Had a lovely day at @PySangamam where I presented my experiences developing @aushadha_emr #ElectronicMedicalRecords or #EMR . Attaching below are some pictures of the event. https://t.co/hJteYzw822
I was pleasantly surprised on how open the crowd and organisers were to a talk delivered by a developer who’s primarily a doctor. It was organised beautifully and thanks specially Mr. Vijayakumar , Mr Abhishek and his team for all the encouragement.
Looking forward to #pysangamam next year at #Coimbatore , my home town
I am happy to inform as promised earlier that AuShadha 2.0, which is a complete rewrite of AuShadha using Python 3.x, PostreSQL, Django 2.x and Dojo1.1x has been started and first major commit pushed.
AuShadha Electronic Medical Records at https://github.com/dreaswar/AuShadha has been seeing very slow development mostly due to pressures on my personal and professional front.
I could get back to development past few days and I have pushed a commit to master after some gap.
The Prescription App for Outpatient visits is ready.
Next stop is to implement Outpatient Reports.
Do check it out and let me know what you think.
You will need #Django1.7.2, #Python2.7x, #Dojo #Javascript Toolkit 1.13
For all those who were following AuShadha Open Source EMR project hosted at GitHub there’s news.
I had paused developing for sometime due to pressure of time.
The development has restarted for past few months (no commits ) and am planning to branch of development into AuShadha2.0 with changes to the core, Dojo 1.12 JavaScript library, Django1.10 support and Python3.x support.
This is a version written with lessons of what were not ideal practices in previous version.
Watch this space. Will post more by the end of this month.
Building the Dijit – UI with PyYAML markup and Django Templating
Get the PyYAML file from Git Hub Repo : get it here.
This is the file that generates the Patient Pane which is brought up after searching.
This is the UI it generates:
This Patient Pane’s UI widgets, layout etc is partly generated from the PyYAML
This pane.yaml file is a Django template that leverages Django’s templating features as well as PyYAML‘s object mark up to generate a rendered JSON. This JSON is then returned on AJAX call to help the UI building. JSON is parsed by the Javascript file here to help build the Dijit UI, Widgets etc…
PyYAML file
Let us examine the PyYAML file markup
Comments and Verbatim Code
At the top, {% verbatim %} Django Template tag allow the developer to put some code / comments
Declaring Variables
Variables that can be used all over the YAML file can be declared at the top. This is where PyYAML markup scores over Django Template. Django Template restricts variable naming and prevents you from doing Python stuff inside the template. This is ok for most templates that output HTML where the relevent code can be put inside the views.py. However, for it is also convenient if the option exists on the template. PyYAML allows us to call random python objects, declare variables that can be used through the template, use aliases in YAML file and even instantiate Python objects. Coupled with Django Template, it can be used powerfully.
# VARS
Variables can be declared with the expected type just to be sure. Aliases created can be used like Variables throughout the YAML file.Of Course we can just use {{{<some_var>}} Django template variable to do the substitution as well without creating any alias.
VARS:
clinic_id: &CLINIC_ID
!!int {{clinic_id}}
patient_id: &PATIENT_ID
!!int {{patient_id}}
URLS:
This calls the Django reverse method and allows calling with arguments. The results is stored as the PATIENT_PANE_URL alias.
pane: &PATIENT_PANE_URL
!!python/object/apply:django.core.urlresolvers.reverse
args: [ render_patient_pane_with_id ]
kwds: { kwargs : { patient_id: *PATIENT_ID } }
Using Django {%url%} template tag, the code below can be rewritten more elegantlyas:
pane: &PATIENT_PANE_URL # creates the Alias of PATIENT_PANE_URL
{% url 'render_patient_pane_with_id' *PATIENT_ID %}
YAML Header and Describing the Layout of the UI, widgets inside each DOM
YAML Header describes which module the pane belongs to, what are requisite modules to be loaded before this loads and whether this loads on AuShadha start. This is something like a basicinformation about the pane.
# YAML
depends_on: [ search ] #Requires that the Search Module
load_after: search #Requires that Search UI should be loaded before this
load_first: !!bool False #Prevents loading this first explicitly
#Following markup start the description of the Patient UI Pane
id : PATIENT #ID of the DOM Element
type : bc # Type of Dijit Layout Widget this is bc = Dijit BorderContainer
title : Patient #Title Attribute
url : *PATIENT_PANE_URL #The URL attribute which equals href of the widget
closable : !!bool True #Whether the tab is closable
widgets: [] #Whether there are child widgets (exludes layout widgets)
panes: #Describes the child layout Panes / DOM Nodes
- id: PATIENT_DETAIL_ACTIONS_ICONS #DOM Element Id of the pane
type: dom #Says that this is only a DOM Node not Dijit
domType: div #Specifies the DOM node type
style: #Specifies the CSS styles
position: relative
top: 10
zIndex: 1000
float: right
width: 200px
height: 1.8em
- id : PATIENT_TOP_CP #Describes a Dijit Layout Widget DOM Id
region: top #Region attribute of the widget
type: cp #Type of widget cp = dijit ContentPane
splitter: False #Splitter attibute
url: *PATIENT_INFO_URL #href attribute
widgets: [] #Contained non-layout widgets
panes: [] #Contained Dijit panes, DOM nodes
class: topContentPane selected #CSS class
style: #CSS styles
height: 1.8em
The resulting PyYAML file can be parsed and UI created by the Javascript file. As you can see the method is easy and the markup is certainly more readable than an HTML file with Dijit declarative markup interspersed with Django template markup etc..
It can certainly be argued about the need for a PyYAML use when HTML can be used. However, to change a layout and to see switching layout / per -user customisation it is much easier to move the YAML blocks to and fro the nested levels than to switch HTML blocks with all the declarative markups. Of course we can use Django Template {% include %} to create a basic HTML file that will do the job. It is up to developer preference. I found this much easier on the eye.
The current limitation is regarding inline javascript. This can be solved through custom Dojo Modules using AMD loader. Dojo’s dojoConfig attribute allows runtime loading. The pane’sattribute can allow import of specifically needed JS modules / classes. This is a thought. I have not implemented this fully. However, the proof of concept of this exists at the Pluggable module aushadha_demographics_us tree.yaml file.
More on that on a later post.
Next Tutorial will be based on the core of AuShadha and its bundled apps
This will generate the application scaffold and populate it with basic import stubs. The folder structure will be as described in the PART 1.
1. Creating the model, views and urls.py
The models will be derived based on the US Demographics requirements here: Demographics
The model class inherits from AuShadhaBaseModel and the model form class will inherit from AuShadhaBaseModelForm class, which gives them some useful methods which they inherit.
Additionally, the AuShadhaModelForm class generates Dijits for display. The Dijits have to be configured in the dijit_widgets_constants.py file which is a python dictionary. This is will give the necessary Dijit declarative directives for generating the form widgets.
Once the models are done, the views and urls.py have nothing AuShadha specific about them. Basically we need views to add, edit, delete, view, json export the objects. The same can be represented in the urls.py
2. Determining the registration of roles
The aushadha.py file registers the role of a particular class in the application. Roles are purely arbitrarily made up by the developer. However, if he needs to register a class for a particualr role that has already been registered, he will need to use the same name so as to override the preexisting class.
For eg> a PatientRegistration model may do the role of Patient Registration in the application. Hence this can be registered for that role. AuShadhaUI class generates an instance per server run and this registers the classes for a particular role on startup.
Registration can be accomplished inside aushadha.py as
UI.register(<class_name>, <role_name_as_string> )
3. Finalise the UI layout with PyYAML
Earlier in AuShadha developement, Django Template with HTML, CSS, and JS was used to generate the layout. This sometimes requires extensive Dijit declarative HTML markup that was not easy on the eye. Additionally interspersed JS and CSS didnt help.
Hence a method of returning the UI layout as a JSON was devised using PyYAML library. On JSON return, this is parsed and the UI dynamically generated using Javascript. This has dramatically reduced the JS files required.
The required PyYAML file is located in the dijit_widgets directory. The pane.yaml and pane.py creates the necessary JSON
PyYAML directives are almost the same as Dijit declarative HTML markup except for the quotations and angled bracket distractions. I will devout an entire tutorial on this and how the JS file parses this. This is very early in AuShadha development so the markup, directive may change, but the principle is the same.
4. Study need for additional JS files
The add-on modules will have a media directory with sub-directories of js, styles, images to house modules of JS, CSS and images. Dojo has the new AMD loader that encourages modular design and the dojoConfig variable can be changed at runtime allowing full flexibility to add modules as needed. This is demonstrated by the grids in the application (Contact, Phone and Guardian grid). The relevent module that should be called by the loader is specified in the pane.yaml under the grid directives as gridStrModule.
5. Integerate or install the application
The application itself needs to be added to the INSTALLED_APPS. Integrating the application (or installing ) requires changes in the settings.py to set the paths for templates, scripts, styles and media. The Root urls.py needs to include the application as well. After the settings are done run syncdb to install the changes.
In case of Stock modules that clash with add-on modules, the stock modules will have to be removed, changes made to settings.py and urls.py to reflect this. This has to be done before syncdb is done.
AuShadha Open Source EMR has been made pluggable – well almost. The au_pluggable branch is meant to make it more pluggable that it was in master branch.
Issues the monolithic AuShadha:
Well, when I started this I myself was new to Django and programming in general. I learnt as I coded and as can be expected, there were code everywhere and it was not very pleasant. So I rewrote the app in many times from ground up before AuShadha came into being. I was at that time building something for myself – to use at my orthopaedic clinic.
When AuShadha was started, it suddenly dawned that there are now people participating; people who have never seen this code, and who probably will be put off on the huge pile of code to digest. Since there is already a lot of code out there, it is difficult for a developer joining a project or someone who does not want the whole AuShadha package to develop , rehash or add packages to it. The entry barrier was very high. I also seemed to be re-creating one of the problems that made me start and EMR project; I had found existing ones tough to customise.
In an ideal world, EMRs should vary. Data collection varies from hospital to hospital, country to country and speciality to speciality and to some extent practioner to practitioner. Except for gross repeatable elements that can be swapped, most of the EMRs have to be different. However, many are not. Its not common in India to see EMRs used by hospitals that do not fit into the Indian way of data gathering and its unique Demographics and other regional specifics. Some EMRs do provide custom form generation to tide over this and some vendors do provide some basic customisation. The solution has to be more robust.
My own experience with getting them to do that for us was poor. This is probably because the code is hardwired and they could not accomodate out request for a feature change easily. From their side it would involve extensive recoding and debugging, man power requirement, that could not be afforded when the system is live at a Hospital.
The user should be provided a decent package out of the box with the option of switching out elements as he / she sees fit, to develop his own variant of AuShadha. This would be the ultimate goal.
Why this tutorial ?
It became quickly clear that I had to do something about it before the project grew. So about 2 months ago I created the au_pluggable branch in an attempt to modularise AuShadha. Thankfully Django encourages pluggable modules. This process was not very difficult; except for the difficulties created by my mangled coding earlier 🙂
The purpose of the write-up is to show developers and other enthusiastic people who want to develop / test out AuShadha how easy it is now to create their own mix- and – match AuShadha brew. There is still a lot of work, but as it stands the process is simple enough for somebody to follow. It is intended to show how easy it is to create modules for AuShadha without knowing the whole codebase that is already out there.
The tutorial would be written in parts. This is the first one.
So, let us start.
As I said, one of the advantages of the current pluggability model it that it allows user to swap in custom implementation of a particular module. All this while retaining the inherent structure of Django. This is important as developers who would get involved with AuShadha should feel that the skill they improve here is usable outside of AuShadha. Therefore the customisations have be done on top of Django with no patching of Django or any hacks.
First, let us familiarise ourselves with AuShadha module directory and file structure. After that we will create a pluggable module for use. For example, if the user wants his own implementation of the Demographics module overriding the stock version he / she will do it as below. The procedure for creating new modules will also be identical to this, which will be examined in subsequent post.
Of course if the reader dosent care and just wants to build a pluggable module for AuShadha using raw Django, then there is not problem. He can just build a regular Django-app and intergrate it as usual and expect it to work; well, after some little configuration. No XML I promise.
Basic AuShadha-app structure
The basic Structure of an AuShadha-pluggable module is typically seen in the patient app ( called aushadha-patient )
models.py, views.py, urls.py, admin.py, media/, templates/ are directly from Django’s own system. Nothing much custom here. Standard Django roles are served by these files.
Custom action is mostly in dijit_widgets/ and its contents, dijit_fields_constants.py, aushadha.py, queries.py, utilities.py
AuShadha uses a system of PyYAML to serialize and generate the UI for each app. Each app can configure the UI layout using Dijit (Dojo) widgets using this markup. Whats’ wrong with HTML ? Well, this is way more readable, we can still use the goodness of Django’s template engine and PyYAML’s python object and function calls including pickling and this reduces the JS files. This way there is less to debug and quick prototyping and customisation of UI is possible. The dijit_widgets folder contains:
Folder Structure and contents inside dijit_widgets folder
pane.py, pane.yaml — > Django view to serve the ‘pane’ for the app. All customisation can be done in the corresponding pane.yaml using django template syntax / PyYaml syntax. It will be serialized as JSON and presented on request. This JSON will autocreate the UI. It is much more easier than using HTML with Django template for UI generation. Of course this traditional approach can be used just to generate Django forms and its validation JS code. This is what is done in the templates/ folder.
tree.py, tree.yaml — > Though not necessary for all apps, apps that do provide a tree structure to the UI can define this and use tree.yaml to generate the structure dynamically. Django template can be used as can PyYAML object notations. The JSON can then be passed to the client on request.
dijit_fields_constants.py — > (WARINING: This is going to be changed soon ) This hold the Python dictionary values for model form fields as Django ModelForm using Dojo/Dijit markup. This was before YAML became widely used in the project. This will be replaced soon with PyYAML markup like the Ui and this file may be moved into the dijit_widgets directory.
aushadha.py –> Every project when server is started creates a shared instance of AuShadhaUI class that lives in . This instance accepts registration of classes for particular roles they will perform in the EMR. Registration for the role and the class is done here. Each module is autoinspected for aushadha.py file on server startup just like admin.py file. The purpose for this is to create a role based central registry that registers classes for roles in EMR. This allow relative role based imports rather than path based module dependant imports allowing free module swappability. No more ImportErrors if that particular module is not present. For eg; if the patient module has been changed by say Author Mr. X and he has named it patient-mr-x and included in installed apps, along with a registration in aushadha.py for “PatientRegistration” role, as long as syncdb has been done, the class is picked up on first load and registered for that role overwriting the stock ‘patient’ app. All modules that need ‘patient_detail’ foreignkey do a relative import of the same in their models.py / views.py. This allows a Zope 3 like Interface like, Role based registrations allowing loose coupling. This is explained by me in my query to Stack Overflow here. Sadly, no answers came. So this solution has been rolled out. http://stackoverflow.com/questions/19100013/using-zope-interface-with-django
LICENSE.txt, MANIFEST.in, README.md, setup.py, docs/ are requirements to make this a python package. This will allow users to easing installation.
Having described the directory structure of AuShadha app and its contents, we will discuss the app creation from scratch in next part of the tutorial
AuShadha Electronic Medical Records project written in Python using Django and Dojo Javascript library has now a dedicated website with integrated Wiki, Blog and Discussion Forum at http://www.aushadha.org/
AuShadha Open Source Electronic Medical Records Project Update:
AuShadha is an electronic medical records project in Python, Django and Dojo.
AuShadha is getting ICD 10 Ready…. Just building an XML parser using elementtree module to parse the ICD 10 codes into a DB.
This is an update to AuShadha on the walk up to Version 1
I am rather busy lately which is why there has not been a post on this; its been quiet for a while, a little longer than I would have liked. The project though, has been far from quiet. Several Improvements both in UI and the back-end has been done and is continuing in a walk up to Version 1 vision put down in the Github Wiki Roadmap.
The gallery below is some samples of the improvements that have come along. These would not have been possible without the help of Dr. Richard Kim, whose constant advice , criticisms helped shape this and continues to do so. Developers involved with the project has been credited and integrated into the UI.
Predominantly the focus is on a balance between minimalism and functionality. It is known that minimalism is beautiful, but in a non-linear system like EMR the issue is that there may not be a workflow to speak off. People often need to random things at various times and expect the UI to keep things within reach. Initially I was not convinced about this, and my focus was more on workflow. Richard convinced me about this and now I see the light. However, my attraction towards minimalism has not been totally abandoned and try to achieve a balance.
As we see version 1 at the horizon, it will be nice to have your feedback. Do leave your comments and criticisms here.
Head over to Github , grab the code and let me know.
Refactored and redesigned Login Screen with repo link and the bottom
License Text along with Credits and About text like Desktop app. Github Wiki will also be included here
Redesigned Patient window with a two-pane design. Tree on the left pane. Horizontal splitter design on the right.
Redesigned Patient window with a two-pane design. Tree on the left pane. Horizontal splitter design on the right. Drop down menu is used to choose the pages and examinations to be added. This keeps the core UI simple and minimalist as possible without losing functionality
My Hospital has requested me to install Electronic Medical Records (EMR).
We are planning, as always, an Open Source Based EMR Solution.
I have desisted from offering my Open Source Electronic Medical Records -AuShadha as one of the options as its still in heavy development.Therefore I have advised two Open Source Implementations that I have short listed after scouring all the available choices that are listed in Wikipedia and Medfloss.
While some of the implementations are not in active development, others are not specifically meant for private clinics like ours. They are for developing nations to keep track of communicable diseases and other specific diseases and treatments. While it is possible to adopt and modify them , there are two Open Source EMR implementations that are reasonably good straight out of the box.
I have to implement and maintain them. I know Python. They are in Python.
Implementation should be easier and so will the maintenance.
Tweaking them to closely fit our hospital’s work flow and adding specific forms for data collection and research work should also be possible.
I personally tend to favour GNU Health, because of installation woes on GNUmed’s previous versions and what I thought was a complicated UI layout but recent communications with Mr. Stephen Hilbert and Mr. Karsten Hilbert, developers of GNUmed and an India doctor who uses GNUmed have forced me to take a second longer look.
This week then I will be installing both on our servers and opening it for use by doctors at our hospital for a month. The user friendliness and ‘tweakability’ will be assessed and then we will decide a month later on which to choose.
Keeping fingers crossed. Will give Installation reports, issues, user experience here once it is through.
AuShadha is undergoing a UI desgin makeover to fit into the present role. I had Open sourced my private EMR, so essentially I am stripping it of personal features and adding in the common use ones that will serve for a multiuser clinic.
Dojo 1.8 migration has already started and is currently in testing.
UI design for the pane controlling an admitted patient is as below. This is a mock up in inkscape and is likely to change.
Dr. Easwar T.R 