Changes between Version 13 and Version 14 of Service_Lab_Plugin


Ignore:
Timestamp:
03/15/2017 10:46:08 PM (5 years ago)
Author:
shan
Comment:

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  • Service_Lab_Plugin

    v13 v14  
    162162- '''paper''' folder in its own plugin (for offline reading of Pubmed papers)
    163163
    164 After ontology is generated, for archiving the generated ontology and protocol variants you have to manually
     164After ontology is generated, for archiving the generated ontology and protocol variants one has to manually
    165165- Place the ''experimentdesignontology.owl'' from experiment design plugin into the Service Lab Main plugin. Also update its version by adding 100 to the ''version'' of the original ontology in experiment design that was used for generating this ontology
    166166- Also add a copy of the local ontology ''localexperimentdesignontology.owl'' with the same version as ''experimentdesignontology.owl'' for compatibility
     
    184184For generating the workspace from latest spread sheet:
    185185- Copy the spread sheet (containing project information) in the doc folder of the Service Lab utility plugin
     186- update the value for variable ''PROJECT_SPREAD_SHEET'' in ''ImportProjectsSheetType3'' class
    186187- Run the ''GRITS.all.lab.service.product'' product from Service Lab utility plugin
    187188- Select or create a new workspace while starting GRITS application
    188189- Right click on popup menu in the project explorer
    189190- Select ''Import Projects''
    190 - Wait for projects and samples to be created and then close GRITS
    191 In the first run it will create a workspace with only projects and sample. Once the values are verified, you can add experiments to this workspace by following the steps:
     191- Wait for projects and samples to be created and then '''close GRITS'''
     192
     193In the first run it will create a workspace with only projects and sample. Once the values are verified, one should make a backup of this workspace so that one does not have to start from scratch if next steps are not done properly. Then one can add experiments to this workspace by following the steps:
     194- delete '''localexperimentdesignontology.owl''' from experiment design config folder
     195 - else could result in duplicate error as it recreates protocols for ''Temporary Category''
    192196- Re-run the ''GRITS.all.lab.service.product'' product from Service Lab utility plugin
    193197- While starting GRITS select the previous workspace that has projects and samples
    194198- Right click on popup menu in the project explorer
    195199- Select ''Import Projects''
    196 - Wait for experiments to be added and then close GRITS
     200- Wait for experiments to be added and then '''close GRITS'''
    197201This would add the experiments in the existing workspace with projects and samples.
    198202
    199203One can also change the combinations of generating workspace to create project and add sample and experiments later (and other such combinations) by changing the enum arguments in ''ImportProjectsHandler''.
     204
     205If some information were not correct and workspace needs to be regenerated then first clean the workspace and then redo the above steps. For cleaning and regenerating the workspace :
     206- Set the variable ''DEFAULT_WORKSPACE'' in ''ImportProjectsHandler'' class to this workspace that is to be cleaned
     207- Run the ''ImportProjectsSheetType3'' class as Java application (when its main method does not receive any argument then it cleans the DEFAULT_WORKSPACE)
     208- then repeat the steps that were described above for creating projects with samples and experiment designs
    200209
    201210== Deployment ==
     
    207216  b. localexperimentdesignontology.owl
    2082172. Make sure the namespace file for Service Lab protocols (''namespaces_servicelab.xml'') is there in the experiment design plugin inside '''namespace''' folder
    209 3. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to export a product as you would normally export
     2183. Use the product "'''GRITS.servicelab.product'''" in Service Lab Main plugin to export a product as one would normally export
    2102194. Test and deploy the exported product in Service Lab computer
    211220
    212221__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.
    213222
    214 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 :
     223Currently one can only generate a new set of protocol variants (it would remove all local protocols and protocol variants) and one 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 and need to be installed then follow the following steps :
    2152241. 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)
    2162252. 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