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Question: How can I build caArray from the source code in the NCI repository?
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The tutorial is designed for use in a Windows environment, but can easily be adapted to work in Linux as well.
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This tutorial is based on the readme.txt file in the NCI caArray source code repository at https://ncisvn.nci.nih.gov/svn/caarray2/tags/2.4.1.1/. |
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- The Java 2 SE Development Kit (JDK) v1.5, available for download at : http://download.oracle.com/otn/java/jdk/1.5.0_22/jdk-1_5_0_22-windows-i586-p.exe
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The build process described in this tutorial only works with version 1.5 of the JDK; it will not work with any other versions, earlier or later. |
- Apache Ant 1.7.0 or later, available for download at : http://mirrors.ibiblio.org/apache//ant/binaries/apache-ant-1.8.3-bin.zip
- MySQL v5.0 or later, available for download at : http://filehippo.com/download/file/3518c972e6317bff1a5caacae83b83cf1057fceca08180ebd44ad9a0ba01444b/
- A command-line Subversion (SVN) client of your choice. The one used in this tutorial is the Collabnet Subversion Command-Line Client v1.74, available for download at : http://www.open.collab.net/servlets/OCNDirector?id=CSVN1.7.4WINC32 (registration required)
2) Once all the above are installed, ensure they are configured as follows:
- The PATH and JAVA_HOME Windows environment variables must be set to the the installation path of the JDK binaries. The default path in Windows is:
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C:\Program Files\Java\jdk1.5.0_22\bin |
- The PATH and ANT_HOME Windows environment variables must be set to the installation path of the Ant binaries. The default path is:
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C:\ant |
- The PATH Windows environment variable must be set to the installation path of the SVN client binaries. The default path in Windows is:
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C:\Program Files\CollabNet Subversion Client |
- The ANT_OPTS environment variable must be set to the value "-Xmx256m"
- The MySQL server must be configured with a secure password for the root user, and this password must be recorded for future reference
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To begin checking out the caArray source code from the NCI repository, first create a new folder (i.e., C:\source), then open up a command-line window, navigate to that folder, and enter the following:
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svn checkout https://ncisvn.nci.nih.gov/svn/caarray2/tags/2.4.1.1/
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You'll know when the checkout is complete when the command-line window shows a message stating, 'Checked out revision x', where x is the revision number, as shown in the screenshot below:
Manually Creating The Requisite Database Schema
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Now, log into the client using the root password you set when installing the database server, then enter the following SQL commands line-by-line, substituting your own database name, username, and password as needed:
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CREATE DATABASE db1 DEFAULT CHARACTER SET latin1;
GRANT ALL ON db1.* TO 'user1'@'localhost' IDENTIFIED BY 'password1' WITH GRANT OPTION;
GRANT ALL ON db1.* TO 'user1'@'%' IDENTIFIED BY 'password1' WITH GRANT OPTION;
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The client will respond with a confirmation that the issued queries were successful, as shown in the screenshot below:
Configuring The 'Properties' Settings Files
The caArray installation settings are mainly specified by a source file, install.properties, whose path is:
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$CAARRAY_HOME/software/master_build/install.properties |
where $CAARRAY_HOME represents the root folder into which the caArray source was checked out (C:\source in this example).
A second file, local.properties, specifies additional settings. This file is not included in the repository -- you must manually create it yourself by opening a plain text editor and saving a blank file with the filename local.properties to the following path:
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$CAARRAY_HOME/software/build/local.properties |
These files must be customized with the settings specific to your local environment before starting the build process. These settings include:
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Refer to the screenshot below for an example of how the local.properties file should be configured:
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The install.properties file contains additional properties which pertain to grid services. These are not covered here, as configuring caArray to utilize a grid service is beyond the scope of this tutorial. For more information, please refer to this KB article:
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Invoking The Build Process From The Command Line
Now that you've checked out the source code, created the database schema, and configured the properties files, you're now ready to start the actual build process. First, open a command-line window and navigate to the following path:
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$CAARRAY_HOME/software/master_build |
Then, enter the following command:
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ant -Dproperties.file=<absolute path to install.properties file> deploy:local:install
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For example, if the path to the install.properties file is:
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C:\source\2.4.1.1\software\master_build\install.properties |
Then the command is:
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ant -Dproperties.file=C:\source\2.4.1.1\software\master_build\install.properties deploy:local:install
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The amount of time needed for the build process to complete can vary anywhere from under 30 minutes to several hours depending on your hardware configuration. For reference, on a Dell Optiplex 765 Windows XP Professional workstation with a Core 2 Quad 6600 CPU running at 2.40 Ghz and approximately 1. 75 GB of memory available at the time of the build, the process took 4 hours, 16 minutes and 51 seconds. The screenshot below shows the command line window after the build process has completed successfully, with the 'BUILD SUCCESSFUL' message at the bottom.
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The time it takes for the Ant build process to complete also depends on the speed of your Internet connection, as Ant retrieves all the JAR dependencies |
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Even if the command line window shows a 'BUILD SUCCESSFUL' message at the end, it is still possible that the build process did not complete successfully. The build process launches several sub-processes, each of which must complete successfully in order for the entire build to complete successfully. If any one of these sub-processes fails, it will display its own 'BUILD FAILED' error message, but the overall build process may still display the 'BUILD SUCCESSFUL' message at the end. The screenshot below illustrates such a case in which a sub-process failed due to an incorrect version of the JDK installed; note the indented 'BUILD FAILED' error message (highlighted in red) several lines above the 'BUILD SUCCESSFUL' message (highlighted in yellow) at the bottom. |
The caArray application is now installed in the path you specified in the install.properties file via the application.base.path property. In our example, the installation path is C:\temp, whose contents are displayed in the screenshot below:
If the contents of your installation path do not match those shown above, it is likely that your build process failed.
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To launch the caArray server, navigate to the following path:
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$INSTALLATION_HOME\jboss-4.0.5.GA\bin |
where $INSTALLATION_HOME is the installation path you specified in install.properties, and run the file run.bat. A command line window will launch showing the progress of the launching of the caArray server. The launch process is not instant and may take anywhere from 20 to 120 seconds, after which the command line will display a message indicating that the JBoss MX Microkernel has started, as shown at the bottom of the screenshot below:
Do not attempt to access the application until you see the messaging message stating that the JBoss kernel has started.
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To access the caArray login page, open up a new tab in your Web browser and enter the following URL in the address bar:
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http://localhost:4721038080/caarray/ |
The login page will now load as shown in the screenshot below from a Mozilla Firefox tab:
The default installation of caArray comes with several pre-configured user accounts built-in. We can log into the application via any of these accounts. In this tutorial, the one we will log in with is 'caarrayadmin', whose corresponding password is 'caArray2!'. You can enter this username and password into their respective fields under the caArray Login panel at the right of the login page, then click on the 'Login' button beneath to log into the application, as shown in the screenshot below:
You will now be directed to the caArray homepage, which shows the 'My Experiment Workspace', as shown in the screenshot below. Congratulations on successfully building and logging into caArray!
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caArray comes with a user provisioning tool (UPT) that allows you to modify the built-in accounts as well as to create additional accounts and assign them varying privileges and access levels. For more information on how to install and use UPT, please visit the UPT user guide at caCORE_CSM_v421_ProgrammersGuide.pdf. |
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Please leave your comment in the caArray End User Forum.
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