Mars installation procedure

Applicable for Release 1.2

 

1. Requirements

Hardware requirements:

Server with at least 1 GBytes of main memory

Software requirements:

Oracle 9i or PostgreSQL 8.x.x for MARS
Oracle 9i or PostgreSQL 8.x.x or MySQL 4.1.xx for the Usermanagement
Java JDK 1.6.x
be sure that JAVA_HOME points to your JDK installation

 

2. Installation Instructions


MARS consists of two components which can run independently on different machines.

  • AAS: provides the central usermanagement and its access controls
  • MARS: is the core application
Security: The communication between the components of MARS is based on http connections
which should be secured by SSL layer security (HTTPS). In order to reduce complexity of this
installation instruction HTTPS adaptations were skipped. In our productive environment all
communications between MARS and the usermanagement are performed over https.


1. Unpacking Mars

1.1. Unpack mars-1.2.x.tar.gz

2.a PostgreSQL installation

 2.a.1. Create 2 new users

  • for MARS (for example:)
                 username: marsdummy
                 password: marsdummy
  • for AAS
                username: usermanagement
                password: usermanagement
 2.a.2. Create new database mars
 2.a.3 Create a new schema called usermanagement (MARS is mapping by default to public)
 2.a.4. Grant the usermanagement user all priviliges for the usermanagement schema
 2.a.5. Use initializeMARS_Oracle.sql to create the tables and insert required data for MARS
           Grant the mars user all priviliges for the public schema


2.b Oracle installation

 2.b.1. Create 2 new tablespaces (MARS and USERMANAGEMENT)

 2.b.2. Create 2 new users like 'Scott'

  • for MARS (for example:)
                 username: marsdummy
                 password: marsdummy
  • for AAS
                username: usermanagement
                password: usermanagement
 2.b.3. Use install/database/sql/initializeMARS1.2_Oracle.sql to create the tables and insert required data for MARS

2.c Mysql AAS Installation

 2.c.1. Create a new schema usermanagement

 2.c.2. Create a new user

  • for AAS (for example)
                username: usermanagement
                password: usermanagement
 2.c.3. Grant the usermanagement user all priviliges for the usermanagement schema


3. Configuring the JBoss for the right database

  • for AAS
                 Copy the database specific userman-XXXX-ds.xml from install/database/config/
                 to $JBOSS_HOME/server/usermanagement/deploy/
                 and change the file corresponding your configuration.
  • for MARS
                Copy the database specific mars-XXXX-ds.xml from install/database/config to
                 $JBOSS_HOME/server/mars/deploy/
                and change the file corresponding your configuration.

4. Starting the AAS

4.1. Go to $JBOSS_HOME/bin

4.2. Start supplied Authentication and Authorization System (AAS) with
             run.bat -c usermanagement (for Windows) or
             run.sh -c usermanagement (for Linux or Solaris)
        and wait until the JBoss started

4.3 Use correct sql file from /install/usermanagement/
         initializeAAS_xxx.sql     to insert required data

5. Create data root

5.1 Create your DATAROOTDIRECTORY. The DATAROOTDIRECTORY is the root path where all the files which are uploaded or can be downloaded from MARS are stored. Pay attention! This volume should be large since all the files are stored there, too!
e.g. /home/marsdata/
5.2. Copy the contents of install/root/ to your created DATAROOTDIRECTORY.
5.3. If you want to connect to CARMAweb as well, copy the keystore file GenomeCA.clientTrust into a subfolder accessable for MARS.

6. Configuring MARS for the AAS (only necessary if AAS is not running on the same machine as MARS, otherwise skip this point)

6.1. Open the files mars.properties and marsQM.properties at $JBOSS_HOME/server/mars/

6.2. Change the localhost behind the http_url= to your AAS address

6.3. If your usermanagement is secured with https change the 

        protocol=HTTP
to 
        protocol=HTTPS
and adapt the parameters 
           ##### HTTPS Protocol #####
           https_url=localhost
           https_port=17433
           keystorefile=/path/to/keystore/keystore

7. Starting MARS

7.1. Go to $JBOSS_HOME/bin

7.3. Start MARS with
     run.bat -c mars (for Windows) or
     run.sh -c mars (for Linux or Solaris)
  and wait until JBoss has started

8. Change the MARS settings and insert the path to the newly created DATAROOTDIRECTORY

8.1. Open http://localhost:20080

8.2. Click on JMX-Console

8.3. Click on service=ServerSettings

8.4. Use the method setProperty (e.g.)

p1 = DATAROOTDIRECTORY
p2 = /home/marsdata/

8.5. Click on invoke

8.6. To check the properties use method „listProperties“


8.7. To the same for the other properties:


PROPERTY_CLIENTTRUST

path to the keystore file GenomeCA.clientTrust

 
GUESTUSERALLOWED

TRUE or FALSE

 
OVERVIEWREFRESHINTERVAL

Time in ms when to update the overview page (default setting is 1 hour)

 
ADMINMAIL

the email address of the MARS administrator

 
SMTPSERVER

your outgoing mail server

 
SMTPPORT

smtp server port

 
PROPERTY_RSERVE_EJBWS_ENDPOINT_ADDRESS

address of the CARMAweb web service

 
DATABASE

ORACLE or POSTGRESQL based on your type of installation

 
DATAROOTDIRECTORY

your data root directory, where all the application data is stored



9. Restart MARS to guarantee that your settings take effect.

10. Get access to the AAS

10.1. Open your Web browser and type http://localhost:17080/UsermanagementWeb

10.2. Login using username: admin password: 12345

(change the password afterwards, since this is the ADMINISTRATOR account for the whole AAS)

10.3. Logout

10.4. Login using username: testmars password: mars!!

(The testmars user is in mars and marsQM Administrator group.)

11. Get access to MARS

11.1. Open your Web browser and type http://localhost:20080/marsWEB

12. Get access to marsQM

12.1. Open your Web browser and type http://localhost:20080/marsQM