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Step

Action

1

Execute the Ant build script build.xml located at
<CANANOLAB_SOURCE>/build with the target install:new:cananolab-db.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant install:new:cananolab-db

Successful execution of the Ant script creates the database schema and seed data required the caNanoLab 2.0 release.

2

If you are NOT using LDAP for user authentication, you can skip this step. If you
are using LDAP for authentication, execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db:ldap:upt:superadmin

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab-db:ldap:upt:superadmin

Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file on page 4.

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Verification

Once the MySQL database has been createdicreatesd, either through a new setup or through data migration (described in the next section), verify that the following numbers of database objects are created:

Tables 72

Example: Issue the following query at the MySQL prompt, logging in as root:

Code Block
mysql> select count

...

(*) from information_schema.tables where

...

 table_schema='canano' and table_type='BASE TABLE';

Data Migration

NOTE:
If you are installing caNanoLab 2.0 for the first time or installing a new caNanoLab release 2.0 schema, you can skip this section.

This installation guide only discusses the steps for migrating from release 1.5.3 or 1.5.4 or 1.5.5.?? in MySQL to release 2.0 in MySQL. If you have previously installed caNanoLab in MySQL prior to release 1.5.1, you 'd have need to migrate to release 1.5.1 first, one release at a time. Please see the install instructions for each release at {+}  http://gforge.nci.nih.gov/frs/?group_id=69+ for details.

Follow these steps to complete the required data migration from release 1.5.3, 1.5.4, or release 1.5.4 5.???  in MySQL to release 2.0 in MySQL:

Step

Action

1

Execute the Ant build script build.xml located at
<CANANOLAB_SOURCE>/build with the target update:cananolab-db.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab-db

Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 2.0 release.

2

If you are NOT using LDAP for user authentication, you can skip this step. If you
are using LDAP for authentication, execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db:ldap:upt:superadmin

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab- db:ldap:upt:superadmin

Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file on page 4.

3

If you are NOT using LDAP for user authentication, you can skip this step. If you
are using LDAP for authentication, and you already have user accounts in the system and you have data created by these users whose login names are not their LDAP login IDs, you'd need to do the following data update:

  1. Update the login_name column of the csm_user table with the LDAP login name for each user in the table:

    Example:     Issue the following query at the MySQL prompt for each user, logging in as root:
    mysql> update csm_user set login_name='' where login_name='';
    ...Where the token should be replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by the old login name.
  1. Update the created_by column of tables containing the column with the LDAP login name:

    Example:     Issue the following query at the MySQL prompt for each table containing the created_by column, logging in as root:
    mysql> update sample set created_by='' where created_by ='';
    ...Where the token should be replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by the old login name.


Note: if the created_by field contains the word "COPY" in it, update it with

have

a prefix

"

:

"

(colon), where the token

should be replaced

isreplaced by the real LDAP login name that corresponds to the old login name who created the data. If you

don't

do not know the original login who created the data, use the LDAP login of a curator. If you need assistance on completing the data updates for this step, please contact the caNanoLab technical team.

After data migration, refer to the Verification section to verify that the migration has been is successful.

caNanoLab Web Application

Assumptions and Requirements

Ant has been installed. is installed, and the Ant build properties have been set up, as described on pages 3 through 5areset up. The database has been is installed and verified, as described on pages 6 through 9. The JBoss application server has been is installed on a system (local or remote) and can be started at a designated port. JBoss install directory is referred to as <JBOSS_HOME> in the document. The JBoss application server host URL is referred as
<APP_SERVER_URL>, for example, cananolab-dev.nci.nih.gov:19080.

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It is possible to configure Apache server to interface with the JBoss server and set up a virtual host for the caNanoLab application, if . If you need assistance, please contact NCICBIIT Application Support (info provided at the end).

Installation and Deployment

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