Changes between Version 9 and Version 10 of Service_Lab_Plugin

Timestamp:

03/14/2017 09:16:15 PM (5 years ago)

Author:

shan

Comment:

--

Service_Lab_Plugin

@@ -141 +141 @@
 - Dialog - dialog/UploadBillDialog
 
+=== Service Lab utility plugin ===
+Currently it does two tasks
+- Ontology generation
+- Workspace generation
+
+=== Ontology Generation ===
+The handler class passes the spread sheet that contains the protocols templates to be added in the ontology. It looks in the '''doc''' folder of its plugin to find this spread sheet. The main class for importing ontologies first copies the standard experiment design ontology from ''experiment design plugin'' as a local ontology in the config folder (''.grits-toolbox/org.grits.toolbox.editor.experimentdesigner/''). It adds protocol templates to this ontology and generates protocol variants in the config folder. It then copies back the local experiment design ontology as standard ontology in the experiment design plugin.
+
+Sometimes excessive HTTP requests for reading Pubmed papers may result in server blocking the operation. To overcome this, one can download the papers using browser and save it in the '''paper''' folder (name being ''PubmedId'' of the paper and file type being ".xml"). Codes have been adjusted to read the papers from this '''paper''' folder if response from HTTP request has certain error phrases.
+
+- Handler - handler/AddOntologyHandler
+- main class - addtoontology/ImportTemplates (short for import protocol templates)
+
+Important locations
+- '''.grits-toolbox/org.grits.toolbox.editor.experimentdesigner/''' is the config folder (for writing to local ontology and generating protocol variants)
+- '''ontology''' folder in experiment design plugin (copies standard ontology as local ontology and once generation is complete, copies back to this folder as standard ontology)
+- '''namespace''' folder in experiment design plugin (adds short namespaces for parameters that were created while adding protocols in the ontology)
+- '''doc''' folder in its own plugin (for protocol spread sheet)
+- '''paper''' folder in its own plugin (for offline reading of Pubmed papers)
+
 
 
@@ -146 +166 @@
 Following steps are to be followed each time GRITS is to be installed in Service Lab:
 
-1. Copy two ontologies before building
+1. Copy two ontologies before exporting
  - copy the two ontologies from '''ontology''' folder of Service Lab main plugin to '''ontology''' folder of Experiment designer plugin
   a. experimentdesignontology.owl
   b. localexperimentdesignontology.owl
 2. Make sure the namespace file for Service Lab protocols (''namespaces_servicelab.xml'') is there in the experiment design plugin inside '''namespace''' folder
-3. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to build a product as you would normally build
-4. Test and deploy the generated product in Service Lab computer
+3. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to export a product as you would normally export
+4. Test and deploy the exported product in Service Lab computer
 
 __Note:__ Service Lab has its own set of ontologies and protocol variants. It cannot work merely with the experiment design ontologies. Each time a product is made for Service lab, the ontologies from the Service Lab Main plugin should be copied to build the product.
 
-Currently you can only generate a new set of protocol variants (it would remove all local protocols and protocol variants) and you do not have the option for adding protocol variants to the existing protocol variants. If a new set of protocol variants were generated for Service Lab then follow the following steps :
+Currently you can only generate a new set of protocol variants (it would remove all local protocols and protocol variants) and you do not have the option for adding protocol variants to the existing protocol variants. If a new set of protocol variants have been generated for Service Lab need to be installed then follow the following steps :
 1. Get a copy of protocol variants from '''protocol variants''' folder of Service Lab main plugin (use the protocol variants with matching version of the ontology that was used in step 1 for deployment)
 2. In Service Lab computer, clean the '''org.grits.toolbox.editor.experimentdesigner''' folder inside config folder and copy the new protocol variants and extract it here