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Installation of OSCAR v9.06 + Ubuntu Hardy

Heron v8.04 LTS

This tutorial covers the installation of the OSCAR McMaster Clinical Management System (CMS), using

the Ubuntu Hardy Heron v8.04 Long Term Support (LTS) operating system.

As this is a mission critical server, we recommend utilizing the latest Ubuntu LTS version as the

foundation for your OSCAR installation, as this will deliver the most trouble free and stable platform for

your OSCAR.

OSCAR can be installed on two or more servers and deployed in a redundant configuration to provide

maximum resiliency in support of your practice. The instructions to install a redundant server

configuration is beyond the scope of this tutorial. However, for the adventurous who are interested in thistopic, build two identical OSCAR servers, and then search the internet on how to configure MySQL

replication for the database, rsync for the filesystem, and cron for the automation. These utilities/tools

will allow you to tie your two or more OSCAR servers together.

Preamble

These instructions are written for an audience comfortable with invoking instructions from the command

line. If you are capable of installing the user friendly Ubuntu GNU/Linux operating system, then you

should be able to follow along with ease.

This installation has been tested with the following standard Ubuntu 8.04 LTS distro packages:

Ubuntu 8.04.1 i386 (32 bit, desktop or server)

tomcat 5.5mysql 5.0.51a-3Ubuntu5.4

java version 1.5.0_16 (Sun’s java 1.5)

OSCAR Install Guide | Indivica | http://indivica.com/?page_id=123

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javac version 1.5.0_16ant version 1.7.0

License

This document, written by David Daley in June 2008, is freely licensed under the Creative Commons

Attribution-Share Alike 3.0 Unported License.

The OSCAR McMaster project, Copyright © 2001 McMaster University, is distributed under the terms of

the GNU General Public License version 2 (GPLv2).

Document Version History

v1.0 – initial public release for OSCAR v2.2 – July, 2008v1.1 – minor modifications, additions, corrections – March, 2009

v1.1a – no content changes (formatted for new webserver) – May, 2009

v1.2 – added specific date stamp to drugref CVS command – May, 2009v1.3 – fixed formating issue related to quotes – May, 2009

v2.0 – initial public release for OSCAR v9.06 – July, 2009

v2.1 – updated the cvs date to include week view feature – July, 2009v2.2 – fixed a wayward hyphen – September, 2009

Getting Started

First, you must install Ubuntu 8.04 LTS. The installation of the base operating system is beyond the scope

of this document. Ubuntu can be downloaded or ordered in disk format directly over the internet.

Ubuntu runs on inexpensive, commodity hardware. To support a small practice with OSCAR, we

recommend a minimum configuration of 200Gb Disk, 2Gb RAM, and a 2GHz Intel Dual Core CPU. For

maximum subsystem compatibility, we suggest that you install the 32bit version of Ubuntu. If you arepurchasing a computer to run OSCAR, one option is to order the machine with Ubuntu pre-installed.

Please note that OSCAR continues to run very well on hardware that is much less powerful than this

practical minumum. For example, OSCAR will run quite reasonably on a machine with a single core

CPU with 512Mb RAM and 20Gb disk.

I am assuming that your target computer is connected to the internet. After installing the operating system,

log into your machine and open a terminal window.

We are now ready to begin.

Updating The Operating System

It is useful to update your system with the latest components and system patches. The first command

below asks Ubuntu to update its database of available packages, and the second command installs the

latest packages based on your current configuration. We run the upgrade command twice to ensure thatany packages that may have post-upgrade dependancies, also have an opportunity to be upgraded.

From the command line, enter the following commands, one at a time.


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sudo apt-get update

sudo apt-get -u upgrade

sudo apt-get -u upgrade

The sudo command is used to run priviledged operations on the Ubuntu platform. The first time you runthe command, it will ask for your password. Subsequently, it will not ask for your password again for a

short period of time (typically 15 minutes).

apt-get is the program Ubuntu uses for managing the system’s packages. When used to manipulate thecore packages of the operating system, it needs to be run in conjunction with the sudo command.

Installing The Infrastructure Packages

In order to support secure remote connections to your server, you will need to install the OpenSSH

package. This package will come in handy in the future to support administrative tasks on the system.

sudo apt-get install openssh-server

To log into a remote computer that is running OpenSSH, you use the ssh username@hostname command,

replacing username with a valid user name on the computer you are trying to log into, and replacinghostname with either the fully qualified host name (e.g. example.com) of your server, or it’s IP address

(e.g. 192.168.0.17).

For example, if your everyday computer is a Mac, and your OSCAR server user account is david, andyour OSCAR server IP address is 192.168.2.200, then you can now log into your server from your Mac,

by opening a terminal window on your Mac and running the command ssh [email protected].

OSCAR is predominately written in the Java programming language and thus requires the Java SDK to bebuilt from source. The Java SDK also supports the Tomcat web framework. The following installs Java,

plus fixes a bug in its default installation program. The server will need to be rebooted to catch this fix, but

we will do this later.

sudo apt-get install sun-java5-jdk

sudo ln -s /usr/lib/jvm/java-1.5.0-sun/jre/lib/i386/libmlib_image.so /usr/lib

sudo ldconfig

The source code compilation process for OSCAR is managed by the Ant package.

sudo apt-get install ant-optional

Your specific CMS data, profiles, and information will all be stored in the MySQL database. Thisinstallation sequence will ask you for a secure password for the database server – remember this password

as you will need it again later in the installation.

sudo apt-get install mysql-server libmysql-java

To support OSCAR’s web based user interface, the system leverages the extensive resources of the

Apache Tomcat web application framework.

sudo apt-get install tomcat5.5 tomcat5.5-admin

sudo ln -s /usr/share/tomcat5.5 /usr/local/tomcat


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OSCAR backup can be configured to use the Pretty Good Privacy subsystem.

sudo apt-get install pgpgpg

Concurrent Versions System (CVS) is used for source code control on the OSCAR Project. You will need

this package to grab the OSCAR source code.

sudo apt-get install cvs

OSCAR’s prescription drug & allergy database, DrugRef, requires the PostgreSQL database.

Please note that the sudo command is not required for the following export and unset commands.

export LC_ALL=C

sudo apt-get install postgresql-8.3 python-pgsql

unset LC_ALL

If you are installing OSCAR on the Ubuntu 8.04 LTS Server Edition, the default package will not include

unzip. We’ll install that now (note: if your Ubuntu is the Desktop Edition, then you can skip this step.

sudo apt-get install unzip

To keep OSCAR’s clock synchronized with the world, we recommend you install the Network Time

Protocol (NTP) service. This will require that your OSCAR maintains a link to the Internet to work.

sudo apt-get install ntp

These are all of the base packages that need to be installed. Now, we will reboot the server.

sudo shutdown -r now

After the server restarts, log in once again, and proceed to the next section.

Configuring The Base Packages

A few environment variables need to be set to support OSCAR.

A note about the following command – ‘vi’ (for visual editor) is a classic unix editor (classic, in the

sense of, you have to know it to really love it). Alternative editors exist. Examples of other Ubuntu

editors include ‘nano’, if you are running in a terminal environment, and ‘gedit’, if you are running

with a GUI. ‘emacs’ lovers need to install the emacs package via apt-get before you can use it as it is not

part of the base distro. If you elect to use an alternative editor, replace ‘vi’ in the commands that follow

with your editor of choice.

sudo vi /etc/profile

If you are configuring OSCAR on a freshly installed Ubuntu server, then you should be safe to add these

lines to end of the file.

JAVA_HOME="/usr/lib/jvm/java-1.5.0-sun"

CATALINA_HOME="/usr/share/tomcat5.5"

ANT_HOME="/usr/share/ant"


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export JAVA_HOME CATALINA_HOME ANT_HOME

To load the new environment variables into your existing terminal, run the following command. Please

note that the sudo command is not required in this case.

source /etc/profile

The infrastructure is now in place and it is time to get the OSCAR source code. The first cvs command

below will ask you for a password – please respond by hitting the Enter key, without adding a password

(ie a null password).

By specifying a specific date/time on the checkout command, you ensure that you get a specific, dated

version that you can track from. The command, run without the datestamp verb -D "2009-06-30

23:59:59" will retrieve the most recent version.

By specifying a particular release, you will get the code from that branch of the code. The command, run

without the release flags, will get you the code from the development branch. If the development stream

code is what you want, run the command without -r and also without -r RELEASE_9_06.

This tutorial is specific to the commands in the following section.

mkdir -p $HOME/src/oscar_source

cd $HOME/src/oscar_source

cvs -d:pserver:[email protected]:/cvsroot/oscarmcmaster login

cvs -z3 -r -d:pserver:[email protected]:/cvsroot

/oscarmcmaster co -r RELEASE_9_06 -D "2009-07-20 23:59:59" oscar_mcmaster

cvs -d:pserver:[email protected]:/cvsroot/oscarmcmaster

logout

It will take a few minutes for the source code to download. Afterwards, compile OSCAR.

cd $HOME/src/oscar_source/oscar_mcmaster/build

ant

You may ignore the warnings from the compiler, however you should expect to receive the message:BUILD SUCCESSFUL.

Copy the resulting WAR files to the web server.

sudo cp $HOME/src/oscar_source/oscar_mcmaster/build/tmp/*.war$CATALINA_HOME/webapps

OSCAR includes scripts to populate the MySQL database. For the following set of commands, you need

to replace ****** with a secure password. Remember this password as it will be required to administerthe database.

cd $HOME/src/oscar_source/oscar_mcmaster/database/mysql

Only run one of the following two database creation commands!

Users that wish to use Ontario’s billing subsystem should run the following command:

./createdatabase_on.sh ****** oscar_mcmaster


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Whereas users who wish to use British Columbia’s billing subsystem should run this command:

./createdatabase.sh ****** oscar_mcmaster

OSCAR users that are from neither Ontario nor BC can run either of the above commands (you must run

one of them), then you will need to adjust the billing system according to your own location.

You will need to move the oscar_*.properties files to $CATALINA_HOME as describe below.

sudo cp $HOME/src/oscar_source/oscar_mcmaster/install/oscar*properties

$CATALINA_HOME

sudo ln -s $CATALINA_HOME/oscar_mcmaster.properties

$CATALINA_HOME/oscar.properties

The oscar.properties file needs to be localized for your specific configuration.

sudo vi $CATALINA_HOME/oscar.properties

Specific configuration variables to consider for modification may include the following (but please review

all properties for your own situtation):

db_password = oscar2003 ### change to your mysql database password

drugref_url = http://localhost:8001 ### points locally

project_home = oscar

backup_path = /usr/local/backups/ ### change to a place for your backup files

SHOW_APPT_REASON=yes ### uncomment by removing the ‘#’

ENABLE_EDIT_APPT_STATUS=yes ### uncomment by removing the ‘#’

#ticklerplus=on ### disable by adding the ‘#’

#clientdropbox=off ### disable by adding the ‘#’

CASEMANAGEMENT=all ### turn on the new echart

CMESort=UP ### make the echart sort nicely

TESTING=yes ### enables the Invoice Report feature

FILTER_ON_FACILITY=false

If you don’t change the default location for the documentation directories in the properties file, you will

need to create the appropriate directories.

sudo mkdir -p /usr/local/tomcat/webapps/OscarDocument/oscar_mcmaster/form/record

sudo chown tomcat55:nogroup -R /usr/local/tomcat/webapps/OscarDocument

/oscar_mcmaster/form

The defaults for MySQL will work fine when you are starting out, but you can tune the database so that itwill run even faster. First, edit it’s configuration file:

sudo vi /etc/mysql/my.cnf


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Find the section that looks like this:

#

# * Fine Tuning

#

key_buffer = 16M

max_allowed_packet = 16M

thread_stack = 128K

thread_cache_size = 8

#max_connections = 100

#table_cache = 64

#thread_concurrency = 10

#

# * Query Cache Configuration

#

query_cache_limit = 1M

query_cache_size = 16M

Assuming that your server has 2Gb RAM and a single, dual core CPU, then the following modifications

are reasonable to help accelerate your OSCAR solution. For the lines that exist in the above block, you

can just adjust their numbers. For the lines that do not exist, add them to your configuration file.

key_buffer = 384M

table_cache = 512

sort_buffer_size = 4M

read_buffer_size = 4M

read_rnd_buffer_size = 16M

myisam_sort_buffer_size = 64M

query_cache_size = 32M

thread_concurrency = 4

After saving the configuration file, you will need to restart MySQL.

sudo /etc/init.d/mysql restart

We will now configure Tomcat. First, adjust the configuration file to allocate more resources to OSCAR.


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sudo vi /etc/default/tomcat5.5

Find the following sections and configure the variables to match what is below. Once again, I am assuming

that you have at least 2Gb RAM.

# Arguments to pass to the Java virtual machine (JVM).

JAVA_OPTS="-Xmx1024m -Xms1024m -XX:MaxPermSize=512m"

# Use the Java security manager? (yes/no)

TOMCAT5_SECURITY=no

Save the configuration file and when you are back to the shell, create the SSL certificate (localize the

specific values noted in this command for your particular situation and change the default password of

“changeit” to something specific for your installation).

sudo $JAVA_HOME/bin/keytool -genkey -dname "CN=192.168.2.200, OU=Indivica,

O=Indivica, L=Toronto, ST=Ontario, C=CA" -alias tomcat -validity 3650 -keyalg RSA

-keystore /root/.keystore -keypass changeit -storepass changeit

Now, modify Tomcat’s server config file to support secure encrypted connections via SSL.

sudo vi $CATALINA_HOME/conf/server.xml

In the server.xml file, look for the SSL HTTP/1.1 Connector entry and enable that block of configurationcode by removing the comment tags (<!– and –>).

Then modify the section to look like the following section.

<!– Define a SSL HTTP/1.1 Connector on port 8443 –>

<Connector port="8443" maxHttpHeaderSize="8192"

maxThreads="150" minSpareThreads="25" maxSpareThreads="75"

enableLookups="false" disableUploadTimeout="true"

acceptCount="100" scheme="https" secure="true"

clientAuth="false"

keystoreFile="/root/.keystore" ### add this line

keystorePass="put-your-password-here" ### add this line – this is the password from the

certificate creation command

sslProtocol="TLS" />

With these changes now configured, we need to restart the Tomcat application server.

sudo /etc/init.d/tomcat5.5 restart

Now we’ll enable the new echart interface.


java -cp .:/usr/local/tomcat/webapps/oscar/WEB-INF/lib/mysql-connector-java-3.0.11-stable-


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bin.jar importCasemgmt /usr/local/tomcat/oscar.properties

mysql -uroot -p****** oscar_mcmaster ### will bring you to the mysql database prompt

insert into issue (code,description,role,update_date) select icd9.icd9, icd9.description,

"doctor", now() from icd9;

quit ### gets you out of mysql

The DrugRef source resides on a different code branch from the main OSCAR system. We will now

download the subsystem.

cd $HOME/src/oscar_source

cvs -d:pserver:[email protected]:/cvsroot/oscarmcmaster login

cvs -z3 -d:pserver:[email protected]:/cvsroot/oscarmcmasterco -P -D "2009-07-20 23:59:59" drugref

cvs -d:pserver:[email protected]:/cvsroot/oscarmcmaster

logout

We need to create some directories for DrugRef and move the code into them.

sudo ln -s /usr/lib/postgresql/8.3 /usr/local/pgsql

sudo mkdir /usr/local/DPD

sudo mkdir /usr/local/drugref-ca_1_5

sudo cp -r $HOME/src/oscar_source/drugref/drugref2/DPD/* /usr/local/DPD

sudo cp -r $HOME/src/oscar_source/drugref/drugref2/drugref-ca_1_5/* /usr/local/drugref-ca_1_5

We now need to give ownership of these files and directories to the postgres account.

sudo chown -R postgres:postgres /usr/local/DPD

sudo chown -R postgres:postgres /usr/local/drugref-ca_1_5

We will log into the postgres account for the next section, but first, we will need to set a password for the

account.

sudo passwd postgres

su - postgres

We need to enable the execution bits on a couple of scripts.

cd /usr/local/DPD

chmod +x create_database.sh

chmod +x import_dpd.sh

The following command will create the database space for the DrugRef information.


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./create_database.sh

The next command will download the latest drug database from Health Canada. This import script will

take some time, so be patient (a good time to get a fresh coffee). You can ignore the ERROR: table

"*****" does not exist CREATE TABLE messages.

./import_dpd.sh

We need to add a new first line to the DrugRef calling program to compensate for a python issue (see:

http://www.python.org/dev/peps/pep-0263/). We also need to be specific about where the druginteractions plugins directory is.

First, edit the file:

vi /usr/local/drugref-ca_1_5/drugref_service.py

And now add as the very first line (including the sharp sign (‘#’)):

# coding: latin-1

Change the following line…

def __init__(self, plugindir="plugins", name = "Drugref Service", version="1.0"):

to reflect the current directory:

def __init__(self, plugindir="/usr/local/drugref-ca_1_5/plugins", name = "Drugref Service",version="1.0"):

Save the file. Finally when you get back to the terminal prompt, we will exit from postgres account.

exit

Now that you are back to your original shell, the last step is to start up the DrugRef subsystem.

We will configure the system so that it always will start when the server is turned on. To do this, we need

to edit a system script.

sudo vi /etc/rc.local

Add the following line to /etc/rc.local (before the exit 0 line):

nohup su -c "/usr/bin/python /usr/local/drugref-ca_1_5/drugref_service.py >> /usr/local/drugref-ca_1_5/drug.log 2>&1 &" postgres

And run the script:

sudo /etc/rc.local

That’s it! Your base OSCAR package is configured.

Trying It Out

We are now ready to log into OSCAR for the first time.

To test the connection, open your web browswer and go to your the web address of your server as shownbelow. You should see the OSCAR login page.


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In the specific example below, replace the IP address of the example URL with the IP address of your

server. To find the IP address of your server you can run the command "ifconfig" from the shell that you

have been using to configure the system.

https://192.168.2.200:8443/oscar/

Your connection to the OSCAR server is encrypted.

Your browser may complain about your unofficial or uncertified certificate. You can ignore these

warnings and avoid them in the future by installing the certificate on your workstation. The instructionsfor doing this is browser specific and beyond the scope of this document.

The default login parameters for OSCAR is as follows:

User Name: oscardoc

Password: mac2002

2nd Level Passcode: 1117

The first thing you will need to do once you log in, is change your passwords from the defaults. Theprimary password is changed via the Pref -> Change Your Password menu. The secondary password is

changed via the Admin -> Search/Edit/Delete Security Records menu.

Configure Your Backup

There are a number of ways to automate your backup. A few areas will need to be considered:

the database

the properties file

the document upload directorythe eforms directory

My recommendation is to automatically backup the database nightly, then use rsync to move all the files,

including the database dump to a remote machine.

First, create a database backup directory, and change the permissions so that only the root user can read

the contents.

sudo mkdir /usr/local/backups

sudo chown tomcat55:nogroup /usr/local/backups

sudo chmod 755 /usr/local/backups

Now we will create a script that we can use to backup the database and create an archive of all thedynamic files on the system. As the archive file of the uploaded files will become quite large over time,

we’ll only keep two copies on hand at any given time. You can, of course, configure your system to keep

more if you like.

First, we will create the file:

sudo vi /usr/local/backups/backupOSCAR.sh

In this file, put the following lines (replacing the ****** with your actual mySQL database password):

#!/bin/sh -e


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#

/usr/bin/mysqldump –add-drop-table -uroot -p****** oscar_mcmaster > /usr/local/backups

/backupOSCAR-`date +%F`.sql

/bin/gzip -f /usr/local/backups/backupOSCAR-`date +%F`.sql

/bin/mv /usr/local/backups/backupOscarFiles.tar.gz /usr/local/backups

/backupOscarFiles.older.tar.gz

/bin/tar cfz /usr/local/backups/backupOscarFiles.tar.gz /usr/local/tomcat/webapps/OscarDocument/oscar_mcmaster /usr/local/tomcat/oscar_mcmaster.properties

Make this file executable.

sudo chmod 700 /usr/local/backups/backupOSCAR.sh

We’ll configure Ubuntu to run the command every day. This is done by creating a cron job for the script

we just made. Run the following command:

sudo crontab -e

And add to the existing file an entry so that the command looks like below:

# m h dom mon dow command

04 04 * * * /usr/local/backups/backupOSCAR.sh

You’ve now configured a daily backup of the mySQL OSCAR database. This backup will run at 4 minutes

after 4 am, each morning. Each backup file will be created in the /usr/local/backups directory and will be

time stamped based on the day it was created.

You will be able to see the contents of the backup directory with the command:

sudo ls /usr/local/backups

These backup files are also viewable/downloadable via the Admin->oscarDatabase/Document Download

tab from within OSCAR.

To restore OSCAR from a backup file, you run this command (once again, inserting your own password in

lieu of the asterisks, and also adjusting the timestamp for the appropriate backup file from your owndirectory):

sudo zcat /usr/local/backups/backupOSCAR-2008-11-20.sql | mysql -uroot -p******

oscar_mcmaster

Finally, lets move the backup files, and the backup database to a remote machine. This is accomplished by

running the following command, and replacing username with a valid username for the remote machine,

and replacing domainname with the FQDN or IP of the remote host:

sudo rsync -azvv -e ssh /usr/local/backups username@domainname:backups

You have now completed a full installation of OSCAR. Keep reading for hints on what to do next.

Getting Started With OSCAR

Now that OSCAR is installed, there are a number of activities that you will need to perform to get the


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most out of your new CMS. Some of these tasks may include:

add users and configure their security and optionally their schedules

configure your clinic information

import your patient demographic recordslocalize your billing templates and update the system to the lastest fees schedule

configure electronic access to your labs

configure your prescription padadd some forms and eforms

Many of these activities are intuitive to configure and most are described in the user guide which is

available on the OSCAR Canada web site.

I will help you through a couple simple tasks to get you started.

Configuring Forms

Log into the OSCAR server as oscardoc.

Select from the menu Admin -> Select Forms. This will open a window which allows you to add andremove the forms that are available via the patient’s Encounter window.

Highlight Discharge Summary from the Selected Forms list, and click Delete. Add the following forms

from the All Available Forms list:

Annual

Annual V2

CHFGrowth 0-36m

Growth Charts

ImmunAllergiesLab Req 2007

Mental Health

MMSEPeriMenopausal

Risk Assessment

RourkeRourke2006

Self Efficacy

T2DiabetesVascular Tracker

To finish your selection, click the Close button.

These forms will now be viewable via the Encounter page of each patient.

Enabling Flowsheets

OSCAR supports a number of flowsheets, including:

INR

HypertensionHIV

Diabetes


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These flowsheets are enabled by configuring the disease registry. First, select Admin -> Customize

Disease Registry Quick List -> Edit Quick List -> default.

Then you enter each of the icd9 codes for the following items and select Add (select Close when you are

finished):

Atrial Fibrillation (code: 42731)

Diabetes Mellitus (code: 250)

Essential Hypertension (code: 401)Human Immuno Virus Dis (code: 042)

HX-VEN Thrombosis/Embols (code: V1251)

Long-Term Use Anticoagul (code: V5861)

And now, to enable a flowsheet for a specific patient, you will select from the patient’s Encounter -> Dx

Registry -> Quick List window the appropriate condition. The appropriate flowsheet will now be enabled

on the Encounter page (you will need to refresh/reload the Encounter page to see the Flowsheet under theMeasurements heading.

OSCAR Install Guide

Comments ( 42 )

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Write comment

Danil

February 15th, 2010REPLY

QUOTE

The database scripts do not work on the mysql version 5, I had to edit them manualy to fix a fewissues. Is it possible to get a compatible dump fom the mysqldump?

1.

David Daley

February 16th, 2010REPLY

QUOTE

the scripts should work if you pull the source from the right place. I would suggest building from thetimestamp/branch noted in the instructions for your first install until you get a handle on the

process, and then when you pull from the “firehose”, you’ll be in better shape to handle the errors

that pop up when dealing with the development branch.

2.

King

February 22nd, 2010REPLY

QUOTE

@David Daley

3.


14 of 27 27-Aug-11 11:37

I also have same problem with the database scripts, initcasidata.sqlAs far as I know, the issues is because of the line: INSERT INTO `intake_node` VALUES from

initcasidata.sql

The table intake_node has 14 columns, but the insert command only has 13 columns.

From one of the page I found, it said the issues had been fixed in 2009, but the most newest source

code still having the same issue.

For the page that discussed about this issue, please refer to: http://old.nabble.com/Unable-to-create-database-td24345159.html

RobFebruary 23rd, 2010

REPLY

QUOTE

This guide has been most helpful.

However, I found this command confusing…

sudo $JAVA_HOME/bin/keytool -genkey -dname “CN=192.168.2.200, OU=Indivica, O=Indivica,L=Toronto, ST=Ontario, C=CA” -alias tomcat -validity 3650 -keyalg RSA -keystore /root/.keystore

-keypass changeit -storepass changeit

because of the dual use of “changeit”… Presumably one is the old hash key, and the other the newhash key, but this could be made clearer with either an annotation, or alternative choices.

Thanks for a great guide.

4.

Carl WiebeMarch 6th, 2010

REPLY

QUOTE

I am a newbie to this but am a little familiar with linux, running Ubuntu on a laptop and desktop at

home. I have used OSCAR for a few years in a GP setting. I’m now specializing and want to set my

own system. I’m following the directions and thank you very much for them. with the command ”./createdatabase.sh ***** oscar_mcmaster” I keep getting the following message; “mysqladmin:

connect to server at ‘localhost’ failed

error: ‘Access denied for user ‘root’@'localhost’ (using password: YES)’ERROR 1045 (28000): Access denied for user ‘root’@'localhost’ (using password: YES)” Any help

or suggestions as to where I can “train up” for this?

Thanks again,Carl Wiebe Vancouver BC

5.

Carl WiebeMarch 6th, 2010

REPLY

QUOTE

6.


15 of 27 27-Aug-11 11:37

I should have added to my Question that I’ve tried all the passwords known and unknown to mysystem in place of the ***** symbols.

RickMarch 8th, 2010

REPLY

QUOTE

Hi David,

I have run into the same problem as posted in Oct but I was unable to see the solution…

i am unable to upload error files into OSCAR and it gives me the following errorWhat i can do about it.

thanks

HTTP Status 404 – /oscar%20/oscarBilling/DocumentErrorReportUpload.do

——————————————————————————–

type Status report

message /oscar%20/oscarBilling/DocumentErrorReportUpload.dodescription The requested resource (/oscar%20/oscarBilling/DocumentErrorReportUpload.do) is

not available.

was there a solution for this problem?

7.

David Daley

March 8th, 2010

REPLYQUOTE

Check the billing directory definition in the oscar.properties file.

8.

David Daley

March 8th, 2010

REPLYQUOTE

The “createdatabase.sh” program creates the databases with the password you used when you first

installed mysql (e.g. “apt-get install mysql”). That is the password the script is looking for.

9.

Alien

March 30th, 2010

REPLYQUOTE

I was triying to get oscar working on Debian Lenny but not good luck with that i get lots of errors

messages so i will need to make more test… i will post the errors i get and see if you can help me…

10.


16 of 27 27-Aug-11 11:37

Thanks…

Anyone of you install oscar succeful on Debian Lenny distro?

KevinApril 2nd, 2010

REPLY

QUOTE

I am in the US, setting up for a birth center. I am running Karmic. This (OSCAR) looks like the cat’s

mew, but I have run into an error when running ant.

“kevin@school-phbc:~/src/oscar_source/oscar_mcmaster/build$ antBuildfile: build.xml

BUILD FAILED

/home/kevin/src/oscar_source/oscar_mcmaster/build/build.xml:385: /usr/share/tomcat6/common/libnot found.”

My system is running tomcat6, obviously, won’t revert to 5.5, and will not set this folder. I can

create the folder, however, I am sure that there is data that should be inlcuded that I need to findsomewhere other.

Please assist any way possible. To further muck this up, I am a newbie-the tutorial level of

information is precisely what I require.

11.

David Daley

April 3rd, 2010

REPLYQUOTE

I would suggest sticking with the infrastructure mentioned in this tutorial unless you are very

adventurous.

Our plan it to update the tutorial in the near future (next few months) to identify the steps to use

OSCAR on the next LTS version of Ubuntu, but the current LTS version is very stable and thus will

give you the best results in a production environment.

12.

Walter

April 3rd, 2010REPLY

QUOTE

I’m running into a problem when trying to log in:

Database connection error: Cannot create PoolableConnectionFactory (Invalid authorization

specification, message from server: “Access dened for user ‘root’@'localhost’ (using password:

YES)”).

Now, I’ve been searching for solutions and most answers tend to point towards the password being

13.


17 of 27 27-Aug-11 11:37

specified incorrectly in oscar.properties – However, I can use the same password to log into mysqlfrom the command-line. An older archive pointed towards renaming oscar.properties to

EMR.properties; I created a symlink but to no avail. What am I missing?

Walter

April 4th, 2010

REPLYQUOTE

@Walter

PS: Additional web search points towards the .war files overriding$CATALINA_HOME/*.properties . I went back and changed the mysql password to the original

one in oscar.properties and now I can connect. I suspect that editing $HOME/src/oscar_source

/oscar_mcmaster/web/WEB-INF/classes/oscar_mcmaster.properties BEFORE running ant shouldhelp resolve the issue. I’ll post an update once I figure out a fix (or if I manage to get it running on

Tomcat6 instead).

14.

Dan CorsilloApril 6th, 2010

REPLY

QUOTE

I’m having difficulty at this instruction set. I have installed Java

sudo $JAVA_HOME/bin/keytool -genkey -dname “CN=192.168.2.200, OU=Indivica, O=Indivica,

L=Toronto, ST=Ontario, C=CA” -alias tomcat -validity 3650 -keyalg RSA -keystore /root/.keystore-keypass changeit -storepass changeit

The error message returns “command not found” and looking in the $JAVA_HOME/bin directory

there is no “keytool” command. I haven’t been able to get past this point. Help would be greatlyappreciated.

15.

David DaleyApril 6th, 2010

REPLY

QUOTE

The keytool is part of the java distribution. It is found on my server:

$ ls $JAVA_HOME/bin/keytool

/usr/lib/jvm/java-1.5.0-sun/bin/keytool

Check to see if you have this file/directory/etc… and if not, try reinstalling your java package

16.

John

April 17th, 2010REPLY

QUOTE

17.


18 of 27 27-Aug-11 11:37

initcaisidata.sql has an error at line 204. Add,NULL

To the end if each insert. It should look like this and then it will work.

INSERT INTO `intake_node` VALUES(1, 1, NULL, 0, NULL, false, 1, 1, NULL, NULL,1,NULL,0,NULL),

(2, 2, NULL, 0, NULL, false, 2, 1, NULL, NULL,2,NULL,0,NULL);

John

April 17th, 2010

REPLYQUOTE

This might help someone

while performing the database conversion:java -cp .:/usr/local/tomcat/webapps/oscar/WEB-INF/lib/mysql-connector-java-3.0.11-stable-bin.jar

importCasemgmt /usr/local/tomcat/oscar.properties

I got the following error:Exception in thread “main” java.lang.UnsupportedClassVersionError: Bad version number in .class

file

Cause: The supplied importCasemgmt.java was compiled by newer compiler version.

Solved by recompiling. cd to the mysql directory and run

javac importCasemgmt.java

then rerunjava -cp .:/usr/local/tomcat/webapps/oscar/WEB-INF/lib/mysql-connector-java-3.0.11-stable-bin.jar

importCasemgmt /usr/local/tomcat/oscar.properties

18.

robApril 21st, 2010

REPLY

QUOTE

java compile of echart

I’m having trouble with the java compile of the echart.

Here’s two attempts, one with the recommended java connector (3.0.11) and one with the 5.1.16connector:


manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$ java -cp .:/usr/local/tomcat

/webapps/oscar/WEB-INF/lib/mysql-connector-java-3.0.11-stable-bin.jar importCasemgmt

/usr/local/tomcat/oscar.propertiesDriver com.mysql.jdbc.Driver

URI jdbc:mysql://localhost/

DB NAME oscar_mcmaster

19.


19 of 27 27-Aug-11 11:37

DB USER rootDB PASSWD XXXXXXXXXXXXX

DB ERROR: com.mysql.jdbc.Driver

java.lang.ClassNotFoundException: com.mysql.jdbc.Driverat java.net.URLClassLoader$1.run(URLClassLoader.java:200)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:188)at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)

at java.lang.ClassLoader.loadClass(ClassLoader.java:252)at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:164)at importCasemgmt.main(importCasemgmt.java:77)

manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$

manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$ java -cp .:/usr/share/java/mysql-connector-java-5.1.16.jar importCasemgmt ‘/usr/local/tomcat/oscar.properties’

Driver com.mysql.jdbc.Driver

URI jdbc:mysql://localhost/DB NAME oscar_mcmaster

DB USER root

DB PASSWD XXXXXXXXXXDB ERROR: com.mysql.jdbc.Driver

java.lang.ClassNotFoundException: com.mysql.jdbc.Driver

at java.net.URLClassLoader$1.run(URLClassLoader.java:200)at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:188)

at java.lang.ClassLoader.loadClass(ClassLoader.java:307)at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)

at java.lang.ClassLoader.loadClass(ClassLoader.java:252)

at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:164)

at importCasemgmt.main(importCasemgmt.java:77)manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$ echo $CLASSPATH

/usr/share/java/mysql-connector-java-5.1.16.jar

manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$

Does anyone see the error of my ways?

RobApril 23rd, 2010

REPLY

QUOTE

@rob

Replacing the 5.1.16 java jar solved that problem.

20.

WombatApril 29th, 2010

REPLY

21.


20 of 27 27-Aug-11 11:37

QUOTE

Hi

I am setting Oscar for the first time, and I have a few issues

1 The CVS setp is broken, it comes up with bad login, so I am forced to download the source codedirectly.

2 The source code has no build.xml file, am I required to create it?

3 Tomcat5.5 package step no longer works, I am assuming tomcat5.5 has been superceeded byTomcat 6. Is Oscar ready for tomcat 6 yet ?

Any chance of updated documentation ?

Ta

Wombat

David DaleyApril 30th, 2010

REPLY

QUOTE

I would suggest for first time installers to explicitly stick to the instructions, including running the

same version of the infrastructure (i.e. 8.04.lts), and the save version of OSCAR (e.g. 9.06)

22.

BashaMay 3rd, 2010

REPLY

QUOTE

@Kevin

Hey Kevin,

I have same your problem , did you FIX ?if you fix please can update how you fixed ?

thank

23.

Mel

May 12th, 2010

REPLYQUOTE

@Wombat

I’ve just run my own first ever download and build, and didn’t encounter the problems you found.Could there have been temporary trouble at sourceforge?

I’m running Ubuntu 9.04.

I anticipate I might have some trouble, since my existing PostgreSQL server is already running

24.


21 of 27 27-Aug-11 11:37

UTF8, (although it didn’t seem to affect the DPD load — fingers crossed.)

Steve Bergman

May 12th, 2010REPLY

QUOTE

Kevin,

Tried dowloading the Aptache Tom cat command, it appears that tere may be a obsolete version out

there now. Please can you recomend a work around. This is my ERROR Message.

“Package tomcat5.5 is not available, but is referred to by another package.This may mean that the package is missing, has been obsoleted, or

is only available from another source

E: Package tomcat5.5 has no installation candidate”

25.

Steve Bergman

May 12th, 2010

REPLYQUOTE

Kevin,

I continued on with the installation and then ran into this…

“administrator@ubuntu:~/src/oscar_source$ cd $HOME/src/oscar_source/oscar_mcmaster/build

administrator@ubuntu:~/src/oscar_source/oscar_mcmaster/build$ ant

Error: JAVA_HOME is not defined correctly.We cannot execute /usr/lib/jvm/java-1.5.0-sun/bin/java”

Do I have to blow the installation out completely and start again? Is this because tomcat was not

found?

Sorry by=ut can you advise…

Thanks.

26.

Steve Bergman

May 12th, 2010

REPLYQUOTE

OK – 8.04.lts is what is required and I have got 10.04.lts – I will start again. Do you know of a

mirror site that still offers 8.04.lts? I have traced it via google and other searches and always end upat the 10.04 version.

Sorry but can you assist me?

27.


22 of 27 27-Aug-11 11:37

Steve Bergman

May 13th, 2010

REPLYQUOTE

My Humble apologies, I re-read carefully your instructions, relaized I had a newer version of

UBUNTU and that cause all the issues with TomCat. Rebuilt the whole configuration – This timecorrectly. There were some issues arround the SUN Java build, I believe i managed arrounf the

issue. BUT….

When doing the Build I did not get BUILD SUCCESSFUL message, after investigation i found thatthe lib directory, in the (/usr/lib/jvm/java-1.5.0-sun-1.5.0.22) it does not exist.

Is their a way I can get this without restarting from the begining…..?

Please let me know.

28.

Gary

May 15th, 2010

REPLYQUOTE

Lots of help, eh? I think we need old Tomcat. Where?

29.

Roy

May 22nd, 2010

REPLYQUOTE

I followed the guide and was able to install Oscar properly, except for one thing :

https://localhost:8443/oscar don’t work.I tried on firefox I get “Firefox can’t establish a connection to the server at localhost:8443.” I

searched for hours to find a solution, but no success. I use tomcat5.5 with java-6-sun. Any idea?

Thanks for this great guide!

30.

David Daley

May 22nd, 2010

REPLYQUOTE

if you are using “localhost”, this would assume that you are running firefox on your local server. if

you are running firefox on your PC/Mac, and OSCAR is on a separate machine, then you need touse the ip address of the server machine

31.

Roy

32.


23 of 27 27-Aug-11 11:37

May 22nd, 2010REPLY

QUOTE

Thank you! Oscar works fine with localhost or IP addresses on my small network, with port 8180(which is unsecured even if redirected toward 8443 right?). The problem is that I can’t have secure

connection, even after following the instructions exactly and verifying many times to make sure

there is no mistakes.

I have installed Oscar on Ubuntu 9.10 Desktop, so maybe Tomcat5.5 is conflicting with something

else?

Also, When I run a port scan (from Network Tools), I find ports 22, 8180 and a few other, but no443 nor 8443. The firewall, ufw, is not blocking port 8443. I do not know where to look anymore to

make this work. If you have any hints, please let me know!

Roy

May 24th, 2010

REPLYQUOTE

Finally I was able to make the https connection work, by creating a certificate at /etc/tomcat5.5

/.keystore instead of /root/.keystore. So changing the location of the keystore made it work,surprisingly…

33.

RKH

May 26th, 2010REPLY

QUOTE

Hi – Does anyone know how to set up the Lab environment on OSCAR? Thanks!

34.

Chod

October 21st, 2010REPLY

QUOTE

Hi all,

I tried to follow this guide explicitly, but must admit I stumbled a few times but it was a good

learning curve.

I have run into a problem I cannot fix though. When I do the ./create_database.sh under postgres, itcomes up with a database creation error saying that the encoding LATIN1 does not match the

server’s locale of en_CA.UTF-8.

This therefore fails to create the tables and ofcourse, cannot proceed to import the drugs fromdrugref.

I tried re-installing postgres and python with export LC_ALL=C and then after installation unset

LC_ALL, but this doesn’t seem to make any difference. Is there anything else I can do to test or

35.


24 of 27 27-Aug-11 11:37

solve my problem?

Thanks,

Chod.

Chod

October 21st, 2010

REPLYQUOTE

@Chod

Fixed.

I had to dpkg –purge Postgres totally and re-install and now the scripts worked fine. Although the

import script only took about 30 seconds… is that right or is something still wrong?

Upon testing, when i go to prescribing a drug, i can search for a drug, but when i click on one itgives an error.

JavaClient: XML-RPC Fault #1: org.apache.xmlrpc.XmlRpcException: :ERROR: operator does not

exist: integer = character varying LINE 1: …ere tc.tc_atc_number = ‘J01CA04′ and tc.drug_code =sd.drug_… ̂HINT: No operator matches the given name and argument type(s). You might need to

add explicit type casts.

Any ideas?

36.

Ahmed Eltawil

October 22nd, 2010

REPLYQUOTE

@Kevin

How did you get over this problem? I am facing the same issue with my installation too. Any help ishighly appreciated.

37.

AmitOctober 29th, 2010

REPLY

QUOTE

@Chod

I am also facing the same problem in selecting a drug. Were you able to find any

solution/workaround?

For others, I am facing problems adding drugs to a prescription. I am able to search for drugs. But, I

get the following error when I try to select it.

38.


25 of 27 27-Aug-11 11:37

JavaClient: XML-RPC Fault #1: org.apache.xmlrpc.XmlRpcException: :ERROR: operator does notexist: integer = character varying LINE 1: …ere tc.tc_atc_number = ‘M01AE01′ and tc.drug_code

= sd.drug_… ̂HINT: No operator matches the given name and argument type(s). You might need

to add explicit type casts.

Any clues?

Thanks

Gordon McCague

November 26th, 2010

REPLYQUOTE

Hi Gang: It seems that Ubuntu is dropping SUN Java for OpenJDK. How do we get the right Java

installed on the server? The command in this document is not working for me.

39.

Roshan

December 13th, 2010

REPLYQUOTE

@Rob

Hi Rob,I am new to this. I am exactly having same problem as you’ve mentioned. But having hard time

figuring out how to replace java jar 5.1.16

Thanks in advance.Roshan

40.

George KruzykJanuary 23rd, 2011

REPLY

QUOTE

@Walter

This worked: change password for root back to original password in file oscar_mcmaster.properties

(“liyi” in the case of my version).

41.

Raj

January 26th, 2011

REPLYQUOTE

Hello – What is the latest version of OSCAR? Is there an upgrade tool that will automatically

upgrade the current OSCAR version to a new one keeping everything intact? Basically looking for aseamless upgrade installer!

Thanks,

42.


26 of 27 27-Aug-11 11:37

Raj.

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OSCAR Install Guide _ Indivica _2