Bell Eapen MD, PhD.

Bringing Digital health & Gen AI research to life!

GIT for doctors (Part 3) – stash, branch, merge, rebase and tag

To continue with our git story: Read the full series on GIT for doctors here

If you think you have made a mistake, you can “stash” the changes. Your file will be returned to the previous state. You have the option of returning to the stash if needed, but this is beyond our scope at present.

Now let us consider another scenario: You have two differential diagnosis for your patient and you want to investigate the patient for both conditions. You may decide to keep two versions of the same case sheet to continue the work up on both differentials. In Git you can create a “branch” for this situation. You can work on branches independently. The main branch or the trunk is called “master” by convention. You can give any name for the other branches.

Embiodea
Embiodea (Photo credit: beapen)

If you decide to consult your colleague, he/she may want to continue working on their copy without changing the “master” file in your possession. So they can work on their “branches” too. Later on if you want to add your differential branch or your colleague’s branch into the master file, you can choose “merge”.

You can create branches of branches. If you want to merge several such branches into the “master”, you have to paste all branches together into a single branch. This is called “rebase”.

If you have to submit a master chart for audit, you can “tag” the chart, so that you can give a name to the current state. “Tagging” for software is generally done when you decide to release a version to the end user.

In the next part, I will discuss how to collaborate with your friends. If you are not on github.com as yet, do register for an account now. If you want to follow someone, let me suggest yours truly: https://github.com/dermatologist

Read the full series on GIT for doctors here

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Facebook and Ajax
Christmas pudding decorated with skimmia rathe...
Christmas pudding decorated with skimmia rather than holly. (Photo credit: Wikipedia)

Today is the last day of my Christmas break and the winter term will officially start tomorrow. I did use my break in a productive way as I mentioned in my post last week. To continue with my exploration, I found out two more things the hard way. So I thought I would share it here so that you guys can probably save some time.

I decided to learn how to make a facebook app. So I registered for a developer account and got my AppID and secret key. I made a word game in php for dermatology and decided to port it to the facebook canvas. The facebook interface asked for the normal application URL and the https URL. Near the https field, it is mentioned that https is a requirement from Oct 11th onwards. Since it is only the beginning of 2014 with a good 10 months to October, I decided to leave the https blank. The form submission was accepted without any problems and I was given a new ‘blank’ canvas.

Despite my best efforts at debugging, the canvas remained perpetually blank. After hours of googling, I found out the bitter truth. The October 11 is not Oct 2014, but Oct 2011 and is over 2 years back! So facebook needs a secure https URL for displaying external apps in the facebook canvas and it is mandatory for the last 2 years. I have no complaints about facebook’s security policies and probably this is a good thing. But why the Oct 11 is still mentioned there without the year, and why the form is getting validated without an https url still!!

The other thing I found out the hard way was the (simple fact 🙂 ) that: Ajax is basically javascript obeying the Same-origin policy. Your backend php script (or any other script) should be on the same server. Again no complaints, but……

Here is my DermGame who could never make it to the facebook, but got a facelift with Ajax. Sorry for the mangled interface and template.

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Deploying Java applications with embedded derby database
Ruby on Rails
Ruby on Rails (Photo credit: Wikipedia)

I have been trying to brush up my programming skills during the christmas break. I recently added the tagline “Dermatologist who codes” to my elevator speech. My plan is to sharpen my java skills and to learn python and ruby on rails. I believe coding real world applications is the best way to learn/sharpen any programming language.

Here is the first innovative application, Dermatology Image Tagger that I made. I believe this would be quite useful to dermatologists for organizing clinical images. Afterwards I made a simple java database application for a colleague. I never explored the deployment of java applications before. I hit google to find useful resources, but found only very few. The one I found most useful was Aparna’s blog. Here she succinctly explains how to use the Java embedded derby database. The only thing I had to figure out the hard way was to use the connection string as below to force creation of the database in the working directory. I also added a ‘create table’ button for initial deployment.

 String host = “jdbc:derby:imfdb;create=true”;
            String uName = “your_username”;
            String uPass= “your_password”;
            con = DriverManager.getConnection(host, uName, uPass);
            stmt = con.createStatement();

She has also written an very useful article on deploying java desktop applications. I followed her instructions to package all required files into a single executable jar file for Mac and an exe file for windows. I have used this for DIT. Thanks Aparna for making life easy for me!

Pink in honor of breast cancer awareness programs
Pink in honor of breast cancer awareness programs (Photo credit: beapen)

I am still exploring python and Ruby on Rails. So far I have been really impressed by the way Ruby on Rails managed to make web application development intuitive. I also learnt git for version tracking and joined github. I have added few learning projects for python and RoR that may be useful applications if developed properly. Feel free to fork, watch or star them and if you are on github too, a follow will not hurt.

So this will be my last post for 2013. Will meet you all again in 2014.

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Running Tomcat as www-data
For last couple of days I have been working on a web based application for skin color measurement as I blogged here. The core of the application is implemented in php as it is much easier to handle. (May be I am more comfortable with it). But the GD image library for php has limited functionality. So I had to rely on Java for border detection and segmentation. So I implemented part of the functionality as a servlet running on tomcat6.

Today's latte, Apache Tomcat.
Today’s latte, Apache Tomcat. (Photo credit: yukop)

Both php and servlet had to read and write same files. But standard configuration does not allow this as php creates files as www-data (apache user) and tomcat creates files as tomcat6 user. I searched the internet for solutions. One suggestion was to create an appropriate umask for both which I could never completely understand. Finally I realised that the easiest solution is to make tomcat run as user www-data so that all created files will have same ownership.

I found this webpage with detailed instructions on how to do this. I would like to add two more steps:
1. Edit /etc/init.d/tomcat6 also to add the user ID and group ID
2. chown var/cache/tomcat6 directory also.

Nina Jablonski - The Evolution of Human Skin Color
Nina Jablonski – The Evolution of Human Skin Color (Photo credit: wagnerfreeinstitute)

BTW the application is hosted on my laptop. If you want to check it out click on the banner below if you see it. You will see it only when my laptop is on.

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