Add documentation

doc/API.rst

@@ -0,0 +1,3 @@
+=====
+API
+=====

doc/Makefile

@@ -0,0 +1,20 @@
+# 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)

doc/_static/custom.css

@@ -0,0 +1,16 @@
+/* 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;
+}

doc/conf.py

@@ -0,0 +1,241 @@
+# 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')
+]

doc/index.rst

@@ -0,0 +1,26 @@
+==================================================
+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`

doc/install.rst

@@ -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

doc/make.bat

@@ -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

doc/models.rst

@@ -0,0 +1,21 @@
+======
+Models
+======
+
+----
+Base
+----
+.. automodule:: lib.models.base
+   :members:
+
+---
+API
+---
+.. automodule:: apps.api.models
+   :members:
+
+-------
+Synthea
+-------
+.. automodule:: apps.synthea.models
+   :members:

doc/requirements.txt

@@ -0,0 +1,2 @@
+Sphinx
+sphinx-markdown-builder

doc/signals.rst

@@ -0,0 +1,9 @@
+=======
+Signals
+=======
+
+---
+API
+---
+.. automodule:: apps.api.signals
+   :members:

doc/utils.rst

@@ -0,0 +1,17 @@
+======
+Utils
+======
+
+-------
+General
+-------
+.. automodule:: lib.utils.general
+   :members:
+.. automodule:: lib.utils.emails
+   :members:
+
+-------
+Synthea
+-------
+.. automodule:: apps.synthea.lib.utils
+   :members:

doc/views.rst

@@ -0,0 +1,6 @@
+=====
+Views
+=====
+
+.. autoclass:: apps.api.views.Info
+   :members:

nginx/synthea_webservice.vhost.conf

@@ -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;
+    }
+}

webservice/apps/api/migrations/0001_initial.py

@@ -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

webservice/apps/api/models.py

@@ -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

webservice/apps/api/signals.py

@@ -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:

webservice/apps/synthea/apps.py

@@ -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:

webservice/apps/synthea/lib/utils.py

@@ -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

webservice/apps/synthea/migrations/0001_initial.py

@@ -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')),
+                ('gender', models.CharField(blank=True, 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')),
+                ('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(help_text='Select the module', max_length=50, verbose_name='Mopdule')),
+                ('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': 'synthea',
-                'verbose_name_plural': 'tokens',
+                'verbose_name_plural': 'synthea',
             },
         ),
     ]

webservice/apps/synthea/migrations/0002_auto_20201116_1457.py

@@ -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'),
-        ),
-    ]

webservice/apps/synthea/models.py

@@ -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 = _('synthea')
-        verbose_name_plural = _('tokens')
+        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
 

webservice/lib/utils/emails.py

@@ -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)

webservice/lib/utils/general.py

@@ -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)

webservice/webservice/.env.example

@@ -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)
+# The base folder where Synthea is installed. This folder should contain the file 'run_synthea.(|bat)'
-DROPOFF_HOSTNAME=http://localhost:8000
+settings.SYNTHEA_BASE_DIR = settings.BASE_DIR / '../synthea'
 
-# What is the Dropoff Upload host
+# The base output folder where Synthea will generate its output. This location will be appended with a unique folder name.
-DROPOFF_UPLOAD_HOST=http://localhost
+settings.SYNTHEA_OUTPUT_DIR = settings.BASE_DIR / '../synthea_output'
 
-# Which file extensions are **NOT** allowed
+# The location where the Synthea modules are located.
-DROPOFF_NOT_ALLOWED_EXTENSIONS=exe,com,bat,lnk,sh
+settings.SYNTHEA_MODULE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/modules/'
 
-# What is the full VRE Portal domains
+# The location where the Synthea resources are located. This should also include the geography data.
-VRE_BROKER_API=http://localhost:8000
+settings.SYNTHEA_RESOURCE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/'
+
+# The output type for Synthea.
+settings.SYNTHEA_EXPORT_TYPE = 'fhir_stu3'