Clean-up of the project. Users info moved to developers info. Added j…

…ar file that was created with Maven in a newly created release folder.
CTMM-TraIT · 174ab2adfe2be1a022b5493b709d42caa32fc297 · wardblonde committed Jun 4, 2015 · Jun 4, 2015 · 174ab2a
1 parent 3dab1a2
commit 174ab2adfe2be1a022b5493b709d42caa32fc297
diff --git a/odm/.classpath b/odm/.classpath
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="gensrc"/>
-	<classpathentry exported="true" kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-snmp-appender.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/sqljdbc4.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/jdom-1.1.2.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.5.jar"/>
-	<classpathentry kind="lib" path="lib/junit-4.8.2.jar"/>
-	<classpathentry kind="lib" path="lib/junit-dep-4.8.2.jar"/>
-	<classpathentry kind="lib" path="lib/jtds-1.2.5.jar"/>
-	<classpathentry kind="lib" path="lib/jackson-core-asl-1.9.3.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="http://jackson.codehaus.org/1.9.3/javadoc/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="lib" path="build/conf"/>
-	<classpathentry kind="output" path="classes"/>
-</classpath>
diff --git a/odm/.project b/odm/.project
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>odm</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-</projectDescription>
diff --git a/odm/build.properties b/odm/build.properties
diff --git a/odm/build_openclinica.xml b/odm/build_openclinica.xml
@@ -1,95 +0,0 @@
-<?xml version="1.0"?>
-
-<project name="odm" default="all" basedir=".">
-
-	<echo message="pulling in property files" />
-	<property file="build.properties" />
-
-	<property name="src.dir" value="${basedir}/src" />
-	<property name="test.dir" value="${basedir}/test" />
-	<property name="lib.dir" value="${basedir}/lib" />
-	<property name="scripts.dir" value="${basedir}/scripts" />
-	<property name="build.dir" value="${basedir}/build" />
-	<property name="deploy.dir" value="redcapui/lib" />
-	<property name="gensrc.dir" value="/gensrc" />
-	<property name="classes.dir" value="${basedir}/classes" />
-	<property name="xsd.dir" value="${basedir}/xsd" />
-
-	<path id="build.classpath">
-		<fileset dir="${lib.dir}">
-			<include name="**/*.jar" />
-		</fileset>
-	</path>
-
-	<target name="all" depends="clean,gensrc,compile,build,deploy" />
-
-	<target name="compile">
-		<mkdir dir="${classes.dir}" />
-		<javac destdir="${classes.dir}" debug="true">
-			<src path="${src.dir}" />
-			<src path="${test.dir}" />
-			<classpath refid="build.classpath" />
-			<compilerarg value="-Xlint" />
-		</javac>
-	</target>
-
-	<target name="gensrc">
-		<mkdir dir="/gensrc" />
-
-		<echo message="calling xjc generation tool: odm" />
-		<exec executable="xjc">
-			<arg value="-d" />
-			<arg value="${gensrc.dir}" />
-			<arg value="-b" />
-			<arg value="${xsd.dir}/OpenClinica-ToODM1-3-0-OC2-0/bindings.xml" />
-			<arg value="${xsd.dir}/OpenClinica-ToODM1-3-0-OC2-0/ODM1-3-0.xsd" />
-			<arg value="${xsd.dir}/OpenClinica-ToODM1-3-0-OC2-0/OpenClinica-ToODM1-3-0-OC2-0.xsd" />
-		</exec>
-
-		<mkdir dir="${classes.dir}" />
-		<javac srcdir="${gensrc.dir}" destdir="${classes.dir}" />
-	</target>
-
-	<target name="build" depends="compile">
-		<mkdir dir="${build.dir}" />
-		<mkdir dir="${build.dir}/lib" />
-		<mkdir dir="${build.dir}/conf" />
-		<mkdir dir="${build.dir}/logs" />
-		<mkdir dir="${build.dir}/files" />
-		<mkdir dir="${build.dir}/files/inbox" />
-		<mkdir dir="${build.dir}/files/archive" />
-
-		<jar destfile="${build.dir}/lib/redcap2i2b2.jar" basedir="${classes.dir}" />
-		<copy todir="${build.dir}/lib">
-			<fileset dir="${lib.dir}">
-				<include name="**/*.jar" />
-			</fileset>
-		</copy>
-
-		<copy todir="${build.dir}">
-			<fileset dir="${scripts.dir}">
-				<include name="*.bat" />
-				<include name="*.sh" />
-			</fileset>
-		</copy>
-
-		<copy todir="${build.dir}/conf">
-			<fileset dir="${src.dir}">
-				<include name="*.properties" />
-			</fileset>
-		</copy>
-	</target>
-
-	<target name="deploy" depends="build">
-		<copy file="${build.dir}/lib/redcap2i2b2.jar" todir="${deploy.dir}" overwrite="true" />
-	</target>
-
-	<target name="clean">
-		<delete failonerror="false">
-			<fileset dir="${classes.dir}" />
-			<fileset dir="/gensrc" />
-			<fileset dir="${build.dir}" />
-		</delete>
-	</target>
-
-</project>
diff --git a/odm/etc/load_clinical_data_R.sh b/odm/etc/load_clinical_data_R.sh
@@ -1,42 +0,0 @@
-#!/bin/sh
-
-StudyID="CAIRO_WARD"
-TopNode="\\Public Studies\\Cairo-Ward\\"
-ColumnMapFile="CAIRO_columns.txt"
-WordMapFile="CAIRO_word_map.txt"
-Security="N"
-
-# Where the tranSMART-ETL repository is
-ETL_HOME="$HOME/repos/tranSMART-ETL"
-
-# The pivot-file which will be uploaded into the database
-OutputFile="output.tsv"
-
-###########################################################################
-# Going to do the work. You should not have the change anything below here.
-
-echo "Start re-arranging input..."
-Rscript ${ETL_HOME}/Postgres/GPL-1.0/R/clinical/load_clinical_data.R studyID=${StudyID} \
-                          					     columnMapFile=${ColumnMapFile} \
-					                             wordMapFile=${WordMapFile} \
-					                             outputFile=${OutputFile}
-echo "re-arranged input stored in file: ${OutputFile}"
-echo ""
-
-echo "Start uploading file: ${OutputFile} into database (tm_lz.lt_src_clinical_data)"
-psql -U tm_lz -w -d transmart <<EIND
-truncate TABLE tm_lz.lt_src_clinical_data;
-\\copy tm_lz.lt_src_clinical_data FROM '${OutputFile}' WITH (FORMAT CSV, DELIMITER E'\t', HEADER);
-select count(*) from tm_lz.lt_src_clinical_data;
-EIND
-echo "File: ${OutputFile} uploaded into database"
-echo ""
-
-echo "Call stored-procedure to put data into i2b2 tables"
-psql -U tm_cz -w -d transmart <<END
-select tm_cz.i2b2_load_clinical_data('${StudyID}', '${TopNode}', '${Security}')
-END
-echo "All done."
-
-# Remove the tempory pivot-file
-#\rm ${OutputFile} 2>&1 >/dev/null
diff --git a/odm/jar/META-INF/MANIFEST.MF b/odm/jar/META-INF/MANIFEST.MF
@@ -1,3 +0,0 @@
-Manifest-Version: 1.0
-Main-Class: com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient
-
diff --git a/odm/jar2/META-INF/MANIFEST.MF b/odm/jar2/META-INF/MANIFEST.MF
@@ -1,6 +0,0 @@
-Manifest-Version: 1.0
-Class-Path: junit-4.8.2.jar junit-dep-4.8.2.jar log4j-snmp-appender.ja
- r sqljdbc4.jar commons-logging-1.1.1.jar log4j.jar commons-lang-2.5.j
- ar jackson-core-asl-1.9.3.jar jdom-1.1.2.jar jtds-1.2.5.jar
-Main-Class: com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient
-
diff --git a/pom.xml b/pom.xml
@@ -19,7 +19,7 @@
     <url>https://github.com/CTMM-TraIT/trait_odm_to_i2b2</url>
     <groupId>nl.vumc.biomedbridges</groupId>
     <artifactId>odm-to-i2b2</artifactId>
-    <version>0.1.0</version>
+    <version>3.0</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -309,6 +309,20 @@
                 <version>${coveralls-maven-plugin.version}</version>
             </plugin>
 
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient</mainClass>
+                        </manifest>
+                    </archive>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                </configuration>
+            </plugin>
+
         </plugins>
     </build>
 
diff --git a/...te_sqlserver_i2b2metadata_table_study.sql → ...te_sqlserver_i2b2metadata_table_study.sql b/...te_sqlserver_i2b2metadata_table_study.sql → ...te_sqlserver_i2b2metadata_table_study.sql
diff --git a/...ripts/create_sqlserver_staging_tables.sql → ...ripts/create_sqlserver_staging_tables.sql b/...ripts/create_sqlserver_staging_tables.sql → ...ripts/create_sqlserver_staging_tables.sql
diff --git a/odm/scripts/create_synonyms.sql → redcap-to-i2b2/scripts/create_synonyms.sql b/odm/scripts/create_synonyms.sql → redcap-to-i2b2/scripts/create_synonyms.sql
diff --git a/odm/scripts/odm2i2b2.bat → redcap-to-i2b2/scripts/odm2i2b2.bat b/odm/scripts/odm2i2b2.bat → redcap-to-i2b2/scripts/odm2i2b2.bat
diff --git a/odm/scripts/redcap2odm.bat → redcap-to-i2b2/scripts/redcap2odm.bat b/odm/scripts/redcap2odm.bat → redcap-to-i2b2/scripts/redcap2odm.bat
diff --git a/releases/release-3.0/odm-to-i2b2-3.0.jar b/releases/release-3.0/odm-to-i2b2-3.0.jar
diff --git a/src/documentation/DevelopersInformation.md b/src/documentation/DevelopersInformation.md
@@ -9,6 +9,64 @@ Linux/Unix. It is supposed to work on OS10 as well. It does not use databases no
 Java Enterprise Edition. The conversion tool only executes file operations. It parses the input ODM/XML file and
 returns as output three tabular text files.
 
+The installation can be executed entirely via the command line and has been tested
+on Ubuntu Linux and on a Windows system. The project is downloaded from GitHub on issuing
+the 'git clone' and 'git checkout' commands, as recommended below. The installation process can be followed
+via the screenshots. Developers who want to use/test the very latest state of the tool should not issue the
+'git checkout tags/v3.0' command.
+
+Requirements:
+-------------
+- internet access
+- git
+```sh
+$ sudo apt-get install git
+```
+- Java 7 or Java 8
+```sh
+$ sudo add-apt-repository ppa:webupd8team/java
+$ sudo apt-get update
+$ sudo apt-get install oracle-java8-installer
+```
+- Maven 3
+```sh
+$ sudo apt-get install maven
+```
+
+Installation
+------------
+Linux:
+```sh
+$ cd /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
+$ cp odm/examples/odm130.XML ../input-ODMs/test.xml
+$ mvn test
+$ mvn exec:java -Dexec.mainClass="com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient" -Dexec.args="/path/to/workspace/ODM-to-i2b2/input-ODMs/test.xml /path/to/workspace/ODM-to-i2b2/output-tabular-files"
+$ cd ../output-tabular-files
+$ ls -l
+```
+
+Screenshots
+-----------
+![Image first commands](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/first_commands.png)
+
+![Image test build success](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/test_build_success.png)
+
+![Image execution success](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/execution_success.png)
+
+![Image find the files](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/find_the_files.png)
+
+![Image Excel view](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/Excel_view.png)
+
+
+
+
 We currently have some information on using git & GitHub (for code management) and Maven (for building the code). To
 enhance and monitor the code quality, we use Checkstyle (code style checker), FindBugs (static code analysis tool),
 PMD (another static code analysis tool), and CPD (copy/paste detector).
diff --git a/src/documentation/UsersInformation.md b/src/documentation/UsersInformation.md
@@ -1,48 +1,7 @@
 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. The installation can be executed entirely via the command line and has been tested
-on Ubuntu Linux and via cmd.exe on a Windows system. The project is downloaded from GitHub on issuing
-the 'git clone' and 'git checkout' commands, as recommended below. The installation process can be followed
-via the screenshots. Users who want to use/test the very latest state of the tool should not issue the
-'git checkout tags/v3.0' command.
-
-Requirements:
--------------
-- internet access
-- git
-```sh
-$ sudo apt-get install git
-```
-- Java 7 or Java 8
-```sh
-$ sudo add-apt-repository ppa:webupd8team/java
-$ sudo apt-get update
-$ sudo apt-get install oracle-java8-installer
-```
-- Maven 3
-```sh
-$ sudo apt-get install maven
-```
-
-Installation
-------------
-Linux:
-```sh
-$ cd /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
-$ cp odm/examples/odm130.XML ../input-ODMs/test.xml
-$ mvn test
-$ mvn exec:java -Dexec.mainClass="com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClient" -Dexec.args="/path/to/workspace/ODM-to-i2b2/input-ODMs/test.xml /path/to/workspace/ODM-to-i2b2/output-tabular-files"
-$ cd ../output-tabular-files
-$ ls -l
-```
+three tabular files.
 
 Windows:
 ```sh
@@ -60,16 +19,3 @@ $ mvn exec:java -Dexec.mainClass="com.recomdata.i2b2.I2B2ODMStudyHandlerCMLClien
 $ cd ..\output-tabular-files
 $ dir
 ```
-
-Screenshots
------------
-![Image first commands](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/first_commands.png)
-
-![Image test build success](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/test_build_success.png)
-
-![Image execution success](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/execution_success.png)
-
-![Image find the files](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/find_the_files.png)
-
-![Image Excel view](https://github.com/CTMM-TraIT/trait_odm_to_i2b2/blob/master/src/documentation/Excel_view.png)
-
diff --git a/odm/examples/CDISC_ODM_example_maxim.xml → src/examples/CDISC_ODM_example_maxim.xml b/odm/examples/CDISC_ODM_example_maxim.xml → src/examples/CDISC_ODM_example_maxim.xml
diff --git a/odm/examples/CDISC_ODM_example_minim.xml → src/examples/CDISC_ODM_example_minim.xml b/odm/examples/CDISC_ODM_example_minim.xml → src/examples/CDISC_ODM_example_minim.xml
diff --git a/odm/examples/CDISC_ODM_example_web1.xml → src/examples/CDISC_ODM_example_web1.xml b/odm/examples/CDISC_ODM_example_web1.xml → src/examples/CDISC_ODM_example_web1.xml
diff --git a/odm/examples/CHB_REDCap_2.xml → src/examples/CHB_REDCap_2.xml b/odm/examples/CHB_REDCap_2.xml → src/examples/CHB_REDCap_2.xml
diff --git a/odm/examples/odm121.XML → src/examples/odm121.XML b/odm/examples/odm121.XML → src/examples/odm121.XML
diff --git a/odm/examples/odm130.XML → src/examples/odm130.XML b/odm/examples/odm130.XML → src/examples/odm130.XML
diff --git a/odm/examples/odm130data.XML → src/examples/odm130data.XML b/odm/examples/odm130data.XML → src/examples/odm130data.XML
diff --git a/odm/examples/odm130valueErrors.xml → src/examples/odm130valueErrors.xml b/odm/examples/odm130valueErrors.xml → src/examples/odm130valueErrors.xml
diff --git a/odm/examples/split_odm_aa.xml → src/examples/split_odm_aa.xml b/odm/examples/split_odm_aa.xml → src/examples/split_odm_aa.xml
diff --git a/src/main/generate-odm-reader-code/build.xml b/src/main/generate-odm-reader-code/build.xml
@@ -8,7 +8,7 @@
 	<property name="src.dir" value="${basedir}/src" />
 	<property name="test.dir" value="${basedir}/test" />
 	<property name="lib.dir" value="${basedir}/lib" />
-	<property name="scripts.dir" value="${basedir}/scripts" />
+	<property name="scripts.dir" value="/redcap-to-i2b2/scripts" />
 	<property name="build.dir" value="${basedir}/build" />
 	<property name="deploy.dir" value="redcapui/lib" />
 	<property name="gensrc.dir" value="/gensrc" />
@@ -69,7 +69,7 @@
 		</copy>
 
 		<copy todir="${build.dir}">
-			<fileset dir="${scripts.dir}">
+			<fileset dir="/redcap-to-i2b2/scripts">
 				<include name="*.bat" />
 				<include name="*.sh" />
 			</fileset>