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Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.
Step 1. Extract caNanoLab
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Extract the GitHub location to a location on your local system, for example, C:\caNanoLab_2.1.1 This location is referred as <CANANOLAB_SOURCE> throughout the document. Verify that the following five folders exist in the directory <CANANOLAB_SOURCE>:
build
cananolab-db
cananolab-grid
cananolab-webapp
common
Step 2. Edit Ant Properties
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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, C:/apps/caNanoLab.
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admin.email | The email address that receives requests for new user accounts, for example, the NCI CBIIT application support email for the NCI CBIIT installation. | |||||
ldap.authentication.enabled | A Boolean flag to indicate whether or not to use LDAP for user authentication. caNanoLab 2.1.1 and beyond does not support LDAP authentication. Set this to | |||||
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 that the user specified above, for example, | |||||
database.system.user | The system database user name with privileges to create a database, create tables, and grant user accesses to a database, for example, | |||||
database.system.password | The password for the system database that the user specified above, for example, | |||||
jboss.server.dir | The Wildfly server directory, for example:
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Installation and Deployment
Step 1.
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DB changes to be deployed to migrate to CSM 5.2
a Execute the following scripts in the order specified below.
- Create the following table:
CREATE TABLE favorite_data (
favorite_data_id bigint(20) DEFAULT NULL,data_id bigint(20) DEFAULT NULL,
data_type varchar(200) DEFAULT NULL,
data_name varchar(200) DEFAULT NULL,
login_name varchar(200) DEFAULT NULL,
protocol_file_id bigint(20) DEFAULT NULL,
pubmed_id bigint(20) DEFAULT NULL,
editable tinyint(1) DEFAULT '0',
description text,
protocol_file_title varchar(200) DEFAULT NULL
https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.0MySQL.sql
- https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.1MySQL.sql
- Execute the following script to reset passwords for all of the accounts:
update csm_user set password = 'zJPWCwDeSgG8j2uyHEABIQ==';
update csm_user set first_time_login = 1;
- Create the following table:
b Migrate encryption from 4.x CSM database.
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CSM 5.0 has introduced using AES encryption to encrpt CSM User information while storing it in CSM_USER table. If you are upgrading CSM from 4.x to 5.x, apart from migrating the database, you would need to run encryption migration. This step expects PASSWORD column values in CSM_USER are not altered from the their original values created through CSM API.
- 1.
- Download the CSM UPT v5.2 distribution file into a designated folder (for example,
c:\csm_52
). Be sure to note the folder name and location.
- Download the CSM UPT v5.2 distribution file into a designated folder (for example,
2. - Extract the contents of the
downloaded csm- downloaded csm_upgrade5.2.
zip into - zip into a designated folder (for example,
c:\csm_52\csm_upgrade5.2
).
- zip into a designated folder (for example,
3. - In the designated folder, find and modify
the upgrade- the upgrade.
properties file- properties file. Database properties must be updated with the upgraded database connection details.
4. - Open the cmd window and navigate
to c- to
c:\csm_52\csm_upgrade5.
- to
2 2
5. - Run "ant -Dproperties.file=upgrade.properties migration:run".
Step 2. caNanoLab installation instructions to upgrade to 2.1.1
Follow these steps to install and deploy caNanoLab.
# | Action | |||||
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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 <CANANOLAB_SOURCE>/build with the target deploy:cananolab-webpp. Example: Issue the following commands to execute the Ant script: C:\>cd C:\caNanoLab_2.1\build 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>. Artifacts generated are also available in the following folder under <CANANOLAB_SOURCE>:
target/dist/cananolab- webapp/caNanoLab.war | |||||
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 <JBOSSfile <JBOSS_HOME>/bin/standalone. conf withconf with the following JAVAfollowing JAVA_OPTS:
This configuration file is read when Wildfly server starts. For a standalone server, you have to pass in the JVM settings either as command line arguments when executing the the | |||||
4 | 1. Create a new directory structure C:/local/content/caNanoLab/artifacts and move the following artifacts.
Create a new directory structure
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5 | Start JBoss application server in Standalone mode. From
The cli scripts assumes the CLI port is running at 19990. If it is different, update the port number at the second line in the script. For Windows environment: jboss-cli.bat --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli and press <ENTER>. For Linux environment: jboss-cli.sh --file= /local/content/caNanoLab/artifacts/caNanoLab_modules.cli and press <ENTER>. Run the remaining caNanoLab_setup.cli and caNanoLab_deploy.cli that deploys the caNanoLab and csmUPT. After successful completion, you should see following output in the window.
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Verification
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Once the deployment artifacts are deployed and the Wildfly application server is correctly configured, shutdown and restart 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.
Step 1. Extract caNanoLab
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.
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· build
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· cananolab-grid
· cananolab-webapp
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