diff --git a/odm/.classpath b/odm/.classpath deleted file mode 100755 index e25fdf4..0000000 --- a/odm/.classpath +++ /dev/null @@ -1,23 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - diff --git a/odm/.project b/odm/.project deleted file mode 100755 index 5a7bd24..0000000 --- a/odm/.project +++ /dev/null @@ -1,17 +0,0 @@ - - - odm - - - - - - org.eclipse.jdt.core.javabuilder - - - - - - org.eclipse.jdt.core.javanature - - diff --git a/odm/build.properties b/odm/build.properties deleted file mode 100755 index e69de29..0000000 diff --git a/odm/build_openclinica.xml b/odm/build_openclinica.xml deleted file mode 100755 index 715ae2f..0000000 --- a/odm/build_openclinica.xml +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/odm/etc/load_clinical_data_R.sh b/odm/etc/load_clinical_data_R.sh deleted file mode 100755 index 52126df..0000000 --- a/odm/etc/load_clinical_data_R.sh +++ /dev/null @@ -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 <&1 >/dev/null diff --git a/odm/jar/META-INF/MANIFEST.MF b/odm/jar/META-INF/MANIFEST.MF deleted file mode 100755 index 05c9218..0000000 --- a/odm/jar/META-INF/MANIFEST.MF +++ /dev/null @@ -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 deleted file mode 100755 index ca568f1..0000000 --- a/odm/jar2/META-INF/MANIFEST.MF +++ /dev/null @@ -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 index 6a32b16..21ad38e 100755 --- a/pom.xml +++ b/pom.xml @@ -19,7 +19,7 @@ https://github.com/CTMM-TraIT/trait_odm_to_i2b2 nl.vumc.biomedbridges odm-to-i2b2 - 0.1.0 + 3.0 jar @@ -309,6 +309,20 @@ ${coveralls-maven-plugin.version} + + maven-assembly-plugin + + + + com/recomdata/i2b2/I2B2ODMStudyHandlerCMLClient + + + + jar-with-dependencies + + + + diff --git a/odm/scripts/create_sqlserver_i2b2metadata_table_study.sql b/redcap-to-i2b2/scripts/create_sqlserver_i2b2metadata_table_study.sql similarity index 100% rename from odm/scripts/create_sqlserver_i2b2metadata_table_study.sql rename to redcap-to-i2b2/scripts/create_sqlserver_i2b2metadata_table_study.sql diff --git a/odm/scripts/create_sqlserver_staging_tables.sql b/redcap-to-i2b2/scripts/create_sqlserver_staging_tables.sql similarity index 100% rename from odm/scripts/create_sqlserver_staging_tables.sql rename to redcap-to-i2b2/scripts/create_sqlserver_staging_tables.sql diff --git a/odm/scripts/create_synonyms.sql b/redcap-to-i2b2/scripts/create_synonyms.sql similarity index 100% rename from odm/scripts/create_synonyms.sql rename to redcap-to-i2b2/scripts/create_synonyms.sql diff --git a/odm/scripts/odm2i2b2.bat b/redcap-to-i2b2/scripts/odm2i2b2.bat similarity index 100% rename from odm/scripts/odm2i2b2.bat rename to redcap-to-i2b2/scripts/odm2i2b2.bat diff --git a/odm/scripts/redcap2odm.bat b/redcap-to-i2b2/scripts/redcap2odm.bat similarity index 100% rename from odm/scripts/redcap2odm.bat rename to 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 new file mode 100755 index 0000000..fb7629c Binary files /dev/null and b/releases/release-3.0/odm-to-i2b2-3.0.jar differ diff --git a/src/documentation/DevelopersInformation.md b/src/documentation/DevelopersInformation.md index b01b113..bd7dd3f 100755 --- 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 index 722503f..766384b 100755 --- 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 b/src/examples/CDISC_ODM_example_maxim.xml similarity index 100% rename from odm/examples/CDISC_ODM_example_maxim.xml rename to src/examples/CDISC_ODM_example_maxim.xml diff --git a/odm/examples/CDISC_ODM_example_minim.xml b/src/examples/CDISC_ODM_example_minim.xml similarity index 100% rename from odm/examples/CDISC_ODM_example_minim.xml rename to src/examples/CDISC_ODM_example_minim.xml diff --git a/odm/examples/CDISC_ODM_example_web1.xml b/src/examples/CDISC_ODM_example_web1.xml similarity index 100% rename from odm/examples/CDISC_ODM_example_web1.xml rename to src/examples/CDISC_ODM_example_web1.xml diff --git a/odm/examples/CHB_REDCap_2.xml b/src/examples/CHB_REDCap_2.xml similarity index 100% rename from odm/examples/CHB_REDCap_2.xml rename to src/examples/CHB_REDCap_2.xml diff --git a/odm/examples/odm121.XML b/src/examples/odm121.XML similarity index 100% rename from odm/examples/odm121.XML rename to src/examples/odm121.XML diff --git a/odm/examples/odm130.XML b/src/examples/odm130.XML similarity index 100% rename from odm/examples/odm130.XML rename to src/examples/odm130.XML diff --git a/odm/examples/odm130data.XML b/src/examples/odm130data.XML similarity index 100% rename from odm/examples/odm130data.XML rename to src/examples/odm130data.XML diff --git a/odm/examples/odm130valueErrors.xml b/src/examples/odm130valueErrors.xml similarity index 100% rename from odm/examples/odm130valueErrors.xml rename to src/examples/odm130valueErrors.xml diff --git a/odm/examples/split_odm_aa.xml b/src/examples/split_odm_aa.xml similarity index 100% rename from odm/examples/split_odm_aa.xml rename to 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 index f87984c..4c114a9 100755 --- a/src/main/generate-odm-reader-code/build.xml +++ b/src/main/generate-odm-reader-code/build.xml @@ -8,7 +8,7 @@ - + @@ -69,7 +69,7 @@ - +