Add documentation

This commit is contained in:
Joshua Rubingh 2020-11-27 12:49:03 +01:00
parent e4c51874dc
commit c9b94ed6c6
26 changed files with 743 additions and 98 deletions

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=====
API
=====

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doc/Makefile Normal file
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# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = output
# 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 $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

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/* override table width restrictions as found on https://github.com/getpelican/pelican/issues/1311 */
.wy-table-responsive table td, .wy-table-responsive table th {
/* !important prevents the common CSS stylesheets from
overriding this as on RTD they are loaded after this stylesheet */
white-space: normal !important;
}
.wy-table-responsive {
overflow: visible !important;
}
/* Add some more space between the function descriptions */
dl.function,
dl.class {
margin-bottom: 1em;
}

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# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../tusd/hooks'))
# Django autodoc
sys.path.insert(0, os.path.abspath('../webservice'))
os.environ['DJANGO_SETTINGS_MODULE'] = 'webservice.settings'
import django
django.setup()
# -- Project information -----------------------------------------------------
project = 'Synthea patient generator webservice'
copyright = '2020, Joshua Rubingh'
author = 'Joshua Rubingh'
# The master toctree document.
master_doc = 'index'
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.napoleon',
'sphinx.ext.autodoc',
'sphinx.ext.viewcode',
'sphinx.ext.coverage',
'sphinx_markdown_builder',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store','build/*']
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'alabaster'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_theme_options = {
'logo': 'RUG_Logo.jpg',
'logo_name' : True
}
# -- Options for LaTeX output ---------------------------------------------
# Install Ubuntu/Debian package(s): texlive-latex-recommended, texlive-fonts-recommended, texlive-latex-extra, netpbm
latex_engine = 'pdflatex'
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
'papersize': 'a4paper',
'releasename':" ",
# Sonny, Lenny, Glenn, Conny, Rejne, Bjarne and Bjornstrup
# 'fncychap': '\\usepackage[Lenny]{fncychap}',
'fncychap': '\\usepackage{fncychap}',
'fontpkg': '\\usepackage{amsmath,amsfonts,amssymb,amsthm}',
'figure_align':'htbp',
# The font size ('10pt', '11pt' or '12pt').
#
'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
'preamble': r'''
%%%%%%%%%%%%%%%%%%%% Meher %%%%%%%%%%%%%%%%%%
%%%add number to subsubsection 2=subsection, 3=subsubsection
%%% below subsubsection is not good idea.
\setcounter{secnumdepth}{3}
%
%%%% Table of content upto 2=subsection, 3=subsubsection
\setcounter{tocdepth}{1}
\usepackage{amsmath,amsfonts,amssymb,amsthm}
\usepackage{graphicx}
%%% reduce spaces for Table of contents, figures and tables
%%% it is used "\addtocontents{toc}{\vskip -1.2cm}" etc. in the document
\usepackage[notlot,nottoc,notlof]{}
\usepackage{color}
\usepackage{transparent}
\usepackage{eso-pic}
\usepackage{lipsum}
\usepackage{footnotebackref} %%link at the footnote to go to the place of footnote in the text
%% spacing between line
\usepackage{setspace}
%%%%\onehalfspacing
%%%%\doublespacing
\singlespacing
%%%%%%%%%%% datetime
\usepackage{datetime}
\newdateformat{MonthYearFormat}{%
\monthname[\THEMONTH], \THEYEAR}
%% RO, LE will not work for 'oneside' layout.
%% Change oneside to twoside in document class
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{}
%%% Alternating Header for oneside
\fancyhead[L]{\ifthenelse{\isodd{\value{page}}}{ \small \nouppercase{\leftmark} }{}}
\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}}}
%%% Alternating Footer for two side
%% %\fancyfoot[RO, RE]{\scriptsize Meher Krishna Patel (mekrip@gmail.com)}
%%% page number
\fancyfoot[CO, CE]{\thepage}
\renewcommand{\headrulewidth}{0.5pt}
\renewcommand{\footrulewidth}{0.5pt}
\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')
]

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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`

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============
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

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@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

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======
Models
======
----
Base
----
.. automodule:: lib.models.base
:members:
---
API
---
.. automodule:: apps.api.models
:members:
-------
Synthea
-------
.. automodule:: apps.synthea.models
:members:

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Sphinx
sphinx-markdown-builder

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=======
Signals
=======
---
API
---
.. automodule:: apps.api.signals
:members:

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======
Utils
======
-------
General
-------
.. automodule:: lib.utils.general
:members:
.. automodule:: lib.utils.emails
:members:
-------
Synthea
-------
.. automodule:: apps.synthea.lib.utils
:members:

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=====
Views
=====
.. autoclass:: apps.api.views.Info
:members:

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##
# 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;
}
}

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@ -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

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@ -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

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@ -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:

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@ -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:

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@ -8,20 +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 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_STATES_DIR / 'demographics.csv', index_col=False)
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})
# Sort on name
states = sorted(states, key=lambda k: k['name'].lower())
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():
@ -29,10 +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

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@ -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',
},
),
]

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@ -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'),
),
]

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@ -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

View 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)

View File

@ -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)

View File

@ -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'