= Sample Ontology =
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== General Information ==
GRITS has a ''sample'' entry. This entry contains information related to samples. This entry is contributed and managed by [https://svn.grits-toolbox.org/trunk/eclipse/org.grits.toolbox.entry.sample Sample Plugin]. The Sample plugin defines the properties of ''sample entry'' and other related information. This plugin also adds an editor for sample entry to display or modify sample information. An object that is used to represent a sample is stored in a ''.xml'' file. Read [wiki:GritsTutorial_ObjectModelGritsSampleEditor this] to learn more about this Sample object. This object has a predefined model that is stored in the ontologies.

Currently there are two ontologies for Sample
- Standard ontology
 - stores information related to samples that is to be used by the sample plugin
- Local ontology
 - an additional ontology that has the same structure as the Standard ontology and has no additional information when GRITS is installed initially. When GRITS is used on a system, the information that is generated and saved is saved locally in this ontology.

__Note:__Classes that manage ontologies in Sample plugin are first supposed to look into the Standard ontology for any information and if some information is missing or additional information is required then it should look into the Local ontology.

== Ontology Structure ==
Each of the ontology (Standard and Local ontology) have the structure as shown below:

[[BR]]
[[Image(sample_ontology.png, 1200)]]
[[BR]]
''__Sample Ontology__''
[[BR]]

For more details also look into the owl files in the sample plugin.

== Classes in Sample plugin for Ontology management ==
Sample plugin can read information from the two ontologies. For writing it can only '''create templates in the local ontology'''. Reading and template creation is managed by the following classes that are in the '''ontologymanager''' package :
- ISampleOntologyApi
 - interface that defines the public APIs to be provided by ''SampleOntologyApi'' class
- SampleOntologyApi
 - implements the public methods defined in ''ISampleOntologyApi''
 - calls methods from ''SampleOntologyManager'' class to read/write information in ontologies
- SampleOntologyManager
 - uses Jena Ontology API to read/write information in ontologies
 - only protected and private methods
 - used by upper layer classes in the same package

Read Javadocs to learn more about specific methods

Sample plugin is not allowed to modify ontologies (except for creating templates in the local ontology) but there is another [https://svn.grits-toolbox.org/trunk/eclipse/org.grits.toolbox.editor.samplemanager Sample Manager Plugin] that can be used for editing information stored in the ontologies.

== Sample Manager Plugin ==
The Sample Manager plugin is an additional plugin that can be used to edit information stored in ontologies. This plugin can modify both standard and local ontologies. It has two modes of operation :
- '''User Mode'''
 - it displays both Standard and Local ontology
 - in this mode only Local ontology can be modified
- '''Admin Mode'''
 - it only displays Standard ontology information
 - in this mode only Standard ontology can be modified

== Updating ontologies ==
One can directly modify the ontologies that are there in the '''ontology''' folder of the ''org.grits.toolbox.entry.sample'' plugin. After updating an ontology submit it to the svn.

OR

One can also use the Sample Manager plugin to modify the ontologies. For modifying using the Sample Manager, follow the steps described below :
- Clean the GRITS Sample config folder ('''.grits-toolbox/org.grits.toolbox.entry.sample''' folder in the home directory)
 - this would ensure that there are no previous local changes prior to modifying the ontology
- Start a GRITS product that has the Sample Manager plugin
 - currently ''"Grits.all.dev.product"'' product file has the Sample Manager plugin while the main ''"Grits.all.product"'' product file for deployment does not include this plugin
- After GRITS is started
 - use menu '''Manager->User Mode''' to modify the Local ontology
 - use menu '''Manager->Admin Mode''' to modify the Standard ontology
- Save the changes in the editor
 - changes would be saved in the ontologies of GRITS Sample config folder ('''.grits-toolbox/org.grits.toolbox.entry.sample''' folder in the home directory)
  - when GRITS is started and it does not find the ontologies in the GRITS Sample config folder then it copies the two ontologies from sample plugin to GRITS Sample config folder
- Copy back the ontologies from GRITS Sample config folder ('''.grits-toolbox/org.grits.toolbox.entry.sample''' folder in the home directory) to '''ontology''' folder of the ''"org.grits.toolbox.entry.sample"'' plugin
- Update the files to svn