CLIENT REGISTRYOpenEMPI: Operations Support Training

SYSNET International, Inc.

OpenEMPI Software Stack• Database Server: PostgreSQL open source database,

version 9.1• Application Server: JBoss version 4.2.3• Web Server: Apache HTTP Server, version 2.4

Overview of Operational Support Tasks

• Starting the Application Server• Stopping the Application Server• Starting the Database Server• Stopping the Database Server• Changing database account passwords• Managing OpenEMPI user accounts• Back-up the application software• Back-up the Client Registry data• Viewing log files• Monitor the server load

Starting the Application Server• JBoss Installation Directory

• /home/sysnet/servers/jboss-4.2.3

• Setting the environment• $ source /home/sysnet/openempi/openempi_env.sh

• Start the server• $ cd /home/sysnet/servers/jboss-4.2.3• $ bin/run.sh

Server’s Memory Configuration• Will be configured appropriately but if necessary,

adjustments can be made over timeIn bin/run.conf

JAVA_OPTS="-Xms128m -Xmx2048m -XX:MaxPermSize=512m …

-Xms: Sets the starting heap size

-Xmx: Sets the maximum heap size

-XX:MaxPermSize: Sets the size of the memory allocated to storing class information

Stopping the Application Server• JBoss Installation Directory

• /home/sysnet/servers/jboss-4.2.3

• Setting the environment$ source /home/sysnet/openempi/openempi_env.sh

• Start the server$ cd /home/sysnet/servers/jboss-4.2.3

$ bin/shutdown.sh --shutdown

Starting/Stopping the Database Server

• PostgreSQL 9.1 installed as Unix service

• Starting the server:$ sudo /etc/init.d/posgresql start

• Stopping the server:$ sudo /etc/init.d/posgresql stop

Database Accounts• Account postgres is privileged; it is created when the

software is installed• Account openempi is created during installation of

OpenEMPI

• To change the openempi password, first connect to Postgres server with client applicationpsql --username=openempi --host=localhost openempi

Change Database Password• Once connected, use the alter user command:

ALTER USER openempi WITH PASSWORD ‘xxxxxxxxx';

Note: ‘xxxxxxxxx’ is just a placeholder for the password; so a strong password

• Must tell OpenEMPI that database password has changed$ cd /home/sysnet/openempi/conf

$ vi jdbc.properties

jdbc.username=openempi

jdbc.password=openempi

Managing OpenEMPI Accounts• Use the security tab to manage accounts and privileges

Manage Roles

From the Security tab select Manager Roles

Manage Roles

Roles have one or more permissions assigned to them.

Backup Database

Postgres includes the pg_dump tool for backups

pg_dump --username=openempi --password \

--host=localhost openempi gzip \

/home/sysnet/backups/openempi-db-backup-mm-dd-yyyy.sql.gz

• Software backs up everything within the database• A script will be developed to automate this process• Backups should be done on a daily basis

Backup Software• All the software that needs to be preserved resides under:

/home/sysnet

• Filesystem backups may be performed at the virtual machine level

• Backup strategy will be refined once the server hosting the client registry is made available to us

Log Files• The primary log file for the Client Registry is:

/home/sysnet/openempi/openempi.log

• Stores operational information at a configurable log level/home/sysnet/openempi/conf/log4j.properties

log4j.rootCategory=warn, R, O• Log level takes the values below (increasing detail):

error, warn, info, debug, trace

• Application server’s log file:/home/sysnet/servers/jboss-4.2.3.GA/server/default/log/server.log

System Monitoring• It is useful to periodically monitor the performance of the

servervmstat 5 (sar is another alternative)

procs -----------memory---------- ---swap-- -----io---- -system-- ----cpu----

r b swpd free buff cache si so bi bo in cs us sy id wa

1 0 769136 166932 21272 2298044 1 1 21 18 3 1 2 2 95 0

4 0 769136 165664 21280 2298392 0 0 1 20 4833 17126 5 11 83 0

0 0 769136 164272 21288 2298392 0 0 0 14 4870 18597 6 12 82 0

You want to verify:• System has plenty of memory• Disk I/O is low• CPU Utilization is not too high (consistently in the %90s).

Why do we need an EMPI?• Patient visits multiple separate healthcare providers

Enterprise MPI

Radiology

Patient known asJohn Smythe

Hospital

Patient known asJohn Smith

Laboratory

Patient known asJ. M. Smith

Patient

ID | John Smith | …

Three entries merged into single record

Approaching Record Matching

Client Registry Architecture• Overview of the software architecture of OpenEMPI

OpenEMPI Architecture• Utilizing the idea of a service, interchangeable

implementations of services can be plugged into the system transparently

Blocking Algorithms• Comparison of records is quadratic in the number of

records• Two files of 300,000 each generate 90 billion pairs

• Blocking variables are used for partitioning• Multiple passes are used to prevent errors• Selecting blocking variables

• High selectivity factor• Preferably uniformly distributed

• Wide variety of blocking algorithms available• Sorted neighborhood• Bigram Indexing• Canopy Clustering

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Field Comparison/Distance Algorithms

• Phonetic Encoding Algorithms• Soundex: oldest and most well known algorithm• Phonex: aims soundex by pre-processing names• Phonix: extension of Phonex with > 100 rules• NYSIIS: New York State Identification Intelligence System• Metaphone/Double Metaphone

• Approximate String Matching• Levenshtein or Edit Distance• Longest Common Substring (LCS)• Q-Grams• Jaro/Jaro-Winkler• Combinations of techniques

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Matching Algorithms• Variety of algorithms available, both deterministic and probabilistic• Fellegi-Sunter is the most popular probabilistic algorithm

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