The End

The semester is coming to an end and I have to formally end this blog at some point.
OpenMRS
Contributing to OpenMRS has been a great time. I have enjoyed the things I have learned by contributing. Many of the things I have experienced on this large project I have actually seen in the work place at my internship. I believe working with this project was invaluable. I would have hoped to contributed a little more but I am glad that I got to contribute something. Every little bit counts right?

Turns out I didnt get a chance to finish my last bug fix. I started to fix the problem as I saw fit but as I dug deeper into the problem it actually turned out to be too large of a bug to handle. I would have not had time to refactor some of the unit tests that needed to be worked on, given the permitted time. I hope that the OpenMRS team has apperciated our team's contributions and I actually hope to contribute again if I have extra time to work on the project. I think I have a lot more to learn and I think OpenMRS would be a great medium to use.

CSCI Software Engineering Practicum
My experiences with this class directly coincide with experiences with OpenMRS. All positive here. I have enjoyed this class and I believe it has really helped me in preparing for working in industry. I recently obtained an internship here locally and many of the tools and techniques discussed and used in this class have been used. This blog itself actually helped me secure my internship and was a great presentation point during my interviews. I think the most important thing learned in this class was how to work with large code bases and large projects. It is a great experience to dive into a large project and have to learn about in a short amount of time. Being able to adapt to a project and educate yourself on it is a very important quality to have in the workplace since more times out of none you this is exactly what will be happening to you (makes you appreciate documentation).




Final Notes:
Please check back on my blogger as I hope to blog about some other experiences as I grow as a computer scientist. This has been a useful tool for me and I want to use it again if I can. Please if you have any questions feel free to email me through my contact Info.

Thanks,

Joshua Walton
Undergraduate
College of Charleston
Department of Computer Science

OpenMRS individual bug fix

So the semester is starting to come to an end and everyone in team handicapped is working on individual bugs to fix in order to contribute to the project as a whole. The OpenMRS project has been changing a lot in the last few weeks. OpenMRS has now moved to a SCRUM like methodology for their main development team. OpenMRS now concentrates on a specific development issue for two weeks at a time. These sprints help the development team conquer individual issues very efficiently. Last sprint's theme was the OpenMRS 2.x UI framework design and development. Here are some stats that were sent out on the dev list:

• 7 people used the 2.x UI framework to create patient dashboard fragments
• Abbas Hachem: patientPrograms
• Darius Jazayeri: personDetails, patientIdentifiers, standardPatientHeader
• Jeremy Keiper: personNames
• Mike Seaton: personAttributes
• Rafal Korytkowski: personAddresses
• Wyclif Luyima: patientProblems
• We did a pretty good job of navigating distributed locations and time zones
• We completed 18 tickets
• the dashboard fragments, and assorted framework improvements I made in response to people's requests
• We didn't get to 3 non-essential tickets
• Each participant made useful suggestions about features the framework needs, improvements to widgets, or to our patient fragment conventions.

It seems to me like these sprints have been very useful for OpenMRS.

There is one problem with the new methodology that I was concerned with. How was team handicapped going to contribute? I promptly asked Ben Wolfe, who is now my go-to-guy for OpenMRS questions, if we had to only work on sprints. Turns out we can work on whatever tickets we want. Sprints are simply the recommended process of contribution.

After my conversation with Ben our group sat down and planned out an individual bug to work on for each of us. Right now I am working on TRUNK-2148. This bug is related to the JUnit tests within OpenMRS. Right now some tests are reporting ERROR to the build log. OpenMRS dev team has requested that they be logged as INFO instead. My job is to find every place the log.error is used within OpenMRS code and change it. No Problem! Just so happens there are 723 matches within eclipse's search. I've got some time to work on the project later this week so i hope to finish parsing the project this week. This fix might take some time because direct communication with some of the lead devs is needed to find out the functionality of each error that is logged.

My plans for contribution later is to somehow contribute to the creation of OpenMRS 2.x. I think there is lots of opportunity there and I would like to dive into it.

Til' next time...Adios.

POSSCON and more...

POSSCON Results
So POSSCON was a huge success in my eyes. It was great to meet people that were very enthusiastic about open source software. I think the open source community is moving in the right direction and I think more and more software solutions are going to become open source. It was interesting to see the input from some various computer scientist veterans about how open source can be useful. I found John "mad dog" Halls speech very interesting. Hall talked about his take on open source and how much money it can really save businesses. I also like that he emphasized the fact that software is only as valuable as someone makes it. If you NEED software badly and it can help you very much, then chances are that software is extremely valuable. This idea is very interesting because when you think open source you think of "free", at least I do. This is not necessarily true. Open source software can be very valuable and can be a point of profit for someone. Overall I believe POSSCON opened my eyes just a little more to the possibilities of open source and most of all reinforced its goodness.

OpenMRS Plans, Future, Work, Etc.
We haven't had much progress as a group on OpenMRS these past few weeks. Bobby Strickland did a feasibility study on our first scheduled bug and discovered the bug is fixed in later versions of OpenMRS. I presented the idea that we could extract the solution and patch it with the requested version since there is a possibility that someone is running an older version and doesn't want or can't update to the latest stable version of OpenMRS. I believe I will try and revert my code to the requested version and offer a patch to the bug submission. Our other goals this week is to find another bug to work on in order to fulfill our requirement. Overall I have become very comfortable with the OpenMRS project and I feel like we are able to get around with the code very well. Better get to contributin' !

POSSCON 2011

A part of the curriculum of CSCI 462 involves attending POSSCON 2011. POSSCON will have many speakers and many different workshops and I hope to attend to attend as many as possible.

Here are a few people I would like to talk to:

1. Jim Jagielski - I think it would be interesting to talk to Jim Jagielski. Jagielski is the current president of the Apache Software Foundation. I think it would be intriguing to talk to Jagielski about future apache projects and which projects he thinks are the most important. Apache has a large amount of software and i think that all of them are very important to the Computer Science world and specifically software engineering.
   
2. Dr. Sam Bowen - I would like to talk to Bowen because of my interest in Open EMR's. This whole semester i have been working on OpenMRS which is another open source EMR. I would like to see his take on the subject and maybe ask him some questions regarding the differences between OpenMRS and OpenMRS.
   
3. David Duggins - I would like to meet Duggins and ask him about startups and his take on using open source to create new businesses. I would like to ask him bout the primary advantages and how much of an actual advantage open source would be. I would also like to see some real world examples of businesses that have started using open source software.

Overall I am very excited to get to POSSCON and get to meet  some of the important figures in the open source world.

The Plan, Stan...

Our latest team goals included coming up with a road map/ schedule for the rest of the semester. This involved finding bugs, features, or other contributions to work on for the rest of the semester. Our team found a few different bugs and features that we are hoping to be able to contribute to.

1. “Password Change” - This is a non-essential bug that needs to be fixed in OpenMRS. This bug allows the administrator to select requirements for a password (numbers, letters, etc.) but the password message always reads “Must be at least 8 characters long, contain an uppercase character, and contain at least one number”. This could be a major error for implementations that create different password properties.
   
   
2. “OpenMRS 2.0 Wishlist” - This is a non-essential fix for a specific implementation of OpenMRS. This implementation is located in Lesotho, which is located in South Africa. The implementation needs a few changes that are important for the locale of the implementation. Our goal for this fix is to fix a few of the changes that are requested, not all of them. This fix is particularly interesting because we would be working on an actual implementation.

Overall I believe all of our goals are achievable and I think it will be a good experience to dive deeper into the OpenMRS project. Our patch for our previous bug was a good intro into OpenMRS API. I believe we have a much better knowledge of OpenMRS.

In addition to finding issues and creating a road map, we also are looking to submit our patch for code-review. We have had the bug assigned to us and hope to upload the patch in the next 24 hours. Lets cross our fingers and hope it was a good fix.

Wish us luck.

OpenMRS Preferred Patient Fix

Progress on the home front...
Our group has finally solved our bug. As described in my previous blogs, OpenMRS does not require that you have a preferred patient ID. Our patch now fixes that and requires that a user enters a preferred patient ID. Our fix required quite a bit of research on our parts to find how OpenMRS uses the SpringMVC framework for patient form validation. After finding out where OpenMRS had their validators placed we were able to go ahead and create a new validator and its entities in order to require that the user input a preferred patient identifier.


Plans for the future
now that we have fixed our bug we are thinking of creating a code repository, which we really didn't need before, in order to handle the changes within our group. Our next process for our bug fix is to post our patch for code review within the OpenMRS ticket system(JIRA). Right now our group has not decided on a contribution for the rest of the semester but we hope to have one chosen and a road map in place by the end of the week.

Playing Catch Up

Whoa! Almost let this blog die...
I have a few things I'd like to catch up on and discuss.


CS Alumni Symposium
First I'll talk about the computer science department's alumni symposium. Our department put on this symposium for current students and in my eyes it was a huge success. Previous graduates came to offer their advice about graduating and getting jobs. I thought all of this advice was very useful. Seeing these graduates and how successful most of them are is a very big eye opener. It reminded me that I am involved in a career field that is constantly in need of new people. It's good to know that finding a job after school will be easier than most. I also got to talk to Jason Youmans of Bibliolabs who gave some good ideas about internships. I think that the main message that i took away from the symposium was that I need to get extracurricular with my computer science and get involved in something I'm passionate about. Overall I thought it was a successful meeting.

Team Project and Bug Fix
Fixing our bug has pretty much been a flop so far. Most of us have had other school work to deal with the past week or so. It has been slow moving. I did make a minor amount of progress the past few days.

I am starting to try and learn Spring MVC which deals with the form submission in OpenMRS. If I can figure out how the form submission redirects when there is an input error I can just use that same technique when the "preferred patient" is not selected. This should be easy to do within the next week. Hope to have a solution very, very soon.

After we get done working out this bug I hope to work on a bigger issue with OpenMRS and make some major contributions with our group for the semester.

TOSS Chapter 7 Exercises
...........................................

Bug Tracking OpenMRS using JIRA

Issue tracking is probably one of the most important aspects of open source software development. Evolution of open source software depends upon a community resolving problems.

OpenMRS is most certainly an open source project, and also has an issue tracker. OpenMRS uses JIRA to track all of it's issues. Issues include a bug, defect, task, improvement, incident, etc. JIRA does a great job of reporting, filtering, and designating issues. I found it very easy to navigate issue tickets and find some information that exercises in "Teaching Open Source" requested.

The oldest bug in OpenMRS:
TRUNK-330 is the oldest ticketed bug in OpenMRS that is still open. The bug is described as the following:

• audit trails for obs - can only change one attribute at a time.
• double data entry

Since I am just getting involved with the project it is hard to tell what the bug's domain and nature is. I hope to figure this out with time. My guess is that it hasn't been solved because the bug is probably insignificant to future development.

Creating a JIRA Account for OpenMRS
I was able to create a JIRA account for OpenMRS very easily and I am now ready to report or solve tickets within OpenMRS. Since our project will most likely involve fixing a minor bug, this is very important.

Reproducing a Bug
First I went into the JIRA issue tracker and picked the revision/version of OpenMRS that i have checked out:  Version 1.9.0 SNAPSHOT Build 18013.
I then searched for a bug that i felt was relatively easy to reproduce. The bug that I tried was known as TRUNK-222. The description of the bug is, "If a patient's first name is less than 3 letters, we cannot search for him without knowing his family or middle name". I thought that this would be an easy bug to reproduce so i went ahead trying.

First i went ahead and created a patient with a 2 letter name "Di":

I then proceeded to try and search for "Di" and could not produce any results, as expected.

Although this bug ticket was not well formatted, it was still easy to reproduce. Also, after reproducing it i think that this is not actually a bug but a design problem.


Bug Triage
Since I'm very new to the OpenMRS project bug triage would be very difficult at the moment. Instead, I'm just going to go through a few bugs on my own and share my thoughts on what bugs are more important than others, a part of the triage process. All of the bugs I'm going to mention are under the category from the JIRA ticket system on OpenMRS as being a "severity" of "3 or 4" (on a scale from 1-4).

Bugs:

1.  "JUnit tests fail if run independent of maven" - This bug is extremely bad. OpenMRS fails to pass the unit test's that are designed. This means that there could be an unforeseen amount of issues with the particular build (1.9.x)
2. "OpenMRS can not be installed with MS SQL Server" - This bug is also extremely bad considering some machines trying to implement the particular build could be running MS SQL Server.
3. "Change default logging levels of service methods" - This bug is import because it affects the logging of everything that happens in an OpenMRS deployment. Logging could be very important if you wanted to track information in a particular deployment of OpenMRS
4. "support names with more than 2 components when going to create patient page" - This bug is a little less important than the first 3, but still has a profound affect on any particular implementation of OpenMRS. This bug will cause the name of  a patient to display and appear to be incomplete.
5. initialsetup: OpenMRS logo text is not correct - This is a less important bug. This bug is simply a cosmetic item in a build that is very new. I think that this could be avoided until some of the tougher bugs are fixed.

This triage was simply an exercise and I hope to learn more about OpenMRS so that my triage can evolve and become better.


Conclusion:
All of these exercises were very helpful for me. They forced me into exploring deeper in to the project that I am working on. I hope to learn more and be able to contribute to OpenMRS.

Getting, Building, & Running "OpenMRS" Part 2

Okay!

Finally managed to deploy OpenMRS locally after a whole flurry of issues. Thank God for Google!

I first had issues with installing the right packages that were needed to install and run OpenMRS. Tomcat6 is used to deploy OpenMRS on a local server. Unfortunately it's not easy to get Tomcat6 working. The Tomcat6 download in the Ubuntu repositories is not a good install and has missing files, in my experience, that are crucial to running Tomcat6. I had to go directly to the apache Tomcat6 website and get a mirror to download the tar.gz file from their repositories. Some of my best researched advice came from "how to geek".

This was easy since all i did was run:

sudo wget http://www.trieuvan.com/apache/tomcat/tomcat-6/v6.0.32/bin/apache-tomcat-6.0.32.tar.gz

sudo tar xvzf  apache-tomcat-6.0.32.tar.gz

sudo mv apache-tomcat-6.0.32.tar.gz usr/share/tomcat6

After installing Tomcat6 properly I had to change a couple .xml files associated with the software in order to get it running. This was fairly simple.

Next was the feat of trying to get OpenMRS deployed on the tomcat server. This took me multiple tries with different settings. The quick installation is known to fail since it was just commited to the OpenMRS Trunk last week. All I had to do was to try and run the advanced install and I finally have OpenMRS running.

I can now start to explore some of OpenMRS and find out how i can contribute to the bug fixes located in their ticket system, implemented with JIRA. I look forward to blogging about more of my experiences.


Here's a screenshot of OpenMRS finally deployed on my system:

OpenMRS FINALLY Deployed

A word of advice for those reading that are trying to Build-->Install-->Deploy OpenMRS on Ubuntu:
Make sure that you get a good Tomcat6 install with /conf directory and make sure you use sun-java-6-sdk. This is crucial to getting OpenMRS deployed correctly.

freeciv2.1 Build, Make, and Install

"Freeciv is a Free and Open Source empire-building strategy game inspired by the history of human civilization."  -taken from Freeciv

As a part of the "Teaching Open Source" book, there is an activity that helps you learn how to build, make, and install open source projects from source code. I went ahead and downloaded freeciv and extracted the files from the .tar.bz2 file. From here building was fairly simple. At first i ran into a problem with dependencies. Luckily the compilation script mentions which dependencies were left out. So i went in search for GTK packages in order to full fill the requirement. This proved to be very, very slow and agonizing. I finally came across a command that would find and download all missing dependencies for the freeciv projects.

sudo apt-get build-dep freeciv

This command worked great. next all i had to do was:

sudo make install

This installed to the default directory "usr/local/bin" and made the project. I got it to run nicely and all went well. This was a very simple exercise since i have commonly used these commands before in the previous course CSCI 360 "Software Engineering" Project.

Here's a screenshot of freeciv up and running:

Freeciv 2.1 Running

Getting, Building, & Running "OpenMRS"

My goal for this week was to checkout the latest version of OpenMRS and try to build and run it. Conveniently OpenMRS had a great guide for developers looking to build and run the source code here.  I found this guide to be very helpful. OpenMRS recommends that you use a couple of integrated pieces of software in eclipse such as m2eclipse and subclipse. subclipse and m2eclipse proved to be very helpful in the building process. Subclipse, which is a subversion client for eclipse, made it very easy to check out the Trunk for OpenMRS. All you have to do is type the repository's link and designate that it is indeed an SVN server. After checking out the code it was also very simple to build the code using m2eclipse, which is a client that maintains dependencies of a "mavenized" project. At first i encountered an issue with version conflicts but that was easily resolved. After resolving these issues i was able to succesfully build the project. Next my goal was to run the built code. This is the hardest part about the project since it has to be built as a web application instead of a piece of software that you use locally. OpenMRS suggests that you use TomCat to mount the OpenMRS web app. This is what i ran into trouble with. TomCat requires that you change permissions to the "users" file. I ran into trouble getting access to the .xml file. I am very close to getting OpenMRS to run and I am very excited to get it running.


I also got a response from one of the core developers and she suggested that we go ahead and resolve some of the ticket issues/bugs. As soon as i get OpenMRS built i will blog my experiences.

Subversion & Me...

For the last week or so I've been reading the Subversion Book that was given to us as a resource in our CSCI 462 class. The book was a great intro into Subversion and I learned a lot just skimming the readings. As a result of reading the Subversion Book i ran into some terminology i have heard before, but never really understood. I took it upon myself to do some research and actually learned quite a bit. A good example of an item i was not familiar with was the idea of an "apache" server. I took some time to look up what this was all about and educated myself on the Apache HTTP server open source project and what it was used for. I have a feeling ill be running into this open source project in the future.


Quickly after skimming through some of the important areas of the Subversion Book I decided to explore some of the commands and play around with Subversion on my machine. I chose not to install a subversion client and just run my subversion commands through the Ubuntu terminal. In my opinion this is much faster and much more clean than having to deal with a SVN Client that might have a GUI. Not to mention I'm starting to like familiarizing myself with terminal commands in Ubuntu. The "Cirdles Playground" provided to us proved to be very useful for this. I played around with some basic commands such as "update", "commit", and "checkout". All of these commands seemed to work without a hitch.


I feel like Subversion is a very efficient system for collaboration. I'm excited to get to work with and develop my skills with it. I think knowing how to use Subversion will be a very important skill to have in the future with a career in the computer science field. 


Heres a little screen shot of my work for all who are interested:

Subversion Work Screenshot

P.S. On our "Cirdles Playground" someone decided to upload some Chuck Norris Facts...I'll leave you with a running list of some Here.

OpenMRS

For our project we chose OpenMRS. After exploring some of the development going on, I'm starting to get a real idea of how big this project actually is. This project has already been implemented in places like Nairobi and India. It's amazing to see how large these projects can actually grow. I emailed some of the leadership team and I am still waiting to hear back from someone on a recommended project to take on. There are lots of modules and little projects that need to be worked on from what I could tell. I am a little nervous about this project as our main project for the class though. It seems that most of the work for OpenMRS has been done and it is already being implemented. This could prove to be difficult to slide right into. I believe what will happen is we are going to be referred to the ticket system they have online. I have high hopes for the project and I hope to get involved soon.

Open Source?

As a Computer Science student, i am slowly becoming more familiar with the idea of open source software. Although i have used plenty of open source software before, I never had a real sense for what it was. As we move forward with the curriculum in this class i am becoming more and more familiar with how these projects work.

Eric S. Raymond's "The Cathedral and The Bazaar" really motivated me to contribute explore open source more deeply and to get a better idea of what open source actually is. Raymond discusses how open source compares to the idea of a "Bazaar", rather than the idea of a "Cathedral". The cathedral compares to projects that are meticulously planned out and have planned releases. The Bazaar compares to open source projects that are released often and have many developers. Raymond's exploration into why these "Bazaar" projects work is very interesting. I think that the exploration into social context and why developers actually tend to contribute is an interesting topic. Why do developers actually devote time to these projects? Raymond's explanations answered these questions well. "The Cathedral and The Bazaar" was a refreshing article and i think it renewed my interest in contributing towards a project for this class.


Class Progress:
Team Handicapped made progress by joining IRC channels for OpenMRS project. It seems that these channels are still very active and that development is still very much alive. Our team also joined mailing list. Funny to me, receiving these emails really reflect the "release and release often" phrase. I am getting about 3 to 4 emails every couple of hours. Seems like OpenMRS will be a valuable project.

Progress...

Thursday January 13 class consisted of exploring possible options for our FOSS projects that will be done throughout the semester.

On our team wiki are the possible projects that our group Team Handicapped discussed during class.

All of these FOSS projects are humanitarian projects. I find this to be very interesting and i feel like contributing to one of these important open source projects could be potentially very fulfilling. For example, working on a project such as OpenMRS, a medical records system, could help thousands of people.

I look forward to choosing a project and exploring what sort of options for contribution are available. Hopefully this project will develop my skills in the field of software engineering.

First Blog!

Here's my first blog for CSCI462. Hope to learn a lot in this class. I registered for POSSCON 2011 and received confirmation that my ticket was purchased. First Class consisted of breaking up into teams and team names. Our team is team Handicapped. Look for more coming from my blog as the semester moves forward.