Life in GSOC

Longitudinal module in lab3

Omar — Fri, 12 Jun 2009 16:01:26 +0000

After the end of a hard semester I’m finally free to code in GSoC so I begun to upload my module in the Lab 3 that Ben give me with the support of Verio

The link is

http://lab3.openmrs.org:8080/openmrs/index.htm

the user is dummy and the password is test13 , so feel free to play with my alpha release a little bit

This week Im going to code some searchs using date ranges using jquery as the glue.

Finally, running 500k observations in my alpha module :D

Omar — Sat, 23 May 2009 08:18:23 +0000

Well, finally , after creating and dropping schemas many times, I can watch my module running some observations from the 500 k already in the obs table of the demo data script

There was a lot of weird issues , for example, I do not how, but my environment variables that I use for the developer environment where dropped in my laptop running windows, after that, the users and names of my two schemas , the one for the openmrs1.4.2 war deployment and the one for the openmrs trunk collide in some way, so I have to drop the both two schemas and finally, proceed to this guide …

After checking that my deployment was correct and before I ran the demo data i wanted to check if my connection was setted properly, so i check the open mrs page and …. I couldn’t acces the open mrs, by the way, at this moment, I add to the runtime properties the next entry

hibernate.show_sql=true

so I can watch wtf was doing hibernate in my database…

well, I see that the users table its the one that stores my username, so I enter and discover that … the username column was empty… that was the reason why I can login in the first place, so I ran a a update sentence in this table to add a user in the username column, and secret answer and secret question for reset the actual password.

After that, and following the link for tue use case when the user forgot his password, I can gain access to the webapp.

After that, I have to remark that I have only ran the createdb from scratch and run the update to lates scripts , so I had no obs, but my search for patients was succesfull, so the next case was to run the demo data script.

Running the demo data script its a huge tas for my mysql gui and my old laptop , so I have to use the mysql console to not put a lot of pressure on my resources, running the mysql in this way was very fast compared to all the previous runs of the script ( usually, on my mysql gui, just open the demo data script takes 10 minutes , and running the script takes another 20 minutes), so, at the end, I have the demo data in my openmrs database using a connection that I already test.

I restart tomcat and openmrs don’twork, I see the stacktrace and see that OpenMRS throw me an exception about the modules folder, basically, now check for default module folder in bewolfe environment, so I correc this with a update in the global_property table
Again, returning to the OpenMRS webapp i get the old message that i can gain access, so I check again the users table and see that the previous issue was already present, so I ran again the same sql update and gain access.

After that, I check for patients and there was a LOT more, so I see that the moment to check my module with dozens of obs for a patient was very close.

At this point, I have to say that my openmrs context was throwing some exceptions about a form entry class that can be found , but I dont understand where this class should be… until I have to load my module, and see a entry about a form entry in my manage modules page… I just realized that was a reference to a module, so I guess it was not such a big deal, and I continue loading my module, and finally Icheck that the module can retrieve obs about a demo patient.

The next pics are images about the process, the issues I found, and the module page with a lot of obs…

ps. tomorrow I hope I can apply some format to this mess.

BOINC

Omar — Fri, 22 May 2009 05:27:26 +0000

These days, with all the final projects and exams I am very close to my Laptop, but eventually one has to go to watch some NBA game or UEFA Champions League matchs, and my laptop finally goes to sleep, well, I look for the BOINC project that erroneously I thought that only ran on PS3, but after click on http://boinc.berkeley.edu/projects.php and fulfill some data,now I’m running the SETI project and the ROSSETA project on the dead periods of my laptop activities.

I think that the Boinc Software with at least the ROSSETA project or the WorldCommunityGrid running is an app that should be present in every desktop with idle times.

Below the links to the projects

http://boinc.bakerlab.org/rosetta/

http://www.worldcommunitygrid.org/

http://setiathome.berkeley.edu/

Weekly Report

Omar — Fri, 08 May 2009 22:38:57 +0000

Well, this week I was very slow because I can’t run the demo data in my OpenMRS Database, My Hibernate throws a lot of exceptions, so, for not stay more time without code I decided to create a little script to add 5 patients and observations associated with them.

After that, I was testing my code when I notice that my module dont compile and that exists a difference between the methods that Eclipse suggests me and the open mrs api javadoc, then I realized that the module wizard in Eclipse creates a module with the 1.2 version of open mrs api, web open mrs api and test open mrs api, so I check that in fact exists a ticket in the developers site http://dev.openmrs.org/ticket/1347 .
An easy fix was run some targets in openmrs trunk project so I can obtain the 3 previous jars in a recent version.
Some changes in classpath and project properties to avoid classpath hell and finally my module compile with the new methods.

Finally, after resolve these inconvenients, I commit my changes and now I’m waiting for get access to a Lab inhttp://openmrs.org/wiki/OpenMRS_Labs so the community can see my first approach to the demo and receive feedback from everybody.

ps
I have already noticed that I never asigned the tag openmrs, , only the category, so I guess that in OpenMRS they never knew about that post… a stupid mistake.

Demo Data problem

Omar — Tue, 05 May 2009 17:48:59 +0000

Following the creation of my module, I have coded some stuff in my jsp page and the associated controller and I need to retrieve some data for my purposes.

To probe my page, Paul Biondich told me about a demo data script in http://openmrs.org/wiki/Downloads with observations about 5k patients, but that script broke my trunk installation, today Justin Miranda has created a ticket for this issue in http://dev.openmrs.org/ticket/1459 . I hope I can deal with this issue soon, because I haven’t touched my module code for 4 days.

PS. Justin Miranda, Ben Wolfe and Joao Portela has suggestions about my trouble, when I can resolve this, I think I can put them has a new post.

First module

Omar — Tue, 28 Apr 2009 17:48:20 +0000

My module space is in http://svn.openmrs.org/openmrs-modules/longitudinaldataviewer/ .
In this moment it’s only a skeleton, but at the end of the week I hope this module can acquire observations for a given patient from the OpenMRS API and render a complete list of all the observations for the patient onto a JSP page which lives in the module.

Swine flu and OpenMRS

Omar — Sun, 26 Apr 2009 20:55:15 +0000

If someone don’t know, last days in Mexico there’s been a flu outbreak .
These days in Mexico City the government set a decree that restricts our rights in nearly all the city area so the Health Minister can make us stay in quarintine if we look suspicious for something like flu.
That means No sports, No concerts and No movie theaters. It’s like a sucession of Sundays one after another.
There are even cases registered in US , and suspicious cases in Canada, Spain, England, Brazil and Israel.

These events remind me why I want to participate in the OpenMRS project, at the end of the day, OpenMRS help people´s health.

Hello GSoC2009

Omar — Tue, 21 Apr 2009 16:16:43 +0000

Welcome to my blog, I´ve been accepted to the Google Summer of Code 2009 in OpenMRS organization to work on the propposal Longitudinal Data Review (Discrete Data Flowsheet) Module (mentor Paul Biondich).

The project would require working on HTML, CSS, JSP, Spring and AJAX/JavaScript coding

More info in this link http://tinyurl.com/d6a7p