Tag: EMR

Developing Pluggable Modules with AuShadha Open Source EMR – UI building with PyYAML – Tutorial – Part 3

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:

Patient Pane
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

Advertisements

Developing Pluggable Modules with AuShadha Open Source EMR – Part 2

Creating a fresh application

For the purpose of this we will create a demographics application with data collection as done is USA.

The end result is available at http://github.com/dreaswar/Au-Pluggables

After activating the virtual environment run

$ python manage.py startapp aushadha_demographics_us --template AuShadha/app_template

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.

The fully developed application for US demographics collection is at http://github.com/dreaswar/Au-Pluggables

Part 3 will deal with PyYAML and auto building the Dijit UI Widgets with PyYAML and Dojo

AuShadha Icon Pack nearing completion !

This is a preview of AuShadha Icon Pack.

AuShadha my Electronic Medical Records project will be using this.

If is nearing completion and soon will be released.

The project is hosted on Bitbucket and is private now.

I am finalising the icon licences and attributions. Hence the watermark on the Screenshot.

Most icons are derived straight / modified from NounProject.

Please keep a watch on http://facebook.com/AuShadha/

Please watch this space as I will announce it here or on Facebook

Image.

AuShadha Open Source Public Health Management EMR System at GitHub has a official logo

Image Image

LICENSE: Image

Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License

AuShadha Project home: http://dreaswar.github.com/AuShadha/

Open Source Public Health Management EMR System in Django at GitHub is ready !

My GitHub repo for Public Health Management Electronic Medical Record is ready !

This is system that should be optimised for small Primary Care Providers especially in India and other developing countries. This is licensed as GNU GPL v3. Written in Django and Dojo

Visit http://dreaswar.github.com/AuShadha/

Guide to Successful Open Source Software Implementation in Hospitals – Some Difficulties That Needs to be Crossed..

      Its the age of Great Leap Forward..

People are happy, work goes on.. life is kind of strange with no BSOD but people are still carrying on.

One thing they are unhappy about.. They have to work. Gone or the days when their trusted OS used to giveway under then leaving them staring at a BSOD so that they could make a quick call to the IT in charge and go out for a coffee.

Excuses for work delay have come down.

So how did we get ourselves in this mess ?

We had to struggle.

What follows is a first hand account and a general guide for all Doctors who wish to implement Open Source Solutions / Software or Linux based systems at their workplace but are afraid to take the plunge.

For the technically minded Mr. Kumaran (http://kums.in) is preparing a more technically heavy note full of implementation details. Please watch that space.

 

Essential Reading

1) How we moved to Open Source at our hospital

2) Intranet &PACS

3) My Open Source EMR

4) EMR Implementation

Planning ::
==========

– Sit down and think what we want our computers to do for us and define a budget.

– This will dictate what software & hardware you need to get that
job done.

– Make the right Hardware and Software Investments. It is very easy to
get convinced by the vendor to invest more in features you may never
use / need.

– You need to choose you FOSS projects carefully.

http://www.ohloh.net/

http://www.sourceforge.net

gives you indices that help you decide the popularity of the software.

– Look Before you Buy: Always check the Linux Compatibility of the
hardware you are going to purchase after you have installed Linux.
While many will work out of the box, some will work after tweaking,
some may not work.

– Get the right persons for the job. There will be an element of luck
here. If you are, then you will find somebody passionate abt this. Consult them.FOSS enthusiasts and ready to help.

– Do your Homework: I worked for 5 years trying out one solution after another before settling on the ones I wanted. Since I know the work flow of my hospital, I naturally know what suits it the best.

– Keep it cheap. It can be done. Cost is important, even if you are willing to pay
more. Bargain hard. Buy only what you want. Dont by what you are
sold.

– Interoperability within and without your office. This is important.
When going down the not-so-beaten-before track. Detractors are many.
Complaints will be raised. It will be irritating. Don’t expect users
to share your idealistic vision. Every complaint needs to be
listened to and most of them can be safely ignored. Some of them
will give an idea of the gap that needs to be bridged.

– After-installation-service – accessibility, response time, ?365X24X7.
This needs support. If you have an in house reponse team that knows
FOSS solutions, then thats good, otherwise you may need to buy
support. My Open Source friends tell me that Red Hat support is good
and is value for the money paid. Decide on support. Lord Murphy is
always watching. Depending on the level of in house support there may be some investment here.

– Staff training had to be spot on so that there is no excuses
to put up your hand and say `open office is too tough`. This is the
most important. Implementation will fail otherwise. Management will
be inundated by complaints of `non-working’ computers. In our
Hospital. Mr. Kumaran cleverly themed Cent-OS to look list Win7.
Most users tech-savviness ends are very `iconic`, so thats all that
will require.

What did we do ::
=================

– Even when we had the WinSystems I stood firm and never let the management invest in MS office. It was unnecessary. Complaints were many ranging from inability to open external files to difficult UI.

Some of the complaints, especially UI related were somewhat relevent, but I decided not to pay heed. These have settled down.

– Avoiding repeated investments to tide over a initial improper investment: The Pros kept telling us to invest in Teminal Server License but we stood firm. I kept telling the management that that takes away the advantage of cost and that I could run it better without any further investment by installing Linux. There needs to be a strong FOSS enthusiast in whom the management has trust. Otherwise the Corporate win.

– Kept to a budget: When we cut off all the frills like antivirus, firewall, terminal license we cut off all the recurring expenses.

Know what you want and buy only that. They will try to sell you more; thats their job. Let them do theirs, and you do yours.

– Choose your FOSS projects you wnt to implement: Now that you have got the courage to implement, use only well maintained and mature FOSS projects. We have Cent OS , Ubuntu, Zope & Plone, mysql, postgresql, dcm4che,JBoss – all mature and well maintained. For EMR you can use Open EMR, Open MRS, GnuMed, GNU-Health. There are several DICOM viewers you can use depending on the data you want : Oviyam, Mayam, Osirix(Mac), Aeskulap, GingkoCADx, inVesalius and many more. ImageJ is useful with its Java plugins for image analysis.

-Use the LTS version of the OS if possible. Install it on the staging system first. Train all the staff, get them to use it everyday and stress the system. This will give you an idea as to what kind of server you need now and when you expand in future.

– Training. It is important to train the staff. This is paramount. Our Admin Officer (AO) who also looks after IT complaints goes around doing all the minor trouble shooting and doubts. Once the staff realise work has to be done with this, they keep quiet and try to learn. We do Plone/Zope training many times a week. The software vendor and our AO do the Hospital Software training. The basic use of a Linux thin client interface has been taught. The theming is very handy for bridging the gap.

– Firewall. Set up a linux firewall and set up basic access rights to prevent unauthorised access to internet. Setup a secure Wireless. This will help access to Intranet, PACS, EMR over mobile and touch devices and also allow remote access.

Accept the Sore Areas:

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

Medical Presentations: Right now its only MS office. Even Mac guys have trouble presenting many times; atleast in India. This will need users to use their personal MS office products to prepare their presentations. Sadly Libreoffice Presenter leaves much to be desired. It can do the basic .ppt export, but cannot be relied upon

Printer Support: This will need you to look before you buy. If you have expensive existing systems please evaluate. We could not use two network printers (Sharp)after switching over. They are both aged, so replacement is an alternative.

External DICOM applications: Many patients come with CDs with bundled DICOM viewer software. This may not work in Linux ; even under wine. Depending on the type of practice this may be a problem. In our current practice most patients come with printed films so it is ok. Some of the DICOM viewers open / the CDs can be opened with Aeskulap, but GE PACS cd usually dont.

.docx files: People send you MS Office files of all kinds. You cannot expect them to save it in a legacy format. Ubiquity of MS Office and Win make them expect a reply when the files are received. MS office 2007 – 2010 files are an issue. Simple ones open. Extensive use of animation, graphics causes improper rendering. Usually Office communications are bland letters which open without an issue. For academic presentation use, we suggest you rely on a personal copy of MS Office in you laptop.

Hopefully these basic guidelines will help people to switch. This is first hand account. That should be encouragement enough.

We have made it happen at our Hospital. It is comfortable. Transition has been very smooth with most users not even knowing the OS has changed. They only feel the computer is faster.

Please feel free to leave comments in case of any implementation queries.
As I said before watch http://kums.in for technical updates.

My Neurology Charter app in HTML and Javascript – Design Preview

An Neurology Charter app in Javascript and HTML.
As of now this is Standalone but this will be integrated into the EMR.
This is still very-much-beta. Design & Functionality will change considerably before I go final.

Neurological Examination App
Neurological Examination App

Django EMR , Dojo (OrthoDocx) – jQuery (OrthoEMR) comparative Interfaces

The entire application interface is basically a tabbed top and bottom container for Patient management.

Patient list grid is basically a list with Datagrid with a jsonRest store. The Django view will return the json. The row click will  fill the bottom tabbed panel with appropriate contact, phone numbers, email, guardian, admission and visit info for that patient.The double click will allow editions / deletion of the patient if the user has the permissions.

Application currently uses Django 1.4, PyYaml, PIL, ReportLab, PISA(html5lib) and Dojo 1.7.2

The icons currently being used are from KDE but that may change.

 

The second sreenshot is the comparative interface in jQuery. There is no bottom pane here. Left sidebar shows the context info on patient selection from the list. The Right sidebar is hidden if the screen resolution is below 1024 and shows itself on zooming out / clicking the icon at the top left.

This interface uses jQuery, jQuery UI and plugins for the table with heavy CSS and jQuery customisation.  The icons used are mostly from the tango project with a few from the silk collection for web. I have made some of my own. Some icons are just place holders and i need to work on them to make my own ones.

Image