Importing data

To add new ways to import data from different file types (say, dicom files), a new module should be made. Labkey is quite verbose on module insertion. Here they elaborate what modules can do. In the list is the pointer to a pipeline based on R scripts. While the concept is based on R scripts, the same can be done also with bash commands and hence with anything that can run in a shell, including compiled code in c++, matlab, etc. I made a dummy module that calls a script in /home/andrej/scripts/ directory with a .IMA file as its argument. The file is actually a zip of the directory structures as it appears in the labkey area. To deploy it, the .module file has to be copied to the /usr/share/labkey/externalModules directory. The only relevant parts are in the pipeline/pipelines and pipeline/tasks directory. The files in the pipelines directory specifies order and name of tasks to be called. They can be a combination of tasks defined in the local tasks directory and labkey defined tasks. Each new task must be defined with an xml script in the tasks directory. The convention is well explained in the link. At this point I am figuring out how to interface the layout of the database to the general shell script.

Setting privilgies

Some tasks (such as project creation) is reserved for site administrators. To add people, go to Admin->Site->Site Permissions, tab to Site Groups, and update Site Administrator list.

Backup

However, a pipeline override can be set to perform data-specific tasks with labkey based or user supplied tools..

Maybe this is more on the point:

Transformation scripts (which are always attached to assay designs) are different from trigger scripts, which are attached to a dataset (database table or query).