A system to migrate from SQL-based databases into OpenMRS
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.settings
src
target
.classpath
.gitignore
.project
README.md
log.log
log4j.xml
pom.xml

README.md

data-migration-system

A system to migrate from SQL-based databases into OpenMRS.

Overview

The main architectural idea is to have a tool that takes a matching file as input, validates the matches, translates them into SQL SELECT, INSERT and/or UPDATE statements (mapping), and execute the resulting mapping.

To accomplish the underlying idea the tool must be:

  • Reusable - Developed once and used when needed. The mapping is created based on input logic
  • Configurable - The migration logic is structured in a user friendly and versatile input worksheet
  • Auditable - Provide feedback to the user and the tool itself
  • General Purpose - Can be used out of the box (evolving OpenMRS as the target database)

Development Environment Specs

For the development of the data migration tool, here are the minimum specs required for the development environment:

  •     Windows OS 7+ (currently being used by the majority)
    
  •     Eclipse IDE (preferably Indigo, Juno, Kepler or Luna)
    
  •     Java 7 (not recommend the Java 8 because there were some compatibility            issues when creating the environment)
    
  •     Apache Maven 3 (http://maven.apache.org/download.cgi)
    
  •     Git (http://git-scm.com/downloads)
    

Optionally:

  •     EGit - plugin for Eclipse (Eclipse Marketplace)
    
  •     GitHub Extensions -  plugin for Eclipse (Eclipse Marketplace)
    
  •     EclEmma - plugin for Eclipse used for test coverage (Eclipse Marketplace)
    
  •     Maven Integration for Eclipse (Eclipse Marketplace)
    

The project is mavenized (maven project). Some dependencies to consider:

  •     JaCoCo - For test coverage control, considering that one of our criteria for the DoD (Definition of Done) is that all code should be 100% test coverage.
    
  •     Mokito - for unit testing without necessarily exist all integrated systems, eg. databases (https://code.google.com/p/mockito/)
    
  •     Jaxcel API - for XLS processing (http://www.vogella.com/tutorials/JavaExcel/article.html)
    
  •     Lambaj - used for flexible manipulation of Javacollections
    
  •     JUnit - For unit and integration tests
    

Mac OS X Setup

You may need to make one or more of the following changes to get the system up and running on OS X.

1. Configure Java version

The code in this repository requires Java 7 to compile, so if you're running multiple versions of Java, you'll need to use something like jenv to ensure that Maven uses the correct Java installation to compile the code.

2. Configure file encoding

The files in this repository use the ISO-8859-1 file encoding. This could cause errors that look like:

[ERROR] Codable.java:[5,14] error: unmappable character for encoding UTF8

If you see such errors, you may need to tell Maven to use the correct encoding by adding <encoding>ISO-8859-1</encoding> to the compiler plugin configuration in pom.xml as follows:

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-compiler-plugin</artifactId>
    <configuration>
        <source>1.7</source>
        <target>1.7</target>
        <encoding>ISO-8859-1</encoding>
    </configuration>
</plugin>

3. Correct Windows-specific file locations

In src/main/resources/config.xml, there are references to C:/EMR_Architecture/OpenMRS_SESP_Matching_Table_210820141022.xls. You'll need to change these to valid locations on your local filesystem in order to run the tests.

Test and Production Environments Specs

In order to execute the system in test environment make sure you have the following tools installed:

  •     Java 7 (http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html) - **Make sure you download a 32 bit JDK (Windows X86)**
    
  •     Apache Maven 3 (http://maven.apache.org/download.cgi)
    
  •     Git (http://git-scm.com/downloads)
    

Perform the following steps using command line:

  1. Clone the project repository from github git clone https://github.com/esaude/data-migration-system.git

  2. Navigate to your project root directory and run the command mvn package. This step will generate the distribution of the tool data-migration-system-[VERSION]-dist.zip in zip format. The generated file will be located in PROJECT_ROOT\target

  3. Extract the distribution file to a suitable location

  4. Configure the input and runtime properties in ...\data-migration-system-[VERSION]\src\main\resources\config.xml

  5. Open command line

  6. Change your PATH to use Java 7 32 bit: path=%PATH%;YOUR_JAVA32_INSTALATION_LOCATION\bin or set the classpath in Environment Variables;

  7. Make sure you are now using Java 7 32 bit: java -version should display the details of your java in the classpath

  8. Execute the data cleaning tool esaude-dct-cleaner.jar for SESP located in ...\data-migration-system-[VERSION]\src\main\resources - use the command java -jar esaude-dct-cleaner.jar and provide the absolute path of your SESP database when requested, e.g. C:/databases/Bkup_CS Namige_2014-09-22 11.28.mdb and press enter key

  9. Execute the jar file PROJECT_ROOT\data-migration-system-1.0-SNAPSHOT.jar located in PROJECT_ROOT\data-migration-system-[VERSION]. Run the command java -jar data-migration-system-[VERSION].jar