From a56dab997dbc1d768542afa04689e99c5ba3de3a Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Mon, 10 Mar 2025 09:10:33 +0000
Subject: [PATCH] (docs) tried sphix but compelx and not automatied. We have
option of pdoc for html or basic markdown using pydoc-markdown, which is
likely sufficient for now. Closes #12
---
docs/api/acmc.md | 35 -----------------------------------
docs/api/acmc/parse.html | 2 +-
docs/api/acmc/phen.html | 2 +-
docs/api/search.js | 2 +-
docs/index.md | 2 +-
pyproject.toml | 12 ++++++------
6 files changed, 10 insertions(+), 45 deletions(-)
delete mode 100644 docs/api/acmc.md
diff --git a/docs/api/acmc.md b/docs/api/acmc.md
deleted file mode 100644
index 9d47c14..0000000
--- a/docs/api/acmc.md
+++ /dev/null
@@ -1,35 +0,0 @@
-
-
-<div>
-
-## Submodules
-
-- [logging_config](acmc/logging_config.html)
-- [main](acmc/main.html)
-- [omop](acmc/omop.html)
-- [parse](acmc/parse.html)
-- [phen](acmc/phen.html)
-- [trud](acmc/trud.html)
-- [util](acmc/util.html)
-
-## API Documentation
-
-[built with [pdoc]{.visually-hidden}](https://pdoc.dev "pdoc: Python API documentation generator"){.attribution
-target="_blank"}
-
-</div>
-
-::: {.pdoc role="main"}
-::: {.section .module-info}
-# acmc {#acmc .modulename}
-
-View Source
-
-::: {.pdoc-code .codehilite}
- 1from importlib.metadata import version
- 2
- 3__version__ = version("acmc")
-:::
-:::
-:::
diff --git a/docs/api/acmc/parse.html b/docs/api/acmc/parse.html
index e393867..791d600 100644
--- a/docs/api/acmc/parse.html
+++ b/docs/api/acmc/parse.html
@@ -773,7 +773,7 @@
<section id="SUPPORTED_CODE_TYPES">
<div class="attr variable">
<span class="name">SUPPORTED_CODE_TYPES</span> =
-<span class="default_value">{'icd10', 'atc', 'read2', 'snomed', 'opcs4', 'read3'}</span>
+<span class="default_value">{'read2', 'opcs4', 'snomed', 'icd10', 'read3', 'atc'}</span>
</div>
diff --git a/docs/api/acmc/phen.html b/docs/api/acmc/phen.html
index c245485..fe5aeb3 100644
--- a/docs/api/acmc/phen.html
+++ b/docs/api/acmc/phen.html
@@ -1910,7 +1910,7 @@
<div class="attr variable">
<span class="name">CONFIG_SCHEMA</span> =
<input id="CONFIG_SCHEMA-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
- <label class="view-value-button pdoc-button" for="CONFIG_SCHEMA-view-value"></label><span class="default_value">{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\d+\\.\\d+\\.\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['icd10', 'atc', 'read2', 'snomed', 'opcs4', 'read3']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}</span>
+ <label class="view-value-button pdoc-button" for="CONFIG_SCHEMA-view-value"></label><span class="default_value">{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\d+\\.\\d+\\.\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['read2', 'opcs4', 'snomed', 'icd10', 'read3', 'atc']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}</span>
</div>
diff --git a/docs/api/search.js b/docs/api/search.js
index 07ea900..22510e2 100644
--- a/docs/api/search.js
+++ b/docs/api/search.js
@@ -1,6 +1,6 @@
window.pdocSearch = (function(){
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this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e<arguments.length;e++)t=arguments[e],~this.indexOf(t)||this.elements.splice(this.locationFor(t),0,t);this.length=this.elements.length},lunr.SortedSet.prototype.toArray=function(){return this.elements.slice()},lunr.SortedSet.prototype.map=function(e,t){return this.elements.map(e,t)},lunr.SortedSet.prototype.forEach=function(e,t){return this.elements.forEach(e,t)},lunr.SortedSet.prototype.indexOf=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var 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- /** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "annotation", "default_value", "signature", "bases", "doc"], "ref": "fullname", "documentStore": {"docs": {"acmc": {"fullname": "acmc", "modulename": "acmc", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config": {"fullname": "acmc.logging_config", "modulename": "acmc.logging_config", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config.DEFAULT_LOG_FILE": {"fullname": "acmc.logging_config.DEFAULT_LOG_FILE", "modulename": "acmc.logging_config", "qualname": "DEFAULT_LOG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'acmc.log'"}, "acmc.logging_config.setup_logger": {"fullname": "acmc.logging_config.setup_logger", "modulename": "acmc.logging_config", "qualname": "setup_logger", "kind": "function", "doc": "<p>Sets up logger as a singleton outputing to file and sysout syserr</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span 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acmc_logger (INFO)>"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace')"}, "acmc.main.trud_install": {"fullname": "acmc.main.trud_install", "modulename": "acmc.main", "qualname": "trud_install", "kind": "function", "doc": "<p>Handle the <code>trud install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_install": {"fullname": "acmc.main.omop_install", "modulename": "acmc.main", "qualname": "omop_install", "kind": "function", "doc": "<p>Handle the <code>omop install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_clear": {"fullname": "acmc.main.omop_clear", "modulename": "acmc.main", "qualname": "omop_clear", "kind": "function", "doc": "<p>Handle the <code>omop clear</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_delete": {"fullname": "acmc.main.omop_delete", "modulename": "acmc.main", "qualname": "omop_delete", "kind": "function", "doc": "<p>Handle the <code>omop delete</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_init": {"fullname": "acmc.main.phen_init", "modulename": "acmc.main", "qualname": "phen_init", "kind": "function", "doc": "<p>Handle the <code>phen init</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_fork": {"fullname": "acmc.main.phen_fork", "modulename": "acmc.main", "qualname": "phen_fork", "kind": "function", "doc": "<p>Handle the <code>phen fork</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_validate": {"fullname": "acmc.main.phen_validate", "modulename": "acmc.main", "qualname": "phen_validate", "kind": "function", "doc": "<p>Handle the <code>phen validate</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_map": {"fullname": "acmc.main.phen_map", "modulename": "acmc.main", "qualname": "phen_map", "kind": "function", "doc": "<p>Handle the <code>phen map</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_export": {"fullname": "acmc.main.phen_export", "modulename": "acmc.main", "qualname": "phen_export", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_publish": {"fullname": "acmc.main.phen_publish", "modulename": "acmc.main", "qualname": "phen_publish", "kind": "function", "doc": "<p>Handle the <code>phen publish</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_copy": {"fullname": "acmc.main.phen_copy", "modulename": "acmc.main", "qualname": "phen_copy", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_diff": {"fullname": "acmc.main.phen_diff", "modulename": "acmc.main", "qualname": "phen_diff", "kind": "function", "doc": "<p>Handle the <code>phen diff</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<h1 id=\"omop-module\">OMOP Module</h1>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.logger": {"fullname": "acmc.omop.logger", "modulename": "acmc.omop", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop')"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p></p>\n", "default_value": "'54'"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54.sqlite'"}, "acmc.omop.DB_PATH": {"fullname": "acmc.omop.DB_PATH", "modulename": "acmc.omop", "qualname": "DB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_54.sqlite')"}, "acmc.omop.VERSION_FILE": {"fullname": "acmc.omop.VERSION_FILE", "modulename": "acmc.omop", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_version.yaml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yaml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'source': 'OHDSI Athena', 'url': 'https://athena.ohdsi.org/vocabulary/list', 'cdm_version': '54', 'version': '', 'vocabularies': [{'id': 1, 'name': 'SNOMED'}, {'id': 2, 'name': 'ICD9CM'}, {'id': 17, 'name': 'Readv2'}, {'id': 21, 'name': 'ATC'}, {'id': 55, 'name': 'OPCS4'}, {'id': 57, 'name': 'HES Specialty'}, {'id': 70, 'name': 'ICD10CM'}, {'id': 75, 'name': 'dm+d'}, {'id': 144, 'name': 'UK Biobank'}, {'id': 154, 'name': 'NHS Ethnic Category'}, {'id': 155, 'name': 'NHS Place of Service'}], 'tables': []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'read2': 'Read', 'read3': None, 'icd10': 'ICD10CM', 'snomed': 'SNOMED', 'opcs4': 'OPCS4', 'atc': 'ATC', 'med': None, 'cprd': None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>Installs the OMOP release csv files in a file-based sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p></p>\n"}, "acmc.parse.logger": {"fullname": "acmc.parse.logger", "modulename": "acmc.parse", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'icd10', 'atc', 'read2', 'snomed', 'opcs4', 'read3'}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[list], pandas.core.series.Series], typing.Callable[[list, pathlib.Path], NoneType]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10.trim_icd10": {"fullname": "acmc.parse.Icd10.trim_icd10", "modulename": "acmc.parse", "qualname": "Icd10.trim_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">'vocab/trud/processed'</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<h1 id=\"phenotype-module\">Phenotype Module</h1>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.logger": {"fullname": "acmc.phen.logger", "modulename": "acmc.phen", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'phen'"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace/phen')"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'map'"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concept-sets'"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/csv')"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/omop')"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p></p>\n", "default_value": "['concepts', 'map', 'concept-sets']"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'config.yaml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'vocab_version.yaml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['major', 'minor', 'patch']"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p></p>\n", "default_value": "'patch'"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p></p>\n", "default_value": "'main'"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'split_col'"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'codes_col'"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'divide_col'"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p></p>\n", "default_value": "['split_col', 'codes_col', 'divide_col']"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.SOURCE_COL_SUFFIX": {"fullname": "acmc.phen.SOURCE_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "SOURCE_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_source'"}, "acmc.phen.TARGET_COL_SUFFIX": {"fullname": "acmc.phen.TARGET_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "TARGET_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_target'"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['icd10', 'atc', 'read2', 'snomed', 'opcs4', 'read3']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.construct_git_url": {"fullname": "acmc.phen.construct_git_url", "modulename": "acmc.phen", "qualname": "construct_git_url", "kind": "function", "doc": "<p>Constructs a git url for github or gitlab including a PAT token environment variable</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.create_empty_git_dir": {"fullname": "acmc.phen.create_empty_git_dir", "modulename": "acmc.phen", "qualname": "create_empty_git_dir", "kind": "function", "doc": "<p>Creates a directory with a .gitkeep file so that it's tracked in git</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.check_delete_dir": {"fullname": "acmc.phen.check_delete_dir", "modulename": "acmc.phen", "qualname": "check_delete_dir", "kind": "function", "doc": "<p>Checks on the command line if a user wants to delete a directory</p>\n\n<p>Args:\n path (Path): path of the directory to be deleted\n msg (str): message to be displayed to the user</p>\n\n<p>Returns:\n Boolean: True if deleted</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<p>Args:\n phen_dir (str): local directory path where the upstream repo is to be cloned\n upstream_url (str): url to the upstream repo\n upstream_version (str): version in the upstream repo to clone\n new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>\n\n<p>Raises:\n ValueError: if the specified version is not in the upstream repo\n ValueError: if the upstream repo is not a valid phenotype repo\n ValueError: if there's any other problems with Git</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.read_table_file": {"fullname": "acmc.phen.read_table_file", "modulename": "acmc.phen", "qualname": "read_table_file", "kind": "function", "doc": "<p>Load Code List File</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">excel_sheet</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">''</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.process_actions": {"fullname": "acmc.phen.process_actions", "modulename": "acmc.phen", "qualname": "process_actions", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.preprocess_source_concepts": {"fullname": "acmc.phen.preprocess_source_concepts", "modulename": "acmc.phen", "qualname": "preprocess_source_concepts", "kind": "function", "doc": "<p>Parses each column individually - Order and length will not be preserved!</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">code_file_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.get_code_type_from_col_name": {"fullname": "acmc.phen.get_code_type_from_col_name", "modulename": "acmc.phen", "qualname": "get_code_type_from_col_name", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">col_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.sql_row_exist": {"fullname": "acmc.phen.sql_row_exist", "modulename": "acmc.phen", "qualname": "sql_row_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">conn</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Connection</span>, </span><span class=\"param\"><span class=\"n\">table</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">column</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">value</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_code_errors": {"fullname": "acmc.phen.write_code_errors", "modulename": "acmc.phen", "qualname": "write_code_errors", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">code_errors</span><span class=\"p\">:</span> <span class=\"nb\">list</span>, </span><span class=\"param\"><span class=\"n\">code_errors_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map_target_code_type": {"fullname": "acmc.phen.map_target_code_type", "modulename": "acmc.phen", "qualname": "map_target_code_type", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">phenotype</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.generate_version_tag": {"fullname": "acmc.phen.generate_version_tag", "modulename": "acmc.phen", "qualname": "generate_version_tag", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">repo</span><span class=\"p\">:</span> <span class=\"n\">git</span><span class=\"o\">.</span><span class=\"n\">repo</span><span class=\"o\">.</span><span class=\"n\">base</span><span class=\"o\">.</span><span class=\"n\">Repo</span>,</span><span class=\"param\">\t<span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span>,</span><span class=\"param\">\t<span class=\"n\">use_v_prefix</span><span class=\"p\">:</span> <span class=\"nb\">bool</span> <span class=\"o\">=</span> <span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.extract_clean_deepdiff_keys": {"fullname": "acmc.phen.extract_clean_deepdiff_keys", "modulename": "acmc.phen", "qualname": "extract_clean_deepdiff_keys", "kind": "function", "doc": "<p>Extracts clean keys from a DeepDiff dictionary.</p>\n\n<p>:param diff: DeepDiff result dictionary\n:param key_type: The type of change to extract (e.g., \"dictionary_item_added\", \"dictionary_item_removed\")\n:return: A set of clean key names</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">diff</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">key_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"n\">Any</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p></p>\n"}, "acmc.trud.logger": {"fullname": "acmc.trud.logger", "modulename": "acmc.trud", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p></p>\n", "default_value": "'isd.digital.nhs.uk'"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud')"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'trud_version.yaml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yaml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/downloads')"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/processed')"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">file_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p></p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 14}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 10}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.trud_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_clear": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_delete": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_init": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_fork": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_validate": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_map": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_export": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_publish": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_copy": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_diff": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 15}, "acmc.omop.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 14}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 11}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 3}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 66, "bases": 0, "doc": 3}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodesError.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 51, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 2, "doc": 17}, "acmc.parse.InvalidCodesException.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 9, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException.error": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 59}, "acmc.parse.Proto.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 44, "bases": 0, "doc": 3}, "acmc.parse.Proto.checks": {"qualname": 2, "fullname": 4, "annotation": 13, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.name": {"qualname": 2, "fullname": 4, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.raise_exception": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 36}, "acmc.parse.Proto.in_database": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 93, "bases": 0, "doc": 3}, "acmc.parse.Proto.process": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 85, "bases": 0, "doc": 14}, "acmc.parse.Proto.verify": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 52, "bases": 0, "doc": 7}, "acmc.parse.Read2": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 40}, "acmc.parse.Read2.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Read3": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Read3.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Icd10.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10.trim_icd10": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 49, "bases": 0, "doc": 3}, "acmc.parse.Snomed": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Snomed.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Opcs4": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Opcs4.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Atc": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Atc.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Med": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Med.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Cprd": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Cprd.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, 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{"acmc.parse.CodesError": {"tf": 1}, "acmc.parse.CodeTypeParser": {"tf": 1}}, "df": 2}}}}, "s": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "l": {"docs": {}, "df": 0, "v": {"docs": {}, "df": 0, "e": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}}, "df": 8, "d": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}}, "df": 1}}}}}, "u": {"docs": {}, "df": 0, "l": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}, "a": {"docs": {}, "df": 0, "d": {"2": {"docs": {"acmc.parse.Read2": {"tf": 1.4142135623730951}}, "df": 1}, "docs": {}, "df": 0}}, "t": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "n": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "s": {"docs": 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{}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}}, "b": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "d": {"docs": {"acmc.omop.install": {"tf": 1}, "acmc.parse.Read2": {"tf": 1}}, "df": 2}}}}, "e": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}, "acmc.phen.check_delete_dir": {"tf": 1.4142135623730951}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.preprocess_source_concepts": {"tf": 1}}, "df": 4, "c": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "e": {"docs": {"acmc.parse.Proto.raise_exception": {"tf": 1}}, "df": 1}}}}}, "t": {"docs": {}, "df": 0, "w": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.phen.diff_phen": {"tf": 1}}, "df": 1}}}}}}, "y": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}, "acmc.phen.publish": {"tf": 1}}, "df": 2}, "o": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "l": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "n": {"docs": {"acmc.phen.check_delete_dir": {"tf": 1}}, "df": 1}}}}}}}, "w": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {"acmc.omop.write_version_file": {"tf": 1}}, "df": 1}}}}}, "h": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}, "acmc.parse.Read2": {"tf": 1}, "acmc.phen.PhenValidationException": {"tf": 1}}, "df": 3}, "r": {"docs": {}, "df": 0, "e": {"docs": {"acmc.phen.fork": {"tf": 1}}, "df": 1}}}, "a": {"docs": {}, "df": 0, "t": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}}, "df": 8}}}, "i": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "h": {"docs": {"acmc.parse.Proto.process": {"tf": 1}, "acmc.phen.create_empty_git_dir": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.init": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 5}}, "l": {"docs": {}, "df": 0, "l": {"docs": {"acmc.phen.preprocess_source_concepts": {"tf": 1}}, "df": 1}}}, "a": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "s": {"docs": {"acmc.phen.check_delete_dir": {"tf": 1}}, "df": 1}}}}}, "e": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "r": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "r": {"docs": {"acmc.parse.CodesError": {"tf": 1}, "acmc.parse.CodeTypeParser": {"tf": 1}}, "df": 2, "s": {"docs": {"acmc.parse.Read2": {"tf": 1}, "acmc.phen.PhenValidationException": {"tf": 1}}, "df": 2}}}}}, "x": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "p": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "n": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}, "acmc.parse.Proto.raise_exception": {"tf": 1.4142135623730951}, "acmc.phen.PhenValidationException": {"tf": 1}}, "df": 3}}}}}}}, "p": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "s": {"docs": {"acmc.parse.Proto.raise_exception": {"tf": 1}}, "df": 1}}}}}}}}, "l": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "t": {"docs": {"acmc.parse.Proto.raise_exception": {"tf": 1}}, "df": 1}}}}, "o": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "s": {"docs": {"acmc.phen.export": {"tf": 1}}, "df": 1}}}}}, "t": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "d": {"docs": {}, "df": 0, "s": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}, "r": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "s": {"docs": {"acmc.phen.extract_concepts": {"tf": 1}, "acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 2}}}}}}}, "n": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}}}}}}}}, "a": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "h": {"docs": {"acmc.phen.preprocess_source_concepts": {"tf": 1}, "acmc.phen.translate_codes": {"tf": 1}}, "df": 2}}}}, "n": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "e": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}, "acmc.phen.extract_concepts": {"tf": 1.4142135623730951}}, "df": 9, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}, "o": {"docs": {}, "df": 0, "t": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Proto.raise_exception": {"tf": 1.7320508075688772}, "acmc.parse.Proto.process": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}, "acmc.phen.fork": {"tf": 1.4142135623730951}, "acmc.phen.preprocess_source_concepts": {"tf": 1}}, "df": 12}, "n": {"docs": {}, "df": 0, "e": {"docs": {"acmc.phen.fork": {"tf": 1}}, "df": 1}}}, "e": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "y": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}}}}, "w": {"docs": {"acmc.phen.fork": {"tf": 1.7320508075688772}}, "df": 1}}}, "g": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "i": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}, "acmc.phen.create_empty_git_dir": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.init": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 5, "h": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "l": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "p": {"docs": {"acmc.phen.create_empty_git_dir": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.trud.download_release_file": {"tf": 1}}, "df": 1}}}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "y": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1.4142135623730951}}, "df": 1, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true};
+ /** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "annotation", "default_value", "signature", "bases", "doc"], "ref": "fullname", "documentStore": {"docs": {"acmc": {"fullname": "acmc", "modulename": "acmc", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config": {"fullname": "acmc.logging_config", "modulename": "acmc.logging_config", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config.DEFAULT_LOG_FILE": {"fullname": "acmc.logging_config.DEFAULT_LOG_FILE", "modulename": "acmc.logging_config", "qualname": "DEFAULT_LOG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'acmc.log'"}, "acmc.logging_config.setup_logger": {"fullname": "acmc.logging_config.setup_logger", "modulename": "acmc.logging_config", "qualname": "setup_logger", "kind": "function", "doc": "<p>Sets up logger as a singleton outputing to file and sysout syserr</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span> <span class=\"o\">=</span> <span class=\"mi\">20</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.logging_config.set_log_level": {"fullname": "acmc.logging_config.set_log_level", "modulename": "acmc.logging_config", "qualname": "set_log_level", "kind": "function", "doc": "<p>Sets the log level for the acmc logger</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main": {"fullname": "acmc.main", "modulename": "acmc.main", "kind": "module", "doc": "<p></p>\n"}, "acmc.main.logger": {"fullname": "acmc.main.logger", "modulename": "acmc.main", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace')"}, "acmc.main.trud_install": {"fullname": "acmc.main.trud_install", "modulename": "acmc.main", "qualname": "trud_install", "kind": "function", "doc": "<p>Handle the <code>trud install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_install": {"fullname": "acmc.main.omop_install", "modulename": "acmc.main", "qualname": "omop_install", "kind": "function", "doc": "<p>Handle the <code>omop install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_clear": {"fullname": "acmc.main.omop_clear", "modulename": "acmc.main", "qualname": "omop_clear", "kind": "function", "doc": "<p>Handle the <code>omop clear</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_delete": {"fullname": "acmc.main.omop_delete", "modulename": "acmc.main", "qualname": "omop_delete", "kind": "function", "doc": "<p>Handle the <code>omop delete</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_init": {"fullname": "acmc.main.phen_init", "modulename": "acmc.main", "qualname": "phen_init", "kind": "function", "doc": "<p>Handle the <code>phen init</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_fork": {"fullname": "acmc.main.phen_fork", "modulename": "acmc.main", "qualname": "phen_fork", "kind": "function", "doc": "<p>Handle the <code>phen fork</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_validate": {"fullname": "acmc.main.phen_validate", "modulename": "acmc.main", "qualname": "phen_validate", "kind": "function", "doc": "<p>Handle the <code>phen validate</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_map": {"fullname": "acmc.main.phen_map", "modulename": "acmc.main", "qualname": "phen_map", "kind": "function", "doc": "<p>Handle the <code>phen map</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_export": {"fullname": "acmc.main.phen_export", "modulename": "acmc.main", "qualname": "phen_export", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_publish": {"fullname": "acmc.main.phen_publish", "modulename": "acmc.main", "qualname": "phen_publish", "kind": "function", "doc": "<p>Handle the <code>phen publish</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_copy": {"fullname": "acmc.main.phen_copy", "modulename": "acmc.main", "qualname": "phen_copy", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_diff": {"fullname": "acmc.main.phen_diff", "modulename": "acmc.main", "qualname": "phen_diff", "kind": "function", "doc": "<p>Handle the <code>phen diff</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<h1 id=\"omop-module\">OMOP Module</h1>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.logger": {"fullname": "acmc.omop.logger", "modulename": "acmc.omop", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop')"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p></p>\n", "default_value": "'54'"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54.sqlite'"}, "acmc.omop.DB_PATH": {"fullname": "acmc.omop.DB_PATH", "modulename": "acmc.omop", "qualname": "DB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_54.sqlite')"}, "acmc.omop.VERSION_FILE": {"fullname": "acmc.omop.VERSION_FILE", "modulename": "acmc.omop", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_version.yaml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yaml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'source': 'OHDSI Athena', 'url': 'https://athena.ohdsi.org/vocabulary/list', 'cdm_version': '54', 'version': '', 'vocabularies': [{'id': 1, 'name': 'SNOMED'}, {'id': 2, 'name': 'ICD9CM'}, {'id': 17, 'name': 'Readv2'}, {'id': 21, 'name': 'ATC'}, {'id': 55, 'name': 'OPCS4'}, {'id': 57, 'name': 'HES Specialty'}, {'id': 70, 'name': 'ICD10CM'}, {'id': 75, 'name': 'dm+d'}, {'id': 144, 'name': 'UK Biobank'}, {'id': 154, 'name': 'NHS Ethnic Category'}, {'id': 155, 'name': 'NHS Place of Service'}], 'tables': []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'read2': 'Read', 'read3': None, 'icd10': 'ICD10CM', 'snomed': 'SNOMED', 'opcs4': 'OPCS4', 'atc': 'ATC', 'med': None, 'cprd': None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>Installs the OMOP release csv files in a file-based sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p></p>\n"}, "acmc.parse.logger": {"fullname": "acmc.parse.logger", "modulename": "acmc.parse", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'read2', 'opcs4', 'snomed', 'icd10', 'read3', 'atc'}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[list], pandas.core.series.Series], typing.Callable[[list, pathlib.Path], NoneType]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10.trim_icd10": {"fullname": "acmc.parse.Icd10.trim_icd10", "modulename": "acmc.parse", "qualname": "Icd10.trim_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">'vocab/trud/processed'</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<h1 id=\"phenotype-module\">Phenotype Module</h1>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.logger": {"fullname": "acmc.phen.logger", "modulename": "acmc.phen", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'phen'"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace/phen')"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'map'"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concept-sets'"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/csv')"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/omop')"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p></p>\n", "default_value": "['concepts', 'map', 'concept-sets']"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'config.yaml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'vocab_version.yaml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['major', 'minor', 'patch']"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p></p>\n", "default_value": "'patch'"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p></p>\n", "default_value": "'main'"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'split_col'"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'codes_col'"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'divide_col'"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p></p>\n", "default_value": "['split_col', 'codes_col', 'divide_col']"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.SOURCE_COL_SUFFIX": {"fullname": "acmc.phen.SOURCE_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "SOURCE_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_source'"}, "acmc.phen.TARGET_COL_SUFFIX": {"fullname": "acmc.phen.TARGET_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "TARGET_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_target'"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['read2', 'opcs4', 'snomed', 'icd10', 'read3', 'atc']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.construct_git_url": {"fullname": "acmc.phen.construct_git_url", "modulename": "acmc.phen", "qualname": "construct_git_url", "kind": "function", "doc": "<p>Constructs a git url for github or gitlab including a PAT token environment variable</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.create_empty_git_dir": {"fullname": "acmc.phen.create_empty_git_dir", "modulename": "acmc.phen", "qualname": "create_empty_git_dir", "kind": "function", "doc": "<p>Creates a directory with a .gitkeep file so that it's tracked in git</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.check_delete_dir": {"fullname": "acmc.phen.check_delete_dir", "modulename": "acmc.phen", "qualname": "check_delete_dir", "kind": "function", "doc": "<p>Checks on the command line if a user wants to delete a directory</p>\n\n<p>Args:\n path (Path): path of the directory to be deleted\n msg (str): message to be displayed to the user</p>\n\n<p>Returns:\n Boolean: True if deleted</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<p>Args:\n phen_dir (str): local directory path where the upstream repo is to be cloned\n upstream_url (str): url to the upstream repo\n upstream_version (str): version in the upstream repo to clone\n new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>\n\n<p>Raises:\n ValueError: if the specified version is not in the upstream repo\n ValueError: if the upstream repo is not a valid phenotype repo\n ValueError: if there's any other problems with Git</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.read_table_file": {"fullname": "acmc.phen.read_table_file", "modulename": "acmc.phen", "qualname": "read_table_file", "kind": "function", "doc": "<p>Load Code List File</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">excel_sheet</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">''</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.process_actions": {"fullname": "acmc.phen.process_actions", "modulename": "acmc.phen", "qualname": "process_actions", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.preprocess_source_concepts": {"fullname": "acmc.phen.preprocess_source_concepts", "modulename": "acmc.phen", "qualname": "preprocess_source_concepts", "kind": "function", "doc": "<p>Parses each column individually - Order and length will not be preserved!</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">code_file_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.get_code_type_from_col_name": {"fullname": "acmc.phen.get_code_type_from_col_name", "modulename": "acmc.phen", "qualname": "get_code_type_from_col_name", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">col_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.sql_row_exist": {"fullname": "acmc.phen.sql_row_exist", "modulename": "acmc.phen", "qualname": "sql_row_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">conn</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Connection</span>, </span><span class=\"param\"><span class=\"n\">table</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">column</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">value</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_code_errors": {"fullname": "acmc.phen.write_code_errors", "modulename": "acmc.phen", "qualname": "write_code_errors", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">code_errors</span><span class=\"p\">:</span> <span class=\"nb\">list</span>, </span><span class=\"param\"><span class=\"n\">code_errors_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map_target_code_type": {"fullname": "acmc.phen.map_target_code_type", "modulename": "acmc.phen", "qualname": "map_target_code_type", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">phenotype</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.generate_version_tag": {"fullname": "acmc.phen.generate_version_tag", "modulename": "acmc.phen", "qualname": "generate_version_tag", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">repo</span><span class=\"p\">:</span> <span class=\"n\">git</span><span class=\"o\">.</span><span class=\"n\">repo</span><span class=\"o\">.</span><span class=\"n\">base</span><span class=\"o\">.</span><span class=\"n\">Repo</span>,</span><span class=\"param\">\t<span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span>,</span><span class=\"param\">\t<span class=\"n\">use_v_prefix</span><span class=\"p\">:</span> <span class=\"nb\">bool</span> <span class=\"o\">=</span> <span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.extract_clean_deepdiff_keys": {"fullname": "acmc.phen.extract_clean_deepdiff_keys", "modulename": "acmc.phen", "qualname": "extract_clean_deepdiff_keys", "kind": "function", "doc": "<p>Extracts clean keys from a DeepDiff dictionary.</p>\n\n<p>:param diff: DeepDiff result dictionary\n:param key_type: The type of change to extract (e.g., \"dictionary_item_added\", \"dictionary_item_removed\")\n:return: A set of clean key names</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">diff</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">key_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"n\">Any</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p></p>\n"}, "acmc.trud.logger": {"fullname": "acmc.trud.logger", "modulename": "acmc.trud", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p></p>\n", "default_value": "'isd.digital.nhs.uk'"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud')"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'trud_version.yaml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yaml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/downloads')"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/processed')"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">file_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p></p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 14}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 10}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.trud_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_clear": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_delete": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_init": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_fork": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_validate": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_map": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_export": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_publish": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_copy": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_diff": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 15}, "acmc.omop.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, 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"df": 0, "p": {"docs": {"acmc.phen.create_empty_git_dir": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.trud.download_release_file": {"tf": 1}}, "df": 1}}}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "y": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1.4142135623730951}}, "df": 1, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true};
// mirrored in build-search-index.js (part 1)
// Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/docs/index.md b/docs/index.md
index 0a6d9d8..ef5cc82 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,7 +9,7 @@
- [Example 1 - Basic local phenotype](./tutorials/example1.md)
- [Example 2 - More complex local phenotype](./tutorials/example2.md)
- [Example 3 - Using a remote git repository](./tutorials/example3.md)
- - [API Reference](./api/acmc.html)
+ - [API Reference](./api.md)
- [Change Log](./changelog.md)
- [Troubleshooting](./troubleshooting.md)
diff --git a/pyproject.toml b/pyproject.toml
index 5406de1..8132caa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,18 +70,18 @@ dependencies = [
"black",
"mypy",
"pdoc",
- "pandoc",
"pydoc-markdown",
- "mkdocs",
- "mkdocstrings",
- "mkdocstrings[python]",
+ "sphinx",
+ "sphinx-rtd-theme",
+ "myst-parser",
+ "sphinx-markdown-builder",
]
[tool.hatch.envs.dev.scripts]
format = "black ."
type = "mypy ."
-docs = "pdoc -o docs/api -d markdown --docformat markdown --include-undocumented acmc"
-pydocs = "pydoc-markdown > docs/api.md"
+docs = "pydoc-markdown > docs/api.md"
+htmldocs = "pdoc -o docs/api -d markdown --docformat markdown --include-undocumented acmc"
precommit = "hatch format && type mypy && hatch docs"
[tool.hatch.build]
--
GitLab