Cleaned up, provided zip file for release 3 and added adequate user i…

…nformation.

ODM-to-i2b2.properties

@@ -2,7 +2,8 @@
 # of the properties after the = signs according to your needs.
 
 # The path to the file with log4j properties for logging errors, warnings, info, etc.
-log4j-properties-file=src/main/resources/log4j.xml
+# log4j-properties-file=src/main/resources/log4j.xml
+log4j-properties-file=log4j.xml
 
 # The property below specifies the maximum length that a clinical data entry may have.
 # Longer strings will be cut off in order to assure that the length of the string does

src/documentation/DevelopersInformation.md

@@ -127,8 +127,8 @@ Maven
 -----
 
 We use [Maven](http://maven.apache.org/) as our build tool. This makes it easier to use certain tools (like Checkstyle
-and FindBugs) and to manage the third-party libraries (dependencies) we use. The pom.xml file for the trait_odm_to_i2b2
-conversion tool is stored in the root directory.
+and FindBugs) and to manage the third-party libraries (dependencies) we use. The pom.xml file that Maven needs
+is stored in the root directory: trait_odm_to_i2b2. All the maven commands need to be executed in this root directory.
 
 Some commonly used Maven commands are
 (see [Introduction to the Build Lifecycle](http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html)
@@ -167,6 +167,28 @@ for an explanation of the build lifecycle and the build phases):
 \# Check for CPD issues (report in target\cpd.xml):<br/>
 **`mvn compile pmd:cpd-check`**
 
+\# Create the jar file in the trait_odm_to_i2b2\target directory
+**`mvn clean compile assembly:single`**
+
+Auto-generating the java files from the ODM-specification
+---------------------------------------------------------
+Java classes are generated for handling ODM files using the JAXB (Java Architecture for XML Binding) related xjc binding
+compiler. The source code of these ODM reader classes are created by the xjc tool with xsd files that describe the ODM
+standard as input. See for example https://jaxb.java.net/2.2.11/docs/ch04.html#tools-xjc or
+https://en.wikipedia.org/wiki/Java_Architecture_for_XML_Binding for more information on xjc and JAXB.
+
+The main schema file (ODM1-3-1.xsd) depends on several other schema files: ODM1-3-1-foundation.xsd, xml.xsd, and
+xmldsig-core-schema.xsd. The bindings file (bindings.xml) modifies the default package names that are used. The Java
+classes are put in two packages: org.cdisk.odm.jaxb (ODM1-3-1.xsd) and org.w3.xmldsig.jaxb (xmldsig-core-schema.xsd).
+
+The call to xjc looks something like this:<br/>
+**`xjc [schema file] -b [bindings file] -d [destination directory]`**
+
+For example, on the Windows platform (with xjc.bat in the jaxb-ri\bin directory at your install location) using ODM 1.3.1,
+you could generate the ODM reader classes like this:<br/>
+**`mkdir java-generated`**<br/>
+**`xjc.bat xsd\cdisc-odm-1.3.1\ODM1-3-1.xsd -b xsd\cdisc-odm-1.3.1\bindings.xml -d java-generated`**
+
 
 Checkstyle
 ----------

src/documentation/UsersInformation.md

@@ -3,19 +3,14 @@ Users information
 This page is meant for users who want to install and use ODM-to-i2b2 in order to convert an ODM file to
 three tabular files.
 
-Windows:
 ```sh
-$ cd C:\path\to\workspace
-$ mkdir ODM-to-i2b2
-$ cd ODM-to-i2b2
-$ mkdir input-ODMs
-$ mkdir output-tabular-files
-$ git clone https://github.com/CTMM-TraIT/trait_odm_to_i2b2.git
-$ cd trait_odm_to_i2b2
-$ git checkout tags/v3.0
-$ copy odm\examples\odm130.XML ..\input-ODMs\test.xml
-$ mvn test
-$ mvn exec:java -Dexec.mainClass="com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient" -Dexec.args="C:\path\to\workspace\ODM-to-i2b2\input-ODMs\test.xml C:\path\to\workspace\ODM-to-i2b2\output-tabular-files"
-$ cd ..\output-tabular-files
-$ dir
+Download odm-to-i2b2-3.0.zip from the [release directory](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/releases/release-3.0) and unzip it.
+Save your ODM file in odm-to-i2b2-3.0\input-ODMs (e.g. odm130.XML)
+Start the command line terminal (e.g. cmd.exe)
+$ cd C:\path\to\odm-to-i2b2-3.0
+$ java -jar odm-to-i2b2-3.0.jar input-ODMs\odm130.XML output-tabular-files
+$ cd output-tabular-files
+$ ls -l
 ```
+
+![Image cmd execution](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/cmd_execution.png)

src/main/java/com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient.java

@@ -91,9 +91,9 @@ public static void main(String[] args) {
         try {
             logger.info("ODM-to-i2b2 version v3.0 (2015-05-28) started running.");
             if (args.length >= 1) {
-                String propertiesFilePath = "ODM-to-i2b2.properties";
+                final String propertiesFilePath = "ODM-to-i2b2.properties";
                 final Configuration configuration = new Configuration(propertiesFilePath);
-                DOMConfigurator.configure(configuration.getLog4jPath());
+                DOMConfigurator.configure(I2B2ODMStudyHandlerCMLClient.class.getResource(configuration.getLog4jPath()));
 
                 if (EXPORT_TO_DATABASE) {
                     logger.info("Initializing database connection...");