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In caNanoLab release 2.1, the Ant build script automatically installs the web application. |
Setting Properties
Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.
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Edit the Ant properties file, build.properties
, at <CANANOLAB_SOURCE>/build
by specifying values for the following properties.
Property | Description | |
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file.repository.dir | A directory on the system that hosts the Wildfly application server for storing uploaded files, for example, NOTE: This directory should be writable by the user that starts the Wildfly server, and this directory should be created prior to starting the application. Use either double-back slashes or a single forward slash / as the file separator if working on Windows platform. | |
admin.email | : The email address that receives requests for new user accounts, for example, the NCICBIIT application support email for the NCICBIIT installation. | |
ldap.authentication.enabled | : A Boolean flag to indicate whether or not to use LDAP for user authentication in caNanoLab, for example, NOTE: Please note that the default value is | |
ldap.host.url | : The URL of the LDAP server used for user authentication. | |
ldap.searchable.base | : The location in the directory from which the LDAP search begins. | |
ldap.userId.label | : The uid label for LDAP, for example, | |
superadmin.login.name | : The LDAP login name for the user account who is the super admin of the UPT tool. See User Provisioning Tool (UPT) for details on setting up UPT. | |
superadmin.first.name | : The LDAP first name for the user account who is the super admin of the UPT tool. | |
superadmin.last.name | : The LDAP last name for the user account who is the super admin of the UPT tool. | |
database.server | : The name of the server hosting the database, for example, | |
database.port | : The database port number, for example, | |
database.user : | The database user name used in the caNanoLab application, for example, | |
database.password | : The password for the database user specified above, for example, | |
database.system.user | : The system database user name with privileges to create a database, create tables, grant user accesses to a database, for example, | |
database.system.password | : The password for the system database user specified above, for example, | |
jboss.server.dir | : The Wildfly server directory, for example, |
Database Technology
Assumptions and Requirements
- The Ant build properties are set as described in section, Step 2. Edit Ant Properties.
- A MySQL database is set up on a system (local or remote) with a system (or root) account.
- The system account matches properties 9) and properties 10)
superadmin.last.name
anddatabase.server
in Step 2. Edit Ant Properties.
For a Previous Installation
If you installed :
- Installed caNanoLab prior to release 2.1 against an MySQL database
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OR
Installed release 1.2, release 1.1.1, or release 1.1 against an Oracle database,
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- AND have associated production data in these schemas
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AND would like to continue to use the same data for caNanoLab release 2.1 in MySQL,- ...review the following database initialization steps, and then go directly to section,
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If you have a previously installed caNanoLab |
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running on a Wildfly server, stop the server before running the database scripts. |
For a New Installation
If you are installing the caNanoLab application for the first time or want to install a new schema for release 2.1, follow the steps below to set up the required MySQL schema objects and the seed data for release 2.1.
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Follow these steps to initialize your MySQL database system:.
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:
Successful execution of the Ant script creates the database schema and seed data required the caNanoLab 2.1 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:
Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file. |
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mysql> select count(*) from information_schema.tables where table_schema='canano' and table_type='BASE TABLE'; |
Data Migration
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If you are installing caNanoLab 2.1 for the first time or installing a new caNanoLab release 2.1 schema, you can skip this section. |
This installation guide only discusses the steps for migrating from release 1.5.3, 1.5.4, or 1.5.5. in MySQL to release 2.1 in MySQL. If you have previously installed caNanoLab in MySQL prior to release 1.5.1, you need to migrate to release 1.5.1 first, one release at a time. The 1.5.5 installation guide is available at the main caNanoLab wiki page caNano Lab Release Notes, but previous installation guides are available at the caNanoLab Archive page.
Follow these steps to complete the required data migration from release 1.5.3, 1.5.4, or 1.5.5. in MySQL to release 2.1 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:
Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 2.1 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:
Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file. | |||||
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 need to perform the following update:
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After data migration, refer to the Verification section to verify that the migration is successful.
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Assumptions and Requirements
- Ant is installed, and the Ant build properties are set up.
- The database is installed and verified.
- The Wildfly application server is installed on a system (local or remote) and can be started at a designated port. Wildfly install directory is referred to as <JBOSS_HOME> in the document. The Wildfly application server host URL is referred as <APP_SERVER_URL>, for example,
cananolab-dev.nci.nih.gov:19080
.
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- The default configuration is used for deploying caNanoLab web archive files.
For example, in wildfly-8.2.0.Final, the default configuration is located at the directory <JBOSS_HOME>/standalone. The caNanoLab web archive file will be deployed at the directory <JBOSS_HOME>standalone/deployments. - It is possible to configure Apache server to interface with the Wildfly server and set up a virtual host for the caNanoLab application. If you need assistance, please contact
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- NCI CBIIT Application Support.
Installation and Deployment
Follow these steps to install and deploy caNanoLab:.
Step | Action | |||||||
1 | Set up an environment variable JBOSS_HOME to point to the Wildfly installation directory.
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2 | Execute the Ant build script build.xml located at Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script generates the following artifacts that include two deployable web archive war files, configuration files and libraries for running the web application in the Wildfly environment, and also places these artifacts in the appropriate directories under <JBOSS_HOME>:
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3 | We recommend increasing the JBoss JVM heap size to 2G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file
This configuration file is read when Wildfly server starts. | |||||||
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5. | Start JBoss application server in Standalone mode. This script assumes the CLI port is running at 19990. If it is different, you need to update port number at the 2nd linesecond line in the script.
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Verification
Once the deployment artifacts are deployed and the Wildfly application server is correctly configured, you can now start the Wildfly application server, which in turn starts the caNanoLab application.
Open the URL http://<APP_SERVER_URL>/caNanoLab/
, for example, http://localhost:8080/caNanoLab
). The Welcome/Login page displays.
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Before a user can log in to the caNanoLab application to submit and search data, you must first create a user account through the UPT web interface. The caNanoLab application makes use of the NCICBIITNCI CBIIT's User Provisioning Tool (UPT), a separate web application, for user account management. The concepts of users, groups, roles, protection groups are defined according the CSM/UPT principles. See the CSM documentation for details on these concepts and the use of the UPT tool.
Since release 1.5.2, as a part of the database seed data, two default user groups are created: Public and Curator. The group Public is assigned role R (read-only) public protocols, samples and publications. The group Curator is assigned role CURD (create, update, read and delete) to all protocols, samples and publications in the system. When a user first logs into caNanoLab, the user is automatically added to the Public group and can see all public data. The user needs to be added to the Curator group in the UPT tool in order to have Curator access.NOTE:
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Since release 1.5.2, a user must be assigned as a caNanoLab administrator to see the ADMINISTRATION menu |
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in the application to log into the UPT tool or update site preferences, such as the site logo. A user must be assigned as a caNanoLab administrator AND assigned to the Curator group to be able to execute the transfer ownership function. |
UPT Example
The following steps illustrate an example use of the UPT tool to create a new user, assign the user to be a caNanoLab administrator, and assign the user to the Curator group.
Step | Action |
1 | Launch the UPT tool at http://<APP_SERVER_URL>/upt52/Home.action and login as the super admin. If you are NOT using LDAP for user authentication, the default user account/password for super admin is superadmin/superadmin. Enter csmupt as the application name when prompted at the UPT log in. If you are using LDAP for user authentication, use the LDAP login name and password of the user assigned as the super admin as specified in the Ant build properties file. Note: The NoteThe user superadmin with initial password superadmin was created as a part of the database setup. Only superadmin can assign users to be caNanoLab administrators. |
2 | If you are using LDAP for user authentication, skip this step. If you are not using LDAP for authentication, follow this step to reset the password for superadmin:
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3 | Log in as the super admin, and follow these steps to create a new user and assign it to be a caNanoLab administrator:
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4 | Before the newly-created user can log into the UPT application, logged in as the super admin, follow these steps to update the required database connection information for the csmupt and caNanoLab applications under the Application tab: Select Application > Select an Existing Application, and click Search. Select csmupt from the application list. Click View Details, then update the following fields:
Note: Please refer to Edit Ant Properties for the appropriate values for these fields. Values for Application Database Dialect and Application Database Driver must be exactly entered as shown above. Repeat the steps to update the database connection information for the caNanoLab application. |
5 | Log out of the UPT tool and log back in as admin. Use caNanoLab as the application name when prompted at the UPT log in. |
6 | Select User > Select an Existing User, and click Search. Select admin from the User list. Click ViewDetails, then AssociatedGroups. Select Curator from the pre-defined group list and assign it to the user. Click UpdateAssociations to commit the change. |
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Contacting Application Support
NCICBIIT Application Support
Send an email to the NCI CBIIT application support group: ncicbiit@mail.nih.gov
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