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Welcome to the caNanoLab 2.1.1 Installation Guide.
Get Support
For any general information about the=
application, support, or to report a bug, contact caNanoLab-Support@ISB-CGC.org=
a>.
Print the Guide
If you want to print a single page, refer to Printing a Page.
Topics in this document include:
For more information about the 2.1.1 updates, refer to the caNanoLab 2.1.1 Release Note= .
Download each of the following tools and follow the installation instruc= tions provided with each respective product for your environment. Assistanc= e from a MySQL database administrator is expected to properly configure the= MySQL database. For MySQL database configuration and maintenance, it is al= so helpful to download the MySQL workbench (suite of GUI tools) at http://www.mysql.com/downloads= /workbench/
Product |
Link |
---|---|
Java Software Development Kit (JDK) version 7= .0 and set JAVA_HOME |
|
Wildfly version 8.2.0.Final |
|
Jakarta Ant version 1.8.x and set ANT_HOME en= vironment variable |
|
MySQL version 5.1.x |
Downloads for caNanoLab are available at caNanoLab GitHub Repository.
The caNanoLab Software License app= lies.
Follow these steps to set the build and deploy properties required for b= uilding and deploying caNanoLab.
Extract the GitHub l= ocation to a location on your local system, for example, C:\caNan= oLab_2.1.1 This location is referred as <CANANOLAB_SOURCE> &nbs= p;throughout the document. Verify that the following five folders exist in = the directory <CANANOLAB_SOURCE> :
build
cananolab-db
cananolab-grid
cananolab-webapp
common
Edit the Ant properties file, build.properties , at&nb= sp; <CANANOLAB_SOURCE>/build by specifying values for the follo= wing properties.
Property |
Description |
---|---|
file.repository.dir |
A directory on the system that hosts the Wildfly application server= for storing uploaded files, for example, C:/apps/caNanoLab . Writable Directory This directory should be writable by the user that starts the Wildfly&nb= sp;server, and this directory should be created prior to starting the appli= cation. Use either double-back slashes or a single forward slash / as the f= ile separator if working on Windows platform. |
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 suppo=
rt 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, <= code>3306. |
database.user |
The database user name used in the caNanoLab =
application, for example, |
database.password |
The password for the database that the user s=
pecified 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 exampl= e:
|
=
CREATE TABLE favorite_data (
&=
nbsp;
favorite_data_id bigint(20) DEFAULT NULL,
data_id bigint(20) DEF=
AULT NULL,
&=
nbsp;
data_type varchar(200) DEFAULT NULL,
&n=
bsp;
data_na=
me varchar(200) DEFAULT NULL,
<=
/code>
login_name varchar(200) DEFAULT NUL=
L,
=
code> 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 NUL=
L
https://github.com/CBIIT/=
common-security-module/blob/master/software/common/resources/db/db-upgrade/=
mysql/MigrationScript5.0MySQL.sql
update csm_user set password =3D 'zJPWCwDeSgG8j2uyHEABIQ=3D=3D';
CSM 5.0 has introduce= d using AES encryption to encrpt CSM User information while storing it in C= SM_USER table. If you are upgrading CSM from 4.x to 5.x, apart from migrati= ng the database, you would need to run encryption migration. This step expe= cts PASSWORD column values in CSM_USER are not altered from the their origi= nal values created through CSM API.
c:\csm_52
). Be sure to note th=
e folder name and location.c:\csm_=
52\csm_upgrade5.2
).c:\csm_52=
\csm_upgrade5.2
Follow these steps to install and deploy caNanoLab.
# |
Action |
---|---|
1 |
Set up an environment= variable JBOSS_HOME to point to the Wildfly installation direc= tory. Windows Platform <= /span>
Use either double back slashes // or a single forward slash / as the file s=
eparator if working on Windows platform, for example, JBOSS_HOME=3DC:=
/wildfly-8.2.0.Final (C:\wildfly-8.2.0.Final would fail).
|
2 |
Execute the Ant build script build.xml located at <CANANOLAB= _SOURCE>/build with the target deploy:cananolab-webpp . <= p class=3D"MsoNormal" style=3D"margin-top: 7.5pt;line-height: 13.5pt;">= 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 th= ese artifacts in the appropriate directories under <JBOSS_HOME >= ;. Artifacts generated are also available in the following folder under <= ;CANANOLAB_SOURCE> : target/dist/cananolab- webapp/caNanoLa=
b.war |
3 |
We recommend increasing t= he JBoss JVM heap size to 2G bytes and permanent generation (permgen) memor= y space to 256M bytes by updating the file <JBOSS_HOME>/bin/stan= dalone.conf with the following JAVA_OPTS:
This configuration file is read when Wildfly server start= s. For a standalone server, pass in the JVM settings either as comman=
d line arguments when executing the |
4 |
1. Create a= new directory structure C:/local/content/caNanoLab/artifacts a= nd move the following artifacts.
Create a new directory structure
|
5 | Start JBoss application server in Standalone = mode. From
= The cli scripts assumes the CLI port is running at 19990. If it is differen= t, update the port number at the second line in the script. = strong> For Windows environment:
F= or Linux environment:
Run the remaining After successful completion, the following output appears in= the window.
|
Once the deployment artifacts are deployed and the Wildfly a= pplication 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>/ca=
NanoLab/
, for example, http://localhost:8080/caNanoLab=
. The Welcome/Login page appears.