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install.rb
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#!/usr/bin/env ruby
require 'genboreeTools'
group_pcalc_resources = 'pcalc_resources'
group_pcalc_public_cache = 'pcalc_cache'
kb_pcalc_resources = 'pcalc_resources'
kb_pcalc_cache = 'pcalc_cache'
# genboree groups
api_put("/REST/v1/grp/#{group_pcalc_resources}")
api_put("/REST/v1/grp/#{group_pcalc_public_cache}")
# access for system users
api_put("/REST/v1/grp/#{group_pcalc_resources}/usr/gbPublicToolUser/role", {"role"=>"subscriber", "permissionBits"=>""})
api_put("/REST/v1/grp/#{group_pcalc_resources}/usr/gbCacheUser/role" , {"role"=>"subscriber", "permissionBits"=>""})
api_put("/REST/v1/grp/#{group_pcalc_public_cache}/usr/gbPublicToolUser/role", {"role"=>"author", "permissionBits"=>""})
api_put("/REST/v1/grp/#{group_pcalc_public_cache}/usr/gbCacheUser/role" , {"role"=>"author", "permissionBits"=>""})
# create KBs
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}")
api_put("/REST/v1/grp/#{group_pcalc_public_cache}/kb/#{kb_pcalc_cache}")
# set KBs as public
genboree_set_kb_public(group_pcalc_resources, kb_pcalc_resources)
genboree_set_kb_public(group_pcalc_public_cache, kb_pcalc_cache)
# create collections for public cache
api_put("/REST/v1/grp/#{group_pcalc_public_cache}/kb/#{kb_pcalc_cache}/coll/ConclusionCache/model", File.read("kb_collections/ConclusionCache.model.json") )
api_put("/REST/v1/grp/#{group_pcalc_public_cache}/kb/#{kb_pcalc_cache}/coll/EvidenceCache/model" , File.read("kb_collections/EvidenceCache.model.json") )
# create collections with resources
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/AllowedTags/model" , File.read("kb_collections/AllowedTags.model.json") )
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/GuidelineRulesMetaRules/model", File.read("kb_collections/GuidelineRulesMetaRules.model.json"))
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/Configuration/model" , File.read("kb_collections/Configuration.model.json"))
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/AlleleSupportingData/model" , File.read("kb_collections/AlleleSupportingData.model.json"))
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/GeneSupportingData/model" , File.read("kb_collections/GeneSupportingData.model.json"))
# load tags, Guideline, transform
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/AllowedTags/doc/ACMG2015-Caps" , File.read("kb_data/ACMG2015-Caps.json") )
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/coll/GuidelineRulesMetaRules/doc/ACMG2015-Guidelines", File.read("kb_data/ACMG2015-Guidelines.json"))
api_put("/REST/v1/grp/#{group_pcalc_resources}/kb/#{kb_pcalc_resources}/trRulesDoc/acmgTransform" , File.read("kb_others/acmgTransform.json"))
# copy dedicated files to correct locations
`./install_app.sh`