secondary: #9ca0a5; // for secondary text\n --color-foreground-muted: #81868d; // for muted text\n --color-foreground-border: #666666; // for content borders\n\n --color-background-primary: #131416; // for content\n --color-background-secondary: #1a1c1e; // for navigation + ToC\n --color-background-hover: #1e2124ff; // for navigation-item hover\n --color-background-hover--transparent: #1e212400;\n --color-background-border: #303335; // for UI borders\n --color-background-item: #444; // for \"background\" items (eg: copybutton)\n\n // Announcements\n --color-announcement-background: #000000dd;\n --color-announcement-text: #eeebee;\n\n // Brand colors\n --color-brand-primary: #2b8cee;\n --color-brand-content: #368ce2;\n\n // Highlighted text (search)\n --color-highlighted-background: #083563;\n\n // GUI Labels\n --color-guilabel-background: #08356380;\n --color-guilabel-border: #13395f80;\n\n // API documentation\n --color-api-keyword: var(--color-foreground-secondary);\n --color-highlight-on-target: #333300;\n\n // Admonitions\n --color-admonition-background: #18181a;\n\n // Cards\n --color-card-border: var(--color-background-secondary);\n --color-card-background: #18181a;\n --color-card-marginals-background: var(--color-background-hover);\n}\n","// This file contains the styling for making the content throughout the page,\n// including fonts, paragraphs, headings and spacing among these elements.\n\nbody\n font-family: var(--font-stack)\npre,\ncode,\nkbd,\nsamp\n font-family: var(--font-stack--monospace)\n\n// Make fonts look slightly nicer.\nbody\n -webkit-font-smoothing: antialiased\n -moz-osx-font-smoothing: grayscale\n\n// Line height from Bootstrap 4.1\narticle\n line-height: 1.5\n\n//\n// Headings\n//\nh1,\nh2,\nh3,\nh4,\nh5,\nh6\n line-height: 1.25\n font-weight: bold\n\n border-radius: 0.5rem\n margin-top: 0.5rem\n margin-bottom: 0.5rem\n margin-left: -0.5rem\n margin-right: -0.5rem\n padding-left: 0.5rem\n padding-right: 0.5rem\n\n + p\n margin-top: 0\n\nh1\n font-size: 2.5em\n margin-top: 1.75rem\n margin-bottom: 1rem\nh2\n font-size: 2em\n margin-top: 1.75rem\nh3\n font-size: 1.5em\nh4\n font-size: 1.25em\nh5\n font-size: 1.125em\nh6\n font-size: 1em\n\nsmall\n opacity: 75%\n font-size: 80%\n\n// Paragraph\np\n margin-top: 0.5rem\n margin-bottom: 0.75rem\n\n// Horizontal rules\nhr.docutils\n height: 1px\n padding: 0\n margin: 2rem 0\n background-color: var(--color-background-border)\n border: 0\n\n.centered\n text-align: center\n\n// Links\na\n text-decoration: underline\n\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline)\n\n &:hover\n color: var(--color-link--hover)\n text-decoration-color: var(--color-link-underline--hover)\n &.muted-link\n color: inherit\n &:hover\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline--hover)\n","// This file contains the styles for the overall layouting of the documentation\n// skeleton, including the responsive changes as well as sidebar toggles.\n//\n// This is implemented as a mobile-last design, which isn't ideal, but it is\n// reasonably good-enough and I got pretty tired by the time I'd finished this\n// to move the rules around to fix this. Shouldn't take more than 3-4 hours,\n// if you know what you're doing tho.\n\n// HACK: Not all browsers account for the scrollbar width in media queries.\n// This results in horizontal scrollbars in the breakpoint where we go\n// from displaying everything to hiding the ToC. We accomodate for this by\n// adding a bit of padding to the TOC drawer, disabling the horizontal\n// scrollbar and allowing the scrollbars to cover the padding.\n// https://www.456bereastreet.com/archive/201301/media_query_width_and_vertical_scrollbars/\n\n// HACK: Always having the scrollbar visible, prevents certain browsers from\n// causing the content to stutter horizontally between taller-than-viewport and\n// not-taller-than-viewport pages.\n\nhtml\n overflow-x: hidden\n overflow-y: scroll\n scroll-behavior: smooth\n\n.sidebar-scroll, .toc-scroll, article[role=main] *\n // Override Firefox scrollbar style\n scrollbar-width: thin\n scrollbar-color: var(--color-foreground-border) transparent\n\n // Override Chrome scrollbar styles\n &::-webkit-scrollbar\n width: 0.25rem\n height: 0.25rem\n &::-webkit-scrollbar-thumb\n background-color: var(--color-foreground-border)\n border-radius: 0.125rem\n\n//\n// Overalls\n//\nhtml,\nbody\n height: 100%\n color: var(--color-foreground-primary)\n background: var(--color-background-primary)\n\narticle\n color: var(--color-content-foreground)\n background: var(--color-content-background)\n overflow-wrap: break-word\n\n.page\n display: flex\n // fill the viewport for pages with little content.\n min-height: 100%\n\n.mobile-header\n width: 100%\n height: var(--header-height)\n background-color: var(--color-header-background)\n color: var(--color-header-text)\n border-bottom: 1px solid var(--color-header-border)\n\n // Looks like sub-script/super-script have this, and we need this to\n // be \"on top\" of those.\n z-index: 10\n\n // We don't show the header on large screens.\n display: none\n\n // Add shadow when scrolled\n &.scrolled\n border-bottom: none\n box-shadow: 0 0 0.2rem rgba(0, 0, 0, 0.1), 0 0.2rem 0.4rem rgba(0, 0, 0, 0.2)\n\n .header-center\n a\n color: var(--color-header-text)\n text-decoration: none\n\n.main\n display: flex\n flex: 1\n\n// Sidebar (left) also covers the entire left portion of screen.\n.sidebar-drawer\n box-sizing: border-box\n\n border-right: 1px solid var(--color-sidebar-background-border)\n background: var(--color-sidebar-background)\n\n display: flex\n justify-content: flex-end\n // These next two lines took me two days to figure out.\n width: calc((100% - #{$full-width}) / 2 + #{$sidebar-width})\n min-width: $sidebar-width\n\n// Scroll-along sidebars\n.sidebar-container,\n.toc-drawer\n box-sizing: border-box\n width: $sidebar-width\n\n.toc-drawer\n background: var(--color-toc-background)\n // See HACK described on top of this document\n padding-right: 1rem\n\n.sidebar-sticky,\n.toc-sticky\n position: sticky\n top: 0\n height: min(100%, 100vh)\n height: 100vh\n\n display: flex\n flex-direction: column\n\n.sidebar-scroll,\n.toc-scroll\n flex-grow: 1\n flex-shrink: 1\n\n overflow: auto\n scroll-behavior: smooth\n\n// Central items.\n.content\n padding: 0 $content-padding\n width: $content-width\n\n display: flex\n flex-direction: column\n justify-content: space-between\n\n.icon\n display: inline-block\n height: 1rem\n width: 1rem\n svg\n width: 100%\n height: 100%\n\n//\n// Accommodate announcement banner\n//\n.announcement\n background-color: var(--color-announcement-background)\n color: var(--color-announcement-text)\n\n height: var(--header-height)\n display: flex\n align-items: center\n overflow-x: auto\n & + .page\n min-height: calc(100% - var(--header-height))\n\n.announcement-content\n box-sizing: border-box\n padding: 0.5rem\n min-width: 100%\n white-space: nowrap\n text-align: center\n\n a\n color: var(--color-announcement-text)\n text-decoration-color: var(--color-announcement-text)\n\n &:hover\n color: var(--color-announcement-text)\n text-decoration-color: var(--color-link--hover)\n\n////////////////////////////////////////////////////////////////////////////////\n// Toggles for theme\n////////////////////////////////////////////////////////////////////////////////\n.no-js .theme-toggle-container // don't show theme toggle if there's no JS\n display: none\n\n.theme-toggle-container\n vertical-align: middle\n\n.theme-toggle\n cursor: pointer\n border: none\n padding: 0\n background: transparent\n\n.theme-toggle svg\n vertical-align: middle\n height: 1rem\n width: 1rem\n color: var(--color-foreground-primary)\n display: none\n\n.theme-toggle-header\n float: left\n padding: 1rem 0.5rem\n\n////////////////////////////////////////////////////////////////////////////////\n// Toggles for elements\n////////////////////////////////////////////////////////////////////////////////\n.toc-overlay-icon, .nav-overlay-icon\n display: none\n cursor: pointer\n\n .icon\n color: var(--color-foreground-secondary)\n height: 1rem\n width: 1rem\n\n.toc-header-icon, .nav-overlay-icon\n // for when we set display: flex\n justify-content: center\n align-items: center\n\n.toc-content-icon\n height: 1.5rem\n width: 1.5rem\n\n.content-icon-container\n float: right\n display: flex\n margin-top: 1.5rem\n margin-left: 1rem\n margin-bottom: 1rem\n gap: 0.5rem\n\n .edit-this-page svg\n color: inherit\n height: 1rem\n width: 1rem\n\n.sidebar-toggle\n position: absolute\n display: none\n// \n.sidebar-toggle[name=\"__toc\"]\n left: 20px\n.sidebar-toggle:checked\n left: 40px\n// \n\n.overlay\n position: fixed\n top: 0\n width: 0\n height: 0\n\n transition: width 0ms, height 0ms, opacity 250ms ease-out\n\n opacity: 0\n background-color: rgba(0, 0, 0, 0.54)\n.sidebar-overlay\n z-index: 20\n.toc-overlay\n z-index: 40\n\n// Keep things on top and smooth.\n.sidebar-drawer\n z-index: 30\n transition: left 250ms ease-in-out\n.toc-drawer\n z-index: 50\n transition: right 250ms ease-in-out\n\n// Show the Sidebar\n#__navigation:checked\n & ~ .sidebar-overlay\n width: 100%\n height: 100%\n opacity: 1\n & ~ .page\n .sidebar-drawer\n top: 0\n left: 0\n // Show the toc sidebar\n#__toc:checked\n & ~ .toc-overlay\n width: 100%\n height: 100%\n opacity: 1\n & ~ .page\n .toc-drawer\n top: 0\n right: 0\n\n////////////////////////////////////////////////////////////////////////////////\n// Back to top\n////////////////////////////////////////////////////////////////////////////////\n.back-to-top\n text-decoration: none\n\n display: none\n position: fixed\n left: 0\n top: 1rem\n padding: 0.5rem\n padding-right: 0.75rem\n border-radius: 1rem\n font-size: 0.8125rem\n\n background: var(--color-background-primary)\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), #6b728080 0px 0px 1px 0px\n\n z-index: 10\n\n margin-left: 50%\n transform: translateX(-50%)\n svg\n height: 1rem\n width: 1rem\n fill: currentColor\n display: inline-block\n\n span\n margin-left: 0.25rem\n\n .show-back-to-top &\n display: flex\n align-items: center\n\n////////////////////////////////////////////////////////////////////////////////\n// Responsive layouting\n////////////////////////////////////////////////////////////////////////////////\n// Make things a bit bigger on bigger screens.\n@media (min-width: $full-width + $sidebar-width)\n html\n font-size: 110%\n\n@media (max-width: $full-width)\n // Collapse \"toc\" into the icon.\n .toc-content-icon\n display: flex\n .toc-drawer\n position: fixed\n height: 100vh\n top: 0\n right: -$sidebar-width\n border-left: 1px solid var(--color-background-muted)\n .toc-tree\n border-left: none\n font-size: var(--toc-font-size--mobile)\n\n // Accomodate for a changed content width.\n .sidebar-drawer\n width: calc((100% - #{$full-width - $sidebar-width}) / 2 + #{$sidebar-width})\n\n@media (max-width: $full-width - $sidebar-width)\n // Collapse \"navigation\".\n .nav-overlay-icon\n display: flex\n .sidebar-drawer\n position: fixed\n height: 100vh\n width: $sidebar-width\n\n top: 0\n left: -$sidebar-width\n\n // Swap which icon is visible.\n .toc-header-icon\n display: flex\n .toc-content-icon, .theme-toggle-content\n display: none\n .theme-toggle-header\n display: block\n\n // Show the header.\n .mobile-header\n position: sticky\n top: 0\n display: flex\n justify-content: space-between\n align-items: center\n\n .header-left,\n .header-right\n display: flex\n height: var(--header-height)\n padding: 0 var(--header-padding)\n label\n height: 100%\n width: 100%\n user-select: none\n\n .nav-overlay-icon .icon,\n .theme-toggle svg\n height: 1.25rem\n width: 1.25rem\n\n // Add a scroll margin for the content\n :target\n scroll-margin-top: var(--header-height)\n\n // Show back-to-top below the header\n .back-to-top\n top: calc(var(--header-height) + 0.5rem)\n\n // Center the page, and accommodate for the header.\n .page\n flex-direction: column\n justify-content: center\n .content\n margin-left: auto\n margin-right: auto\n\n@media (max-width: $content-width + 2* $content-padding)\n // Content should respect window limits.\n .content\n width: 100%\n overflow-x: auto\n\n@media (max-width: $content-width)\n .content\n padding: 0 $content-padding--small\n // Don't float sidebars to the right.\n article aside.sidebar\n float: none\n width: 100%\n margin: 1rem 0\n","//\n// The design here is strongly inspired by mkdocs-material.\n.admonition, .topic\n margin: 1rem auto\n padding: 0 0.5rem 0.5rem 0.5rem\n\n background: var(--color-admonition-background)\n\n border-radius: 0.2rem\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), 0 0 0.0625rem rgba(0, 0, 0, 0.1)\n\n font-size: var(--admonition-font-size)\n\n overflow: hidden\n page-break-inside: avoid\n\n // First element should have no margin, since the title has it.\n > :nth-child(2)\n margin-top: 0\n\n // Last item should have no margin, since we'll control that w/ padding\n > :last-child\n margin-bottom: 0\n\n.admonition p.admonition-title,\np.topic-title\n position: relative\n margin: 0 -0.5rem 0.5rem\n padding-left: 2rem\n padding-right: .5rem\n padding-top: .4rem\n padding-bottom: .4rem\n\n font-weight: 500\n font-size: var(--admonition-title-font-size)\n line-height: 1.3\n\n // Our fancy icon\n &::before\n content: \"\"\n position: absolute\n left: 0.5rem\n width: 1rem\n height: 1rem\n\n// Default styles\np.admonition-title\n background-color: var(--color-admonition-title-background)\n &::before\n background-color: var(--color-admonition-title)\n mask-image: var(--icon-admonition-default)\n mask-repeat: no-repeat\n\np.topic-title\n background-color: var(--color-topic-title-background)\n &::before\n background-color: var(--color-topic-title)\n mask-image: var(--icon-topic-default)\n mask-repeat: no-repeat\n\n//\n// Variants\n//\n.admonition\n border-left: 0.2rem solid var(--color-admonition-title)\n\n @each $type, $value in $admonitions\n &.#{$type}\n border-left-color: var(--color-admonition-title--#{$type})\n > .admonition-title\n background-color: var(--color-admonition-title-background--#{$type})\n &::before\n background-color: var(--color-admonition-title--#{$type})\n mask-image: var(--icon-#{nth($value, 2)})\n\n.admonition-todo > .admonition-title\n text-transform: uppercase\n","// This file stylizes the API documentation (stuff generated by autodoc). It's\n// deeply nested due to how autodoc structures the HTML without enough classes\n// to select the relevant items.\n\n// API docs!\ndl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)\n // Tweak the spacing of all the things!\n dd\n margin-left: 2rem\n > :first-child\n margin-top: 0.125rem\n > :last-child\n margin-bottom: 0.75rem\n\n // This is used for the arguments\n .field-list\n margin-bottom: 0.75rem\n\n // \"Headings\" (like \"Parameters\" and \"Return\")\n > dt\n text-transform: uppercase\n font-size: var(--font-size--small)\n\n dd:empty\n margin-bottom: 0.5rem\n dd > ul\n margin-left: -1.2rem\n > li\n > p:nth-child(2)\n margin-top: 0\n // When the last-empty-paragraph follows a paragraph, it doesn't need\n // to augument the existing spacing.\n > p + p:last-child:empty\n margin-top: 0\n margin-bottom: 0\n\n // Colorize the elements\n > dt\n color: var(--color-api-overall)\n\n.sig:not(.sig-inline)\n font-weight: bold\n\n font-size: var(--api-font-size)\n font-family: var(--font-stack--monospace)\n\n margin-left: -0.25rem\n margin-right: -0.25rem\n padding-top: 0.25rem\n padding-bottom: 0.25rem\n padding-right: 0.5rem\n\n // These are intentionally em, to properly match the font size.\n padding-left: 3em\n text-indent: -2.5em\n\n border-radius: 0.25rem\n\n background: var(--color-api-background)\n transition: background 100ms ease-out\n\n &:hover\n background: var(--color-api-background-hover)\n\n // adjust the size of the [source] link on the right.\n a.reference\n .viewcode-link\n font-weight: normal\n width: 3.5rem\n\nem.property\n font-style: normal\n &:first-child\n color: var(--color-api-keyword)\n.sig-name\n color: var(--color-api-name)\n.sig-prename\n font-weight: normal\n color: var(--color-api-pre-name)\n.sig-paren\n color: var(--color-api-paren)\n.sig-param\n font-style: normal\n\n.versionmodified\n font-style: italic\ndiv.versionadded, div.versionchanged, div.deprecated\n p\n margin-top: 0.125rem\n margin-bottom: 0.125rem\n\n// Align the [docs] and [source] to the right.\n.viewcode-link, .viewcode-back\n float: right\n text-align: right\n",".line-block\n margin-top: 0.5rem\n margin-bottom: 0.75rem\n .line-block\n margin-top: 0rem\n margin-bottom: 0rem\n padding-left: 1rem\n","// Captions\narticle p.caption,\ntable > caption,\n.code-block-caption\n font-size: var(--font-size--small)\n text-align: center\n\n// Caption above a TOCTree\n.toctree-wrapper.compound\n .caption, :not(.caption) > .caption-text\n font-size: var(--font-size--small)\n text-transform: uppercase\n\n text-align: initial\n margin-bottom: 0\n\n > ul\n margin-top: 0\n margin-bottom: 0\n","// Inline code\ncode.literal, .sig-inline\n background: var(--color-inline-code-background)\n border-radius: 0.2em\n // Make the font smaller, and use padding to recover.\n font-size: var(--font-size--small--2)\n padding: 0.1em 0.2em\n\n pre.literal-block &\n font-size: inherit\n padding: 0\n\n p &\n border: 1px solid var(--color-background-border)\n\n.sig-inline\n font-family: var(--font-stack--monospace)\n\n// Code and Literal Blocks\n$code-spacing-vertical: 0.625rem\n$code-spacing-horizontal: 0.875rem\n\n// Wraps every literal block + line numbers.\ndiv[class*=\" highlight-\"],\ndiv[class^=\"highlight-\"]\n margin: 1em 0\n display: flex\n\n .table-wrapper\n margin: 0\n padding: 0\n\npre\n margin: 0\n padding: 0\n overflow: auto\n\n // Needed to have more specificity than pygments' \"pre\" selector. :(\n article[role=\"main\"] .highlight &\n line-height: 1.5\n\n &.literal-block,\n .highlight &\n font-size: var(--code-font-size)\n padding: $code-spacing-vertical $code-spacing-horizontal\n\n // Make it look like all the other blocks.\n &.literal-block\n margin-top: 1rem\n margin-bottom: 1rem\n\n border-radius: 0.2rem\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n\n// All code is always contained in this.\n.highlight\n width: 100%\n border-radius: 0.2rem\n\n // Make line numbers and prompts un-selectable.\n .gp, span.linenos\n user-select: none\n pointer-events: none\n\n // Expand the line-highlighting.\n .hll\n display: block\n margin-left: -$code-spacing-horizontal\n margin-right: -$code-spacing-horizontal\n padding-left: $code-spacing-horizontal\n padding-right: $code-spacing-horizontal\n\n/* Make code block captions be nicely integrated */\n.code-block-caption\n display: flex\n padding: $code-spacing-vertical $code-spacing-horizontal\n\n border-radius: 0.25rem\n border-bottom-left-radius: 0\n border-bottom-right-radius: 0\n font-weight: 300\n border-bottom: 1px solid\n\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n border-color: var(--color-background-border)\n\n + div[class]\n margin-top: 0\n pre\n border-top-left-radius: 0\n border-top-right-radius: 0\n\n// When `html_codeblock_linenos_style` is table.\n.highlighttable\n width: 100%\n display: block\n tbody\n display: block\n\n tr\n display: flex\n\n // Line numbers\n td.linenos\n background-color: var(--color-code-background)\n color: var(--color-code-foreground)\n padding: $code-spacing-vertical $code-spacing-horizontal\n padding-right: 0\n border-top-left-radius: 0.2rem\n border-bottom-left-radius: 0.2rem\n\n .linenodiv\n padding-right: $code-spacing-horizontal\n font-size: var(--code-font-size)\n box-shadow: -0.0625rem 0 var(--color-foreground-border) inset\n\n // Actual code\n td.code\n padding: 0\n display: block\n flex: 1\n overflow: hidden\n\n .highlight\n border-top-left-radius: 0\n border-bottom-left-radius: 0\n\n// When `html_codeblock_linenos_style` is inline.\n.highlight\n span.linenos\n display: inline-block\n padding-left: 0\n padding-right: $code-spacing-horizontal\n margin-right: $code-spacing-horizontal\n box-shadow: -0.0625rem 0 var(--color-foreground-border) inset\n","// Inline Footnote Reference\n.footnote-reference\n font-size: var(--font-size--small--4)\n vertical-align: super\n\n// Definition list, listing the content of each note.\n// docutils <= 0.17\ndl.footnote.brackets\n font-size: var(--font-size--small)\n color: var(--color-foreground-secondary)\n\n display: grid\n grid-template-columns: max-content auto\n dt\n margin: 0\n > .fn-backref\n margin-left: 0.25rem\n\n &:after\n content: \":\"\n\n .brackets\n &:before\n content: \"[\"\n &:after\n content: \"]\"\n\n dd\n margin: 0\n padding: 0 1rem\n\n// docutils >= 0.18\naside.footnote\n font-size: var(--font-size--small)\n color: var(--color-foreground-secondary)\n\naside.footnote > span,\ndiv.citation > span\n float: left\n font-weight: 500\n padding-right: 0.25rem\n\naside.footnote > p,\ndiv.citation > p\n margin-left: 2rem\n","//\n// Figures\n//\nimg\n box-sizing: border-box\n max-width: 100%\n height: auto\n\narticle\n figure, .figure\n border-radius: 0.2rem\n\n margin: 0\n :last-child\n margin-bottom: 0\n\n .align-left\n float: left\n clear: left\n margin: 0 1rem 1rem\n\n .align-right\n float: right\n clear: right\n margin: 0 1rem 1rem\n\n .align-default,\n .align-center\n display: block\n text-align: center\n margin-left: auto\n margin-right: auto\n\n // WELL, table needs to be stylised like a table.\n table.align-default\n display: table\n text-align: initial\n",".genindex-jumpbox, .domainindex-jumpbox\n border-top: 1px solid var(--color-background-border)\n border-bottom: 1px solid var(--color-background-border)\n padding: 0.25rem\n\n.genindex-section, .domainindex-section\n h2\n margin-top: 0.75rem\n margin-bottom: 0.5rem\n ul\n margin-top: 0\n margin-bottom: 0\n","ul,\nol\n padding-left: 1.2rem\n\n // Space lists out like paragraphs\n margin-top: 1rem\n margin-bottom: 1rem\n // reduce margins within li.\n li\n > p:first-child\n margin-top: 0.25rem\n margin-bottom: 0.25rem\n\n > p:last-child\n margin-top: 0.25rem\n\n > ul,\n > ol\n margin-top: 0.5rem\n margin-bottom: 0.5rem\n\nol\n &.arabic\n list-style: decimal\n &.loweralpha\n list-style: lower-alpha\n &.upperalpha\n list-style: upper-alpha\n &.lowerroman\n list-style: lower-roman\n &.upperroman\n list-style: upper-roman\n\n// Don't space lists out when they're \"simple\" or in a `.. toctree::`\n.simple,\n.toctree-wrapper\n li\n > ul,\n > ol\n margin-top: 0\n margin-bottom: 0\n\n// Definition Lists\n.field-list,\n.option-list,\ndl:not([class]),\ndl.simple,\ndl.footnote,\ndl.glossary\n dt\n font-weight: 500\n margin-top: 0.25rem\n + dt\n margin-top: 0\n\n .classifier::before\n content: \":\"\n margin-left: 0.2rem\n margin-right: 0.2rem\n\n dd\n > p:first-child,\n ul\n margin-top: 0.125rem\n\n ul\n margin-bottom: 0.125rem\n",".math-wrapper\n width: 100%\n overflow-x: auto\n\ndiv.math\n position: relative\n text-align: center\n\n .headerlink,\n &:focus .headerlink\n display: none\n\n &:hover .headerlink\n display: inline-block\n\n span.eqno\n position: absolute\n right: 0.5rem\n top: 50%\n transform: translate(0, -50%)\n z-index: 1\n","// Abbreviations\nabbr[title]\n cursor: help\n\n// \"Problematic\" content, as identified by Sphinx\n.problematic\n color: var(--color-problematic)\n\n// Keyboard / Mouse \"instructions\"\nkbd:not(.compound)\n margin: 0 0.2rem\n padding: 0 0.2rem\n border-radius: 0.2rem\n border: 1px solid var(--color-foreground-border)\n color: var(--color-foreground-primary)\n vertical-align: text-bottom\n\n font-size: var(--font-size--small--3)\n display: inline-block\n\n box-shadow: 0 0.0625rem 0 rgba(0, 0, 0, 0.2), inset 0 0 0 0.125rem var(--color-background-primary)\n\n background-color: var(--color-background-secondary)\n\n// Blockquote\nblockquote\n border-left: 4px solid var(--color-background-border)\n background: var(--color-background-secondary)\n\n margin-left: 0\n margin-right: 0\n padding: 0.5rem 1rem\n\n .attribution\n font-weight: 600\n text-align: right\n\n &.pull-quote,\n &.highlights\n font-size: 1.25em\n\n &.epigraph,\n &.pull-quote\n border-left-width: 0\n border-radius: 0.5rem\n\n &.highlights\n border-left-width: 0\n background: transparent\n\n// Center align embedded-in-text images\np .reference img\n vertical-align: middle\n","p.rubric\n line-height: 1.25\n font-weight: bold\n font-size: 1.125em\n\n // For Numpy-style documentation that's got rubrics within it.\n // https://github.com/pradyunsg/furo/discussions/505\n dd &\n line-height: inherit\n font-weight: inherit\n\n font-size: var(--font-size--small)\n text-transform: uppercase\n","article .sidebar\n float: right\n clear: right\n width: 30%\n\n margin-left: 1rem\n margin-right: 0\n\n border-radius: 0.2rem\n background-color: var(--color-background-secondary)\n border: var(--color-background-border) 1px solid\n\n > *\n padding-left: 1rem\n padding-right: 1rem\n\n > ul, > ol // lists need additional padding, because bullets.\n padding-left: 2.2rem\n\n .sidebar-title\n margin: 0\n padding: 0.5rem 1rem\n border-bottom: var(--color-background-border) 1px solid\n\n font-weight: 500\n\n// TODO: subtitle\n// TODO: dedicated variables?\n",".table-wrapper\n width: 100%\n overflow-x: auto\n margin-top: 1rem\n margin-bottom: 0.5rem\n padding: 0.2rem 0.2rem 0.75rem\n\ntable.docutils\n border-radius: 0.2rem\n border-spacing: 0\n border-collapse: collapse\n\n box-shadow: 0 0.2rem 0.5rem rgba(0, 0, 0, 0.05), 0 0 0.0625rem rgba(0, 0, 0, 0.1)\n\n th\n background: var(--color-table-header-background)\n\n td,\n th\n // Space things out properly\n padding: 0 0.25rem\n\n // Get the borders looking just-right.\n border-left: 1px solid var(--color-table-border)\n border-right: 1px solid var(--color-table-border)\n border-bottom: 1px solid var(--color-table-border)\n\n p\n margin: 0.25rem\n\n &:first-child\n border-left: none\n &:last-child\n border-right: none\n\n // MyST-parser tables set these classes for control of column alignment\n &.text-left\n text-align: left\n &.text-right\n text-align: right\n &.text-center\n text-align: center\n",":target\n scroll-margin-top: 0.5rem\n\n@media (max-width: $full-width - $sidebar-width)\n :target\n scroll-margin-top: calc(0.5rem + var(--header-height))\n\n // When a heading is selected\n section > span:target\n scroll-margin-top: calc(0.8rem + var(--header-height))\n\n// Permalinks\n.headerlink\n font-weight: 100\n user-select: none\n\nh1,\nh2,\nh3,\nh4,\nh5,\nh6,\ndl dt,\np.caption,\nfigcaption p,\ntable > caption,\n.code-block-caption\n > .headerlink\n margin-left: 0.5rem\n visibility: hidden\n &:hover > .headerlink\n visibility: visible\n\n // Don't change to link-like, if someone adds the contents directive.\n > .toc-backref\n color: inherit\n text-decoration-line: none\n\n// Figure and table captions are special.\nfigure:hover > figcaption > p > .headerlink,\ntable:hover > caption > .headerlink\n visibility: visible\n\n:target >, // Regular section[id] style anchors\nspan:target ~ // Non-regular span[id] style \"extra\" anchors\n h1,\n h2,\n h3,\n h4,\n h5,\n h6\n &:nth-of-type(1)\n background-color: var(--color-highlight-on-target)\n // .headerlink\n // visibility: visible\n code.literal\n background-color: transparent\n\ntable:target > caption,\nfigure:target\n background-color: var(--color-highlight-on-target)\n\n// Inline page contents\n.this-will-duplicate-information-and-it-is-still-useful-here li :target\n background-color: var(--color-highlight-on-target)\n\n// Code block permalinks\n.literal-block-wrapper:target .code-block-caption\n background-color: var(--color-highlight-on-target)\n\n// When a definition list item is selected\n//\n// There isn't really an alternative to !important here, due to the\n// high-specificity of API documentation's selector.\ndt:target\n background-color: var(--color-highlight-on-target) !important\n\n// When a footnote reference is selected\n.footnote > dt:target + dd,\n.footnote-reference:target\n background-color: var(--color-highlight-on-target)\n",".guilabel\n background-color: var(--color-guilabel-background)\n border: 1px solid var(--color-guilabel-border)\n color: var(--color-guilabel-text)\n\n padding: 0 0.3em\n border-radius: 0.5em\n font-size: 0.9em\n","// This file contains the styles used for stylizing the footer that's shown\n// below the content.\n\nfooter\n font-size: var(--font-size--small)\n display: flex\n flex-direction: column\n\n margin-top: 2rem\n\n// Bottom of page information\n.bottom-of-page\n display: flex\n align-items: center\n justify-content: space-between\n\n margin-top: 1rem\n padding-top: 1rem\n padding-bottom: 1rem\n\n color: var(--color-foreground-secondary)\n border-top: 1px solid var(--color-background-border)\n\n line-height: 1.5\n\n @media (max-width: $content-width)\n text-align: center\n flex-direction: column-reverse\n gap: 0.25rem\n\n .left-details\n font-size: var(--font-size--small)\n\n .right-details\n display: flex\n flex-direction: column\n gap: 0.25rem\n text-align: right\n\n .icons\n display: flex\n justify-content: flex-end\n gap: 0.25rem\n font-size: 1rem\n\n a\n text-decoration: none\n\n svg,\n img\n font-size: 1.125rem\n height: 1em\n width: 1em\n\n// Next/Prev page information\n.related-pages\n a\n display: flex\n align-items: center\n\n text-decoration: none\n &:hover .page-info .title\n text-decoration: underline\n color: var(--color-link)\n text-decoration-color: var(--color-link-underline)\n\n svg.furo-related-icon,\n svg.furo-related-icon > use\n flex-shrink: 0\n\n color: var(--color-foreground-border)\n\n width: 0.75rem\n height: 0.75rem\n margin: 0 0.5rem\n\n &.next-page\n max-width: 50%\n\n float: right\n clear: right\n text-align: right\n\n &.prev-page\n max-width: 50%\n\n float: left\n clear: left\n\n svg\n transform: rotate(180deg)\n\n.page-info\n display: flex\n flex-direction: column\n overflow-wrap: anywhere\n\n .next-page &\n align-items: flex-end\n\n .context\n display: flex\n align-items: center\n\n padding-bottom: 0.1rem\n\n color: var(--color-foreground-muted)\n font-size: var(--font-size--small)\n text-decoration: none\n","// This file contains the styles for the contents of the left sidebar, which\n// contains the navigation tree, logo, search etc.\n\n////////////////////////////////////////////////////////////////////////////////\n// Brand on top of the scrollable tree.\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-brand\n display: flex\n flex-direction: column\n flex-shrink: 0\n\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n text-decoration: none\n\n.sidebar-brand-text\n color: var(--color-sidebar-brand-text)\n overflow-wrap: break-word\n margin: var(--sidebar-item-spacing-vertical) 0\n font-size: 1.5rem\n\n.sidebar-logo-container\n margin: var(--sidebar-item-spacing-vertical) 0\n\n.sidebar-logo\n margin: 0 auto\n display: block\n max-width: 100%\n\n////////////////////////////////////////////////////////////////////////////////\n// Search\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-search-container\n display: flex\n align-items: center\n margin-top: var(--sidebar-search-space-above)\n\n position: relative\n\n background: var(--color-sidebar-search-background)\n &:hover,\n &:focus-within\n background: var(--color-sidebar-search-background--focus)\n\n &::before\n content: \"\"\n position: absolute\n left: var(--sidebar-item-spacing-horizontal)\n width: var(--sidebar-search-icon-size)\n height: var(--sidebar-search-icon-size)\n\n background-color: var(--color-sidebar-search-icon)\n mask-image: var(--icon-search)\n\n.sidebar-search\n box-sizing: border-box\n\n border: none\n border-top: 1px solid var(--color-sidebar-search-border)\n border-bottom: 1px solid var(--color-sidebar-search-border)\n\n padding-top: var(--sidebar-search-input-spacing-vertical)\n padding-bottom: var(--sidebar-search-input-spacing-vertical)\n padding-right: var(--sidebar-search-input-spacing-horizontal)\n padding-left: calc(var(--sidebar-item-spacing-horizontal) + var(--sidebar-search-input-spacing-horizontal) + var(--sidebar-search-icon-size))\n\n width: 100%\n\n color: var(--color-sidebar-search-foreground)\n background: transparent\n z-index: 10\n\n &:focus\n outline: none\n\n &::placeholder\n font-size: var(--sidebar-search-input-font-size)\n\n//\n// Hide Search Matches link\n//\n#searchbox .highlight-link\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal) 0\n margin: 0\n text-align: center\n\n a\n color: var(--color-sidebar-search-icon)\n font-size: var(--font-size--small--2)\n\n////////////////////////////////////////////////////////////////////////////////\n// Structure/Skeleton of the navigation tree (left)\n////////////////////////////////////////////////////////////////////////////////\n.sidebar-tree\n font-size: var(--sidebar-item-font-size)\n margin-top: var(--sidebar-tree-space-above)\n margin-bottom: var(--sidebar-item-spacing-vertical)\n\n ul\n padding: 0\n margin-top: 0\n margin-bottom: 0\n\n display: flex\n flex-direction: column\n\n list-style: none\n\n li\n position: relative\n margin: 0\n\n > ul\n margin-left: var(--sidebar-item-spacing-horizontal)\n\n .icon\n color: var(--color-sidebar-link-text)\n\n .reference\n box-sizing: border-box\n color: var(--color-sidebar-link-text)\n\n // Fill the parent.\n display: inline-block\n line-height: var(--sidebar-item-line-height)\n text-decoration: none\n\n // Don't allow long words to cause wrapping.\n overflow-wrap: anywhere\n\n height: 100%\n width: 100%\n\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n\n &:hover\n background: var(--color-sidebar-item-background--hover)\n\n // Add a nice little \"external-link\" arrow here.\n &.external::after\n content: url('data:image/svg+xml,')\n margin: 0 0.25rem\n vertical-align: middle\n color: var(--color-sidebar-link-text)\n\n // Make the current page reference bold.\n .current-page > .reference\n font-weight: bold\n\n label\n position: absolute\n top: 0\n right: 0\n height: var(--sidebar-item-height)\n width: var(--sidebar-expander-width)\n\n cursor: pointer\n user-select: none\n\n display: flex\n justify-content: center\n align-items: center\n\n .caption, :not(.caption) > .caption-text\n font-size: var(--sidebar-caption-font-size)\n color: var(--color-sidebar-caption-text)\n\n font-weight: bold\n text-transform: uppercase\n\n margin: var(--sidebar-caption-space-above) 0 0 0\n padding: var(--sidebar-item-spacing-vertical) var(--sidebar-item-spacing-horizontal)\n\n // If it has children, add a bit more padding to wrap the content to avoid\n // overlapping with the
    + + + + + + + + + \ No newline at end of file diff --git a/index.html b/index.html index ef7d60d..a187f2f 100644 --- a/index.html +++ b/index.html @@ -1,177 +1,309 @@ + + + + + + + + + cycquery documentation + + + + + + + - - - - - - - - - - - Welcome to cyclops-query’s documentation! — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    Welcome to cycquery’s documentation!

    Contents:

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    -
    - + + +
    +
    - - - +
    + + + + + + + + + + + \ No newline at end of file diff --git a/intro.html b/intro.html index c5c2863..f13dbd5 100644 --- a/intro.html +++ b/intro.html @@ -1,199 +1,316 @@ + + + + + + + + + cycquery - cycquery documentation + + + + + + + - - - - - - - - - - - cyclops-query — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    cycquery

    +

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

    +

    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 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

    +

    🐣 Getting Started

    +
    +

    Installing cycquery using pip

    python3 -m pip install cycquery
    -

    Query postgresql database

    +

    Query postgresql database

    from cycquery import DatasetQuerier
 import cycquery.ops as qo
 
@@ -230,24 +347,19 @@ 
    Query postgresql database
-
    🧑🏿‍💻 Developing
    
+
    🧑🏿‍💻 Developing
    
 
    
-
    Using poetry
    
-
    The development environment can be set up using
-poetry. Hence, make
-sure it is installed and then run:
    
+
    Using poetry
    
+
    The development environment can be set up using poetry. Hence, make sure it is installed and then run:
    
 
    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:
    
 
    python3 -m poetry install --with test
 
    
 
    
-
    API documentation is built using
-Sphinx and can be locally
-built by:
    
+
    API documentation is built using Sphinx and can be locally built by:
    
 
    python3 -m poetry install --with docs
 cd docs
 make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
@@ -255,93 +367,78 @@ 
    Using poetry
-
    Contributing
    
-
    Contributing to cyclops-query is welcomed. See
-Contributing
-for guidelines.
    
+
    Contributing
    
+
    Contributing to cycquery is welcomed. See Contributing for guidelines.
    -

    📚 Documentation

    -
    -
    -

    🎓 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

    - -
    + +
    +
    - + + +
    +
    - - - + + + + + + + + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv index 082e8d5..6cd4717 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/page.html b/page.html new file mode 100644 index 0000000..04bf18d --- /dev/null +++ b/page.html @@ -0,0 +1,346 @@ + + + + + + + + - cycquery documentation + + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.base.DatasetQuerier.html b/reference/api/_autosummary/cycquery.base.DatasetQuerier.html index e6af04e..98f4441 100644 --- a/reference/api/_autosummary/cycquery.base.DatasetQuerier.html +++ b/reference/api/_autosummary/cycquery.base.DatasetQuerier.html @@ -1,198 +1,311 @@ + + + + + + + + + cycquery.base.DatasetQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.base.DatasetQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    cycquery.base.DatasetQuerier

    -class DatasetQuerier(dbms, user='', password='', host='', port=None, database='')[source]
    +class DatasetQuerier(dbms, user='', password='', host='', port=None, database='')[source]

    Bases: object

    Base class to query EHR datasets.

    -db
    +db

    ORM Database used to run queries.

    @@ -217,6 +330,7 @@

    cycquery.base.DatasetQuerierMethods

    +
    @@ -236,9 +350,10 @@

    cycquery.base.DatasetQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)[source]
    +get_table(schema_name, table_name, cast_timestamp_cols=True)[source]

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -261,7 +376,7 @@

    cycquery.base.DatasetQuerier
    -list_columns(schema_name, table_name)[source]
    +list_columns(schema_name, table_name)[source]

    List columns in a table.

    Parameters:
    @@ -281,7 +396,7 @@

    cycquery.base.DatasetQuerier
    -list_custom_tables()[source]
    +list_custom_tables()[source]

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -295,7 +410,7 @@

    cycquery.base.DatasetQuerier
    -list_schemas()[source]
    +list_schemas()[source]

    List schemas in the database to query.

    Returns:
    @@ -309,7 +424,7 @@

    cycquery.base.DatasetQuerier
    -list_tables(schema_name=None)[source]
    +list_tables(schema_name=None)[source]

    List table methods that can be queried using the database.

    Parameters:
    @@ -328,66 +443,97 @@

    cycquery.base.DatasetQuerier + +
    +
    + Next +
    +
    cycquery.mimiciii
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.base
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.base.html b/reference/api/_autosummary/cycquery.base.html index 5f69e96..da4e1b5 100644 --- a/reference/api/_autosummary/cycquery.base.html +++ b/reference/api/_autosummary/cycquery.base.html @@ -1,190 +1,306 @@ + + + + + + + + + cycquery.base - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.base — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    cycquery.base

    Base querier class.

    Classes

    +

    get_table

    @@ -192,68 +308,73 @@

    DatasetQuerier
    +

    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.eicu.EICUQuerier.html b/reference/api/_autosummary/cycquery.eicu.EICUQuerier.html index ce00c39..02791b8 100644 --- a/reference/api/_autosummary/cycquery.eicu.EICUQuerier.html +++ b/reference/api/_autosummary/cycquery.eicu.EICUQuerier.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.eicu.EICUQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.eicu.EICUQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    cycquery.eicu.EICUQuerier

    -class EICUQuerier(dbms, user='', password='', host='', port=None, database='')[source]
    +class EICUQuerier(dbms, user='', password='', host='', port=None, database='')[source]

    Bases: DatasetQuerier

    EICU dataset querier.

    Methods

    +
    @@ -214,9 +324,10 @@

    cycquery.eicu.EICUQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)
    +get_table(schema_name, table_name, cast_timestamp_cols=True)

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -239,7 +350,7 @@

    cycquery.eicu.EICUQuerier
    -list_columns(schema_name, table_name)
    +list_columns(schema_name, table_name)

    List columns in a table.

    Parameters:
    @@ -259,7 +370,7 @@

    cycquery.eicu.EICUQuerier
    -list_custom_tables()
    +list_custom_tables()

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -273,7 +384,7 @@

    cycquery.eicu.EICUQuerier
    -list_schemas()
    +list_schemas()

    List schemas in the database to query.

    Returns:
    @@ -287,7 +398,7 @@

    cycquery.eicu.EICUQuerier
    -list_tables(schema_name=None)
    +list_tables(schema_name=None)

    List table methods that can be queried using the database.

    Parameters:
    @@ -306,66 +417,96 @@

    cycquery.eicu.EICUQuerier + +
    +
    + Next +
    +
    cycquery.omop
    +
    + +     + + +
    +
    + Previous +
    + +
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    + +
    +     + +
    +
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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.eicu.html b/reference/api/_autosummary/cycquery.eicu.html index 6444649..48d4f3b 100644 --- a/reference/api/_autosummary/cycquery.eicu.html +++ b/reference/api/_autosummary/cycquery.eicu.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.eicu - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.eicu — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +

    cycquery.eicu

    EICU-CRD query module.

    Supports querying of eICU.

    Classes

    +

    get_table

    @@ -197,68 +309,73 @@

    EICUQuerier
    +
    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.html b/reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.html index cfaa6bf..3c5f6b6 100644 --- a/reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.html +++ b/reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.html @@ -1,142 +1,261 @@ + + + + + + + + + cycquery.gemini.GEMINIQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.gemini.GEMINIQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +

    cycquery.gemini.GEMINIQuerier

    -class GEMINIQuerier(dbms, user='', password='', host='', port=None, database='')[source]
    +class GEMINIQuerier(dbms, user='', password='', host='', port=None, database='')[source]

    Bases: DatasetQuerier

    GEMINI dataset querier.

    Methods

    +
    @@ -228,9 +339,10 @@

    cycquery.gemini.GEMINIQuerier
    -care_units()[source]
    +care_units()[source]

    Query care unit data, fetches transfer info from multiple tables.

    Returns:
    @@ -244,7 +356,7 @@

    cycquery.gemini.GEMINIQuerier
    -diagnoses()[source]
    +diagnoses()[source]

    Query diagnosis data.

    Returns:
    @@ -258,7 +370,7 @@

    cycquery.gemini.GEMINIQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)
    +get_table(schema_name, table_name, cast_timestamp_cols=True)

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -281,7 +393,7 @@

    cycquery.gemini.GEMINIQuerier
    -imaging()[source]
    +imaging()[source]

    Query imaging reports data.

    Returns:
    @@ -295,7 +407,7 @@

    cycquery.gemini.GEMINIQuerier
    -ip_admin()[source]
    +ip_admin()[source]

    Query GEMINI patient encounters.

    Returns:
    @@ -309,7 +421,7 @@

    cycquery.gemini.GEMINIQuerier
    -list_columns(schema_name, table_name)
    +list_columns(schema_name, table_name)

    List columns in a table.

    Parameters:
    @@ -329,7 +441,7 @@

    cycquery.gemini.GEMINIQuerier
    -list_custom_tables()
    +list_custom_tables()

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -343,7 +455,7 @@

    cycquery.gemini.GEMINIQuerier
    -list_schemas()
    +list_schemas()

    List schemas in the database to query.

    Returns:
    @@ -357,7 +469,7 @@

    cycquery.gemini.GEMINIQuerier
    -list_tables(schema_name=None)
    +list_tables(schema_name=None)

    List table methods that can be queried using the database.

    Parameters:
    @@ -374,7 +486,7 @@

    cycquery.gemini.GEMINIQuerier
    -room_transfer()[source]
    +room_transfer()[source]

    Query room transfer data.

    Returns:
    @@ -390,65 +502,93 @@

    cycquery.gemini.GEMINIQuerier + + + +
    +
    + Previous +
    + +
    cycquery.gemini
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.gemini.html b/reference/api/_autosummary/cycquery.gemini.html index 50a4ea2..da52211 100644 --- a/reference/api/_autosummary/cycquery.gemini.html +++ b/reference/api/_autosummary/cycquery.gemini.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.gemini - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.gemini — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
    +

    cycquery.gemini

    GEMINI query module.

    Classes

    +

    care_units

    @@ -196,68 +308,73 @@

    GEMINIQuerier
    +
    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.interface.QueryInterface.html b/reference/api/_autosummary/cycquery.interface.QueryInterface.html index c0e3bd0..75c0b90 100644 --- a/reference/api/_autosummary/cycquery.interface.QueryInterface.html +++ b/reference/api/_autosummary/cycquery.interface.QueryInterface.html @@ -1,193 +1,306 @@ + + + + + + + + + cycquery.interface.QueryInterface - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.interface.QueryInterface — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
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    +
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    + + + + + Back to top + +
    + +
    + +
    + +
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    +
    +

    cycquery.interface.QueryInterface

    -class QueryInterface(database, query)[source]
    +class QueryInterface(database, query)[source]

    Bases: object

    An interface dataclass to wrap queries, and run them.

    @@ -200,6 +313,7 @@

    cycquery.interface.QueryInterfaceMethods

    +
    @@ -225,7 +339,9 @@

    cycquery.interface.QueryInterfaceAttributes

    +

    clear_data

    @@ -233,15 +349,16 @@

    cycquery.interface.QueryInterface
    -__init__(database, query)[source]
    +__init__(database, query)[source]

    Initialize the QueryInterface object, join and chain operations.

    -clear_data()[source]
    +clear_data()[source]

    Clear data container.

    Sets the data attribute to None, thus clearing the dataframe contained.

    @@ -253,13 +370,13 @@

    cycquery.interface.QueryInterface
    -property data: DataFrame | None
    +property data: DataFrame | None

    Get data.

    -join(join_table, on=None, on_to_type=None, cond=None, table_cols=None, join_table_cols=None, isouter=False)[source]
    +join(join_table, on=None, on_to_type=None, cond=None, table_cols=None, join_table_cols=None, isouter=False)[source]

    Join the query with another table.

    Parameters:
    @@ -284,7 +401,7 @@

    cycquery.interface.QueryInterface
    -ops(ops)[source]
    +ops(ops)[source]

    Chain operations with the query.

    Parameters:
    @@ -301,7 +418,7 @@

    cycquery.interface.QueryInterface
    -run(limit=None, index_col=None, batch_mode=False, batch_size=1000000, dtype_backend='pyarrow')[source]
    +run(limit=None, index_col=None, batch_mode=False, batch_size=1000000, dtype_backend='pyarrow')[source]

    Run the query, and fetch data.

    Parameters:
    @@ -319,14 +436,14 @@

    cycquery.interface.QueryInterface

    Query result.

    Return type:
    -

    pandas.DataFrame or Generator[pandas.DataFrame, None, None]

    +

    pandas.DataFrame or Generator[pandas.DataFrame, None, None]

    -save(path, file_format='parquet')[source]
    +save(path, file_format='parquet')[source]

    Save the query.

    Parameters:
    @@ -346,7 +463,7 @@

    cycquery.interface.QueryInterface
    -union(other)[source]
    +union(other)[source]

    Union the query with another query.

    Parameters:
    @@ -363,7 +480,7 @@

    cycquery.interface.QueryInterface
    -union_all(other)[source]
    +union_all(other)[source]

    Union all the query with another query.

    Parameters:
    @@ -382,66 +499,100 @@

    cycquery.interface.QueryInterface + +
    +
    + Next +
    +
    cycquery.ops
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.interface
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.interface.html b/reference/api/_autosummary/cycquery.interface.html index 1bf1fc1..86d6950 100644 --- a/reference/api/_autosummary/cycquery.interface.html +++ b/reference/api/_autosummary/cycquery.interface.html @@ -1,190 +1,306 @@ + + + + + + + + + cycquery.interface - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.interface — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +
    +

    cycquery.interface

    A query interface class to wrap database objects and queries.

    Classes

    +

    data

    @@ -192,68 +308,73 @@

    QueryInterface
    +

    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.html b/reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.html index 5e8d978..52d475e 100644 --- a/reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.html +++ b/reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.mimiciii.MIMICIIIQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.mimiciii.MIMICIIIQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
    +

    cycquery.mimiciii.MIMICIIIQuerier

    -class MIMICIIIQuerier(dbms, user='', password='', host='', port=None, database='')[source]
    +class MIMICIIIQuerier(dbms, user='', password='', host='', port=None, database='')[source]

    Bases: DatasetQuerier

    MIMIC-III dataset querier.

    Methods

    +
    @@ -223,9 +333,10 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -chartevents()[source]
    +chartevents()[source]

    Query MIMICIII chartevents data.

    Returns:
    @@ -239,7 +350,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -diagnoses()[source]
    +diagnoses()[source]

    Query MIMICIII diagnosis data.

    Returns:
    @@ -253,7 +364,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)
    +get_table(schema_name, table_name, cast_timestamp_cols=True)

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -276,7 +387,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -labevents()[source]
    +labevents()[source]

    Query MIMICIII labevents data.

    Returns:
    @@ -290,7 +401,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -list_columns(schema_name, table_name)
    +list_columns(schema_name, table_name)

    List columns in a table.

    Parameters:
    @@ -310,7 +421,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -list_custom_tables()
    +list_custom_tables()

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -324,7 +435,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -list_schemas()
    +list_schemas()

    List schemas in the database to query.

    Returns:
    @@ -338,7 +449,7 @@

    cycquery.mimiciii.MIMICIIIQuerier
    -list_tables(schema_name=None)
    +list_tables(schema_name=None)

    List table methods that can be queried using the database.

    Parameters:
    @@ -357,66 +468,99 @@

    cycquery.mimiciii.MIMICIIIQuerier + +
    +
    + Next +
    +
    cycquery.mimiciv
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.mimiciii
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.mimiciii.html b/reference/api/_autosummary/cycquery.mimiciii.html index 2b85773..fca3676 100644 --- a/reference/api/_autosummary/cycquery.mimiciii.html +++ b/reference/api/_autosummary/cycquery.mimiciii.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.mimiciii - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.mimiciii — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
    +

    cycquery.mimiciii

    MIMIC-III query module.

    Supports querying of MIMIC-III.

    Classes

    +

    chartevents

    @@ -197,68 +309,73 @@

    MIMICIIIQuerier
    +
    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html b/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html index 51a85f5..acc45e2 100644 --- a/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html +++ b/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.mimiciv.MIMICIVQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.mimiciv.MIMICIVQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +

    cycquery.mimiciv.MIMICIVQuerier

    -class MIMICIVQuerier(dbms, user='', password='', host='', port=None, database='')[source]
    +class MIMICIVQuerier(dbms, user='', password='', host='', port=None, database='')[source]

    Bases: DatasetQuerier

    MIMICIV dataset querier.

    Methods

    +
    @@ -229,9 +339,10 @@

    cycquery.mimiciv.MIMICIVQuerier
    -chartevents()[source]
    +chartevents()[source]

    Query ICU chart events from the ICU module.

    Returns:
    @@ -245,7 +356,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -diagnoses_icd()[source]
    +diagnoses_icd()[source]

    Query MIMIC diagnosis data.

    Returns:
    @@ -259,7 +370,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)
    +get_table(schema_name, table_name, cast_timestamp_cols=True)

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -282,7 +393,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -labevents()[source]
    +labevents()[source]

    Query lab events from the hospital module.

    Returns:
    @@ -296,7 +407,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -list_columns(schema_name, table_name)
    +list_columns(schema_name, table_name)

    List columns in a table.

    Parameters:
    @@ -316,7 +427,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -list_custom_tables()
    +list_custom_tables()

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -330,7 +441,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -list_schemas()
    +list_schemas()

    List schemas in the database to query.

    Returns:
    @@ -344,7 +455,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -list_tables(schema_name=None)
    +list_tables(schema_name=None)

    List table methods that can be queried using the database.

    Parameters:
    @@ -361,7 +472,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -patients()[source]
    +patients()[source]

    Query MIMIC patient data.

    Returns:
    @@ -380,7 +491,7 @@

    cycquery.mimiciv.MIMICIVQuerier
    -procedures_icd()[source]
    +procedures_icd()[source]

    Query MIMIC procedures data.

    Returns:
    @@ -396,66 +507,101 @@

    cycquery.mimiciv.MIMICIVQuerier + +
    +
    + Next +
    +
    cycquery.eicu
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.mimiciv
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.mimiciv.html b/reference/api/_autosummary/cycquery.mimiciv.html index 9812c5d..7e2e7ed 100644 --- a/reference/api/_autosummary/cycquery.mimiciv.html +++ b/reference/api/_autosummary/cycquery.mimiciv.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.mimiciv - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.mimiciv — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    cycquery.mimiciv

    MIMIC-IV query module.

    Supports querying of MIMICIV-2.0.

    Classes

    +

    chartevents

    @@ -197,68 +309,73 @@

    MIMICIVQuerier
    +
    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.omop.OMOPQuerier.html b/reference/api/_autosummary/cycquery.omop.OMOPQuerier.html index 9ea4da0..0f6378d 100644 --- a/reference/api/_autosummary/cycquery.omop.OMOPQuerier.html +++ b/reference/api/_autosummary/cycquery.omop.OMOPQuerier.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.omop.OMOPQuerier - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.omop.OMOPQuerier — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
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    +
    cycquery documentation
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    + + + + + Back to top + +
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    +
    +

    cycquery.omop.OMOPQuerier

    -class OMOPQuerier(database, user, password, dbms='postgresql', host='localhost', port=5432, schema_name='omop')[source]
    +class OMOPQuerier(database, user, password, dbms='postgresql', host='localhost', port=5432, schema_name='omop')[source]

    Bases: DatasetQuerier

    OMOP querier.

    Methods

    +
    @@ -232,9 +342,10 @@

    cycquery.omop.OMOPQuerier
    -get_table(schema_name, table_name, cast_timestamp_cols=True)
    +get_table(schema_name, table_name, cast_timestamp_cols=True)

    Get a table and possibly map columns to have standard names.

    Standardizing column names allows for columns to be recognized in downstream processing.

    @@ -257,7 +368,7 @@

    cycquery.omop.OMOPQuerier
    -list_columns(schema_name, table_name)
    +list_columns(schema_name, table_name)

    List columns in a table.

    Parameters:
    @@ -277,7 +388,7 @@

    cycquery.omop.OMOPQuerier
    -list_custom_tables()
    +list_custom_tables()

    List custom tables methods provided by the dataset API.

    Returns:
    @@ -291,7 +402,7 @@

    cycquery.omop.OMOPQuerier
    -list_schemas()
    +list_schemas()

    List schemas in the database to query.

    Returns:
    @@ -305,7 +416,7 @@

    cycquery.omop.OMOPQuerier
    -list_tables(schema_name=None)
    +list_tables(schema_name=None)

    List table methods that can be queried using the database.

    Parameters:
    @@ -322,7 +433,7 @@

    cycquery.omop.OMOPQuerier
    -map_concept_ids_to_name(src_table, src_cols, dst_cols=None)[source]
    +map_concept_ids_to_name(src_table, src_cols, dst_cols=None)[source]

    Map concept IDs in a source table to concept names from concept table.

    For each concept ID column with a name like somecol_concept_ID, the mapped concept name column will be named somecol_concept_name. If dst_cols is @@ -347,7 +458,7 @@

    cycquery.omop.OMOPQuerier
    -measurement()[source]
    +measurement()[source]

    Query OMOP measurement table.

    Returns:
    @@ -361,7 +472,7 @@

    cycquery.omop.OMOPQuerier
    -observation()[source]
    +observation()[source]

    Query OMOP observation table.

    Returns:
    @@ -375,7 +486,7 @@

    cycquery.omop.OMOPQuerier
    -person()[source]
    +person()[source]

    Query OMOP person table.

    Returns:
    @@ -389,7 +500,7 @@

    cycquery.omop.OMOPQuerier
    -visit_detail()[source]
    +visit_detail()[source]

    Query OMOP visit_detail table.

    Returns:
    @@ -403,7 +514,7 @@

    cycquery.omop.OMOPQuerier
    -visit_occurrence()[source]
    +visit_occurrence()[source]

    Query OMOP visit_occurrence table.

    Returns:
    @@ -419,66 +530,102 @@

    cycquery.omop.OMOPQuerier + +
    +
    + Next +
    +
    cycquery.gemini
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.omop
    + +
    +     + +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.omop.html b/reference/api/_autosummary/cycquery.omop.html index 276d46a..986540a 100644 --- a/reference/api/_autosummary/cycquery.omop.html +++ b/reference/api/_autosummary/cycquery.omop.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery.omop - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.omop — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
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    +
    +
    +

    cycquery.omop

    OMOP query API.

    Classes

    +

    get_table

    @@ -196,68 +308,73 @@

    OMOPQuerier
    +
    - -
    + +
    +
    - + + +
    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.AddColumn.html b/reference/api/_autosummary/cycquery.ops.AddColumn.html index 01e86ad..a575327 100644 --- a/reference/api/_autosummary/cycquery.ops.AddColumn.html +++ b/reference/api/_autosummary/cycquery.ops.AddColumn.html @@ -1,137 +1,195 @@ + + + + + + + + + cycquery.ops.AddColumn - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.AddColumn — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
    +
    +
    +

    cycquery.ops.AddColumn

    -class AddColumn(add_to, col, negative=False, new_col_labels=None)[source]
    +class AddColumn(add_to, col, negative=False, new_col_labels=None)[source]

    Bases: QueryOp

    Add a column to some columns.

    @@ -257,13 +328,15 @@

    cycquery.ops.AddColumn

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -282,66 +355,92 @@

    cycquery.ops.AddColumn - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.AddDeltaColumn.html b/reference/api/_autosummary/cycquery.ops.AddDeltaColumn.html index 43a8ff7..768a5d4 100644 --- a/reference/api/_autosummary/cycquery.ops.AddDeltaColumn.html +++ b/reference/api/_autosummary/cycquery.ops.AddDeltaColumn.html @@ -1,138 +1,196 @@ + + + + + + + + + cycquery.ops.AddDeltaColumn - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.AddDeltaColumn — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
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    +
    +

    cycquery.ops.AddDeltaColumn

    -class AddDeltaColumn(add_to, negative=False, new_col_labels=None, **delta_kwargs)[source]
    +class AddDeltaColumn(add_to, negative=False, new_col_labels=None, **delta_kwargs)[source]

    Bases: QueryOp

    Construct and add an interval column to some columns.

    @@ -251,13 +322,15 @@

    cycquery.ops.AddDeltaColumnMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -276,66 +349,92 @@

    cycquery.ops.AddDeltaColumn + +
    +
    + Next +
    +
    cycquery.ops.AddDeltaConstant
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.AddColumn
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.AddDeltaConstant.html b/reference/api/_autosummary/cycquery.ops.AddDeltaConstant.html index 584e7f1..3c3f637 100644 --- a/reference/api/_autosummary/cycquery.ops.AddDeltaConstant.html +++ b/reference/api/_autosummary/cycquery.ops.AddDeltaConstant.html @@ -1,139 +1,197 @@ + + + + + + + + + cycquery.ops.AddDeltaConstant - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.AddDeltaConstant — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
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    +
    cycquery documentation
     +
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    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.AddDeltaConstant

    -class AddDeltaConstant(add_to, delta, new_col_labels=None)[source]
    +class AddDeltaConstant(add_to, delta, new_col_labels=None)[source]

    Bases: QueryOp

    Construct and add a datetime.timedelta object to some columns.

    @@ -249,13 +320,15 @@

    cycquery.ops.AddDeltaConstantMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -274,66 +347,92 @@

    cycquery.ops.AddDeltaConstant + +
    +
    + Next +
    +
    cycquery.ops.AddNumeric
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.AddDeltaColumn
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.AddNumeric.html b/reference/api/_autosummary/cycquery.ops.AddNumeric.html index f1a3df4..e862615 100644 --- a/reference/api/_autosummary/cycquery.ops.AddNumeric.html +++ b/reference/api/_autosummary/cycquery.ops.AddNumeric.html @@ -1,140 +1,198 @@ + + + + + + + + + cycquery.ops.AddNumeric - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.AddNumeric — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +
    +

    cycquery.ops.AddNumeric

    -class AddNumeric(add_to, add, new_col_labels=None)[source]
    +class AddNumeric(add_to, add, new_col_labels=None)[source]

    Bases: QueryOp

    Add a numeric value to some columns.

    @@ -251,13 +322,15 @@

    cycquery.ops.AddNumeric

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -276,66 +349,92 @@

    cycquery.ops.AddNumeric - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.And.html b/reference/api/_autosummary/cycquery.ops.And.html index 3d8912f..86214c5 100644 --- a/reference/api/_autosummary/cycquery.ops.And.html +++ b/reference/api/_autosummary/cycquery.ops.And.html @@ -1,141 +1,199 @@ + + + + + + + + + cycquery.ops.And - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.And — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Apply.html b/reference/api/_autosummary/cycquery.ops.Apply.html index d95c265..afe2eaf 100644 --- a/reference/api/_autosummary/cycquery.ops.Apply.html +++ b/reference/api/_autosummary/cycquery.ops.Apply.html @@ -1,142 +1,200 @@ + + + + + + + + + cycquery.ops.Apply - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Apply — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
    +

    cycquery.ops.Apply

    -class Apply(cols, funcs, new_cols=None)[source]
    +class Apply(cols, funcs, new_cols=None)[source]

    Bases: QueryOp

    Apply function(s) to column(s).

    The function can take a sqlalchemy column object and also return a column object. @@ -255,13 +326,15 @@

    cycquery.ops.ApplyMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -280,66 +353,92 @@

    cycquery.ops.Apply + +
    +
    + Next +
    +
    cycquery.ops.Cast
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.And
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Cast.html b/reference/api/_autosummary/cycquery.ops.Cast.html index 3bc1237..6093365 100644 --- a/reference/api/_autosummary/cycquery.ops.Cast.html +++ b/reference/api/_autosummary/cycquery.ops.Cast.html @@ -1,143 +1,201 @@ + + + + + + + + + cycquery.ops.Cast - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Cast — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +

    cycquery.ops.Cast

    -class Cast(cols, type_)[source]
    +class Cast(cols, type_)[source]

    Bases: QueryOp

    Cast columns to a specified type.

    Currently supporting conversions to str, int, float, date, bool and timestamp.

    @@ -251,13 +322,15 @@

    cycquery.ops.CastMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -276,66 +349,92 @@

    cycquery.ops.Cast + +
    +
    + Next +
    +
    cycquery.ops.ConditionAfterDate
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.Apply
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionAfterDate.html b/reference/api/_autosummary/cycquery.ops.ConditionAfterDate.html index 682d60d..1a41ca0 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionAfterDate.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionAfterDate.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionAfterDate - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionAfterDate — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionAfterDate

    -class ConditionAfterDate(timestamp_col, timestamp, not_=False, binarize_col=None)[source]
    +class ConditionAfterDate(timestamp_col, timestamp, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows based on a timestamp being after some date.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionAfterDateMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionAfterDate + +
    +
    + Next +
    +
    cycquery.ops.ConditionBeforeDate
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.Cast
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.html b/reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.html index 7566985..6201542 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionBeforeDate - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionBeforeDate — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
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    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionBeforeDate

    -class ConditionBeforeDate(timestamp_col, timestamp, not_=False, binarize_col=None)[source]
    +class ConditionBeforeDate(timestamp_col, timestamp, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows based on a timestamp being before some date.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionBeforeDateMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionBeforeDate + +
    +
    + Next +
    +
    cycquery.ops.ConditionEndsWith
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionAfterDate
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionEndsWith.html b/reference/api/_autosummary/cycquery.ops.ConditionEndsWith.html index fcfbc2a..62680a6 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionEndsWith.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionEndsWith.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionEndsWith - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionEndsWith — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
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    + +
    +
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    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionEndsWith

    -class ConditionEndsWith(col, string, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionEndsWith(col, string, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on ending with some string.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionEndsWithMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionEndsWith + +
    +
    + Next +
    +
    cycquery.ops.ConditionEquals
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionBeforeDate
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionEquals.html b/reference/api/_autosummary/cycquery.ops.ConditionEquals.html index 80df546..9f232e5 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionEquals.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionEquals.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionEquals - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionEquals — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
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    +
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     +
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    + + + + + Back to top + +
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    + +
    +
    +
    +

    cycquery.ops.ConditionEquals

    -class ConditionEquals(col, value, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionEquals(col, value, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on being equal, or not equal, to some value.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionEqualsMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionEquals + +
    +
    + Next +
    +
    cycquery.ops.ConditionGreaterThan
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionEndsWith
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.html b/reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.html index 1060bbc..c651d5f 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionGreaterThan - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionGreaterThan — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +
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     +
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    +
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    +
    +
    + + + + + Back to top + +
    + +
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    +
    +
    +

    cycquery.ops.ConditionGreaterThan

    -class ConditionGreaterThan(col, value, equal=False, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionGreaterThan(col, value, equal=False, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on greater than (or equal), to some value.

    @@ -250,13 +321,15 @@

    cycquery.ops.ConditionGreaterThanMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -278,66 +351,92 @@

    cycquery.ops.ConditionGreaterThan + +
    +
    + Next +
    +
    cycquery.ops.ConditionIn
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionEquals
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionIn.html b/reference/api/_autosummary/cycquery.ops.ConditionIn.html index ca09260..c922c6c 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionIn.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionIn.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionIn - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionIn — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
    +
    +
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     +
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    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionIn

    -class ConditionIn(col, values, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionIn(col, values, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on having a value in list of values.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionInMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionIn + +
    +
    + Next +
    +
    cycquery.ops.ConditionInMonths
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionGreaterThan
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionInMonths.html b/reference/api/_autosummary/cycquery.ops.ConditionInMonths.html index ec4d4bc..d0e052a 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionInMonths.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionInMonths.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionInMonths - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionInMonths — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    +
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     +
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    + +
    +
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    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionInMonths

    -class ConditionInMonths(timestamp_col, months, not_=False, binarize_col=None)[source]
    +class ConditionInMonths(timestamp_col, months, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows based on a timestamp being in a list of years.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionInMonthsMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionInMonths + +
    +
    + Next +
    +
    cycquery.ops.ConditionInYears
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionIn
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionInYears.html b/reference/api/_autosummary/cycquery.ops.ConditionInYears.html index cfa1c06..ae78609 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionInYears.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionInYears.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionInYears - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionInYears — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
    +
    +
    cycquery documentation
     +
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    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionInYears

    -class ConditionInYears(timestamp_col, years, not_=False, binarize_col=None)[source]
    +class ConditionInYears(timestamp_col, years, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows based on a timestamp column being in a list of years.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionInYearsMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionInYears + +
    +
    + Next +
    +
    cycquery.ops.ConditionLessThan
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionInMonths
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionLessThan.html b/reference/api/_autosummary/cycquery.ops.ConditionLessThan.html index 83e024f..944f777 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionLessThan.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionLessThan.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionLessThan - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionLessThan — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionLessThan

    -class ConditionLessThan(col, value, equal=False, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionLessThan(col, value, equal=False, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on less than (or equal), to some value.

    @@ -250,13 +321,15 @@

    cycquery.ops.ConditionLessThanMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -278,66 +351,92 @@

    cycquery.ops.ConditionLessThan + +
    +
    + Next +
    +
    cycquery.ops.ConditionLike
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionInYears
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionLike.html b/reference/api/_autosummary/cycquery.ops.ConditionLike.html index 70e3d03..747159e 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionLike.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionLike.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionLike - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionLike — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    + +
    +
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    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionLike

    -class ConditionLike(col, pattern, not_=False, binarize_col=None)[source]
    +class ConditionLike(col, pattern, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows by a LIKE condition.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionLikeMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionLike + +
    +
    + Next +
    +
    cycquery.ops.ConditionRegexMatch
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionLessThan
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.html b/reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.html index 47128de..97cb714 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionRegexMatch - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionRegexMatch — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionRegexMatch

    -class ConditionRegexMatch(col, regex, not_=False, binarize_col=None)[source]
    +class ConditionRegexMatch(col, regex, not_=False, binarize_col=None)[source]

    Bases: QueryOp

    Filter rows based on matching a regular expression.

    @@ -248,13 +319,15 @@

    cycquery.ops.ConditionRegexMatchMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -276,66 +349,92 @@

    cycquery.ops.ConditionRegexMatch + +
    +
    + Next +
    +
    cycquery.ops.ConditionStartsWith
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionLike
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionStartsWith.html b/reference/api/_autosummary/cycquery.ops.ConditionStartsWith.html index 1e22a39..23c3989 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionStartsWith.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionStartsWith.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionStartsWith - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionStartsWith — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionStartsWith

    -class ConditionStartsWith(col, string, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionStartsWith(col, string, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows based on starting with some string.

    @@ -249,13 +320,15 @@

    cycquery.ops.ConditionStartsWithMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -277,66 +350,92 @@

    cycquery.ops.ConditionStartsWith + +
    +
    + Next +
    +
    cycquery.ops.ConditionSubstring
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionRegexMatch
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ConditionSubstring.html b/reference/api/_autosummary/cycquery.ops.ConditionSubstring.html index dfaacb7..b8653a9 100644 --- a/reference/api/_autosummary/cycquery.ops.ConditionSubstring.html +++ b/reference/api/_autosummary/cycquery.ops.ConditionSubstring.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ConditionSubstring - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ConditionSubstring — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ConditionSubstring

    -class ConditionSubstring(col, substrings, any_=True, not_=False, binarize_col=None, **cond_kwargs)[source]
    +class ConditionSubstring(col, substrings, any_=True, not_=False, binarize_col=None, **cond_kwargs)[source]

    Bases: QueryOp

    Filter rows on based on having substrings.

    Can be specified whether it must have any or all of the specified substrings. @@ -254,13 +325,15 @@

    cycquery.ops.ConditionSubstringMethods

    +
    +
    -__call__(table, return_cond=False)[source]
    +__call__(table, return_cond=False)[source]

    Process the table.

    Parameters:
    @@ -282,66 +355,92 @@

    cycquery.ops.ConditionSubstring + +
    +
    + Next +
    +
    cycquery.ops.Count
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.ConditionStartsWith
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Count.html b/reference/api/_autosummary/cycquery.ops.Count.html index 110498c..015395f 100644 --- a/reference/api/_autosummary/cycquery.ops.Count.html +++ b/reference/api/_autosummary/cycquery.ops.Count.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Count - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Count — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
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    +
    cycquery documentation
     +
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    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Distinct.html b/reference/api/_autosummary/cycquery.ops.Distinct.html index e728f24..d53ed9f 100644 --- a/reference/api/_autosummary/cycquery.ops.Distinct.html +++ b/reference/api/_autosummary/cycquery.ops.Distinct.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Distinct - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Distinct — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    cycquery documentation
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.Distinct

    -class Distinct(cols)[source]
    +class Distinct(cols)[source]

    Bases: QueryOp

    Get distinct rows.

    @@ -243,13 +314,15 @@

    cycquery.ops.Distinct

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -268,66 +341,92 @@

    cycquery.ops.Distinct - -

    + +
    + +
    - + + +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Drop.html b/reference/api/_autosummary/cycquery.ops.Drop.html index 7f4426f..6484a21 100644 --- a/reference/api/_autosummary/cycquery.ops.Drop.html +++ b/reference/api/_autosummary/cycquery.ops.Drop.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Drop - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Drop — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
    +
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    +
    + + + + + Back to top + +
    + +
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    + +
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    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.DropEmpty.html b/reference/api/_autosummary/cycquery.ops.DropEmpty.html index 5a14ae0..9148fdf 100644 --- a/reference/api/_autosummary/cycquery.ops.DropEmpty.html +++ b/reference/api/_autosummary/cycquery.ops.DropEmpty.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.DropEmpty - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.DropEmpty — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.DropEmpty

    -class DropEmpty(cols)[source]
    +class DropEmpty(cols)[source]

    Bases: QueryOp

    Remove rows with empty values in some specified columns.

    @@ -243,13 +314,15 @@

    cycquery.ops.DropEmpty

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -268,66 +341,92 @@

    cycquery.ops.DropEmpty - -

    + +
    + +
    - + + +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.DropNulls.html b/reference/api/_autosummary/cycquery.ops.DropNulls.html index 83a5a59..f6d547b 100644 --- a/reference/api/_autosummary/cycquery.ops.DropNulls.html +++ b/reference/api/_autosummary/cycquery.ops.DropNulls.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.DropNulls - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.DropNulls — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + +
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    +
    cycquery documentation
     +
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    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.DropNulls

    -class DropNulls(cols)[source]
    +class DropNulls(cols)[source]

    Bases: QueryOp

    Remove rows with null values in some specified columns.

    @@ -243,13 +314,15 @@

    cycquery.ops.DropNulls

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -268,66 +341,92 @@

    cycquery.ops.DropNulls - -

    + +
    + +
    - + + +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.html b/reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.html index da0277b..7881b78 100644 --- a/reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.html +++ b/reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ExtractTimestampComponent - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ExtractTimestampComponent — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
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    +
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    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.ExtractTimestampComponent

    -class ExtractTimestampComponent(timestamp_col, extract_str, label)[source]
    +class ExtractTimestampComponent(timestamp_col, extract_str, label)[source]

    Bases: QueryOp

    Extract a component such as year or month from a timestamp column.

    @@ -247,13 +318,15 @@

    cycquery.ops.ExtractTimestampComponentMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -272,66 +345,92 @@

    cycquery.ops.ExtractTimestampComponent + +
    +
    + Next +
    +
    cycquery.ops.FillNull
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.DropNulls
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.FillNull.html b/reference/api/_autosummary/cycquery.ops.FillNull.html index 8c59b9e..ab95385 100644 --- a/reference/api/_autosummary/cycquery.ops.FillNull.html +++ b/reference/api/_autosummary/cycquery.ops.FillNull.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.FillNull - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.FillNull — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
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    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.FillNull

    -class FillNull(cols, fill_values, new_col_names=None)[source]
    +class FillNull(cols, fill_values, new_col_names=None)[source]

    Bases: QueryOp

    Fill NULL values with a given value.

    @@ -248,13 +319,15 @@

    cycquery.ops.FillNull

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Fill NULL values with a given value.

    Parameters:
    @@ -273,66 +346,92 @@

    cycquery.ops.FillNull - -

    + +
    + +
    - + + +
    - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.GroupByAggregate.html b/reference/api/_autosummary/cycquery.ops.GroupByAggregate.html index ee9d7b1..0ce8efe 100644 --- a/reference/api/_autosummary/cycquery.ops.GroupByAggregate.html +++ b/reference/api/_autosummary/cycquery.ops.GroupByAggregate.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.GroupByAggregate - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.GroupByAggregate — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.GroupByAggregate

    -class GroupByAggregate(groupby_cols, aggfuncs, aggseps=None)[source]
    +class GroupByAggregate(groupby_cols, aggfuncs, aggseps=None)[source]

    Bases: QueryOp

    Aggregate over a group by object.

    @@ -256,13 +327,15 @@

    cycquery.ops.GroupByAggregateMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -281,66 +354,92 @@

    cycquery.ops.GroupByAggregate + +
    +
    + Next +
    +
    cycquery.ops.Join
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.FillNull
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Join.html b/reference/api/_autosummary/cycquery.ops.Join.html index 5c64465..e783323 100644 --- a/reference/api/_autosummary/cycquery.ops.Join.html +++ b/reference/api/_autosummary/cycquery.ops.Join.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Join - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Join — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
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    +
    cycquery documentation
     +
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    + +
    +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.Join

    -class Join(join_table, on=None, on_to_type=None, cond=None, table_cols=None, join_table_cols=None, isouter=False)[source]
    +class Join(join_table, on=None, on_to_type=None, cond=None, table_cols=None, join_table_cols=None, isouter=False)[source]

    Bases: QueryOp

    Join a table with another table.

    @@ -262,13 +333,15 @@

    cycquery.ops.JoinMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -287,66 +360,92 @@

    cycquery.ops.Join + +
    +
    + Next +
    +
    cycquery.ops.Keep
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.GroupByAggregate
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Keep.html b/reference/api/_autosummary/cycquery.ops.Keep.html index 2aa823c..26d7e6e 100644 --- a/reference/api/_autosummary/cycquery.ops.Keep.html +++ b/reference/api/_autosummary/cycquery.ops.Keep.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Keep - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Keep — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
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    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Limit.html b/reference/api/_autosummary/cycquery.ops.Limit.html index db77bf0..e9c97d7 100644 --- a/reference/api/_autosummary/cycquery.ops.Limit.html +++ b/reference/api/_autosummary/cycquery.ops.Limit.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Limit - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Limit — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    + + + + + Back to top + +
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    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Literal.html b/reference/api/_autosummary/cycquery.ops.Literal.html index 388a32b..e941440 100644 --- a/reference/api/_autosummary/cycquery.ops.Literal.html +++ b/reference/api/_autosummary/cycquery.ops.Literal.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Literal - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Literal — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
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    +
    cycquery documentation
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    + +
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    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.Literal

    -class Literal(value, col)[source]
    +class Literal(value, col)[source]

    Bases: QueryOp

    Add a literal column to a table.

    @@ -245,13 +316,15 @@

    cycquery.ops.Literal

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -270,66 +343,92 @@

    cycquery.ops.Literal - -

    + +
    + +
    - + + +
    - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Or.html b/reference/api/_autosummary/cycquery.ops.Or.html index 82e8027..d0080ea 100644 --- a/reference/api/_autosummary/cycquery.ops.Or.html +++ b/reference/api/_autosummary/cycquery.ops.Or.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Or - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Or — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.OrderBy.html b/reference/api/_autosummary/cycquery.ops.OrderBy.html index 8746ead..ee5b3e2 100644 --- a/reference/api/_autosummary/cycquery.ops.OrderBy.html +++ b/reference/api/_autosummary/cycquery.ops.OrderBy.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.OrderBy - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.OrderBy — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    cycquery.ops.OrderBy

    -class OrderBy(cols, ascending=None)[source]
    +class OrderBy(cols, ascending=None)[source]

    Bases: QueryOp

    Order, or sort, the rows of a table by some columns.

    @@ -249,13 +320,15 @@

    cycquery.ops.OrderBy

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -274,66 +347,92 @@

    cycquery.ops.OrderBy - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.QueryOp.html b/reference/api/_autosummary/cycquery.ops.QueryOp.html index d3ccab2..104c6a5 100644 --- a/reference/api/_autosummary/cycquery.ops.QueryOp.html +++ b/reference/api/_autosummary/cycquery.ops.QueryOp.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.QueryOp - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.QueryOp — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    cycquery documentation
     +
    +
    +
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    + + + + + Back to top + +
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    +
    +

    cycquery.ops.QueryOp

    -class QueryOp(*args, **kwargs)[source]
    +class QueryOp(*args, **kwargs)[source]

    Bases: object

    Base class for query operations.

    Methods

    +
    +
    -abstract __call__(*args, **kwargs)[source]
    +abstract __call__(*args, **kwargs)[source]

    Implement a calling function.

    Return type:
    @@ -252,66 +325,92 @@

    cycquery.ops.QueryOp - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.RandomizeOrder.html b/reference/api/_autosummary/cycquery.ops.RandomizeOrder.html index 265d504..cb62efd 100644 --- a/reference/api/_autosummary/cycquery.ops.RandomizeOrder.html +++ b/reference/api/_autosummary/cycquery.ops.RandomizeOrder.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.RandomizeOrder - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.RandomizeOrder — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
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    +
    +

    cycquery.ops.RandomizeOrder

    -class RandomizeOrder(*args, **kwargs)[source]
    +class RandomizeOrder(*args, **kwargs)[source]

    Bases: QueryOp

    Randomize order of table rows.

    Useful when the data is ordered, so certain rows cannot @@ -243,13 +314,15 @@

    cycquery.ops.RandomizeOrderMethods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -268,66 +341,92 @@

    cycquery.ops.RandomizeOrder + +
    +
    + Next +
    +
    cycquery.ops.Rename
    +
    + +     + + +
    +
    + Previous +
    + +
    cycquery.ops.QueryOp
    + +
    +     +

    +
    +
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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Rename.html b/reference/api/_autosummary/cycquery.ops.Rename.html index 9d2ef72..46385d6 100644 --- a/reference/api/_autosummary/cycquery.ops.Rename.html +++ b/reference/api/_autosummary/cycquery.ops.Rename.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Rename - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Rename — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Reorder.html b/reference/api/_autosummary/cycquery.ops.Reorder.html index 0f7287c..2f8a50b 100644 --- a/reference/api/_autosummary/cycquery.ops.Reorder.html +++ b/reference/api/_autosummary/cycquery.ops.Reorder.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Reorder - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Reorder — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    cycquery.ops.Reorder

    -class Reorder(cols)[source]
    +class Reorder(cols)[source]

    Bases: QueryOp

    Reorder the columns in a table.

    @@ -242,13 +313,15 @@

    cycquery.ops.Reorder

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -267,66 +340,92 @@

    cycquery.ops.Reorder - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.ReorderAfter.html b/reference/api/_autosummary/cycquery.ops.ReorderAfter.html index 27edc75..ab6da5f 100644 --- a/reference/api/_autosummary/cycquery.ops.ReorderAfter.html +++ b/reference/api/_autosummary/cycquery.ops.ReorderAfter.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.ReorderAfter - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.ReorderAfter — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Sequential.html b/reference/api/_autosummary/cycquery.ops.Sequential.html index 13a30dd..82f6a2f 100644 --- a/reference/api/_autosummary/cycquery.ops.Sequential.html +++ b/reference/api/_autosummary/cycquery.ops.Sequential.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Sequential - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Sequential — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +

    cycquery.ops.Sequential

    -class Sequential(*ops: QueryOp)[source]
    +class Sequential(*ops: QueryOp)[source]
    class Sequential(ops: List[QueryOp])
    @@ -249,6 +320,7 @@

    cycquery.ops.Sequential

    Methods

    +
    @@ -265,9 +337,10 @@

    cycquery.ops.Sequential

    append
    +
    -__add__(other)[source]
    +__add__(other)[source]

    Add two Sequential objects.

    Parameters:
    @@ -284,7 +357,7 @@

    cycquery.ops.Sequential
    -__call__(table)[source]
    +__call__(table)[source]

    Execute the query operations on the table.

    Parameters:
    @@ -301,7 +374,7 @@

    cycquery.ops.Sequential
    -__init__(*args)[source]
    +__init__(*args)[source]

    Initialize the class.

    Parameters:
    @@ -312,7 +385,7 @@

    cycquery.ops.Sequential
    -append(op_)[source]
    +append(op_)[source]

    Append a given query op to the end.

    Parameters:
    @@ -329,7 +402,7 @@

    cycquery.ops.Sequential
    -extend(sequential)[source]
    +extend(sequential)[source]

    Extend the sequential query op with another sequential query op.

    Parameters:
    @@ -346,7 +419,7 @@

    cycquery.ops.Sequential
    -insert(index, op_)[source]
    +insert(index, op_)[source]

    Insert a given query op at the given index.

    Parameters:
    @@ -366,7 +439,7 @@

    cycquery.ops.Sequential
    -pop(key)[source]
    +pop(key)[source]

    Pop the query op at the given index.

    Parameters:
    @@ -385,66 +458,98 @@

    cycquery.ops.Sequential - -

    + +
    + +
    - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Substring.html b/reference/api/_autosummary/cycquery.ops.Substring.html index f73f7aa..210310c 100644 --- a/reference/api/_autosummary/cycquery.ops.Substring.html +++ b/reference/api/_autosummary/cycquery.ops.Substring.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Substring - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Substring — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +

    cycquery.ops.Substring

    -class Substring(col, start_index, stop_index, new_col_label=None)[source]
    +class Substring(col, start_index, stop_index, new_col_label=None)[source]

    Bases: QueryOp

    Get substring of a string column.

    @@ -248,13 +319,15 @@

    cycquery.ops.Substring

    Methods

    +
    +
    -__call__(table)[source]
    +__call__(table)[source]

    Process the table.

    Parameters:
    @@ -273,66 +346,92 @@

    cycquery.ops.Substring - -

    + +
    + + - + + + - - - + + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Trim.html b/reference/api/_autosummary/cycquery.ops.Trim.html index e74743b..07ef4cc 100644 --- a/reference/api/_autosummary/cycquery.ops.Trim.html +++ b/reference/api/_autosummary/cycquery.ops.Trim.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Trim - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Trim — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    + Copyright © 2024, Vector AI Engineering +
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    +
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    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.Union.html b/reference/api/_autosummary/cycquery.ops.Union.html index cb7badd..cced471 100644 --- a/reference/api/_autosummary/cycquery.ops.Union.html +++ b/reference/api/_autosummary/cycquery.ops.Union.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops.Union - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops.Union — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    + Copyright © 2024, Vector AI Engineering +
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    +
    +
    + + + + + + +
    -
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/_autosummary/cycquery.ops.html b/reference/api/_autosummary/cycquery.ops.html index f548c49..d51d468 100644 --- a/reference/api/_autosummary/cycquery.ops.html +++ b/reference/api/_autosummary/cycquery.ops.html @@ -1,136 +1,194 @@ + + + + + + + + + cycquery.ops - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery.ops — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    + +
    +
    +
    +

    cycquery.ops

    Query operations.

    Classes

    +
    @@ -360,68 +434,73 @@

    AddColumn
    +
    - -
    + +
    +
    - + + +
    +
    - - - +
    + + + + + + + + + \ No newline at end of file diff --git a/reference/api/cycquery.html b/reference/api/cycquery.html index c1a0009..2181fa1 100644 --- a/reference/api/cycquery.html +++ b/reference/api/cycquery.html @@ -1,143 +1,261 @@ + + + + + + + + + cycquery - cycquery documentation + + + + + + + - - - - - - - - - - - cycquery — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
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    +
    cycquery documentation
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    + +
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    + +
    + +
    + +
    +
    +
    +

    cycquery

    The query API provides classes to query EHR databases.

    +
    @@ -199,8 +313,10 @@

    interface
    +
    -

    dataset APIs

    +

    dataset APIs

    +
    @@ -220,69 +336,93 @@

    dataset APIs + +
    +
    + Next +
    +
    cycquery.interface
    +
    + +     + + +
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    + Previous +
    + +
    API Reference
    + +
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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
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    + - - - + + + + + + + + + + \ No newline at end of file diff --git a/search.html b/search.html index 4dd9a93..c24cb39 100644 --- a/search.html +++ b/search.html @@ -1,245 +1,358 @@ + + + + + + + Search - cycquery documentation + + + + + + - - - - - - - - - - Search — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "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.": [[67, "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 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]]}, "indexentries": {"cycquery.base": [[4, "module-cycquery.base"]], "module": [[4, "module-cycquery.base"], [6, "module-cycquery.eicu"], [8, "module-cycquery.gemini"], [10, "module-cycquery.interface"], [12, "module-cycquery.mimiciii"], [14, "module-cycquery.mimiciv"], [16, "module-cycquery.omop"], [18, "module-cycquery.ops"], [62, "module-cycquery"]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier"]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db"]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table"]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns"]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables"]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas"]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier"]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table"]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns"]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables"]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas"]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier"]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units"]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses"]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table"]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging"]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin"]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns"]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables"]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas"]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables"]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface"]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__"]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data"]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data"]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join"]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops"]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run"]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save"]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union"]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier"]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents"]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses"]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table"]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents"]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns"]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables"]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas"]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier"]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents"]], "diagnoses_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd"]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table"]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents"]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns"]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables"]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas"]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables"]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients"]], "procedures_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.procedures_icd"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier"]], "get_table() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.get_table"]], "list_columns() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_columns"]], "list_custom_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_custom_tables"]], "list_schemas() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_schemas"]], "list_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_tables"]], "map_concept_ids_to_name() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.map_concept_ids_to_name"]], "measurement() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.measurement"]], "observation() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.observation"]], "person() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.person"]], "visit_detail() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_detail"]], "visit_occurrence() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_occurrence"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "addcolumn (class in cycquery.ops)": [[19, "cycquery.ops.AddColumn"]], "__call__() (addcolumn method)": [[19, "cycquery.ops.AddColumn.__call__"]], "adddeltacolumn (class in cycquery.ops)": [[20, "cycquery.ops.AddDeltaColumn"]], "__call__() (adddeltacolumn method)": [[20, "cycquery.ops.AddDeltaColumn.__call__"]], "adddeltaconstant (class in cycquery.ops)": [[21, "cycquery.ops.AddDeltaConstant"]], "__call__() (adddeltaconstant method)": [[21, "cycquery.ops.AddDeltaConstant.__call__"]], "addnumeric (class in cycquery.ops)": [[22, "cycquery.ops.AddNumeric"]], "__call__() (addnumeric method)": [[22, "cycquery.ops.AddNumeric.__call__"]], "and (class in cycquery.ops)": [[23, "cycquery.ops.And"]], "__call__() (and method)": [[23, "cycquery.ops.And.__call__"]], "apply (class in cycquery.ops)": [[24, "cycquery.ops.Apply"]], "__call__() (apply method)": [[24, "cycquery.ops.Apply.__call__"]], "cast (class in cycquery.ops)": [[25, "cycquery.ops.Cast"]], "__call__() (cast method)": [[25, "cycquery.ops.Cast.__call__"]], "conditionafterdate (class in cycquery.ops)": [[26, "cycquery.ops.ConditionAfterDate"]], "__call__() (conditionafterdate method)": [[26, "cycquery.ops.ConditionAfterDate.__call__"]], "conditionbeforedate (class in cycquery.ops)": [[27, "cycquery.ops.ConditionBeforeDate"]], "__call__() (conditionbeforedate method)": [[27, "cycquery.ops.ConditionBeforeDate.__call__"]], "conditionendswith (class in cycquery.ops)": [[28, "cycquery.ops.ConditionEndsWith"]], "__call__() (conditionendswith method)": [[28, "cycquery.ops.ConditionEndsWith.__call__"]], "conditionequals (class in cycquery.ops)": [[29, "cycquery.ops.ConditionEquals"]], "__call__() (conditionequals method)": [[29, "cycquery.ops.ConditionEquals.__call__"]], "conditiongreaterthan (class in cycquery.ops)": [[30, "cycquery.ops.ConditionGreaterThan"]], "__call__() (conditiongreaterthan method)": [[30, "cycquery.ops.ConditionGreaterThan.__call__"]], "conditionin (class in cycquery.ops)": [[31, "cycquery.ops.ConditionIn"]], "__call__() (conditionin method)": [[31, "cycquery.ops.ConditionIn.__call__"]], "conditioninmonths (class in cycquery.ops)": [[32, "cycquery.ops.ConditionInMonths"]], "__call__() (conditioninmonths method)": [[32, "cycquery.ops.ConditionInMonths.__call__"]], "conditioninyears (class in cycquery.ops)": [[33, "cycquery.ops.ConditionInYears"]], "__call__() (conditioninyears method)": [[33, "cycquery.ops.ConditionInYears.__call__"]], "conditionlessthan (class in cycquery.ops)": [[34, "cycquery.ops.ConditionLessThan"]], "__call__() (conditionlessthan method)": [[34, "cycquery.ops.ConditionLessThan.__call__"]], "conditionlike (class in cycquery.ops)": [[35, "cycquery.ops.ConditionLike"]], "__call__() (conditionlike method)": [[35, "cycquery.ops.ConditionLike.__call__"]], "conditionregexmatch (class in cycquery.ops)": [[36, "cycquery.ops.ConditionRegexMatch"]], "__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__"]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith"]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__"]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring"]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__"]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count"]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__"]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct"]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__"]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop"]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__"]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty"]], "__call__() (dropempty method)": [[42, "cycquery.ops.DropEmpty.__call__"]], "dropnulls (class in cycquery.ops)": [[43, "cycquery.ops.DropNulls"]], "__call__() (dropnulls method)": [[43, "cycquery.ops.DropNulls.__call__"]], "extracttimestampcomponent (class in cycquery.ops)": [[44, "cycquery.ops.ExtractTimestampComponent"]], "__call__() (extracttimestampcomponent method)": [[44, "cycquery.ops.ExtractTimestampComponent.__call__"]], "fillnull (class in cycquery.ops)": [[45, "cycquery.ops.FillNull"]], "__call__() (fillnull method)": [[45, "cycquery.ops.FillNull.__call__"]], "groupbyaggregate (class in cycquery.ops)": [[46, "cycquery.ops.GroupByAggregate"]], "__call__() (groupbyaggregate method)": [[46, "cycquery.ops.GroupByAggregate.__call__"]], "join (class in cycquery.ops)": [[47, "cycquery.ops.Join"]], "__call__() (join method)": [[47, "cycquery.ops.Join.__call__"]], "keep (class in cycquery.ops)": [[48, "cycquery.ops.Keep"]], "__call__() (keep method)": [[48, "cycquery.ops.Keep.__call__"]], "limit (class in cycquery.ops)": [[49, "cycquery.ops.Limit"]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__"]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal"]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__"]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or"]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__"]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy"]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__"]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp"]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__"]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder"]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__"]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename"]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__"]], "reorder (class in cycquery.ops)": [[56, "cycquery.ops.Reorder"]], "__call__() (reorder method)": [[56, "cycquery.ops.Reorder.__call__"]], "reorderafter (class in cycquery.ops)": [[57, "cycquery.ops.ReorderAfter"]], "__call__() (reorderafter method)": [[57, "cycquery.ops.ReorderAfter.__call__"]], "sequential (class in cycquery.ops)": [[58, "cycquery.ops.Sequential"]], "__add__() (sequential method)": [[58, "cycquery.ops.Sequential.__add__"]], "__call__() (sequential method)": [[58, "cycquery.ops.Sequential.__call__"]], "__init__() (sequential method)": [[58, "cycquery.ops.Sequential.__init__"]], "append() (sequential method)": [[58, "cycquery.ops.Sequential.append"]], "extend() (sequential method)": [[58, "cycquery.ops.Sequential.extend"]], "insert() (sequential method)": [[58, "cycquery.ops.Sequential.insert"]], "pop() (sequential method)": [[58, "cycquery.ops.Sequential.pop"]], "substring (class in cycquery.ops)": [[59, "cycquery.ops.Substring"]], "__call__() (substring method)": [[59, "cycquery.ops.Substring.__call__"]], "trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim"]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__"]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union"]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__"]], "cycquery": [[62, "module-cycquery"]]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "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.": [[67, "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."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. 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"teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials.html b/tutorials.html index a2ae51b..636107a 100644 --- a/tutorials.html +++ b/tutorials.html @@ -1,132 +1,180 @@ + + + + + + + + + Tutorials - cycquery documentation + + + + + + + - - - - - - - - - - - Tutorials — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    +

    Tutorials

    +

    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.

    @@ -192,7 +316,7 @@

    TutorialsImports and instantiate MIMICIVQuerier
  • Example 1. Get all patient admissions from 2021 or later (approx year of admission)
  • Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.
    • -
  • 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.
  • Example 4. Get routine vital signs for patients from year 2015.
  • Example 5. Get hemoglobin lab tests for patients from year 2009.
  • Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.
    • @@ -229,66 +353,72 @@

    Tutorials + +
    +
    + Next +
    +
    MIMIC-III tutorial
    +
    + +     + + +
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    + Previous +
    + +
    Contributing to cycquery
    + +
    +     +

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    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo + +
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    -
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    - - - + + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index 923da9e..f580f8d 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -1,189 +1,302 @@ + + + + + + + + + eICU-CRD tutorial - cycquery documentation + + + + + + + - - - - - - - - - - - eICU-CRD tutorial — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
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    -

    eICU-CRD tutorial

    -

    This notebook shows examples of how to use the cyclops-query tool on eicu-CRD.

    +

    eICU-CRD tutorial

    +

    This notebook shows examples of how to use the cycquery tool on eicu-CRD.

    Each query is limit to 100 rows (for quick results).

    • First, setup the eICU database according to the instructions in eicu-code.

    • The database is assumed to be hosted using postgres. Update the config parameters such as username and password, passed to EICUQuerier accordingly.

    -

    Imports and instantiate EICUQuerier

    +

    Imports and instantiate EICUQuerier

    [1]:
    @@ -478,7 +591,7 @@

    Imports and instantiate 
    -2024-03-08 10:05:14,376 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-17 15:12:30,977 INFO cycquery.orm    - Database setup, ready to run queries!

    @@ -522,7 +635,7 @@

    Imports and instantiate

    -

    Example 1. Get all female patients discharged in 2014 (limit to 100 rows).

    +

    Example 1. Get all female patients discharged in 2014 (limit to 100 rows).

    [2]:
    @@ -542,7 +655,7 @@

    Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
    -2024-03-08 10:05:15,276 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:31,857 INFO cycquery.orm    - Query returned successfully!

    @@ -550,7 +663,7 @@

    Example 1. Get all female patients discharged in 2014 (limit to 100 rows). 
    -2024-03-08 10:05:15,277 INFO cycquery.utils.profile - Finished executing function run_query in 0.052928 s
+2024-04-17 15:12:31,859 INFO cycquery.utils.profile - Finished executing function run_query in 0.054049 s

    @@ -563,7 +676,7 @@

    Example 1. Get all female patients discharged in 2014 (limit to 100 rows).

    -

    Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.

    +

    Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.

    [3]:
    @@ -585,7 +698,7 @@

    Example 2. Get all patient encounters with diagnoses ( 
    -2024-03-08 10:05:15,369 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:31,963 INFO cycquery.orm    - Query returned successfully!

    @@ -593,7 +706,7 @@

    Example 2. Get all patient encounters with diagnoses ( 
    -2024-03-08 10:05:15,370 INFO cycquery.utils.profile - Finished executing function run_query in 0.070819 s
+2024-04-17 15:12:31,965 INFO cycquery.utils.profile - Finished executing function run_query in 0.084577 s

    @@ -606,7 +719,7 @@

    Example 2. Get all patient encounters with diagnoses ( -

    Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.

    +

    Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.

    [4]:
    @@ -634,7 +747,7 @@

    Example 3. Get potassium lab tests for patients discharged in the year 2014, 

    -2024-03-08 10:05:15,432 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:32,037 INFO cycquery.orm    - Query returned successfully!
    @@ -642,7 +755,7 @@

    Example 3. Get potassium lab tests for patients discharged in the year 2014, 

    -2024-03-08 10:05:15,433 INFO cycquery.utils.profile - Finished executing function run_query in 0.039567 s
+2024-04-17 15:12:32,038 INFO cycquery.utils.profile - Finished executing function run_query in 0.043745 s

    @@ -655,7 +768,7 @@

    Example 3. Get potassium lab tests for patients discharged in the year 2014,

    -

    Example 4. Get glucose medications (substring search) for female patients discharged in 2014.

    +

    Example 4. Get glucose medications (substring search) for female patients discharged in 2014.

    [5]:
    @@ -681,7 +794,7 @@

    Example 4. Get glucose medications (substring search) for female patients di 

    -2024-03-08 10:05:15,625 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:32,221 INFO cycquery.orm    - Query returned successfully!
    @@ -689,7 +802,7 @@

    Example 4. Get glucose medications (substring search) for female patients di 

    -2024-03-08 10:05:15,626 INFO cycquery.utils.profile - Finished executing function run_query in 0.168468 s
+2024-04-17 15:12:32,222 INFO cycquery.utils.profile - Finished executing function run_query in 0.162660 s
    @@ -703,66 +816,95 @@

    Example 4. Get glucose medications (substring search) for female patients di - -

    + +
    + +
    - + + + - - - + + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index 9dee54c..000fa2f 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -13,7 +13,7 @@ "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", @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:13.066986Z", - "iopub.status.busy": "2024-03-08T15:05:13.066463Z", - "iopub.status.idle": "2024-03-08T15:05:15.209180Z", - "shell.execute_reply": "2024-03-08T15:05:15.207588Z" + "iopub.execute_input": "2024-04-17T19:12:29.764524Z", + "iopub.status.busy": "2024-04-17T19:12:29.764005Z", + "iopub.status.idle": "2024-04-17T19:12:31.788493Z", + "shell.execute_reply": "2024-04-17T19:12:31.786859Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:14,376 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-17 15:12:30,977 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -124,10 +124,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:15.215967Z", - "iopub.status.busy": "2024-03-08T15:05:15.215335Z", - "iopub.status.idle": "2024-03-08T15:05:15.282228Z", - "shell.execute_reply": "2024-03-08T15:05:15.281145Z" + "iopub.execute_input": "2024-04-17T19:12:31.795439Z", + "iopub.status.busy": "2024-04-17T19:12:31.794487Z", + "iopub.status.idle": "2024-04-17T19:12:31.864869Z", + "shell.execute_reply": "2024-04-17T19:12:31.863453Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,276 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:31,857 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,277 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.052928 s\n" + "2024-04-17 15:12:31,859 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.054049 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:15.289122Z", - "iopub.status.busy": "2024-03-08T15:05:15.288592Z", - "iopub.status.idle": "2024-03-08T15:05:15.373284Z", - "shell.execute_reply": "2024-03-08T15:05:15.372593Z" + "iopub.execute_input": "2024-04-17T19:12:31.870737Z", + "iopub.status.busy": "2024-04-17T19:12:31.870162Z", + "iopub.status.idle": "2024-04-17T19:12:31.968896Z", + "shell.execute_reply": "2024-04-17T19:12:31.967980Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,369 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:31,963 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,370 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.070819 s\n" + "2024-04-17 15:12:31,965 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.084577 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:15.381182Z", - "iopub.status.busy": "2024-03-08T15:05:15.380823Z", - "iopub.status.idle": "2024-03-08T15:05:15.438153Z", - "shell.execute_reply": "2024-03-08T15:05:15.437236Z" + "iopub.execute_input": "2024-04-17T19:12:31.976270Z", + "iopub.status.busy": "2024-04-17T19:12:31.975774Z", + "iopub.status.idle": "2024-04-17T19:12:32.042718Z", + "shell.execute_reply": "2024-04-17T19:12:32.041789Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,432 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:32,037 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,433 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.039567 s\n" + "2024-04-17 15:12:32,038 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.043745 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:15.444922Z", - "iopub.status.busy": "2024-03-08T15:05:15.444412Z", - "iopub.status.idle": "2024-03-08T15:05:15.632012Z", - "shell.execute_reply": "2024-03-08T15:05:15.630782Z" + "iopub.execute_input": "2024-04-17T19:12:32.047085Z", + "iopub.status.busy": "2024-04-17T19:12:32.046621Z", + "iopub.status.idle": "2024-04-17T19:12:32.227812Z", + "shell.execute_reply": "2024-04-17T19:12:32.226421Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,625 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:32,221 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:15,626 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.168468 s\n" + "2024-04-17 15:12:32,222 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.162660 s\n" ] }, { diff --git a/tutorials/gemini.html b/tutorials/gemini.html index 0fc7dd3..e009f98 100644 --- a/tutorials/gemini.html +++ b/tutorials/gemini.html @@ -1,189 +1,302 @@ + + + + + + + + + GEMINI tutorial - cycquery documentation + + + + + + + - - - - - - - - - - - GEMINI tutorial — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    +
    +
    -

    GEMINI tutorial

    -

    This notebook shows examples of how to use the cyclops-query tool on GEMINI.

    +

    GEMINI tutorial

    +

    This notebook shows examples of how to use the cycquery tool on GEMINI.

    -

    Imports and instantiate GEMINIQuerier.

    +

    Imports and instantiate GEMINIQuerier.

    [1]:
    @@ -471,7 +584,7 @@

    Imports and instantiate 
    -2023-09-21 09:17:45,449 INFO cyclops.query.orm - Database setup, ready to run queries!
+2023-09-21 09:17:45,449 INFO cycquery.orm - Database setup, ready to run queries!

    @@ -518,7 +631,7 @@

    Imports and instantiate

    -

    Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.

    +

    Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.

    [2]:
    @@ -541,8 +654,8 @@

    Example 1a. Create a table with only one hospitalization per patient, keepin 

    -2023-09-21 09:17:51,902 INFO cyclops.query.orm - Query returned successfully!
-2023-09-21 09:17:51,903 INFO cyclops.utils.profile - Finished executing function run_query in 6.093352 s
+2023-09-21 09:17:51,902 INFO cycquery.orm - Query returned successfully!
+2023-09-21 09:17:51,903 INFO cycquery.utils.profile - Finished executing function run_query in 6.093352 s
    @@ -555,7 +668,7 @@

    Example 1a. Create a table with only one hospitalization per patient, keepin

    -

    Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.

    +

    Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.

    [3]:
    @@ -577,8 +690,8 @@

    Example 1b. From the above set of encounters, take a subset of patients who 

    -2023-09-21 09:17:52,591 INFO cyclops.query.orm - Query returned successfully!
-2023-09-21 09:17:52,592 INFO cyclops.utils.profile - Finished executing function run_query in 0.675141 s
+2023-09-21 09:17:52,591 INFO cycquery.orm - Query returned successfully!
+2023-09-21 09:17:52,592 INFO cycquery.utils.profile - Finished executing function run_query in 0.675141 s
    @@ -591,7 +704,7 @@

    Example 1b. From the above set of encounters, take a subset of patients who

    -

    Example 1c. From the above set of encounters, get the total number of admissions for each hospital.

    +

    Example 1c. From the above set of encounters, get the total number of admissions for each hospital.

    [4]:
    @@ -607,8 +720,8 @@

    Example 1c. From the above set of encounters, get the total number of admiss 

    -2023-09-21 09:17:52,856 INFO cyclops.query.orm - Query returned successfully!
-2023-09-21 09:17:52,857 INFO cyclops.utils.profile - Finished executing function run_query in 0.145693 s
+2023-09-21 09:17:52,856 INFO cycquery.orm - Query returned successfully!
+2023-09-21 09:17:52,857 INFO cycquery.utils.profile - Finished executing function run_query in 0.145693 s
    @@ -621,7 +734,7 @@

    Example 1c. From the above set of encounters, get the total number of admiss

    -

    Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?

    +

    Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?

    [5]:
    @@ -652,8 +765,8 @@

    Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31 

    -2023-09-21 09:26:19,814 INFO cyclops.query.orm - Query returned successfully!
-2023-09-21 09:26:19,815 INFO cyclops.utils.profile - Finished executing function run_query in 506.939296 s
+2023-09-21 09:26:19,814 INFO cycquery.orm - Query returned successfully!
+2023-09-21 09:26:19,815 INFO cycquery.utils.profile - Finished executing function run_query in 506.939296 s
    @@ -669,66 +782,95 @@

    Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31

    - -
    + +
    + +
    - + + + - - - + + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/gemini.ipynb b/tutorials/gemini.ipynb index 53797d6..759a3fc 100644 --- a/tutorials/gemini.ipynb +++ b/tutorials/gemini.ipynb @@ -13,7 +13,7 @@ "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/)." ] }, { @@ -34,7 +34,7 @@ "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" ] }, { @@ -116,8 +116,8 @@ "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" ] }, { @@ -159,8 +159,8 @@ "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" ] }, { @@ -201,8 +201,8 @@ "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" ] }, { @@ -237,8 +237,8 @@ "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" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index 7305a33..336d859 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -1,189 +1,302 @@ + + + + + + + + + MIMIC-III tutorial - cycquery documentation + + + + + + + - - - - - - - - - - - MIMIC-III tutorial — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
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    + +
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    +
    -

    MIMIC-III tutorial

    -

    This notebook shows examples of how to use the cyclops-query tool on MIMIC-III v1.4.

    +

    MIMIC-III tutorial

    +

    This notebook shows examples of how to use the cycquery tool on MIMIC-III v1.4.

    Each query is limit to 100 rows (for quick results).

    • First, setup the MIMIC-III database according to the instructions in mimic-code.

    • The database is assumed to be hosted using postgres. Update the config parameters such as username and password, passed to MIMICIIIQuerier accordingly.

    -

    Imports and instantiate MIMICIIIQuerier

    +

    Imports and instantiate MIMICIIIQuerier

    [1]:
    @@ -478,7 +591,7 @@

    Imports and instantiate 
    -2024-03-08 10:05:23,625 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-17 15:12:41,249 INFO cycquery.orm    - Database setup, ready to run queries!

    @@ -492,7 +605,7 @@

    Imports and instantiate

    -

    Example 1. Get all male patients with a mortality outcome.

    +

    Example 1. Get all male patients with a mortality outcome.

    [2]:
    @@ -512,7 +625,7 @@

    Example 1. Get all male patients with a mortality outcome. 
    -2024-03-08 10:05:30,478 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:48,210 INFO cycquery.orm    - Query returned successfully!

    @@ -520,7 +633,7 @@

    Example 1. Get all male patients with a mortality outcome. 
    -2024-03-08 10:05:30,480 INFO cycquery.utils.profile - Finished executing function run_query in 0.039255 s
+2024-04-17 15:12:48,212 INFO cycquery.utils.profile - Finished executing function run_query in 0.044270 s

    @@ -533,7 +646,7 @@

    Example 1. Get all male patients with a mortality outcome. -

    Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).

    +

    Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).

    [3]:
    @@ -560,7 +673,7 @@

    Example 2. Get all female patient encounters with diagnoses ( 
    -2024-03-08 10:05:30,604 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:48,350 INFO cycquery.orm    - Query returned successfully!

    @@ -568,7 +681,7 @@

    Example 2. Get all female patient encounters with diagnoses ( 
    -2024-03-08 10:05:30,605 INFO cycquery.utils.profile - Finished executing function run_query in 0.097194 s
+2024-04-17 15:12:48,351 INFO cycquery.utils.profile - Finished executing function run_query in 0.102949 s

    @@ -581,7 +694,7 @@

    Example 2. Get all female patient encounters with diagnoses ( -

    Example 3. Get potassium lab tests for female patients.

    +

    Example 3. Get potassium lab tests for female patients.

    [4]:
    @@ -600,7 +713,7 @@

    Example 3. Get potassium lab tests for female patients. 
    -2024-03-08 10:05:30,665 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:12:48,417 INFO cycquery.orm    - Query returned successfully!

    @@ -608,7 +721,7 @@

    Example 3. Get potassium lab tests for female patients. 
    -2024-03-08 10:05:30,667 INFO cycquery.utils.profile - Finished executing function run_query in 0.032749 s
+2024-04-17 15:12:48,418 INFO cycquery.utils.profile - Finished executing function run_query in 0.034705 s

    @@ -621,7 +734,7 @@

    Example 3. Get potassium lab tests for female patients.
    -

    Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.

    +

    Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.

    [5]:
    @@ -645,7 +758,7 @@

    Example 4. Get AaDO2 carevue chart events for male patients that have a 
    -2024-03-08 10:06:41,183 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:13:59,173 INFO cycquery.orm    - Query returned successfully!

    @@ -653,7 +766,7 @@

    Example 4. Get AaDO2 carevue chart events for male patients that have a 
    -2024-03-08 10:06:41,185 INFO cycquery.utils.profile - Finished executing function run_query in 70.485521 s
+2024-04-17 15:13:59,175 INFO cycquery.utils.profile - Finished executing function run_query in 70.722001 s

    @@ -667,66 +780,95 @@

    Example 4. Get AaDO2 carevue chart events for male patients that have a

    - -

    + +
    + +

    - + + +
    - - - + + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index c398d5e..ce3359e 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -13,7 +13,7 @@ "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", @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:18.088479Z", - "iopub.status.busy": "2024-03-08T15:05:18.087921Z", - "iopub.status.idle": "2024-03-08T15:05:30.428783Z", - "shell.execute_reply": "2024-03-08T15:05:30.426826Z" + "iopub.execute_input": "2024-04-17T19:12:34.552849Z", + "iopub.status.busy": "2024-04-17T19:12:34.552345Z", + "iopub.status.idle": "2024-04-17T19:12:48.154112Z", + "shell.execute_reply": "2024-04-17T19:12:48.152540Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:23,625 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-17 15:12:41,249 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -94,10 +94,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:30.435198Z", - "iopub.status.busy": "2024-03-08T15:05:30.434569Z", - "iopub.status.idle": "2024-03-08T15:05:30.486731Z", - "shell.execute_reply": "2024-03-08T15:05:30.484996Z" + "iopub.execute_input": "2024-04-17T19:12:48.161108Z", + "iopub.status.busy": "2024-04-17T19:12:48.160378Z", + "iopub.status.idle": "2024-04-17T19:12:48.218425Z", + "shell.execute_reply": "2024-04-17T19:12:48.217000Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,478 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:48,210 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,480 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.039255 s\n" + "2024-04-17 15:12:48,212 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.044270 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:30.494201Z", - "iopub.status.busy": "2024-03-08T15:05:30.493860Z", - "iopub.status.idle": "2024-03-08T15:05:30.611720Z", - "shell.execute_reply": "2024-03-08T15:05:30.610105Z" + "iopub.execute_input": "2024-04-17T19:12:48.224747Z", + "iopub.status.busy": "2024-04-17T19:12:48.224219Z", + "iopub.status.idle": "2024-04-17T19:12:48.357641Z", + "shell.execute_reply": "2024-04-17T19:12:48.356365Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,604 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:48,350 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,605 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.097194 s\n" + "2024-04-17 15:12:48,351 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.102949 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:30.620848Z", - "iopub.status.busy": "2024-03-08T15:05:30.620296Z", - "iopub.status.idle": "2024-03-08T15:05:30.672685Z", - "shell.execute_reply": "2024-03-08T15:05:30.671319Z" + "iopub.execute_input": "2024-04-17T19:12:48.363867Z", + "iopub.status.busy": "2024-04-17T19:12:48.363394Z", + "iopub.status.idle": "2024-04-17T19:12:48.423621Z", + "shell.execute_reply": "2024-04-17T19:12:48.422526Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,665 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:12:48,417 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:05:30,667 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.032749 s\n" + "2024-04-17 15:12:48,418 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.034705 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:05:30.680136Z", - "iopub.status.busy": "2024-03-08T15:05:30.679553Z", - "iopub.status.idle": "2024-03-08T15:06:41.191220Z", - "shell.execute_reply": "2024-03-08T15:06:41.189906Z" + "iopub.execute_input": "2024-04-17T19:12:48.429451Z", + "iopub.status.busy": "2024-04-17T19:12:48.428903Z", + "iopub.status.idle": "2024-04-17T19:13:59.180520Z", + "shell.execute_reply": "2024-04-17T19:13:59.179457Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:41,183 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:13:59,173 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:41,185 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 70.485521 s\n" + "2024-04-17 15:13:59,175 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 70.722001 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index 4dd6c2c..3f81542 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -1,193 +1,302 @@ + + + + + + + + + MIMIC-IV tutorial - cycquery documentation + + + + + + + - - - - - - - - - - - MIMIC-IV tutorial — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
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    +
    cycquery documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    -

    MIMIC-IV tutorial

    -

    This notebook shows examples of how to use the cyclops-query tool on MIMIC-IV v2.0.

    +

    MIMIC-IV tutorial

    +

    This notebook shows examples of how to use the cycquery tool on MIMIC-IV v2.0.

    Each query is limit to 100 rows (for quick results).

    • First, setup the MIMIC-IV database according to the instructions in mimic-code.

    • The database is assumed to be hosted using postgres. Update the config parameters such as username and password, passed to MIMICIVQuerier accordingly.

    -

    Imports and instantiate MIMICIVQuerier

    +

    Imports and instantiate MIMICIVQuerier

    [1]:
    @@ -482,7 +591,7 @@

    Imports and instantiate 
    -2024-03-08 10:06:46,575 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-17 15:14:03,964 INFO cycquery.orm    - Database setup, ready to run queries!

    @@ -505,7 +614,7 @@

    Imports and instantiate

    -

    Example 1. Get all patient admissions from 2021 or later (approx year of admission)

    +

    Example 1. Get all patient admissions from 2021 or later (approx year of admission)

    [2]:
    @@ -527,7 +636,7 @@

    Example 1. Get all patient admissions from 2021 or later (approx year of adm 

    -2024-03-08 10:06:49,687 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:14:05,263 INFO cycquery.orm    - Query returned successfully!
    @@ -535,7 +644,7 @@

    Example 1. Get all patient admissions from 2021 or later (approx year of adm 

    -2024-03-08 10:06:49,688 INFO cycquery.utils.profile - Finished executing function run_query in 0.307097 s
+2024-04-17 15:14:05,265 INFO cycquery.utils.profile - Finished executing function run_query in 0.195802 s
    @@ -548,7 +657,7 @@

    Example 1. Get all patient admissions from 2021 or later (approx year of adm

    -

    Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.

    +

    Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.

    [3]:
    @@ -580,7 +689,7 @@

    Example 2. Get all patient encounters with diagnoses ( 
    -2024-03-08 10:06:50,600 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:14:05,977 INFO cycquery.orm    - Query returned successfully!

    @@ -588,7 +697,7 @@

    Example 2. Get all patient encounters with diagnoses ( 
    -2024-03-08 10:06:50,601 INFO cycquery.utils.profile - Finished executing function run_query in 0.874461 s
+2024-04-17 15:14:05,979 INFO cycquery.utils.profile - Finished executing function run_query in 0.674020 s

    @@ -600,8 +709,8 @@

    Example 2. Get all patient encounters with diagnoses ( -

    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.

    [4]:
    @@ -633,7 +742,7 @@

    Example 3. Advanced - uses 
    -2024-03-08 10:06:52,133 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:14:07,490 INFO cycquery.orm    - Query returned successfully!

    @@ -641,7 +750,7 @@

    Example 3. Advanced - uses 
    -2024-03-08 10:06:52,134 INFO cycquery.utils.profile - Finished executing function run_query in 1.491402 s
+2024-04-17 15:14:07,491 INFO cycquery.utils.profile - Finished executing function run_query in 1.468321 s

    @@ -654,7 +763,7 @@

    Example 3. Advanced - uses

    -

    Example 4. Get routine vital signs for patients from year 2015.

    +

    Example 4. Get routine vital signs for patients from year 2015.

    [5]:
    @@ -682,7 +791,7 @@

    Example 4. Get routine vital signs for patients from year 2015. 
    -2024-03-08 10:08:14,529 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:15:30,600 INFO cycquery.orm    - Query returned successfully!

    @@ -690,7 +799,7 @@

    Example 4. Get routine vital signs for patients from year 2015. 
    -2024-03-08 10:08:14,530 INFO cycquery.utils.profile - Finished executing function run_query in 82.349428 s
+2024-04-17 15:15:30,601 INFO cycquery.utils.profile - Finished executing function run_query in 83.074736 s

    @@ -703,7 +812,7 @@

    Example 4. Get routine vital signs for patients from year 2015. -

    Example 5. Get hemoglobin lab tests for patients from year 2009.

    +

    Example 5. Get hemoglobin lab tests for patients from year 2009.

    [6]:
    @@ -731,7 +840,7 @@

    Example 5. Get hemoglobin lab tests for patients from year 2009. 
    -2024-03-08 10:09:25,677 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:41,506 INFO cycquery.orm    - Query returned successfully!

    @@ -739,7 +848,7 @@

    Example 5. Get hemoglobin lab tests for patients from year 2009. 
    -2024-03-08 10:09:25,678 INFO cycquery.utils.profile - Finished executing function run_query in 71.109498 s
+2024-04-17 15:16:41,508 INFO cycquery.utils.profile - Finished executing function run_query in 70.871534 s

    @@ -752,7 +861,7 @@

    Example 5. Get hemoglobin lab tests for patients from year 2009. -

    Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.

    +

    Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.

    [7]:
    @@ -786,7 +895,7 @@

    Example 6. Get radiology reports and filter on keywords 
    -2024-03-08 10:09:33,639 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:49,512 INFO cycquery.orm    - Query returned successfully!

    @@ -794,7 +903,7 @@

    Example 6. Get radiology reports and filter on keywords 
    -2024-03-08 10:09:33,640 INFO cycquery.utils.profile - Finished executing function run_query in 7.937612 s
+2024-04-17 15:16:49,513 INFO cycquery.utils.profile - Finished executing function run_query in 7.972264 s

    @@ -807,7 +916,7 @@

    Example 6. Get radiology reports and filter on keywords -

    Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.

    +

    Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.

    [8]:
    @@ -837,7 +946,7 @@

    Example 7. Get all female patient encounters from year 2015, and return batc 

    -2024-03-08 10:09:33,979 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:49,909 INFO cycquery.orm    - Query returned successfully!
    @@ -845,7 +954,7 @@

    Example 7. Get all female patient encounters from year 2015, and return batc 

    -2024-03-08 10:09:33,981 INFO cycquery.utils.profile - Finished executing function run_query in 0.304018 s
+2024-04-17 15:16:49,910 INFO cycquery.utils.profile - Finished executing function run_query in 0.354782 s

    @@ -858,7 +967,7 @@

    Example 7. Get all female patient encounters from year 2015, and return batc

    -

    Example 8. Running a raw SQL string.

    +

    Example 8. Running a raw SQL string.

    [9]:
    @@ -873,7 +982,7 @@

    Example 8. Running a raw SQL string. 
    -2024-03-08 10:09:34,257 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:50,182 INFO cycquery.orm    - Query returned successfully!

    @@ -881,7 +990,7 @@

    Example 8. Running a raw SQL string. 
    -2024-03-08 10:09:34,258 INFO cycquery.utils.profile - Finished executing function run_query in 0.007239 s
+2024-04-17 15:16:50,183 INFO cycquery.utils.profile - Finished executing function run_query in 0.006886 s

    @@ -895,66 +1004,99 @@

    Example 8. Running a raw SQL string. + +
    +
    + Next +
    +
    eICU-CRD tutorial
    +
    + +     + + +
    +
    + Previous +
    + +
    MIMIC-III tutorial
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo +
    -
    +
    - - - + + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index 5eee7b1..dba14e0 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -13,7 +13,7 @@ "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", @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:06:43.096855Z", - "iopub.status.busy": "2024-03-08T15:06:43.096201Z", - "iopub.status.idle": "2024-03-08T15:06:49.354693Z", - "shell.execute_reply": "2024-03-08T15:06:49.353077Z" + "iopub.execute_input": "2024-04-17T19:14:01.103971Z", + "iopub.status.busy": "2024-04-17T19:14:01.103037Z", + "iopub.status.idle": "2024-04-17T19:14:05.051667Z", + "shell.execute_reply": "2024-04-17T19:14:05.051032Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:46,575 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-17 15:14:03,964 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -105,10 +105,10 @@ "id": "cdfadaa4-6fd6-4fd7-85cf-e012aa0799e1", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:06:49.360825Z", - "iopub.status.busy": "2024-03-08T15:06:49.360137Z", - "iopub.status.idle": "2024-03-08T15:06:49.692748Z", - "shell.execute_reply": "2024-03-08T15:06:49.691723Z" + "iopub.execute_input": "2024-04-17T19:14:05.056775Z", + "iopub.status.busy": "2024-04-17T19:14:05.056501Z", + "iopub.status.idle": "2024-04-17T19:14:05.270542Z", + "shell.execute_reply": "2024-04-17T19:14:05.269320Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:49,687 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:14:05,263 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:49,688 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.307097 s\n" + "2024-04-17 15:14:05,265 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.195802 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:06:49.697449Z", - "iopub.status.busy": "2024-03-08T15:06:49.697069Z", - "iopub.status.idle": "2024-03-08T15:06:50.606949Z", - "shell.execute_reply": "2024-03-08T15:06:50.605802Z" + "iopub.execute_input": "2024-04-17T19:14:05.275944Z", + "iopub.status.busy": "2024-04-17T19:14:05.275527Z", + "iopub.status.idle": "2024-04-17T19:14:05.984878Z", + "shell.execute_reply": "2024-04-17T19:14:05.983619Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:50,600 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:14:05,977 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:50,601 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.874461 s\n" + "2024-04-17 15:14:05,979 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.674020 s\n" ] }, { @@ -216,7 +216,7 @@ "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." ] }, { @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:06:50.612539Z", - "iopub.status.busy": "2024-03-08T15:06:50.612008Z", - "iopub.status.idle": "2024-03-08T15:06:52.140537Z", - "shell.execute_reply": "2024-03-08T15:06:52.138848Z" + "iopub.execute_input": "2024-04-17T19:14:05.990878Z", + "iopub.status.busy": "2024-04-17T19:14:05.990231Z", + "iopub.status.idle": "2024-04-17T19:14:07.495479Z", + "shell.execute_reply": "2024-04-17T19:14:07.494735Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:52,133 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:14:07,490 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:06:52,134 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.491402 s\n" + "2024-04-17 15:14:07,491 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.468321 s\n" ] }, { @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:06:52.147292Z", - "iopub.status.busy": "2024-03-08T15:06:52.146802Z", - "iopub.status.idle": "2024-03-08T15:08:14.535902Z", - "shell.execute_reply": "2024-03-08T15:08:14.534822Z" + "iopub.execute_input": "2024-04-17T19:14:07.501898Z", + "iopub.status.busy": "2024-04-17T19:14:07.501542Z", + "iopub.status.idle": "2024-04-17T19:15:30.606475Z", + "shell.execute_reply": "2024-04-17T19:15:30.605389Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:08:14,529 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:15:30,600 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:08:14,530 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 82.349428 s\n" + "2024-04-17 15:15:30,601 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 83.074736 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:08:14.541464Z", - "iopub.status.busy": "2024-03-08T15:08:14.541064Z", - "iopub.status.idle": "2024-03-08T15:09:25.683755Z", - "shell.execute_reply": "2024-03-08T15:09:25.682695Z" + "iopub.execute_input": "2024-04-17T19:15:30.610308Z", + "iopub.status.busy": "2024-04-17T19:15:30.609839Z", + "iopub.status.idle": "2024-04-17T19:16:41.512935Z", + "shell.execute_reply": "2024-04-17T19:16:41.512177Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:25,677 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:41,506 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:25,678 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 71.109498 s\n" + "2024-04-17 15:16:41,508 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 70.871534 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:25.687388Z", - "iopub.status.busy": "2024-03-08T15:09:25.687113Z", - "iopub.status.idle": "2024-03-08T15:09:33.644388Z", - "shell.execute_reply": "2024-03-08T15:09:33.643602Z" + "iopub.execute_input": "2024-04-17T19:16:41.519081Z", + "iopub.status.busy": "2024-04-17T19:16:41.518622Z", + "iopub.status.idle": "2024-04-17T19:16:49.517389Z", + "shell.execute_reply": "2024-04-17T19:16:49.516562Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:33,639 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:49,512 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:33,640 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.937612 s\n" + "2024-04-17 15:16:49,513 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 7.972264 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:33.647545Z", - "iopub.status.busy": "2024-03-08T15:09:33.647164Z", - "iopub.status.idle": "2024-03-08T15:09:34.244879Z", - "shell.execute_reply": "2024-03-08T15:09:34.244087Z" + "iopub.execute_input": "2024-04-17T19:16:49.522046Z", + "iopub.status.busy": "2024-04-17T19:16:49.521507Z", + "iopub.status.idle": "2024-04-17T19:16:50.171152Z", + "shell.execute_reply": "2024-04-17T19:16:50.170446Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:33,979 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:49,909 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:33,981 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.304018 s\n" + "2024-04-17 15:16:49,910 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.354782 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:34.250264Z", - "iopub.status.busy": "2024-03-08T15:09:34.249882Z", - "iopub.status.idle": "2024-03-08T15:09:34.262831Z", - "shell.execute_reply": "2024-03-08T15:09:34.261806Z" + "iopub.execute_input": "2024-04-17T19:16:50.175372Z", + "iopub.status.busy": "2024-04-17T19:16:50.175089Z", + "iopub.status.idle": "2024-04-17T19:16:50.188896Z", + "shell.execute_reply": "2024-04-17T19:16:50.187288Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:34,257 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:50,182 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:34,258 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.007239 s\n" + "2024-04-17 15:16:50,183 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.006886 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index 8ebfc63..2c6fee0 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -1,190 +1,302 @@ + + + + + + + + + OMOP tutorial - cycquery documentation + + + + + + + - - - - - - - - - - - OMOP tutorial — cyclops-query documentation - - - - + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
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    +
    cycquery documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    -

    OMOP tutorial

    -

    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).

    +

    OMOP tutorial

    +

    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).

    We showcase the examples on:

    1. Synthea in OMOP format.

      @@ -454,7 +566,7 @@

      OMOP tutorial -

      Imports and instantiate OMOPQuerier.

      +

      Imports and instantiate OMOPQuerier.

      Pass in the schema_name which is the name of the postgres schema which houses all the OMOP tables.

      [1]:
@@ -487,7 +599,7 @@ 
      Imports and instantiate 
 
      
 
      -2024-03-08 10:09:38,117 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-17 15:16:54,201 INFO cycquery.orm    - Database setup, ready to run queries!
      @@ -544,7 +656,7 @@

      Imports and instantiate

    -

    Example 1. Get all patient visits in or after 2010.

    +

    Example 1. Get all patient visits in or after 2010.

    [2]:
    @@ -562,7 +674,7 @@

    Example 1. Get all patient visits in or after 2010. 
    -2024-03-08 10:09:38,772 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:55,699 INFO cycquery.orm    - Query returned successfully!

    @@ -570,7 +682,7 @@

    Example 1. Get all patient visits in or after 2010. 
    -2024-03-08 10:09:38,774 INFO cycquery.utils.profile - Finished executing function run_query in 0.052621 s
+2024-04-17 15:16:55,701 INFO cycquery.utils.profile - Finished executing function run_query in 0.061462 s

    @@ -607,7 +719,7 @@

    Example 1. Get all patient visits in or after 2010.

    -

    Example 2. Get measurements for all visits in or after 2020.

    +

    Example 2. Get measurements for all visits in or after 2020.

    [3]:
    @@ -628,7 +740,7 @@

    Example 2. Get measurements for all visits in or after 2020. 
    -2024-03-08 10:09:38,898 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:16:55,828 INFO cycquery.orm    - Query returned successfully!

    @@ -636,7 +748,7 @@

    Example 2. Get measurements for all visits in or after 2020. 
    -2024-03-08 10:09:38,899 INFO cycquery.utils.profile - Finished executing function run_query in 0.059497 s
+2024-04-17 15:16:55,829 INFO cycquery.utils.profile - Finished executing function run_query in 0.058665 s

    @@ -657,7 +769,7 @@

    Example 2. Get measurements for all visits in or after 2020. -

    Imports and instantiate OMOPQuerier.

    +

    Imports and instantiate OMOPQuerier.

    Pass in the schema_name which is the name of the postgres schema which houses all the OMOP tables.

    [4]:
@@ -682,7 +794,7 @@ 
    Imports and instantiate 
 
    
 
    -2024-03-08 10:09:42,134 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-17 15:16:58,478 INFO cycquery.orm    - Database setup, ready to run queries!
    @@ -696,7 +808,7 @@

    Imports and instantiate
    -

    Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.

    +

    Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.

    [5]:
    @@ -722,7 +834,7 @@

    Example 1. Get all patient visits that ended in a mortality outcome in or af 

    -2024-03-08 10:09:48,662 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:17:05,260 INFO cycquery.orm    - Query returned successfully!
    @@ -730,7 +842,7 @@

    Example 1. Get all patient visits that ended in a mortality outcome in or af 

    -2024-03-08 10:09:48,663 INFO cycquery.utils.profile - Finished executing function run_query in 0.930822 s
+2024-04-17 15:17:05,261 INFO cycquery.utils.profile - Finished executing function run_query in 0.978384 s

    @@ -743,7 +855,7 @@

    Example 1. Get all patient visits that ended in a mortality outcome in or af

    -

    Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.

    +

    Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.

    [6]:
    @@ -786,7 +898,7 @@

    Example 2. Get all measurements for female patient visits with 
    -2024-03-08 10:10:04,641 INFO cycquery.orm    - Query returned successfully!
+2024-04-17 15:17:21,347 INFO cycquery.orm    - Query returned successfully!

    @@ -794,7 +906,7 @@

    Example 2. Get all measurements for female patient visits with 
    -2024-03-08 10:10:04,642 INFO cycquery.utils.profile - Finished executing function run_query in 15.905970 s
+2024-04-17 15:17:21,348 INFO cycquery.utils.profile - Finished executing function run_query in 16.013580 s

    @@ -828,66 +940,96 @@

    Example 2. Get all measurements for female patient visits with + +
    +
    + Next +
    +
    GEMINI tutorial
    +
    + +     + + +
    +
    + Previous +
    + +
    eICU-CRD tutorial
    + +
    +     +

    +
    +
    +
    + Copyright © 2024, Vector AI Engineering +
    + Made with Sphinx and @pradyunsg's + + Furo +
    -
    +
    - - - +
    + + + + + + + + + + + \ No newline at end of file diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb index b8131ec..a0239b4 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -13,7 +13,7 @@ "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", @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:36.551881Z", - "iopub.status.busy": "2024-03-08T15:09:36.551235Z", - "iopub.status.idle": "2024-03-08T15:09:38.704205Z", - "shell.execute_reply": "2024-03-08T15:09:38.702703Z" + "iopub.execute_input": "2024-04-17T19:16:52.372473Z", + "iopub.status.busy": "2024-04-17T19:16:52.371960Z", + "iopub.status.idle": "2024-04-17T19:16:55.606910Z", + "shell.execute_reply": "2024-04-17T19:16:55.605253Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:38,117 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-17 15:16:54,201 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -151,10 +151,10 @@ "id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:38.709726Z", - "iopub.status.busy": "2024-03-08T15:09:38.709261Z", - "iopub.status.idle": "2024-03-08T15:09:38.794240Z", - "shell.execute_reply": "2024-03-08T15:09:38.792994Z" + "iopub.execute_input": "2024-04-17T19:16:55.613864Z", + "iopub.status.busy": "2024-04-17T19:16:55.613175Z", + "iopub.status.idle": "2024-04-17T19:16:55.720733Z", + "shell.execute_reply": "2024-04-17T19:16:55.719346Z" } }, "outputs": [ @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:38,772 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:55,699 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:38,774 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.052621 s\n" + "2024-04-17 15:16:55,701 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.061462 s\n" ] }, { @@ -227,10 +227,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:38.799732Z", - "iopub.status.busy": "2024-03-08T15:09:38.799367Z", - "iopub.status.idle": "2024-03-08T15:09:38.905025Z", - "shell.execute_reply": "2024-03-08T15:09:38.903822Z" + "iopub.execute_input": "2024-04-17T19:16:55.727323Z", + "iopub.status.busy": "2024-04-17T19:16:55.726777Z", + "iopub.status.idle": "2024-04-17T19:16:55.833883Z", + "shell.execute_reply": "2024-04-17T19:16:55.832847Z" } }, "outputs": [ @@ -238,14 +238,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:38,898 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:16:55,828 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:38,899 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.059497 s\n" + "2024-04-17 15:16:55,829 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.058665 s\n" ] }, { @@ -303,10 +303,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:38.911289Z", - "iopub.status.busy": "2024-03-08T15:09:38.910855Z", - "iopub.status.idle": "2024-03-08T15:09:47.708515Z", - "shell.execute_reply": "2024-03-08T15:09:47.707840Z" + "iopub.execute_input": "2024-04-17T19:16:55.840051Z", + "iopub.status.busy": "2024-04-17T19:16:55.839627Z", + "iopub.status.idle": "2024-04-17T19:17:04.240624Z", + "shell.execute_reply": "2024-04-17T19:17:04.238675Z" }, "tags": [] }, @@ -315,7 +315,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:42,134 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-17 15:16:58,478 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -357,10 +357,10 @@ "id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:47.713562Z", - "iopub.status.busy": "2024-03-08T15:09:47.713359Z", - "iopub.status.idle": "2024-03-08T15:09:48.666856Z", - "shell.execute_reply": "2024-03-08T15:09:48.666244Z" + "iopub.execute_input": "2024-04-17T19:17:04.248067Z", + "iopub.status.busy": "2024-04-17T19:17:04.247444Z", + "iopub.status.idle": "2024-04-17T19:17:05.265514Z", + "shell.execute_reply": "2024-04-17T19:17:05.264715Z" }, "tags": [] }, @@ -369,14 +369,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:48,662 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:17:05,260 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:09:48,663 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.930822 s\n" + "2024-04-17 15:17:05,261 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.978384 s\n" ] }, { @@ -419,10 +419,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:09:48.673731Z", - "iopub.status.busy": "2024-03-08T15:09:48.673379Z", - "iopub.status.idle": "2024-03-08T15:10:04.647600Z", - "shell.execute_reply": "2024-03-08T15:10:04.646443Z" + "iopub.execute_input": "2024-04-17T19:17:05.271669Z", + "iopub.status.busy": "2024-04-17T19:17:05.271286Z", + "iopub.status.idle": "2024-04-17T19:17:21.352068Z", + "shell.execute_reply": "2024-04-17T19:17:21.351401Z" }, "tags": [] }, @@ -431,14 +431,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:10:04,641 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-17 15:17:21,347 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-03-08 10:10:04,642 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 15.905970 s\n" + "2024-04-17 15:17:21,348 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 16.013580 s\n" ] }, { @@ -488,10 +488,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2024-03-08T15:10:04.653090Z", - "iopub.status.busy": "2024-03-08T15:10:04.652548Z", - "iopub.status.idle": "2024-03-08T15:10:04.663848Z", - "shell.execute_reply": "2024-03-08T15:10:04.662593Z" + "iopub.execute_input": "2024-04-17T19:17:21.355875Z", + "iopub.status.busy": "2024-04-17T19:17:21.355544Z", + "iopub.status.idle": "2024-04-17T19:17:21.364321Z", + "shell.execute_reply": "2024-04-17T19:17:21.363213Z" }, "tags": [] },

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