Service Lab Documentation

Service Lab has a GRITS installation in its lab. This installation has some additional features added specifically for the lab. It is a short documentation of additional functionalities provided to the lab and their management in GRITS.

Plugins

GRITS provides some specialized functionalities for Service Lab. Currently there are two plugins that have been created for this purpose.

• Service Lab main plugin
• Service Lab utility plugin

Service Lab main plugin

This plugin provides functionalities related to accounting and management in Service Lab. This plugin should be added to the product file when creating a deployment for the lab. Currently this plugin has following functionalities:

• Invoice Generation
  • price management for protocols and generation of invoice for projects
• Project Validation
  • Task assignment to individual samples in projects, verification of experiments in samples and files in archives
• Management of Task and File Upload information
• Upload of final Bill for projects

This plugin also contains

• the set of latest experiment designer's ontology provided to Service Lab
• the protocol variants provided to Service Lab
• product files that generate GRITS products for deployment
  • GRITS.servicelab.product - to deploy in lab
  • GRITS.servicelab.dev.product - for developers use before deployment (has the additional developers fragment)

Service Lab utility plugin

This plugin is used for generation of GRITS workspace projects from spread sheets. It is also used for adding new protocols to ontology from a spread sheet and for generating its protocol variants. This plugin should not be added to any product file that would be deployed for use. Currently this plugin adds two commands to GRITS in the popup menu of the project explorer:

• Import Projects
• Add Ontology

This plugin contains

• Protocol spread sheet for generation of ontology
  • name would be Protocol Set <SET_NUMBER> Rev<REVISION_NUMBER>.xlsx
• Sample spread sheet for creating descriptors from sample names while generating workspace
• a product file GRITS.all.lab.service.product for ontology and workspace generation.

Note: For data privacy, the spread sheet containing project information for generating workspace is not added to the svn and is used locally. For generating workspace from the 3rd type (latest version) spread sheet, the spread sheet should be placed in the doc folder of this plugin.

Deployment

Steps for deploying GRITS in Service Lab is described below :

1. Copy two ontologies before building - copy the two ontologies from ontology folder of Service Lab main plugin to ontology folder of Experiment designer plugin
   1. experimentdesignontology.owl
   2. localexperimentdesignontology.owl
2. Use the product "GRITS.servicelab.product" in Service Lab Main plugin to build a product
3. Deploy the product in Service Lab computer

Adding new protocol variants (it would remove all local protocols and protocol variants)

1. Get a copy of protocol variants from protocol variants folder of Service Lab main plugin (use the variants with matching version of the ontology that was used for deployment in step 1)
2. Clean the org.grits.toolbox.editor.experimentdesigner folder inside config folder and copy the new protocol variants and extract it here

Tutorials

GRITS Users

Useful tutorials for Service Lab users can be found here:

• Invoice Generation Tutorial
• Project Validation Tutorial