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3 Commits
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c9b94ed6c6
| Author | SHA1 | Date |
|---|---|---|
 Joshua Rubingh
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c9b94ed6c6 | |
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Joshua Rubingh
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e4c51874dc | |
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Joshua Rubingh
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5f5becdf9d |
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=====
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API
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=====
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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
|
||||
# from the environment for the first two.
|
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SPHINXOPTS ?=
|
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SPHINXBUILD ?= sphinx-build
|
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SOURCEDIR = .
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BUILDDIR = output
|
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|
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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|
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.PHONY: help Makefile
|
||||
|
||||
# Catch-all target: route all unknown targets to Sphinx using the new
|
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
|
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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After Width: | Height: | Size: 53 KiB |
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/* override table width restrictions as found on https://github.com/getpelican/pelican/issues/1311 */
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.wy-table-responsive table td, .wy-table-responsive table th {
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/* !important prevents the common CSS stylesheets from
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overriding this as on RTD they are loaded after this stylesheet */
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white-space: normal !important;
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}
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.wy-table-responsive {
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overflow: visible !important;
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}
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/* Add some more space between the function descriptions */
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dl.function,
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dl.class {
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margin-bottom: 1em;
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}
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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../tusd/hooks'))
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# Django autodoc
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sys.path.insert(0, os.path.abspath('../webservice'))
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os.environ['DJANGO_SETTINGS_MODULE'] = 'webservice.settings'
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import django
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django.setup()
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# -- Project information -----------------------------------------------------
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project = 'Synthea patient generator webservice'
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copyright = '2020, Joshua Rubingh'
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author = 'Joshua Rubingh'
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# The master toctree document.
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master_doc = 'index'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
|
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# ones.
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extensions = [
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'sphinx.ext.napoleon',
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'sphinx.ext.autodoc',
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'sphinx.ext.viewcode',
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'sphinx.ext.coverage',
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'sphinx_markdown_builder',
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store','build/*']
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
|
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# a list of builtin themes.
|
||||
#
|
||||
html_theme = 'alabaster'
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|
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# Add any paths that contain custom static files (such as style sheets) here,
|
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# relative to this directory. They are copied after the builtin static files,
|
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_theme_options = {
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'logo': 'RUG_Logo.jpg',
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'logo_name' : True
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}
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# -- Options for LaTeX output ---------------------------------------------
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# Install Ubuntu/Debian package(s): texlive-latex-recommended, texlive-fonts-recommended, texlive-latex-extra, netpbm
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latex_engine = 'pdflatex'
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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'papersize': 'a4paper',
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'releasename':" ",
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# Sonny, Lenny, Glenn, Conny, Rejne, Bjarne and Bjornstrup
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# 'fncychap': '\\usepackage[Lenny]{fncychap}',
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'fncychap': '\\usepackage{fncychap}',
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'fontpkg': '\\usepackage{amsmath,amsfonts,amssymb,amsthm}',
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'figure_align':'htbp',
|
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# The font size ('10pt', '11pt' or '12pt').
|
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#
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'pointsize': '10pt',
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|
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# Additional stuff for the LaTeX preamble.
|
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#
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'preamble': r'''
|
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%%%%%%%%%%%%%%%%%%%% Meher %%%%%%%%%%%%%%%%%%
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%%%add number to subsubsection 2=subsection, 3=subsubsection
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%%% below subsubsection is not good idea.
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\setcounter{secnumdepth}{3}
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%
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%%%% Table of content upto 2=subsection, 3=subsubsection
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\setcounter{tocdepth}{1}
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|
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\usepackage{amsmath,amsfonts,amssymb,amsthm}
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\usepackage{graphicx}
|
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|
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%%% reduce spaces for Table of contents, figures and tables
|
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%%% it is used "\addtocontents{toc}{\vskip -1.2cm}" etc. in the document
|
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\usepackage[notlot,nottoc,notlof]{}
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\usepackage{color}
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\usepackage{transparent}
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\usepackage{eso-pic}
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\usepackage{lipsum}
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\usepackage{footnotebackref} %%link at the footnote to go to the place of footnote in the text
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%% spacing between line
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\usepackage{setspace}
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%%%%\onehalfspacing
|
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%%%%\doublespacing
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\singlespacing
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|
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%%%%%%%%%%% datetime
|
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\usepackage{datetime}
|
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|
||||
\newdateformat{MonthYearFormat}{%
|
||||
\monthname[\THEMONTH], \THEYEAR}
|
||||
|
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|
||||
%% RO, LE will not work for 'oneside' layout.
|
||||
%% Change oneside to twoside in document class
|
||||
\usepackage{fancyhdr}
|
||||
\pagestyle{fancy}
|
||||
\fancyhf{}
|
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|
||||
%%% Alternating Header for oneside
|
||||
\fancyhead[L]{\ifthenelse{\isodd{\value{page}}}{ \small \nouppercase{\leftmark} }{}}
|
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\fancyhead[R]{\ifthenelse{\isodd{\value{page}}}{}{ \small \nouppercase{\rightmark} }}
|
||||
|
||||
%%% Alternating Header for two side
|
||||
%\fancyhead[RO]{\small \nouppercase{\rightmark}}
|
||||
%\fancyhead[LE]{\small \nouppercase{\leftmark}}
|
||||
|
||||
%% for oneside: change footer at right side. If you want to use Left and right then use same as header defined above.
|
||||
%% \fancyfoot[R]{\ifthenelse{\isodd{\value{page}}}{{\tiny Meher Krishna Patel} }{\href{http://pythondsp.readthedocs.io/en/latest/pythondsp/toc.html}{\tiny PythonDSP}}}
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%%% Alternating Footer for two side
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%% %\fancyfoot[RO, RE]{\scriptsize Meher Krishna Patel (mekrip@gmail.com)}
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%%% page number
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\fancyfoot[CO, CE]{\thepage}
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\renewcommand{\headrulewidth}{0.5pt}
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\renewcommand{\footrulewidth}{0.5pt}
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||||
|
||||
\RequirePackage{tocbibind} %%% comment this to remove page number for following
|
||||
\addto\captionsenglish{\renewcommand{\contentsname}{Table of contents}}
|
||||
%% \addto\captionsenglish{\renewcommand{\listfigurename}{List of figures}}
|
||||
%% \addto\captionsenglish{\renewcommand{\listtablename}{List of tables}}
|
||||
%% % \addto\captionsenglish{\renewcommand{\chaptername}{Chapter}}
|
||||
|
||||
|
||||
%%reduce spacing for itemize
|
||||
\usepackage{enumitem}
|
||||
\setlist{nosep}
|
||||
|
||||
%%%%%%%%%%% Quote Styles at the top of chapter
|
||||
%% \usepackage{epigraph}
|
||||
%% \setlength{\epigraphwidth}{0.8\columnwidth}
|
||||
%% \newcommand{\chapterquote}[2]{\epigraphhead[60]{\epigraph{\textit{#1}}{\textbf {\textit{--#2}}}}}
|
||||
%%%%%%%%%%% Quote for all places except Chapter
|
||||
%% \newcommand{\sectionquote}[2]{{\quote{\textit{``#1''}}{\textbf {\textit{--#2}}}}}
|
||||
''',
|
||||
|
||||
|
||||
'maketitle': r'''
|
||||
\pagenumbering{Roman} %%% to avoid page 1 conflict with actual page 1
|
||||
|
||||
\begin{titlepage}
|
||||
|
||||
\begingroup % for PDF information dictionary
|
||||
\def\endgraf{ }\def\and{\& }%
|
||||
\pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup
|
||||
\hypersetup{pdfauthor={\@author}, pdftitle={\@title}}%
|
||||
\endgroup
|
||||
|
||||
\centering
|
||||
|
||||
\vspace*{40mm} %%% * is used to give space from top
|
||||
\textbf{\Huge {UMCG Synthea patient generator webservice} }
|
||||
|
||||
\vspace{0mm}
|
||||
\begin{figure}[!h]
|
||||
\centering
|
||||
\includegraphics[scale=0.4]{RUG_Logo.jpg}
|
||||
\end{figure}
|
||||
|
||||
\vspace{100mm}
|
||||
\Large \textbf{{Joshua Rubingh}}
|
||||
|
||||
|
||||
\small Created on : November, 2020
|
||||
|
||||
\vspace*{0mm}
|
||||
\small Last updated : \MonthYearFormat\today
|
||||
|
||||
|
||||
%% \vfill adds at the bottom
|
||||
\vfill
|
||||
%% \small \textit{More documents are freely available at }{\href{http://pythondsp.readthedocs.io/en/latest/pythondsp/toc.html}{PythonDSP}}
|
||||
\end{titlepage}
|
||||
|
||||
\clearpage
|
||||
\pagenumbering{roman}
|
||||
\tableofcontents
|
||||
\listoffigures
|
||||
\listoftables
|
||||
\clearpage
|
||||
\pagenumbering{arabic}
|
||||
''',
|
||||
|
||||
# Latex figure (float) alignment
|
||||
#
|
||||
# 'figure_align': 'htbp',
|
||||
'sphinxsetup': \
|
||||
'hmargin={0.7in,0.7in}, vmargin={1in,1in}, \
|
||||
verbatimwithframe=true, \
|
||||
TitleColor={rgb}{0,0,0}, \
|
||||
HeaderFamily=\\rmfamily\\bfseries, \
|
||||
InnerLinkColor={rgb}{0,0,1}, \
|
||||
OuterLinkColor={rgb}{0,0,1}',
|
||||
|
||||
'tableofcontents':' ',
|
||||
}
|
||||
|
||||
latex_logo = '_static/RUG_Logo.jpg'
|
||||
|
||||
# Grouping the document tree into LaTeX files. List of tuples
|
||||
# (source start file, target name, title,
|
||||
# author, documentclass [howto, manual, or own class]).
|
||||
latex_documents = [
|
||||
(master_doc, 'documentation.tex', project,
|
||||
author, 'report')
|
||||
]
|
||||
Binary file not shown.
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==================================================
|
||||
Synthea patient generator webservice documentation
|
||||
==================================================
|
||||
|
||||
Here you can read more information about the UMCG Synthea patient generator webservice.
|
||||
|
||||
This webservice uses `Django <https://django.com>`_ for the front-end and `Synthea <https://github.com/dHealthNL/synthea>`_ for the patient generating.
|
||||
|
||||
.. toctree::
|
||||
:caption: Table of Contents
|
||||
:maxdepth: 2
|
||||
|
||||
install
|
||||
models
|
||||
views
|
||||
API
|
||||
utils
|
||||
signals
|
||||
|
||||
------------------
|
||||
Indices and tables
|
||||
------------------
|
||||
|
||||
* :ref:`genindex`
|
||||
* :ref:`modindex`
|
||||
* :ref:`search`
|
||||
|
|
@ -0,0 +1,98 @@
|
|||
============
|
||||
Installation
|
||||
============
|
||||
|
||||
In order to install this Virtual Research Environment project, we use the following packages / software.
|
||||
|
||||
* Synthea
|
||||
* NGINX
|
||||
* Django
|
||||
|
||||
First we need to checkout the code.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
git clone https://git.web.rug.nl/P300021/synthea_webservice /opt/deploy/synthea_webservice
|
||||
|
||||
|
||||
-------
|
||||
Synthea
|
||||
-------
|
||||
TODO: Make clear setup for synthea. As we are using NL demographical data.
|
||||
|
||||
-----
|
||||
NGINX
|
||||
-----
|
||||
Install NGINX through the package manager. For Ubuntu this would be
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
sudo apt install nginx
|
||||
|
||||
Also configure SSL to make the connections secure. This is outside this installation scope.
|
||||
|
||||
Setup
|
||||
-----
|
||||
After installation of the packages, create a symbolic link in the `/etc/nginx/sites-enabled` so that a new VHost is created.
|
||||
|
||||
Important parts of the VHost configuration:
|
||||
|
||||
.. literalinclude:: ../nginx/synthea_webservice.vhost.conf
|
||||
:language: bash
|
||||
|
||||
In order to test if NGINX is configured correctly run `nginx -t` and it should give an OK message:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
nginx: the configuration file /etc/nginx/nginx.conf syntax is ok
|
||||
nginx: configuration file /etc/nginx/nginx.conf test is successful
|
||||
|
||||
------
|
||||
Django
|
||||
------
|
||||
We install Django with standard settings. We could run it in Aync way, but then you need some more steps: https://docs.djangoproject.com/en/3.0/howto/deployment/asgi/ So for now, we keep it simple.
|
||||
|
||||
Install
|
||||
=======
|
||||
Create a python virtual environment
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
cd /opt/deploy/synthea_webservice
|
||||
python3 -m venv venv
|
||||
source venv/bin/activate
|
||||
|
||||
Finally we install the required Python modules
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
pip install -r requirements
|
||||
|
||||
This will install all the needed Python modules we need to run this Django project.
|
||||
|
||||
Settings
|
||||
--------
|
||||
The settings for Django are set in an `.env` file so that you can easily change the environment from production to testing. There is an `.env.example` file that could be used as a template.
|
||||
|
||||
.. literalinclude:: ../webservice/webservice/.env.example
|
||||
:language: jproperties
|
||||
|
||||
Next we have to make the database structure. If you are using SQLite3 as a backend, make sure the database file **DOES** exist on disk.
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
touch /opt/deploy/synthea_webservice/webservice/db.sqlite3
|
||||
|
||||
Then in the Python virtual environment we run the following commands:
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
./manage.py migrate
|
||||
./manage.py createsuperuser
|
||||
./manage.py collectstatic
|
||||
|
||||
And finally you should be able to start the Django application
|
||||
|
||||
.. code-block:: console
|
||||
|
||||
./manage.py runserver
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
@ECHO OFF
|
||||
|
||||
pushd %~dp0
|
||||
|
||||
REM Command file for Sphinx documentation
|
||||
|
||||
if "%SPHINXBUILD%" == "" (
|
||||
set SPHINXBUILD=sphinx-build
|
||||
)
|
||||
set SOURCEDIR=.
|
||||
set BUILDDIR=_build
|
||||
|
||||
if "%1" == "" goto help
|
||||
|
||||
%SPHINXBUILD% >NUL 2>NUL
|
||||
if errorlevel 9009 (
|
||||
echo.
|
||||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
|
||||
echo.installed, then set the SPHINXBUILD environment variable to point
|
||||
echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
||||
echo.may add the Sphinx directory to PATH.
|
||||
echo.
|
||||
echo.If you don't have Sphinx installed, grab it from
|
||||
echo.http://sphinx-doc.org/
|
||||
exit /b 1
|
||||
)
|
||||
|
||||
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
|
||||
goto end
|
||||
|
||||
:help
|
||||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
|
||||
|
||||
:end
|
||||
popd
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
======
|
||||
Models
|
||||
======
|
||||
|
||||
----
|
||||
Base
|
||||
----
|
||||
.. automodule:: lib.models.base
|
||||
:members:
|
||||
|
||||
---
|
||||
API
|
||||
---
|
||||
.. automodule:: apps.api.models
|
||||
:members:
|
||||
|
||||
-------
|
||||
Synthea
|
||||
-------
|
||||
.. automodule:: apps.synthea.models
|
||||
:members:
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
Sphinx
|
||||
sphinx-markdown-builder
|
||||
|
|
@ -0,0 +1,9 @@
|
|||
=======
|
||||
Signals
|
||||
=======
|
||||
|
||||
---
|
||||
API
|
||||
---
|
||||
.. automodule:: apps.api.signals
|
||||
:members:
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
======
|
||||
Utils
|
||||
======
|
||||
|
||||
-------
|
||||
General
|
||||
-------
|
||||
.. automodule:: lib.utils.general
|
||||
:members:
|
||||
.. automodule:: lib.utils.emails
|
||||
:members:
|
||||
|
||||
-------
|
||||
Synthea
|
||||
-------
|
||||
.. automodule:: apps.synthea.lib.utils
|
||||
:members:
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
=====
|
||||
Views
|
||||
=====
|
||||
|
||||
.. autoclass:: apps.api.views.Info
|
||||
:members:
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
##
|
||||
# You should look at the following URL's in order to grasp a solid understanding
|
||||
# of Nginx configuration files in order to fully unleash the power of Nginx.
|
||||
# https://www.nginx.com/resources/wiki/start/
|
||||
# https://www.nginx.com/resources/wiki/start/topics/tutorials/config_pitfalls/
|
||||
# https://wiki.debian.org/Nginx/DirectoryStructure
|
||||
#
|
||||
# In most cases, administrators will remove this file from sites-enabled/ and
|
||||
# leave it as reference inside of sites-available where it will continue to be
|
||||
# updated by the nginx packaging team.
|
||||
#
|
||||
# This file will automatically load configuration files provided by other
|
||||
# applications, such as Drupal or Wordpress. These applications will be made
|
||||
# available underneath a path with that package name, such as /drupal8.
|
||||
#
|
||||
# Please see /usr/share/doc/nginx-doc/examples/ for more detailed examples.
|
||||
##
|
||||
|
||||
# Default server configuration
|
||||
#
|
||||
|
||||
server {
|
||||
listen 80;
|
||||
listen [::]:80;
|
||||
|
||||
# SSL configuration
|
||||
#
|
||||
# listen 443 ssl default_server;
|
||||
# listen [::]:443 ssl default_server;
|
||||
#
|
||||
# Note: You should disable gzip for SSL traffic.
|
||||
# See: https://bugs.debian.org/773332
|
||||
#
|
||||
# Read up on ssl_ciphers to ensure a secure configuration.
|
||||
# See: https://bugs.debian.org/765782
|
||||
#
|
||||
# Self signed certs generated by the ssl-cert package
|
||||
# Don't use them in a production server!
|
||||
#
|
||||
# include snippets/snakeoil.conf;
|
||||
|
||||
root /var/www/html;
|
||||
|
||||
# Add index.php to the list if you are using PHP
|
||||
index index.html index.htm index.nginx-debian.html;
|
||||
|
||||
server_name localhost;
|
||||
|
||||
access_log /var/log/nginx/synthea_webservice.access.log;
|
||||
error_log /var/log/nginx/synthea_webservice.error.log;
|
||||
|
||||
location /static {
|
||||
alias /opt/deploy/synthea_webservice/webservice/static;
|
||||
}
|
||||
|
||||
location / {
|
||||
# First attempt to serve request as file, then
|
||||
# as directory, then fall back to displaying a 404.
|
||||
# try_files $uri $uri/ =404;
|
||||
|
||||
proxy_pass http://localhost:8000;
|
||||
proxy_http_version 1.1;
|
||||
proxy_set_header Upgrade $http_upgrade;
|
||||
proxy_set_header Connection "upgrade";
|
||||
|
||||
proxy_redirect off;
|
||||
proxy_set_header Host $host;
|
||||
proxy_set_header X-Real-IP $remote_addr;
|
||||
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
|
||||
proxy_set_header X-Forwarded-Host $sent_http_host;
|
||||
proxy_set_header X-Forwarded-Proto $scheme;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
# Generated by Django 3.0.8 on 2020-07-30 14:15
|
||||
# Generated by Django 3.1.3 on 2020-11-27 11:47
|
||||
|
||||
import apps.api.models
|
||||
from django.conf import settings
|
||||
|
|
|
|||
|
|
@ -55,7 +55,7 @@ class Token(MetaDataModel):
|
|||
"""Boolean check if the token is belonging to a user with super user rights. Then this token is a super token.
|
||||
|
||||
Returns:
|
||||
bool: Returns true when the token belongs to a super user.
|
||||
Boolean: Returns true when the token belongs to a super user.
|
||||
"""
|
||||
# TODO: Is it allowed to be a super user and researcher? Could give conflict of interests. With the API token you can read other researchers data...
|
||||
return self.user.is_superuser == True
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ def create_user_token(sender, instance=None, created=False, **kwargs):
|
|||
instance: :attr:`~django.contrib.auth.models.User`
|
||||
The newly created user model data
|
||||
|
||||
created : boolean
|
||||
created : Boolean
|
||||
Wether the object was created (True) or updated (False).
|
||||
"""
|
||||
if created:
|
||||
|
|
|
|||
|
|
@ -1,3 +1,10 @@
|
|||
from django.contrib import admin
|
||||
from .models import Synthea
|
||||
|
||||
# Register your models here.
|
||||
@admin.register(Synthea)
|
||||
class SyntheaAdmin(admin.ModelAdmin):
|
||||
list_display = ('id', 'state','population', 'gender','age','module')
|
||||
ordering = ('-created_at', )
|
||||
search_fields = ('state', 'module',)
|
||||
readonly_fields = ('created_at', 'updated_at')
|
||||
|
|
@ -27,21 +27,12 @@ class SyntheaConfig(AppConfig):
|
|||
# We only load this setting, if it is not available in the overall settings.py file
|
||||
settings.SYNTHEA_MODULE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/modules/'
|
||||
|
||||
|
||||
try:
|
||||
assert settings.SYNTHEA_RESOURCE_DIR
|
||||
except AttributeError:
|
||||
# We only load this setting, if it is not available in the overall settings.py file
|
||||
settings.SYNTHEA_RESOURCE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/'
|
||||
|
||||
try:
|
||||
assert settings.SYNTHEA_STATES_DIR
|
||||
except AttributeError:
|
||||
# We only load this setting, if it is not available in the overall settings.py file
|
||||
settings.SYNTHEA_STATES_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/geography/'
|
||||
|
||||
|
||||
|
||||
try:
|
||||
assert settings.SYNTHEA_EXPORT_TYPE
|
||||
except AttributeError:
|
||||
|
|
|
|||
|
|
@ -8,21 +8,31 @@ import json
|
|||
from django.conf import settings
|
||||
from uuid import uuid4
|
||||
|
||||
|
||||
def available_states():
|
||||
"""This method will return a sorted list of available states based on the 'geography/demographics.csv' in the `settings.SYNTHEA_RESOURCE_DIR` folder.
|
||||
|
||||
Returns:
|
||||
List: Sorted list on state name with dicts holding the id and name of the state.
|
||||
"""
|
||||
|
||||
states = []
|
||||
# Read the timezones.csv file from the Synthea resources. This should give us all the 'state' on the first column
|
||||
df = pd.read_csv(settings.SYNTHEA_STATES_DIR / 'timezones.csv', index_col=False)
|
||||
for state in df[df.columns[0]].to_list():
|
||||
# Read the demographics.csv file from the Synthea resources and get all the unique state names
|
||||
# Important, the state name for synthea is case sensitive (field id)
|
||||
df = pd.read_csv(settings.SYNTHEA_RESOURCE_DIR / 'geography/demographics.csv', index_col=False)
|
||||
for state in df.STNAME.unique():
|
||||
states.append({'id' : state , 'name' : state})
|
||||
|
||||
#states = df[df.columns[0]].to_list()
|
||||
# Sort on name
|
||||
states = sorted(states, key=lambda k: k['name'].lower())
|
||||
#states.sort()
|
||||
states = sorted(states, key=lambda s: s['name'].lower())
|
||||
return states
|
||||
|
||||
def available_modules():
|
||||
"""This method will load all the available modules that are in the folder `settings.SYNTHEA_MODULE_DIR`. Only files ending on .json will be loaded.
|
||||
|
||||
Returns:
|
||||
List: Sorted list on module name with dicts holding the id and name of the module.
|
||||
"""
|
||||
|
||||
# Assumption here: Only .json files in the main folder are modules. The rest are submodules...
|
||||
modules = []
|
||||
for module in settings.SYNTHEA_MODULE_DIR.iterdir():
|
||||
|
|
@ -30,10 +40,29 @@ def available_modules():
|
|||
data = json.loads(module.read_text())
|
||||
modules.append({'id' : module.name.replace('.json',''), 'name' : data['name']})
|
||||
|
||||
modules = sorted(modules, key=lambda k: k['name'].lower())
|
||||
modules = sorted(modules, key=lambda m: m['name'].lower())
|
||||
return modules
|
||||
|
||||
def run_synthea(state = None, population = None, gender = None, age = None, module = None):
|
||||
def run_synthea(state, population = 50, gender = None, age = None, module = None):
|
||||
"""This module will run the Synthea application on the background. This method expects Synthea to be installed on the `settings.SYNTHEA_BASE_DIR` location.
|
||||
|
||||
The output will be written to a unique folder in `settings.SYNTHEA_OUTPUT_DIR` that will be zipped and returned.
|
||||
|
||||
It will return the log and the zipfile location for futher processing. The zip file will not be deleted afterwards. So cleanup needs to be done manually.
|
||||
|
||||
Args:
|
||||
state (str, required): The state where to generate synthetic patient data for.
|
||||
population (int, optional): The amount of patients to generate. Defaults to 50.
|
||||
gender (str, optional): Either generate only male(m), only female(f), or None for both. Defaults to None.
|
||||
age (str, optional): This is the age range of the generated patients. Input is always like [min_age]-[max_age]. Defaults to None.
|
||||
module (str, optional): The module to use for generating patient data When None, all modules are used. Defaults to None.
|
||||
|
||||
Raises:
|
||||
Exception: When the Synthea run fails it will return an Exception witht he Java error in it.
|
||||
|
||||
Returns:
|
||||
(str,Path): The returning zipfile has the enabled options in the file name.
|
||||
"""
|
||||
# Add a unique dir to the output, so multiple Synthea processes can run parallel
|
||||
temp_id = uuid4().hex
|
||||
output_folder = settings.SYNTHEA_OUTPUT_DIR / temp_id
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
# Generated by Django 3.1.3 on 2020-11-13 09:36
|
||||
# Generated by Django 3.1.3 on 2020-11-27 11:47
|
||||
|
||||
from django.db import migrations, models
|
||||
import uuid
|
||||
|
|
@ -18,15 +18,16 @@ class Migration(migrations.Migration):
|
|||
('created_at', models.DateTimeField(auto_now_add=True, help_text='The date and time this model has been created', verbose_name='Date created')),
|
||||
('updated_at', models.DateTimeField(auto_now=True, help_text='The date and time this model has been updated', verbose_name='Date updated')),
|
||||
('id', models.UUIDField(default=uuid.uuid4, editable=False, help_text='A unique id', primary_key=True, serialize=False, unique=True, verbose_name='ID')),
|
||||
('state', models.CharField(help_text='The state for which synthea generate data.', max_length=200, verbose_name='Stage')),
|
||||
('state', models.CharField(help_text='The state for which synthea generate data.', max_length=200, verbose_name='State')),
|
||||
('population', models.PositiveSmallIntegerField(default=50, help_text='The size of the population', verbose_name='Population')),
|
||||
('gender', models.CharField(help_text='Select the gender type', max_length=1, verbose_name='Gender')),
|
||||
('age', models.CharField(help_text='Select the age range', max_length=10, verbose_name='Age range')),
|
||||
('module', models.CharField(help_text='Select the module', max_length=50, verbose_name='Mopdule')),
|
||||
('gender', models.CharField(blank=True, help_text='Select the gender type', max_length=1, verbose_name='Gender')),
|
||||
('age', models.CharField(blank=True, default='18-100', help_text='Select the age range. Enter [min age]-[max age]', max_length=10, verbose_name='Age range')),
|
||||
('module', models.CharField(blank=True, help_text='Select the module', max_length=50, verbose_name='Module')),
|
||||
('log', models.TextField(blank=True, help_text='Synthea logfile output', verbose_name='Log')),
|
||||
],
|
||||
options={
|
||||
'verbose_name': 'token',
|
||||
'verbose_name_plural': 'tokens',
|
||||
'verbose_name': 'synthea',
|
||||
'verbose_name_plural': 'synthea',
|
||||
},
|
||||
),
|
||||
]
|
||||
|
|
|
|||
|
|
@ -1,38 +0,0 @@
|
|||
# Generated by Django 3.1.3 on 2020-11-16 13:57
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('synthea', '0001_initial'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='synthea',
|
||||
name='log',
|
||||
field=models.TextField(blank=True, help_text='Synthea logfile output', verbose_name='Log'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='synthea',
|
||||
name='age',
|
||||
field=models.CharField(blank=True, default='18-100', help_text='Select the age range. Enter [min age]-[max age]', max_length=10, verbose_name='Age range'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='synthea',
|
||||
name='gender',
|
||||
field=models.CharField(blank=True, help_text='Select the gender type', max_length=1, verbose_name='Gender'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='synthea',
|
||||
name='module',
|
||||
field=models.CharField(blank=True, help_text='Select the module', max_length=50, verbose_name='Module'),
|
||||
),
|
||||
migrations.AlterField(
|
||||
model_name='synthea',
|
||||
name='state',
|
||||
field=models.CharField(help_text='The state for which synthea generate data.', max_length=200, verbose_name='State'),
|
||||
),
|
||||
]
|
||||
|
|
@ -13,10 +13,32 @@ import uuid
|
|||
|
||||
# Create your models here.
|
||||
class Synthea(MetaDataModel):
|
||||
"""Synthea model that holds some iformation about a generated output.
|
||||
|
||||
Attributes
|
||||
----------
|
||||
id : uuid
|
||||
A unique ID for every Synthea run. Leave empty for auto generating a new value.
|
||||
state : str
|
||||
The state for which you want to generate Synthea patient data
|
||||
population : int
|
||||
The amount of patients you want to generate
|
||||
gender : datetime
|
||||
Generate only male (m), only female(f) or leave empty for male and female
|
||||
age : str
|
||||
The age range for the patients. Enter like [min_age]-[max_age]
|
||||
module : str
|
||||
The module to use for patient generating. Leave empty for random use by Synthea
|
||||
log : str
|
||||
The outcome of a single patient generating run. This can be read in the admin area.
|
||||
|
||||
Returns:
|
||||
Synthea: A new Synthea model
|
||||
"""
|
||||
|
||||
class Meta:
|
||||
verbose_name = _('token')
|
||||
verbose_name_plural = _('tokens')
|
||||
verbose_name = _('synthea')
|
||||
verbose_name_plural = _('synthea')
|
||||
|
||||
id = models.UUIDField(_('ID'), primary_key=True, unique=True, default=uuid.uuid4, editable=False, help_text=_('A unique id'))
|
||||
state = models.CharField(_('State'), max_length=200, help_text=_('The state for which synthea generate data.'))
|
||||
|
|
@ -26,8 +48,15 @@ class Synthea(MetaDataModel):
|
|||
module = models.CharField(_('Module'),blank=True, max_length=50, help_text=_('Select the module'))
|
||||
log = models.TextField(_('Log'),blank=True, help_text=_('Synthea logfile output'))
|
||||
|
||||
|
||||
def generate(self):
|
||||
"""Run the patient generation. This will return a logfile and a zipfile location for download.
|
||||
|
||||
The log will be stored in the model when done. This log can then be seen/readed in the admin section of Django
|
||||
|
||||
Returns:
|
||||
str: The zip file location on disk.
|
||||
"""
|
||||
# Start generating patient data.
|
||||
log,zip_file = run_synthea(
|
||||
self.state,
|
||||
self.population,
|
||||
|
|
@ -35,10 +64,9 @@ class Synthea(MetaDataModel):
|
|||
self.age,
|
||||
self.module
|
||||
)
|
||||
|
||||
# Store the log from the Synthea run in the database.
|
||||
self.log = log
|
||||
|
||||
self.save()
|
||||
|
||||
# Return the zip file locaton for download
|
||||
return zip_file
|
||||
|
||||
|
|
|
|||
|
|
@ -8,15 +8,30 @@ from django.conf import settings
|
|||
|
||||
# Source: https://djangosnippets.org/snippets/2215/
|
||||
class EmailMultiRelated(EmailMultiAlternatives):
|
||||
"""
|
||||
A version of EmailMessage that makes it easy to send multipart/related
|
||||
"""A version of EmailMessage that makes it easy to send multipart/related
|
||||
messages. For example, including text and HTML versions with inline images.
|
||||
|
||||
Returns:
|
||||
EmailMultiAlternatives: EmailMultiAlternatives class
|
||||
"""
|
||||
|
||||
related_subtype = 'related'
|
||||
|
||||
def __init__(self, subject='', body='', from_email=None, to=None, bcc=None,
|
||||
connection=None, attachments=None, headers=None, alternatives=None):
|
||||
# self.related_ids = []
|
||||
"""Create a new email object that can holds text and HTML content.
|
||||
|
||||
Args:
|
||||
subject (str, optional): The subject of the email. Defaults to ''.
|
||||
body (str, optional): The body of the email. Defaults to ''.
|
||||
from_email (str, optional): [description]. Defaults to None.
|
||||
to ([type], optional): [description]. Defaults to None.
|
||||
bcc ([type], optional): [description]. Defaults to None.
|
||||
connection ([type], optional): [description]. Defaults to None.
|
||||
attachments ([type], optional): [description]. Defaults to None.
|
||||
headers ([type], optional): [description]. Defaults to None.
|
||||
alternatives ([type], optional): [description]. Defaults to None.
|
||||
"""
|
||||
self.related_attachments = []
|
||||
super(EmailMultiRelated, self).__init__(subject, body, from_email, to, bcc, connection, attachments, headers, alternatives)
|
||||
|
||||
|
|
@ -27,7 +42,13 @@ class EmailMultiRelated(EmailMultiAlternatives):
|
|||
|
||||
If the first parameter is a MIMEBase subclass it is inserted directly
|
||||
into the resulting message attachments.
|
||||
|
||||
Args:
|
||||
filename ([type], optional): [description]. Defaults to None.
|
||||
content ([type], optional): [description]. Defaults to None.
|
||||
mimetype ([type], optional): [description]. Defaults to None.
|
||||
"""
|
||||
|
||||
if isinstance(filename, MIMEBase):
|
||||
assert content == mimetype == None
|
||||
self.related_attachments.append(filename)
|
||||
|
|
|
|||
|
|
@ -2,25 +2,67 @@ import re
|
|||
import random
|
||||
import string
|
||||
|
||||
def remove_html_tags(text):
|
||||
"""Remove html tags from a string"""
|
||||
clean = re.compile('<.*?>')
|
||||
return re.sub(clean, '', text)
|
||||
|
||||
def get_random_int_value(length = 6):
|
||||
return ''.join(list(map(lambda x: str(random.randint(1,9)), list(range(length)))))
|
||||
|
||||
def get_random_string(length = 8):
|
||||
return ''.join(random.choices(string.ascii_uppercase + string.digits + string.ascii_lowercase, k=length))
|
||||
|
||||
def generate_encryption_key(length = 32):
|
||||
"""Generate a new encryption key of `length` chars. This is done by using the :func:`get_random_string` function with a default of 32 chars.
|
||||
|
||||
Args:
|
||||
length (int, optional): The length in chars of the encryption key. Defaults to 32.
|
||||
|
||||
Returns:
|
||||
str: A string of `length` chars.
|
||||
"""
|
||||
return get_random_string(length)
|
||||
|
||||
def get_ip_address(request):
|
||||
""" use requestobject to fetch client machine's IP Address """
|
||||
"""Get the IP address of the requesting viewer. This is done by looking into the following variables in the headers.
|
||||
|
||||
1. HTTP_X_FORWARDED_FOR
|
||||
2. REMOTE_ADDR
|
||||
|
||||
Args:
|
||||
request (BaseRequest): The Django request.
|
||||
|
||||
Returns:
|
||||
str: IP address of the request
|
||||
"""
|
||||
x_forwarded_for = request.META.get('HTTP_X_FORWARDED_FOR', None)
|
||||
if x_forwarded_for:
|
||||
ip = x_forwarded_for.split(',')[0]
|
||||
else:
|
||||
ip = request.META.get('REMOTE_ADDR') ### Real IP address of client Machine
|
||||
return ip
|
||||
return ip
|
||||
|
||||
def get_random_int_value(length = 6):
|
||||
"""Generate a random number of `length` length numbers.
|
||||
|
||||
Args:
|
||||
length (int, optional): The length of the random number in amount of numbers. Defaults to 6.
|
||||
|
||||
Returns:
|
||||
int: Returns a random number of 'length' numbers.
|
||||
"""
|
||||
return int(''.join(list(map(lambda x: str(random.randint(1,9)), list(range(length))))))
|
||||
|
||||
def get_random_string(length = 8):
|
||||
"""Generate a random string of `length` length characters.
|
||||
|
||||
Args:
|
||||
length (int, optional): The length of the random string in amount of characters. Defaults to 8.
|
||||
|
||||
Returns:
|
||||
str: Returns a random string of 'length' characters.
|
||||
"""
|
||||
return ''.join(random.choices(string.ascii_uppercase + string.digits + string.ascii_lowercase, k=length))
|
||||
|
||||
def remove_html_tags(text):
|
||||
"""Remove HTML tags and code from the input text
|
||||
|
||||
Args:
|
||||
text (str): Input text to be cleaned from HTML
|
||||
|
||||
Returns:
|
||||
str: Cleaned HTML.
|
||||
"""
|
||||
|
||||
clean = re.compile('<.*?>')
|
||||
return re.sub(clean, '', text)
|
||||
|
|
@ -1,8 +1,8 @@
|
|||
# A uniquely secret key
|
||||
SECRET_KEY=@wb=#(f4uc0l%e!5*eo+aoflnxb(@!l9!=c5w=4b+x$=!8&vy%'
|
||||
SECRET_KEY=@wb=#(f4vc0l(e!5*eo+a@flnxb2@!l9!=c6w=4b+x$=!8&vy%'
|
||||
|
||||
# Disable debug in production
|
||||
DEBUG=False
|
||||
DEBUG=True
|
||||
|
||||
# Allowed hosts that Django does server. Take care when NGINX is proxying infront of Django
|
||||
ALLOWED_HOSTS=127.0.0.1,localhost
|
||||
|
|
@ -11,7 +11,7 @@ ALLOWED_HOSTS=127.0.0.1,localhost
|
|||
INTERNAL_IPS=127.0.0.1
|
||||
|
||||
# Enter the database url connection: https://github.com/jacobian/dj-database-url
|
||||
DATABASE_URL=sqlite:////opt/deploy/VRE/VirtualResearchEnvironment/db.sqlite3
|
||||
DATABASE_URL=sqlite:////opt/deploy/synthea_webservice/webservice/db.sqlite3
|
||||
|
||||
# The location on disk where the static files will be placed during deployment. Setting is required
|
||||
STATIC_ROOT=
|
||||
|
|
@ -25,29 +25,32 @@ TIME_ZONE=Europe/Amsterdam
|
|||
EMAIL_HOST=
|
||||
|
||||
# Email user name
|
||||
EMAIL_HOST_USER=
|
||||
EMAIL_HOST_USER=na
|
||||
|
||||
# Email password
|
||||
EMAIL_HOST_PASSWORD=
|
||||
EMAIL_HOST_PASSWORD=na
|
||||
|
||||
# Email server port number to use
|
||||
EMAIL_PORT=25
|
||||
|
||||
# Does the email server supports TLS?
|
||||
EMAIL_USE_TLS=
|
||||
EMAIL_USE_TLS=yes
|
||||
|
||||
# The sender address. This needs to be one of the allowed domains due to SPF checks
|
||||
# The code will use a reply-to header to make sure that replies goes to the researcher and not this address
|
||||
EMAIL_FROM_ADDRESS=Do not reply<no-reply@rug.nl>
|
||||
|
||||
# What is the Dropoff hostname (webinterface)
|
||||
DROPOFF_HOSTNAME=http://localhost:8000
|
||||
# The base folder where Synthea is installed. This folder should contain the file 'run_synthea.(|bat)'
|
||||
settings.SYNTHEA_BASE_DIR = settings.BASE_DIR / '../synthea'
|
||||
|
||||
# What is the Dropoff Upload host
|
||||
DROPOFF_UPLOAD_HOST=http://localhost
|
||||
# The base output folder where Synthea will generate its output. This location will be appended with a unique folder name.
|
||||
settings.SYNTHEA_OUTPUT_DIR = settings.BASE_DIR / '../synthea_output'
|
||||
|
||||
# Which file extensions are **NOT** allowed
|
||||
DROPOFF_NOT_ALLOWED_EXTENSIONS=exe,com,bat,lnk,sh
|
||||
# The location where the Synthea modules are located.
|
||||
settings.SYNTHEA_MODULE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/modules/'
|
||||
|
||||
# What is the full VRE Portal domains
|
||||
VRE_BROKER_API=http://localhost:8000
|
||||
# The location where the Synthea resources are located. This should also include the geography data.
|
||||
settings.SYNTHEA_RESOURCE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/'
|
||||
|
||||
# The output type for Synthea.
|
||||
settings.SYNTHEA_EXPORT_TYPE = 'fhir_stu3'
|
||||
Loading…
Reference in New Issue