CLC Server File System Locations

Data storage configuration is done via the web interface. When logged in as a user with administrative privileges, navigate to the Configuration tab, click on the Main configuration tab, and then click on the File system locations heading to expand that section. See figure 3.3.

Configuring CLC Server File System Locations, where data imported to the CLC Server or results generated using the CLC Server are usually stored, is done by going to:

        Configuration (Image configuration_16) | Main configuration (Image main_configuration_16) | File system locations

See figure 3.3. File System Locations already configured are listed in this area. Those with a P in a blue box have permissions enabled.

Image filelocation
Figure 3.3: Three CLC Server File system Locations have been configured. Two have permissions settings enabled, as indicated by the Ps in blue boxes. One location, CLCServerLoc1, is disabled, as indicated by its name being in light grey text.

Each File System Locations that is enabled is included in the navigation area on the left of the web client. Interacting with data stored in these areas is described in Browsing CLC Server File System Locations.

Adding and configuring CLC Server File System Locations

Add a new location
Click on the Add New File Location button and then specify the path to the folder where data imported into or created by the CLC Server will be stored. The path provided should point to an existing folder on the server machine that the user running the server process has read and write access to.

If a CLC Server File System Location with the name CLC_References is configured, users logged into a CLC Server from a CLC Genomics Workbench will be able to download data directly to this server area using the Workbench's Reference Data Manager tool. Special conditions apply to this file system location. These are outlined in the section on Reference data management.

Enable or disable access for all users
The checkbox to the left the Path is used to control whether or not this location should be available to users. Access is enabled by default. Unchecking this box and saving the configuration makes the location unavailable for use via any client software. For example, in a CLC Workbench connected to the CLC Server, each enabled location is visible in the Navigation Area, but disabled locations are not.

Disabled locations are listed in light grey text, as shown for CLCServerLoc1 in figure 3.4. As expected for a disabled location, it is not listed in the top left side of the web client, whereas the two enabled locations are listed.

Image filelocationdisabled
Figure 3.4: When the checkbox to the left of the Path is unchecked, the file system location is disabled. This makes it unavailable to users. Under the Main Configuration tab, disabled locations are listed using light grey text.

Permissions enabled
When this box is checked, permissions can be configured for that location (figure 3.5).

Changes to permissions settings first take effect after the server is restarted.

Note: Permissions can be configured for any file system location unless it has the name CLC_References (the section on Reference data management).

Image filelocation-permssettings
Figure 3.5: A P in a blue box is shown the location listing for CLC Server File System Locations with permissions enabled, as seen here for CLCServerLoc2. When the Permissions enabled checkbox is checked in the Edit file location dialog, permissions settings are made visible.

Group-based permissions
After selecting this option, group-level read and write permissions can be configured for the file system location using a CLC Workbench client, as described in Controlling access to data. Until such access is granted, the file system location and its contents are available only to admin users.

User homes
The file system location will be used for user home folders. These are top-level folders with names matching users' usernames. A user is granted write access only to the folder with a name matching their username. Admin users continue to have access to all folders.
  • Auto-create user homes When selected, a user folder is created automatically by the CLC Server when a user first logs in. To create folders only for specific users, deselect this option and use the mkdir command of the CLC Server Command Line Tools, specifying the file system location as the target and providing a user's username as the name of the folder to create.
  • Allow global read access to user homes When selected, all users are granted read access to all user home folders on this file system location. When not selected, users only have access to their own user home area.

When enabling the "User homes" option, please note that:

  • Data elements stored directly under the file system location will be readable, but not writable, by all users. While it should only be possible for admin users to place data in this area, if the file system location was in use before the User homes option was selected, then existing data stored at the top level will be accessible to all users.
  • Any folder at the top level of a CLC Server file system location with a name matching a user's username will be treated as a user home area, with read and write access granted to that user on that folder and its contents.
  • A user logged into the CLC Server from a CLC Workbench will see their user home at the top of the list of user home directories. (Folders a user has access to are listed at the top of a given CLC location.)

Remove a file system location
Clicking on the Remove Location button beside a particular file system location removes it from the CLC Server. The underlying folder and its contents are not deleted. To re-enable access via the CLC Server, simply configure the same folder as a file system location again.

Rebuild the index
The CLC Server maintains an index in each CLC Server File System location of the elements in that location. This is used when searching for data. For more details, see Rebuilding the index.