Category Archives: openMRS

OpenMRS Radiology Progress

For those that haven’t been keeping up with the blog, I joined the OpenMRS team as part of a class project. Over time, I have encountered some issues with the software.

3 weeks ago, Ivo, a member of the OpenMRS Radiology team from Austria, showed us how to run the OpenMRS software properly. I found the Skype tutorial somewhat interesting, and I figured I’d use his information to help me with the ticket we were given recently.

2 weeks ago, I started catching up to the rest of my team by installing the software necessary to install the OpenMRS Radiology code as well as the puppet software. Although I had no problems installing, part of the conflict for that Monday was mainly the wireless network and its slow download speed at the time.

Last week, I tried to run the puppet software through Vagrant and VirtualBox, the 2 programs I needed to run the software. Unfortunately, after about 2 minutes of getting the virtual machine running, the Vagrant software times out trying to boot. A discussion with a classmate and Dr. Wurst later, we thought my issue had to deal with the internet connection. I was running my PC on the school’s wireless connection at the time.

As soon as I got home that Friday, I tried running Vagrant again, only to have the software time me out again trying to boot the virtual machine. This time, I was running the software from my home’s wireless connection. I hope next week, if problems persist, I can try running the software on a wired connection. I’ll keep up to date next week.

From the blog cs-wsu – jdongamer by jd22292 and used with permission of the author. All other rights reserved by the author.

Setting Up OpenMRS Core

This task seemed fairly simple at a glance, detailed instructions, clear screenshots, and a group of classmates doing it together; what could be so difficult? To start off I had cloned the openmrs-core repository from github into my eclipse workspace. After doing so I had imported it as a git project from a local repository. After doing so I needed to convert the project into a maven project. After doing so I was able to run the project as maven clean then maven install with build success! Doing this was just the beginning. Next was to get it to work on command line and be able to run the UI for the EMR that we will soon be creating modules for. After getting into the top level of my openmrs-core directory I ran mvn clean install with another build success. Next I needed to download MySQL in order to have access to storing patient information and to also import the demo data that was given to test the EMR. After installing MySQL and then moving one level down into the webapp folder I ran mvn jetty:run. This connected me to the jetty server where I could see the UI. After going to the EMR setup I had found out that the UI was not  installed with the latest version of OpenMRS. I had to clone another git hub repository with the UI and run mvn clean install from command line to create an .omod file. This was then moved to my appdata directory inside the modules directory of OpenMRS. Finally! The last step was to go back into webapp and connect to the jetty server. I was now able to sign into the EMR and get OpenMRS core working. All that is left is to find out what tickets need to be worked on in the Radiology module.This was very time consuming as the project instructions were out of date or missing some information that would have helped along the way. The OpenMRS project is a great tool to help people around the globe and I hope to contribute meaningful work to this project!

From the blog CS@worcester – Greg Tzikas by Greg Tzikas and used with permission of the author. All other rights reserved by the author.

The return

I suppose it’s time I wipe the dust off this inactive blog and bring it back as I start working on a new project. As far as I know, the project is called OpenMRS. More details will come as I find out more.

For those that don’t know me, hello. I am John Donas, Computer Science senior at Worcester State University. I transferred to this school in 2013 after graduating with an Associates at Quinsigamond Community College. My experience in the field includes a project in QCC called AutoeXplorer, an internet browser designed with the intent of allowing users to record their browsing and play it back at any time.

OpenMRS seems interesting based on what I’ve seen of it. I hope to work more with it as this semester continues.

From the blog cs-wsu – jdongamer by jd22292 and used with permission of the author. All other rights reserved by the author.

Sabbatical Restart

Summer is over, and it’s time to really get to work on my Sabbatical project.

I did do some work this summer – I’ve read 3 of the books on my Sabbatical Reading List (and added a few more to the list) and I’ve finally de-lurked on the OpenMRS developer mailing list and in some of the online meetings, and I’ve made a decision to convert all of my course materials to Markdown (the better to track changes on GitHub – see a future post). But, it’s all been pretty passive.

So, the Friday before the Labor Day Weekend, I decided it was time to get back to the “develop code in OpenMRS” part of the project.

Since it had been a couple of months since I had set up  my development environment and tried to build the OpenMRS code, I decided that starting over from scratch (mostly) would not be a bad idea. Here is what I did:

  1. Read OpenMRS’s Getting Started as a Developer wiki page. I had already set up my OpenMRS ID, and signed up for the developer mailing list. I already had a GitHub account, as well.
  2. Read Development ProcessfromOpenMRS Developers’ Guide, and got the code:
    1. Fork openmrs-core repository.
    2. Clone my fork onto my computer.
    3. Set the OpenMRS repository as my upstream remote so that I can pull changes from the main project into my local working copy.
  3. Set up development environment based on Get Set Up from the OpenMRS Developers’ Guide. I chose the section on Manual Installation because Iwantto be able to develop code fortheOpenMRS core application. I followed the general outline of this section, but went about some of the software installations differently.
    1. Install MySQL. Because I am setting up my development environment on a Mac, I installed MySQL using Homebrew
    2. Install Maven using Homebrew
    3. Install Git using Homebrew (actually, I already had Git installed, but I made sure it was up-to-date)
    4. BuildtheOpenMRS code: 
      cd openmrs-core
maven clean install
    5. RuntheOpenMRS web app through the jetty server: 
      cd webapp
mvn jetty:run
    6. The first time you run the web app, it will take you through the Setup wizard
  4. Set up Eclipse. I already had Eclipse installed, but I made sure that my version was up-to-date. Eclipse had been updated to a new major version (Luna) since the last version I installed (Kepler). 1
  5. Git IDE Integration: Since EGit is already installed in current versions of Eclipse, and I’ve already forked and cloned the repository, I really only needed to do the To import as a Maven project section, to get the the projected into Eclipse.
  6. Build the OpenMRS code under Eclipse. I followed the steps in the following section:
    1. How to run the build
    2. How to run Junit
    3. How to Run Web Application

Now that I have a working environment that builds and runs, the next step is to choose a ticket to work on.

  1. In the past, I had just downloaded the newest version, and replaced what I already had installed. I figured that there must be a way to do the update without having to reinstall and reconfigure all of my plugins. It turns out that you can add the release’s repository to the Available Software Sites: http://wiki.eclipse.org/FAQ_How_do_I_upgrade_Eclipse%3F ↩

From the blog On becoming an Eccentric Professor... » CS@Worcester by Karl R. Wurst and used with permission of the author. All other rights reserved by the author.

De-lurking…

I have been lurking in the OpenMRS project for the last 6 months or so. I have read wiki pages, installed the development environment, cloned the repository and built the code, and listened in on a number of OpenMRS weekly developer meetings.

As I begin my sabbatical, I realized that it was time to finally introduce myself to the project members. So here’s what I posted to the OpenMRS Developers mailing list, and to OpenMRS Talk:

My name is Karl Wurst and I am a Professor of Computer Science at Worcester State University in Worcester, MA, USA (about 80 km west of Boston.)

Our university has recently created a concentration in Software Development for our Computer Science majors, and I am one of the primary instructors for the courses in this concentration. I am currently on sabbatical (no teaching responsibilities) from June through December 2014 and my plan is to participate in OpenMRS to improve my somewhat outdated Software Engineering skills.

I have installed the development environment, built the openmrs-core code, and now I will begin looking for tickets that I can work on. I am excited that the 1.10 beta release is imminent, and hope that I can be of some help in that sprint. I am also very interested in the development, testing, integration, and release processes as a way of seeing “real-life” examples of many of the tools and technologies that I have been reading about, but not had any hands-on experience with.

I am also part of the Foss2Serve/POSSE (foss2serve.org) group that is encouraging faculty to have students participate in Humanitarian FOSS projects as part of their coursework, and have been doing that primarily with our senior project course with varying amounts of success. I would like to have my students participate in OpenMRS beginning with the Spring 2015 semester (January through May 2015.) I want to get familiar with the project myself, first, so that I can direct them.

I also want to use OpenMRS for examples in our courses on software process and management, and testing and QA. We also have an installed server instance that we hope to use for the Health Informatics course that we teach for our Nursing students so that they can get some hands-on time with an EMR system.

I’ve already learned a lot just by exploring and listening. I’m looking
forward to learning even more by contributing.

A note to my students: Introducing yourself to a new group of people is hard, even for faculty members! I have put this introduction off for a while. I may be a Professor, but these people are real experts – they do this stuff all the time, and many of them do it for a living! But, as I’ve often found, once I forced myself to write my introduction and pressed the send button, I’ve gotten back only helpful, welcoming responses. Open Source communities really are welcoming groups that are genuinely happy to have you join, want your help, and will help you succeed. You’ll see…

From the blog On becoming an Eccentric Professor... » CS@Worcester by Karl R. Wurst and used with permission of the author. All other rights reserved by the author.

Fall 2014 Sabbatical

I am spending the Fall 2014 semester on sabbatical1. This is the proposal I submitted to request my sabbatical leave:

I will use my sabbatical to become more expert in the area of Software Development/Software Engineering. The Computer Science Department recently created a Concentration in Software Development, which has expanded our course offerings in this area from two courses to four courses. This expansion does not simply expand the number of hours we spend on Software Development topics, but adds many topics that we have not been covering at all. Many of these topics are outside the expertise of any of the faculty in the department.

I am the only member of the Computer Science Department who has worked as a professional software developer, but have not worked professionally in that field for over 20 years. Many of the current processes, techniques, and tools were not in use at that time. The members of the department have worked to learn these new skills so that we can teach them to our students, but have only an academic/theoretical knowledge of many of them – we lack the practical experience of using these skills in a professional environment.

During my sabbatical, I will learn the processes, techniques, and tools of modern software development, and apply them in a professional context by working as a full-time (but unpaid) developer within an open source software project. I will work with Dr. Heidi Ellis at Western New England University and Dr. Gregory Hislop at Drexel University to get the academic perspective on how to teach these skills to undergraduate students, and to take advantage of their experience working with, and their contacts within, open source projects.

Drs. Ellis and Hislop are both well-known software engineering researchers and software engineering education researchers. They have been on the forefront of work to help students develop professional software engineering skills by working with open source software projects. They have a particular interest in having students work within projects with a humanitarian aspect. I have done some work with them in this area over the last 4 years, but have not had the time to work exclusively and intensively on developing these skills myself. In addition, Dr. Hislop served on the committee that developed the SE 2004 software engineering curriculum for the ACM and IEEE, and is currently serving on the committee that is updating those standards. I have already tapped his expertise in developing our new curriculum, and plan to do so again as we develop the new courses in the curriculum.

Proposal
  1. Develop a list of processes, techniques, skills, and tools that are necessary for modern software development. Thislistwill bedevelopedin consultationwithDrs. EllisandHislop, by reviewingtheSLOs of our newly approved Software Development Concentration courses, and by reviewing the SE 2004 Curriculum and any publicly released drafts of the new ACM/IEEE Software Engineering curriculum. This list will include,atminimum:
    • Agile development processes
    • Automated build environments
    • Automated test environments
    • Version control systems
    • Software architectures
    • Design patterns
    • Requirements elicitation
    • Software licensing and intellectual property
    • Project planning and estimation
    • Risk management
    • Analysis techniques
    • Test planning, strategies and techniques
    • Test coverage
    • Code reviews
    • Quality assurance
    • Project and team management
  2. Select an appropriate humanitarian open source project to participate in. The project will be one which
    • Allows me to experience the full range of processes, techniques, skills and tools from the list above. (Or as many as possible.)
    • Allows me to use tool and language skills I already possess to minimize the number of new tools and languages I need to learn.
    • I can continue to use with students in the Software Development Capstone course, and with other courses in the concentration.
    • At this point, the two projects that seem most likely for my participation are:
      OpenMRS (http://openmrs.org/)
      “The global OpenMRS community works together to build the world’s leading open source enterprise electronic medical record system platform.
      We’ve come together to specifically respond to those actively building and managing health systems in the developing world, where AIDS, tuberculosis, and malaria afflict the lives of millions of people.
      Our mission is to improve health care delivery in resource-constrained environments by coordinating a global community to create and support this software.”
      Ushahidi (http://www.ushahidi.com/)
      “We are a non-profit tech company that specializes in developing free and open source software for information collection, visualization and interactive mapping. We build tools for democratizing information, increasing transparency and lowering the barriers for individuals to share their stories.
      “Ushahidi”, which means “testimony” in Swahili, was a website that was initially developed to map reports of violence in Kenya after the post-election fallout at the beginning of 2008. Since then, the name “Ushahidi” has come to represent the people behind the “Ushahidi Platform”. Our roots are in the collaboration of Kenyan citizen journalists during a time of crisis. The original website was used to map incidents of violence and peace efforts throughout the country based on reports submitted via the web and mobile phones. This website had 45,000 users in Kenya, and was the catalyst for us realizing there was a need for a platform based on it, which could be used by others around the world.”
  3. Participate in the selected project. Iwillparticipate in the selected project on a full-time (unpaid) basis, contributing to the project in whatever ways I can including:
    • Participation in planning and design meetings
    • Writing code
    • Testing
    • Writing documentation
    • Helping with support
  4. Participate in Western New England University course. I would like to observe or help teach a software engineering course at WNEU so that I can see what pedagogy is used in the course, and adapt it to our own courses.
  5. Blog about my experiences. I will write about my sabbatical experiences on my blog (http://blog.karl.w-sts.com/). This will allow me to document and reflect on what I am learning and how I can use it in our own courses.
Preparation for this Sabbatical
  • Participant in POSSE (Professors’ Open Source Summer Experience) in 2010, 2011, and 2013 – A workshop designed to prepare faculty to support students working within open source software projects. The summer 2013 workshop group is continuing to work together over the 2013-2014 academic year.
  • Participant in SoftHum (Software for Humanity) workshop in 2011 – A workshop with faculty working to design materials for use in their courses.
  • One of the organizers of Teaching Open Source Symposium in 2012
  • Participant in OpenFE Materials Sprint in 2013 – A workshop to develop materials for teaching POSSE workshops
Relevant Courses
  • Introduction to Programming
  • Software Construction, Design and Architecture
  • Software Process Management
  • Software Quality Assurance and Testing
  • Software Development Capstone
  • Software Development Process
Benefits to the Computer Science Department and to the University

The department will benefit by having a faculty member who has relevant professional experience in software development, with contacts within at least one open source software project, and with the academic experience of applying that experience to courses. I will be able to use that experience and those contacts in order to give students the opportunity to gain valuable practical experience working within a large software project on the same types of tasks and using the same kinds of skills that they will be expected to use in their professional careers.

The University will benefit through a strengthened Computer Science program, by having a higher profile in the software development world, and being recognized as an organization that has donated a semester’s-worth of work of a full-time faculty member to further the mission of a humanitarian project.

There have been some changes since I wrote the proposal and it was approved:

  1. IchoseOpenMRS as the project that I will be working within.WhileUshahidi seems like a very interesting project,OpenMRS seemed to fit better with my goals for the following reasons:
    • It is written primarily in Java, which is the language that we use most in our Computer Science courses. (Ushahidi is written primarily in PHP, which we do not teach at all.)
    • OpenMRS seems to have a more “formal” software development process and tooling, which I think covers more of the topics on the list of what I want to learn.
    • We can use OpenMRS as a tool in the Health Informatics course that we teach for the Nursing majors, to provide an Electronic Medical Record system for the Nursing students to try out.
  2. I participated in the Teaching Open Source Symposium at SIGCSE 2014 and in POSSE 2014.
  3. I increased my use of Open Source tools both in my own work, and introduced them in our first-year courses.
  4. Students in my Spring 2014 capstone course did some work within the OpenMRS project.
  5. I started attending OpenMRS online meetings to familiarize myself with the project.

I will be writing more about sabbatical as the summer and the semester move along.

  1. For those not familiar with the ways of academia, a sabbatical is a paid leave awarded every 7 years to allow a faculty member time for research or updating skills. ↩

From the blog On becoming an Eccentric Professor... » CS@Worcester by Karl R. Wurst and used with permission of the author. All other rights reserved by the author.

OpenMRS DB issues

I wrote a detailed blog on what I have done since my last entry and in an attempt to undo a paste I hit cmd+z and it deleted everything I wrote. In my anger and frustration I will not be redoing it in as much detail. Essentially what I have been working on was trying to get the correct configuration for the mySQL database. I initially installed mySQL with homebrew. I think this led to some configuration issues so what I did was uninstall the homebrew version of mySQL and re-installed it with the mySQL .dmg that is provided from the mySQL official page. Once this was done there were several steps to take to configure mySQL. I used the instructions provided here for the installation, and here for the post installation configuration. Finally I followed the instructions here to change the root password. Once mySQL was all set up I started tomcat and hit the openMRS site. This launched the initial configuration to the DB, I chose the simple setup with the demo data. Once this was complete I found that I did not seem to have any of the data. To solve this I followed the instructions here. Once the data was added I was able to search for a patient and find one. After that I was able to add a drug regiment which was what we needed to be able to test.

Once we added the drug to a patient we could see where the drugs that a patient is on are populated and the buttons that come along with them. This lead us to decide to redesign how our functionality was implemented. We added a button at the bottom that will have a box open where you can select a drug that a patient is on (a feature that we found doesn’t work as we thought), modify the dosage and how often they should take it. We want to move this box up so that it comes more inline with the buttons that are present with each drug.

This is how it currently looks:
You click the button next to the green arrow and the content in the green box comes up.

We want it to look more like this:

This is what we will be working on now.

From the blog A blog about things by TRStaake and used with permission of the author. All other rights reserved by the author.

A blog about things 2014-04-07 14:03:00

Since my last post Matt and I have accomplished a few things. One we finalized the layout of the modify dosage feature we are looking to add. What we did was mimic the layout of the section used to add a new drug regimen. When you click on the modify dosage button a box opens up in the current window that has an area to modify the a drug regimen. The box contains a drop down populated with all the current drugs that the patient is on. There is also a text box to modify the dosage. There are some drop downs to modify the frequencey of drug administration, There is a “start date” box that will pop up a calendar that you can use to select a date. We added a Submit button that should submit the data and a clear button that will clear all fields.

Since the layout is all set now all we need to do is test. This is where we are coming into some issues. We are not able to add drug regimens to a patient. This makes it impossible to see if our drop down will populate with all the medications that the patient is on. Since we can not add a drug regimen we can not modify one. We are currently working to find out what is the issue here. My guess is that it has to do with the DB that we are connecting to.

Another thing that we have done was create a build script that reduces the time to deployment. Initially, when we run a maven clean/install it takes about 8 minutes to build and deploy. This means that any changes we make and want to see will take at least 8 minutes. We cut this down to about 1 minute by running the maven install with the skip tests flag.

  • mvn install -Dmaven.test.skip=true

While this helps in development we realize that the unit tests are important and so once we have reached a state that we are happy with we run the build with the tests as normal.

From the blog A blog about things by TRStaake and used with permission of the author. All other rights reserved by the author.

A blog about things 2014-03-10 14:03:00

Since my last Blog I have done a lot of work to get my workspace up and running. I first had to download and install java EE version of Eclipse from http://www.eclipse.org/downloads/. 

Once I had the EE version of eclipse i set out to make sure that EGit was installed and configured. It was already installed out of the box. So I cloned my project and then imported it into eclipse as a maven project. All this was done by following these instructions. 
Once that project was in my eclipse I built it by right clicking on the project -> Run As->Maven Clean. Then right clicking on the project -> Run As->Maven install. 
This kicks out a open.war to webapps/target folder. Then I deploy the openmrs.war to webapps folder in tomcat and am able to access the site via localhost:8080/openmrs. 

From the blog A blog about things by TRStaake and used with permission of the author. All other rights reserved by the author.