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RoboCop auto lint and refactor
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@syphax-bouazzouni
syphax-bouazzouni committed Mar 4, 2022
1 parent efb330f commit 47fedc8
Showing 1 changed file with 52 additions and 50 deletions.
102 changes: 52 additions & 50 deletions lib/ontologies_linked_data/config/config.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,28 +3,32 @@

module LinkedData
extend self

attr_reader :settings

@settings = OpenStruct.new
@settings_run = false

DEFAULT_PREFIX = 'http://data.bioontology.org/'.freeze

def config(&block)
return if @settings_run

@settings_run = true

overide_connect_goo = false

# Set defaults
@settings.goo_backend_name ||= "4store"
@settings.goo_backend_name ||= '4store'
@settings.goo_port ||= 9000
@settings.goo_host ||= "localhost"
@settings.goo_path_query ||= "/sparql/"
@settings.goo_path_data ||= "/data/"
@settings.goo_path_update ||= "/update/"
@settings.search_server_url ||= "http://localhost:8983/solr/term_search_core1"
@settings.property_search_server_url ||= "http://localhost:8983/solr/prop_search_core1"
@settings.repository_folder ||= "./test/data/ontology_files/repo"
@settings.rest_url_prefix ||= "http://data.bioontology.org/"
@settings.goo_host ||= 'localhost'
@settings.goo_path_query ||= '/sparql/'
@settings.goo_path_data ||= '/data/'
@settings.goo_path_update ||= '/update/'
@settings.search_server_url ||= 'http://localhost:8983/solr/term_search_core1'
@settings.property_search_server_url ||= 'http://localhost:8983/solr/prop_search_core1'
@settings.repository_folder ||= './test/data/ontology_files/repo'
@settings.rest_url_prefix ||= DEFAULT_PREFIX
@settings.enable_security ||= false
@settings.enable_slices ||= false

Expand All @@ -35,47 +39,47 @@ def config(&block)
# @settings.redis_port ||= 6379
# ###

@settings.ui_host ||= "bioportal.bioontology.org"
@settings.replace_url_prefix ||= false
@settings.id_url_prefix ||= "http://data.bioontology.org/"
@settings.ui_host ||= 'bioportal.bioontology.org'
@settings.replace_url_prefix ||= false
@settings.id_url_prefix ||= DEFAULT_PREFIX
@settings.queries_debug ||= false
@settings.enable_monitoring ||= false
@settings.cube_host ||= "localhost"
@settings.cube_host ||= 'localhost'
@settings.cube_port ||= 1180

# Caching http
@settings.enable_http_cache ||= false
@settings.http_redis_host ||= "localhost"
@settings.http_redis_host ||= 'localhost'
@settings.http_redis_port ||= 6379

#Caching goo
@settings.goo_redis_host ||= "localhost"
@settings.goo_redis_host ||= 'localhost'
@settings.goo_redis_port ||= 6379

#Ontology Analytics Redis
@settings.ontology_analytics_redis_host ||= "localhost"
@settings.ontology_analytics_redis_host ||= 'localhost'
@settings.ontology_analytics_redis_port ||= 6379

# PURL server config parameters
@settings.enable_purl ||= false
@settings.purl_host ||= "purl.bioontology.org"
@settings.purl_host ||= 'purl.bioontology.org'
@settings.purl_port ||= 80
@settings.purl_username ||= ""
@settings.purl_password ||= ""
@settings.purl_maintainers ||= ""
@settings.purl_target_url_prefix ||= "http://bioportal.bioontology.org"
@settings.purl_username ||= ''
@settings.purl_password ||= ''
@settings.purl_maintainers ||= ''
@settings.purl_target_url_prefix ||= 'http://bioportal.bioontology.org'

# Email settings
@settings.enable_notifications ||= false
@settings.email_sender ||= "[email protected]" # Default sender for emails
@settings.email_override ||= "[email protected]" # By default, all email gets sent here. Disable with email_override_disable.
@settings.enable_notifications ||= false
@settings.email_sender ||= '[email protected]' # Default sender for emails
@settings.email_override ||= '[email protected]' # By default, all email gets sent here. Disable with email_override_disable.
@settings.email_disable_override ||= false
@settings.smtp_host ||= "localhost"
@settings.smtp_host ||= 'localhost'
@settings.smtp_port ||= 25
@settings.smtp_user ||= "user"
@settings.smtp_password ||= "password"
@settings.smtp_user ||= 'user'
@settings.smtp_password ||= 'password'
@settings.smtp_auth_type ||= :none # :none, :plain, :login, :cram_md5
@settings.smtp_domain ||= "localhost.localhost"
@settings.smtp_domain ||= 'localhost.localhost'
@settings.enable_starttls_auto ||= false # set to true for use with gmail

# number of times to retry a query when empty records are returned
Expand All @@ -89,20 +93,18 @@ def config(&block)

unless @settings.redis_host.nil?
puts "Error: 'redis_host' is not a valid conf parameter."
puts " Redis databases were split into multiple hosts (09/22/13)."
raise Exception, "redis_host is not a valid conf parameter."
puts ' Redis databases were split into multiple hosts (09/22/13).'
raise StandardError, 'redis_host is not a valid conf parameter.'
end

# Check to make sure url prefix has trailing slash
@settings.rest_url_prefix = @settings.rest_url_prefix + "/" unless @settings.rest_url_prefix[-1].eql?("/")
@settings.rest_url_prefix = "#{@settings.rest_url_prefix}/" unless @settings.rest_url_prefix[-1].eql?('/')

puts "(LD) >> Using rdf store #{@settings.goo_host}:#{@settings.goo_port}"
puts "(LD) >> Using term search server at #{@settings.search_server_url}"
puts "(LD) >> Using property search server at #{@settings.property_search_server_url}"
puts "(LD) >> Using HTTP Redis instance at "+
"#{@settings.http_redis_host}:#{@settings.http_redis_port}"
puts "(LD) >> Using Goo Redis instance at "+
"#{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
puts "(LD) >> Using HTTP Redis instance at #{@settings.http_redis_host}:#{@settings.http_redis_port}"
puts "(LD) >> Using Goo Redis instance at #{@settings.goo_redis_host}:#{@settings.goo_redis_port}"

connect_goo unless overide_connect_goo
end
Expand Down Expand Up @@ -132,15 +134,14 @@ def connect_goo
port: @settings.goo_redis_port)

if @settings.enable_monitoring
puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:"+
"#{@settings.cube_port}"
puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:#{@settings.cube_port}"
conf.enable_cube do |opts|
opts[:host] = @settings.cube_host
opts[:port] = @settings.cube_port
end
end
end
rescue Exception => e
rescue StandardError => e
abort("EXITING: Cannot connect to triplestore and/or search server:\n #{e}\n#{e.backtrace.join("\n")}")
end
end
Expand All @@ -150,26 +151,27 @@ def connect_goo
# We do this at initial runtime because goo needs namespaces for its DSL
def goo_namespaces
Goo.configure do |conf|
conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#"))
conf.add_namespace(:skos, RDF::Vocabulary.new("http://www.w3.org/2004/02/skos/core#"))
conf.add_namespace(:owl, RDF::Vocabulary.new("http://www.w3.org/2002/07/owl#"))
conf.add_namespace(:omv, RDF::Vocabulary.new('http://omv.ontoware.org/2005/05/ontology#'))
conf.add_namespace(:skos, RDF::Vocabulary.new('http://www.w3.org/2004/02/skos/core#'))
conf.add_namespace(:owl, RDF::Vocabulary.new('http://www.w3.org/2002/07/owl#'))
conf.add_namespace(:rdfs, RDF::Vocabulary.new("http://www.w3.org/2000/01/rdf-schema#"))
conf.add_namespace(:rdfs, RDF::Vocabulary.new('http://www.w3.org/2000/01/rdf-schema#'))
conf.add_namespace(:metadata,
RDF::Vocabulary.new("http://data.bioontology.org/metadata/"),
RDF::Vocabulary.new('http://data.bioontology.org/metadata/'),
default = true)
conf.add_namespace(:metadata_def,
RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
conf.add_namespace(:dc, RDF::Vocabulary.new("http://purl.org/dc/elements/1.1/"))
conf.add_namespace(:xsd, RDF::Vocabulary.new("http://www.w3.org/2001/XMLSchema#"))
RDF::Vocabulary.new('http://data.bioontology.org/metadata/def/'))
conf.add_namespace(:dc, RDF::Vocabulary.new('http://purl.org/dc/elements/1.1/'))
conf.add_namespace(:xsd, RDF::Vocabulary.new('http://www.w3.org/2001/XMLSchema#'))
conf.add_namespace(:oboinowl_gen,
RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
conf.add_namespace(:obo_purl, RDF::Vocabulary.new("http://purl.obolibrary.org/obo/"))
RDF::Vocabulary.new('http://www.geneontology.org/formats/oboInOwl#'))
conf.add_namespace(:obo_purl, RDF::Vocabulary.new('http://purl.obolibrary.org/obo/'))
conf.add_namespace(:umls,
RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
conf.id_prefix = "http://data.bioontology.org/"
RDF::Vocabulary.new('http://bioportal.bioontology.org/ontologies/umls/'))
conf.id_prefix = DEFAULT_PREFIX
conf.pluralize_models(true)
end
end
self.goo_namespaces
goo_namespaces

end

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