Changes between Version 9 and Version 10 of Service_Lab_Plugin


Ignore:
Timestamp:
03/14/2017 09:16:15 PM (5 years ago)
Author:
shan
Comment:

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  • Service_Lab_Plugin

    v9 v10  
    141141- Dialog - dialog/UploadBillDialog
    142142
     143=== Service Lab utility plugin ===
     144Currently it does two tasks
     145- Ontology generation
     146- Workspace generation
     147
     148=== Ontology Generation ===
     149The 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.
     150
     151Sometimes 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.
     152
     153- Handler - handler/AddOntologyHandler
     154- main class - addtoontology/ImportTemplates (short for import protocol templates)
     155
     156Important locations
     157- '''.grits-toolbox/org.grits.toolbox.editor.experimentdesigner/''' is the config folder (for writing to local ontology and generating protocol variants)
     158- '''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)
     159- '''namespace''' folder in experiment design plugin (adds short namespaces for parameters that were created while adding protocols in the ontology)
     160- '''doc''' folder in its own plugin (for protocol spread sheet)
     161- '''paper''' folder in its own plugin (for offline reading of Pubmed papers)
     162
    143163
    144164
     
    146166Following steps are to be followed each time GRITS is to be installed in Service Lab:
    147167
    148 1. Copy two ontologies before building
     1681. Copy two ontologies before exporting
    149169 - copy the two ontologies from '''ontology''' folder of Service Lab main plugin to '''ontology''' folder of Experiment designer plugin
    150170  a. experimentdesignontology.owl
    151171  b. localexperimentdesignontology.owl
    1521722. Make sure the namespace file for Service Lab protocols (''namespaces_servicelab.xml'') is there in the experiment design plugin inside '''namespace''' folder
    153 3. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to build a product as you would normally build
    154 4. Test and deploy the generated product in Service Lab computer
     1733. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to export a product as you would normally export
     1744. Test and deploy the exported product in Service Lab computer
    155175
    156176__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.
    157177
    158 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 :
     178Currently 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 :
    1591791. 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)
    1601802. 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