Getting Started with DME CLU

This page is a work in progress.

If you decide to use the CLU to perform various activities in DME, the following steps are pre-requisites:

If you are using Windows, install Cygwin as described in the following site: https://www.cygwin.com/

For best results, run Cygwin.bat from C:\cygwin64\ rather than from the Windows Start menu.
Check which version of Java is currently installed:
```
java –version
```
The command output should display the version of Java. DME requires Java 1.8.x.
If Java 1.8.x is not installed, perform the following steps:
1. Download Java 1.8.x from the following page: https://www.java.com/en/download/
2. Install Java, as described in the following installation instructions: https://www.java.com/en/download/help/index_installing.xml
3. Update your PATH system variable with the Java executable folder (such as c:/jdk1.8_13/bin). For details, refer to the following instructions: https://java.com/en/download/help/path.xml
4. Check whether you have performed the previous steps correctly by repeating the java -version command.
If the latest version of JDK is not installed, perform the following steps:
1. Download JDK from the following page:
  https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
2. Install JDK. For information, refer to the following page:
  https://www.oracle.com/technetwork/java/javase/documentation/index.html
In a cmd or shell window, type the following command in your working directory to clone DME utilities to your local machine:
```
Git clone https://github.com/CBIIT/HPC_DME_APIs
```
The system creates a subdirectory (HPC_DME_APIs) containing all files from that GitHub repository.

In the HPC_DME_APIs/utils/ folder, create a copy of the sample configuration file (hpcdme.properties-sample) and rename it (as hpcdme.properties). Edit your hpcdme.properties file to make the following configuration changes:

Property	Instructions
Server settings	If you want to connect to the Production tier, uncomment the Production server settings and comment out the UAT server settings. By default, the UAT server settings are enabled.
hpc.ssl.keystore.password	Contact NCIDataVault@mail.nih.gov to request this password.
hpc.user	Specify your NIH username.
hpc.default.globus.endpoint	If you intend to transfer files using Globus, specify the UUID of the Globus endpoint that you want to use.
Other properties not mentioned above	These properties are for special cases and internal use only. If you have questions about these properties, contact NCIDataVault@mail.nih.gov.

.

Configure environment variables:
1. Navigate to your ~/.bashrc or ~/.profile file, where ~ represents your home directory. For example:
```
C:\cygwin64\home\<username>
```
2. Edit your ~/.bashrc or ~/.profile file to append the following commands, where <client_utils_home> is the absolute path to the HPC_DME_APIs\utils\ folder. The following commands define the HPC_DM_UTILS environment variable and update the PATH environment variable to include the path to the scripts folder:
```
export HPC_DM_UTILS="<client_utils_home>"
export PATH=$HPC_DM_UTILS/scripts/:$PATH
```
If you are using Cygwin on Windows, run the following commands in Cygwin to change end of line delimiters from Windows standard to Unix standard in any files involved in CLU setup:
1. Adjust the line delimiters in the file with your export commands (~/.bashrc or ~/.profile). For example:
```
sed -i "s/\r$//" ~/.bashrc
```
2. Adjust the line delimiters in all files in the scripts folder. Use the following command:
```
sed -i "s/\r$//" $HPC_DM_UTILS/scripts/*
```
To make the above changes take effect in current Bash session, source the modified file (~/.bashrc or ~/.profile). For example:
```
source ~/.bashrc
```
Generate a DME API authentication token, as described in Generating a DME API Authentication Token.

The following DME CLU commands are available:

dm_add_bookmark
dm_delete_collection
dm_delete_datafile
dm_download_async
dm_download_dataobject_sync
dm_download_s3
dm_generate_token
dm_get_collection
dm_get_dataobject
dm_register_collection
dm_register_dataobject
dm_register_directory
dm_register_globus_directory
dm_register_user
dm_rename
dm_update_user

To view usage information for any DME CLU command (except dm_generate_token), type the command on the command line without any parameters. For more information, refer to the User Guide in the following location:

https://github.com/CBIIT/HPC_DME_APIs/tree/master/doc/guides

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