First commit

parents
Pipeline #47330521 failed with stages
in 1 minute and 33 seconds
[distutils]
index-servers=pypi
[pypi]
repository = https://upload.pypi.org/legacy/
username =rickardhultgren
Copyright 2019 Rickard Verner Hultgren
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
An interpreter for the language lympha
This diff is collapsed.
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M [email protected] "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 9052ab3327789825ea39fc4190a4226c
tags: 645f666f9bcd5a90fca523b33c5a78b7
Installation
============
This is the documentation of the lympha-interpreter written in python. You can find documentation for the language itself on:
`http://lympha.readthedocs.io <http://lympha.readthedocs.io/>`_
There are to ways to install the interpreter:
- download it from
`https://gitlab.com/rickardhultgren/lympha/blob/master/ <https://gitlab.com/rickardhultgren/lympha/blob/master/>`_
- or run
.. code-block:: none
pip install lympha
For graphical rendering Graphviz is required:
`https://www.graphviz.org/ <https://www.graphviz.org/>`_
Manual
======
Depending on if you only download the interpreter, or if you install it on the entire system through e.g. ``pip`` you will call the programme by either ``./lympha`` or ``lympha``.
prompt syntax
-------------
.. code-block:: bash
lympha -f <FILE NAME.lympha> -start <START STATEMENT> -steps <INTEGER> -graph -exe
.. csv-table:: "Arguments"
:widths: 5, 20
:header: "Argument", "Description"
"``-f``", "In the current version of the interpreter, only one file is read, and must hance contain both the algorithm and the patient data."
"``-start``", "The name of the statement that should be considered as the first."
"``-steps``", "The number of steps (``->``) begginning from 1."
"``-graph``", "Graphical representation of statements, where statements with the value of 1 are yellow."
"``-exe``", "For each statement with the value of 1, a prompt call with the same name as the statment is made."
Syntax
======
Clinical work flow
------------------
The clinical workflow is a series of events. In lympha this is formulated as statements divided by ``->``. A series of statements ends with semicolon as follows:
.. code-block:: none
statement -> statement -> statement ;
The name of the statement consists of one word, made of letters a-z, A-Z, digits 0-9, full stop (``.``), question mark, hyphen (``-``) and underscore (``_``).
Some events are procedures that should be executed. In lympha, these events are called *procedures*. Some events do not directly involve the patient, but data derived from diagnostics. Those events are called *factors*. Hence there are two types of statements in lympha: procedures and factors.
Differences between procedrues and factors
------------------------------------------
The name of a procedure always ends with a full stop (``.``) meanwhile, factors always end with a question mark (``?``).
Depending on if a procedure should be executed or not, it has a *value* of ``1`` or ``0``. By default, all procedures have the value set to ``1``.
The value of a factor can be declared in three ways:
- Make it equal to a real number (ℝ). Example:
.. code-block:: none
body_temperature_in_C? = 35.8 ;
- The value of the factor can also be dependent upon other factors. These dependent factors are called *binary factors*. The binary factor name in question is followed by one equal sign (``=``). Then follows a tipping point. After that, there is an operator. Below are valid operators listed:
.. csv-table:: Valid rational operators
:widths: 15, 10
:header: "relational operator", "read as"
"``==``", "if and only if (≡)"
"``>``", "greater than"
"``>=``", "greater than or equal (≥)"
"``<``", "lesser than"
"``<=``", "less than or equal (≤)"
"``!=``", "not equal to (≠)"
After the operator follows either the name of a non-binary factor or a series of binary factors.
* In the case where the binary factor depends on a non-binary factor:
.. code-block:: none
binary-factor = tipping-point operator non-binary-factor ;
Example:
.. code-block:: none
hypothermia? = 36 < body_temperature_in_C? ;
* In the case where the binary factor depends on a non-binary factor:
.. code-block:: none
binary-factor = tipping-point operator |{non-binary-factors}|
Example:
.. code-block:: none
resp? = 1 < |{tachypnea?, pCO2_blood_less4.3?}| ;
SIRS? = 2 =< |{ hypothermia?, temp_above_38?, HR_greater_90?, resp?, wbc_less4000?, wbc_greater12000? }| ;
.. toctree::
:caption: Table of Contents
:name: mastertoc
:hidden:
:maxdepth: 1
Installation<index>
manual
This diff is collapsed.
This diff is collapsed.
/* This file intentionally left blank. */
/*
* doctools.js
* ~~~~~~~~~~~
*
* Sphinx JavaScript utilities for all documentation.
*
* :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* make the code below compatible with browsers without
* an installed firebug like debugger
if (!window.console || !console.firebug) {
var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
"dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
"profile", "profileEnd"];
window.console = {};
for (var i = 0; i < names.length; ++i)
window.console[names[i]] = function() {};
}
*/
/**
* small helper function to urldecode strings
*/
jQuery.urldecode = function(x) {
return decodeURIComponent(x).replace(/\+/g, ' ');
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var bbox = span.getBBox();
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
var parentOfText = node.parentNode.parentNode;
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
/**
* Small JavaScript module for the documentation.
*/
var Documentation = {
init : function() {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
this.initOnKeyListeners();
}
},
/**
* i18n support
*/
TRANSLATIONS : {},
PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
if (typeof translated === 'undefined')
return string;
return (typeof translated === 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
if (typeof translated === 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
addTranslations : function(catalog) {
for (var key in catalog.messages)
this.TRANSLATIONS[key] = catalog.messages[key];
this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
this.LOCALE = catalog.locale;
},
/**
* add context elements like header anchor links
*/
addContextElements : function() {
$('div[id] > :header:first').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this headline')).
appendTo(this);
});
$('dt[id]').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this definition')).
appendTo(this);
});
},
/**
* workaround a firefox stupidity
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
if (document.location.hash && $.browser.mozilla)
window.setTimeout(function() {
document.location.href += '';
}, 10);
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords : function() {
var params = $.getQueryParameters();
var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
if (terms.length) {
var body = $('div.body');
if (!body.length) {
body = $('body');
}
window.setTimeout(function() {
$.each(terms, function() {
body.highlightText(this.toLowerCase(), 'highlighted');
});
}, 10);
$('<p class="highlight-link"><a href="javascript:Documentation.' +
'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
.appendTo($('#searchbox'));
}
},
/**
* init the domain index toggle buttons
*/
initIndexTable : function() {
var togglers = $('img.toggler').click(function() {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
if (src.substr(-9) === 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
}).css('display', '');
if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
togglers.click();
}
},
/**
* helper function to hide the search marks again
*/
hideSearchWords : function() {
$('#searchbox .highlight-link').fadeOut(300);
$('span.highlighted').removeClass('highlighted');
},
/**
* make the url absolute
*/
makeURL : function(relativeURL) {
return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
},
/**
* get the current relative url
*/
getCurrentURL : function() {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
if (this === '..')
parts.pop();
});
var url = parts.join('/');
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
},
initOnKeyListeners: function() {
$(document).keyup(function(event) {
var activeElementType = document.activeElement.tagName;
// don't navigate when in search box or textarea
if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
switch (event.keyCode) {
case 37: // left
var prevHref = $('link[rel="prev"]').prop('href');
if (prevHref) {
window.location.href = prevHref;
return false;
}
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
}
}
});
}
};
// quick alias for translations
_ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
});
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: 'lympha-interpreter',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false,
};
\ No newline at end of file
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #8f5902; font-style: italic } /* Comment */
.highlight .err { color: #a40000; border: 1px solid #ef2929 } /* Error */
.highlight .g { color: #000000 } /* Generic */
.highlight .k { color: #004461; font-weight: bold } /* Keyword */
.highlight .l { color: #000000 } /* Literal */
.highlight .n { color: #000000 } /* Name */
.highlight .o { color: #582800 } /* Operator */
.highlight .x { color: #000000 } /* Other */
.highlight .p { color: #000000; font-weight: bold } /* Punctuation */
.highlight .ch { color: #8f5902; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #8f5902; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #8f5902 } /* Comment.Preproc */
.highlight .cpf { color: #8f5902; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #8f5902; font-style: italic } /* Comment.Single */
.highlight .cs { color: #8f5902; font-style: italic } /* Comment.Special */
.highlight .gd { color: #a40000 } /* Generic.Deleted */
.highlight .ge { color: #000000; font-style: italic } /* Generic.Emph */
.highlight .gr { color: #ef2929 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #745334 } /* Generic.Prompt */
.highlight .gs { color: #000000; font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #a40000; font-weight: bold } /* Generic.Traceback */
.highlight .kc { color: #004461; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #004461; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #004461; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #004461; font-weight: bold } /* Keyword.Pseudo */
.highlight .kr { color: #004461; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #004461; font-weight: bold } /* Keyword.Type */
.highlight .ld { color: #000000 } /* Literal.Date */
.highlight .m { color: #990000 } /* Literal.Number */
.highlight .s { color: #4e9a06 } /* Literal.String */
.highlight .na { color: #c4a000 } /* Name.Attribute */
.highlight .nb { color: #004461 } /* Name.Builtin */
.highlight .nc { color: #000000 } /* Name.Class */
.highlight .no { color: #000000 } /* Name.Constant */
.highlight .nd { color: #888888 } /* Name.Decorator */
.highlight .ni { color: #ce5c00 } /* Name.Entity */
.highlight .ne { color: #cc0000; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #000000 } /* Name.Function */
.highlight .nl { color: #f57900 } /* Name.Label */
.highlight .nn { color: #000000 } /* Name.Namespace */
.highlight .nx { color: #000000 } /* Name.Other */
.highlight .py { color: #000000 } /* Name.Property */
.highlight .nt { color: #004461; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #000000 } /* Name.Variable */
.highlight .ow { color: #004461; font-weight: bold } /* Operator.Word */
.highlight .w { color: #f8f8f8; text-decoration: underline } /* Text.Whitespace */
.highlight .mb { color: #990000 } /* Literal.Number.Bin */
.highlight .mf { color: #990000 } /* Literal.Number.Float */
.highlight .mh { color: #990000 } /* Literal.Number.Hex */
.highlight .mi { color: #990000 } /* Literal.Number.Integer */
.highlight .mo { color: #990000 } /* Literal.Number.Oct */
.highlight .sb { color: #4e9a06 } /* Literal.String.Backtick */
.highlight .sc { color: #4e9a06 } /* Literal.String.Char */
.highlight .sd { color: #8f5902; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #4e9a06 } /* Literal.String.Double */
.highlight .se { color: #4e9a06 } /* Literal.String.Escape */
.highlight .sh { color: #4e9a06 } /* Literal.String.Heredoc */
.highlight .si { color: #4e9a06 } /* Literal.String.Interpol */
.highlight .sx { color: #4e9a06 } /* Literal.String.Other */
.highlight .sr { color: #4e9a06 } /* Literal.String.Regex */
.highlight .s1 { color: #4e9a06 } /* Literal.String.Single */
.highlight .ss { color: #4e9a06 } /* Literal.String.Symbol */
.highlight .bp { color: #3465a4 } /* Name.Builtin.Pseudo */
.highlight .vc { color: #000000 } /* Name.Variable.Class */
.highlight .vg { color: #000000 } /* Name.Variable.Global */
.highlight .vi { color: #000000 } /* Name.Variable.Instance */
.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
\ No newline at end of file
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>