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hData Importer

Proof of concept for CCR and CDA validation techniques and import to a Mongo database

Install Steps

  1. install org.projecthdata.hdata-schemas with command (in cmd, not powershell):
mvn install:install  
     or  
mvn install:install-file -DgroupId=org.projecthdata -DartifactId=hdata-schemas -Dversion=1.0-SNAPSHOT -Dpackaging=jar -Dfile=C:/Projects/IEHR/hData/hdata-schemas/target/hdata-schemas-1.0-SNAPSHOT.jar -DgeneratePom=true
  1. install org.projecthdata.java-hstore with command (in cmd, not powershell):
mvn install:install-file -DgroupId=org.projecthdata -DartifactId=java-hstore -Dversion=1.0-SNAPSHOT -Dpackaging=jar -Dfile=C:\Projects\IEHR\hData\java-hstore\target\java-hstore-1.0-SNAPSHOT.jar -DgeneratePom=true
  1. Use local repo with:
mvn install:install-file -DlocalRepositoryPath=repo -DcreateChecksum=true -Dpackaging=jar -Dfile=C:/Projects/IEHR/hData/hdata-schemas/target/hdata-schemas-1.0-SNAPSHOT.jar -DgroupId=org.projecthdata -DartifactId=hdata-schemas -Dversion=1.0-SNAPSHOT  
mvn install:install-file -DlocalRepositoryPath=repo -DcreateChecksum=true -Dpackaging=jar -Dfile=C:/Projects/IEHR/hData/java-hstore/target/java-hstore-1.0-SNAPSHOT.jar -DgroupId=org.projecthdata -DartifactId=java-hstore -Dversion=1.0-SNAPSHOT
  1. Install LVG2012:
CREATE USER 'lvg'@'localhost' IDENTIFIED BY 'lvg';

NOTE: set root password to something without special characters
Recommended settings of my.ini for a large database

query_cache_size=100M  
query_cache_limit=3M  
myisam_sort_buffer_size=200M  
bulk_insert_buffer_size=100M  
join_buffer_size=100M  
key_buffer_size=600M  
read_buffer_size=200M  
sort_buffer_size=500M

Disable InnoDB/transaction support.
NOTE: Do not create database lvg2012 as described in online documentation. This step is done automatically by the scripts used later.
EDIT E:\lvg\lvg2012\loadDb\sources\gov\nih\nlm\nls\lvg\loadDb\MySql\db.cfg

#-------------------  
#DB_DRIVER = org.gjt.mm.mysql.Driver  
DB_DRIVER=com.mysql.jdbc.Driver  
DB_HOST = localhost  
DB_NAME = lvg2012  
DB_USERNAME = lvg  
DB_PASSWORD = lvg  
#-------------------  
DBA_USERNAME=root  
DBA_PASSWORD=MYPASSWORD  
#-------------------  
LVG_DIR = LVG_DIR =E:/lvg/lvg2012

Edit and run E:\lvg\lvg2012\loadDb\bin\1.SetupMySql_win.bat

set LVG_DIR=E:\lvg\lvg2012\
set JDBC=C:\Users\gaineys.FWT2HS1\Downloads\mysql-connector-java-5.1.22-bin.jar

cd ${LVG_DIR}/loadDb/bin/
.\1.SetupMySql_win.bat

Build LoadDB project with Ant. Edit and run E:\lvg\lvg2012\loadDb\bin\2.LoadDb_win.bat

set LVG_DIR=E:\lvg\lvg2012\
set JDBC=C:\Users\gaineys.FWT2HS1\Downloads\mysql-connector-java-5.1.22-bin.jar

.\2.LoadDb_win.bat

Edit and run E:\lvg\lvg2012\loadDb\bin\3.TestDb_win.bat

set LVG_DIR=E:\lvg\lvg2012\
set JDBC=C:\Users\gaineys.FWT2HS1\Downloads\mysql-connector-java-5.1.22-bin.jar

.\3.TestDb_win.bat
  1. Install MongoDB and edit config/mongo.properties to match local configuration.
  2. Run with
mvn jetty:run
  1. Access hData rest page at http://localhost:8080/webresources/12345/allergies/doc1

##Notes

JAXP in 1.6 has a SAXParserFactory that doesn't override setSchema().

This may be a version of org.apache.xerces.jaxp.SAXParserFactoryImpl before 2.7.0, so set the parser factory manually with

    System.setProperty("javax.xml.parsers.SAXParserFactory", "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");

Before calling SAXParserFactory.newInstance().

##References http://www.projecthdata.org/documents/pubs/hData%20Record%20Format-v8.pdf

License

sethrylan.mit-license.org