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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 this topic, 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 5.5 mysql 5.0.51a-3Ubuntu5.4 java version 1.5.0_16 (Suns java 1.5)

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javac version 1.5.0_16 ant 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, 2008 v1.1 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, 2009 v1.3 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, 2009 v2.2 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 are purchasing 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 that any 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 run the 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 systems packages. When used to manipulate the core 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 replacing hostname with either the fully qualified host name (e.g. example.com) of your server, or its 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, and your 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 david@192.168.2.200. OSCAR is predominately written in the Java programming language and thus requires the Java SDK to be built 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. This installation 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 OSCARs 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 OSCARs 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. Well install that now (note: if your Ubuntu is the Desktop Edition, then you can skip this step. sudo apt-get install unzip To keep OSCARs 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:anonymous@oscarmcmaster.cvs.sourceforge.net:/cvsroot/oscarmcmaster login cvs -z3 -r -d:pserver:anonymous@oscarmcmaster.cvs.sourceforge.net:/cvsroot /oscarmcmaster co -r RELEASE_9_06 -D "2009-07-20 23:59:59" oscar_mcmaster cvs -d:pserver:anonymous@oscarmcmaster.cvs.sourceforge.net:/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 administer the 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 Ontarios billing subsystem should run the following command: ./createdatabase_on.sh ****** oscar_mcmaster
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Whereas users who wish to use British Columbias 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 dont 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 it will run even faster. First, edit its 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 Tomcats 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 configuration code 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 well enable the new echart interface. cd $HOME/src/oscar_source/oscar_mcmaster/database/mysql 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:anonymous@oscarmcmaster.cvs.sourceforge.net:/cvsroot/oscarmcmaster login cvs -z3 -d:pserver:anonymous@oscarmcmaster.cvs.sourceforge.net:/cvsroot/oscarmcmaster co -P -D "2009-07-20 23:59:59" drugref cvs -d:pserver:anonymous@oscarmcmaster.cvs.sourceforge.net:/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/drugrefca_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 drug interactions 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 Thats 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 shown below. 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 instructions for 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. The primary 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 directory the 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 the dynamic files on the system. As the archive file of the uploaded files will become quite large over time, well 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 Well 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 Youve 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 own directory): 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 records localize your billing templates and update the system to the lastest fees schedule configure electronic access to your labs configure your prescription pad add 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 and remove the forms that are available via the patients 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 CHF Growth 0-36m Growth Charts ImmunAllergies Lab Req 2007 Mental Health MMSE PeriMenopausal Risk Assessment Rourke Rourke2006 Self Efficacy T2Diabetes Vascular 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 Hypertension HIV 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 patients 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 the Measurements heading. OSCAR Install Guide Comments ( 42 ) Trackbacks ( 0 ) Write comment

1. Danil February 15th, 2010 REPLY QUOTE The database scripts do not work on the mysql version 5, I had to edit them manualy to fix a few issues. Is it possible to get a compatible dump fom the mysqldump?

2. David Daley February 16th, 2010 REPLY QUOTE the scripts should work if you pull the source from the right place. I would suggest building from the timestamp/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, youll be in better shape to handle the errors that pop up when dealing with the development branch.

3. King February 22nd, 2010 REPLY QUOTE @David Daley

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I also have same problem with the database scripts, initcasidata.sql As 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-createdatabase-td24345159.html

4. Rob February 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 new hash key, but this could be made clearer with either an annotation, or alternative choices. Thanks for a great guide.

5. Carl Wiebe March 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. Im now specializing and want to set my own system. Im 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

6. Carl Wiebe March 6th, 2010 REPLY QUOTE

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

7. Rick March 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 error What i can do about it. thanks HTTP Status 404 /oscar%20/oscarBilling/DocumentErrorReportUpload.do type Status report message /oscar%20/oscarBilling/DocumentErrorReportUpload.do description The requested resource (/oscar%20/oscarBilling/DocumentErrorReportUpload.do) is not available. was there a solution for this problem?

8. David Daley March 8th, 2010 REPLY QUOTE Check the billing directory definition in the oscar.properties file.

9. David Daley March 8th, 2010 REPLY QUOTE 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.

10. Alien March 30th, 2010 REPLY QUOTE 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

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Thanks Anyone of you install oscar succeful on Debian Lenny distro?

11. Kevin April 2nd, 2010 REPLY QUOTE I am in the US, setting up for a birth center. I am running Karmic. This (OSCAR) looks like the cats mew, but I have run into an error when running ant. kevin@school-phbc:~/src/oscar_source/oscar_mcmaster/build$ ant Buildfile: build.xml BUILD FAILED /home/kevin/src/oscar_source/oscar_mcmaster/build/build.xml:385: /usr/share/tomcat6/common/lib not found. My system is running tomcat6, obviously, wont 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 find somewhere 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.

12. David Daley April 3rd, 2010 REPLY QUOTE 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.

13. Walter April 3rd, 2010 REPLY QUOTE Im 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, Ive been searching for solutions and most answers tend to point towards the password being

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specified incorrectly in oscar.properties However, I can use the same password to log into mysql from 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?

14. Walter April 4th, 2010 REPLY QUOTE @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 should help resolve the issue. Ill post an update once I figure out a fix (or if I manage to get it running on Tomcat6 instead).

15. Dan Corsillo April 6th, 2010 REPLY QUOTE Im 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 havent been able to get past this point. Help would be greatly appreciated.

16. David Daley April 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

17. John April 17th, 2010 REPLY QUOTE


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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);

18. John April 17th, 2010 REPLY QUOTE 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 rerun 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

19. rob April 21st, 2010 REPLY QUOTE java compile of echart Im having trouble with the java compile of the echart. Heres two attempts, one with the recommended java connector (3.0.11) and one with the 5.1.16 connector: cd $HOME/src/oscar_source/oscar_mcmaster/database/mysql manya@manya:~/src/oscar_source/oscar_mcmaster/database/mysql$ 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.properties Driver com.mysql.jdbc.Driver URI jdbc:mysql://localhost/ DB NAME oscar_mcmaster

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DB USER root DB PASSWD XXXXXXXXXXXXX DB 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$ 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 XXXXXXXXXX DB 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?

20. Rob April 23rd, 2010 REPLY QUOTE @rob Replacing the 5.1.16 java jar solved that problem.

21. Wombat April 29th, 2010 REPLY

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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 code directly. 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 by Tomcat 6. Is Oscar ready for tomcat 6 yet ? Any chance of updated documentation ? Ta Wombat

22. David Daley April 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)

23. Basha May 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

24. Mel May 12th, 2010 REPLY QUOTE @Wombat Ive just run my own first ever download and build, and didnt encounter the problems you found. Could there have been temporary trouble at sourceforge? Im running Ubuntu 9.04. I anticipate I might have some trouble, since my existing PostgreSQL server is already running

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UTF8, (although it didnt seem to affect the DPD load fingers crossed.)

25. Steve Bergman May 12th, 2010 REPLY 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

26. Steve Bergman May 12th, 2010 REPLY QUOTE 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.

27. Steve Bergman May 12th, 2010 REPLY QUOTE 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 up at the 10.04 version. Sorry but can you assist me?

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28. Steve Bergman May 13th, 2010 REPLY QUOTE 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 time correctly. 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 that the 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.

29. Gary May 15th, 2010 REPLY QUOTE Lots of help, eh? I think we need old Tomcat. Where?

30. Roy May 22nd, 2010 REPLY QUOTE I followed the guide and was able to install Oscar properly, except for one thing : https://localhost:8443/oscar dont work. I tried on firefox I get Firefox cant 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!

31. David Daley May 22nd, 2010 REPLY QUOTE 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 to use the ip address of the server machine

32. Roy
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May 22nd, 2010 REPLY 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 cant 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 no 443 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!

33. Roy May 24th, 2010 REPLY QUOTE 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

34. RKH May 26th, 2010 REPLY QUOTE Hi Does anyone know how to set up the Lab environment on OSCAR? Thanks!

35. Chod October 21st, 2010 REPLY 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, it comes up with a database creation error saying that the encoding LATIN1 does not match the servers locale of en_CA.UTF-8. This therefore fails to create the tables and ofcourse, cannot proceed to import the drugs from drugref. I tried re-installing postgres and python with export LC_ALL=C and then after installation unset LC_ALL, but this doesnt seem to make any difference. Is there anything else I can do to test or

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solve my problem? Thanks, Chod.

36. Chod October 21st, 2010 REPLY QUOTE @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 it gives 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?

37. Ahmed Eltawil October 22nd, 2010 REPLY QUOTE @Kevin How did you get over this problem? I am facing the same issue with my installation too. Any help is highly appreciated.

38. Amit October 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.

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

39. Gordon McCague November 26th, 2010 REPLY QUOTE 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.

40. Roshan December 13th, 2010 REPLY QUOTE @Rob Hi Rob, I am new to this. I am exactly having same problem as youve mentioned. But having hard time figuring out how to replace java jar 5.1.16 Thanks in advance. Roshan

41. George Kruzyk January 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).

42. Raj January 26th, 2011 REPLY QUOTE 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 a seamless upgrade installer! Thanks,
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