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Merge pull request #130 from ontoportal-lirmm/pl/add-java-heap-size-c…
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…onfiguration-variable

Add java heap size configuration variable
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@alexskr
alexskr authored Mar 9, 2022
2 parents da2bfd2 + 0568286 commit fc90752
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Showing 4 changed files with 38 additions and 34 deletions.
2 changes: 1 addition & 1 deletion config/config.rb.sample
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ LinkedData.config do |config|
config.repository_folder = "./test/data/ontology_files/repo"
config.rest_url_prefix = "http://data.bioontology.org/"
config.enable_security = false

config.java_max_heap_size = '10240M'
#PURL server config parameters
config.enable_purl = false
config.purl_host = "purl.bioontology.org"
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64 changes: 33 additions & 31 deletions lib/ontologies_linked_data/config/config.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -15,67 +15,69 @@ def config(&block)
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 ||= 'http://data.bioontology.org/'
@settings.enable_security ||= false
@settings.enable_slices ||= false

# Java/JVM options
@settings.java_max_heap_size ||= '10240M'
### these params should be not ussed any more
# removed so that dependencies shout
#
# @settings.redis_host ||= "localhost"
# @settings.redis_port ||= 6379
# ###

@settings.ui_host ||= "bioportal.bioontology.org"
@settings.ui_host ||= 'bioportal.bioontology.org'
@settings.replace_url_prefix ||= false
@settings.id_url_prefix ||= "http://data.bioontology.org/"
@settings.id_url_prefix ||= 'http://data.bioontology.org/'
@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.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 @@ -89,19 +91,19 @@ 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 Exception, '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 "+
puts '(LD) >> Using HTTP Redis instance at '+
"#{@settings.http_redis_host}:#{@settings.http_redis_port}"
puts "(LD) >> Using Goo Redis instance at "+
puts '(LD) >> Using Goo Redis instance at '+
"#{@settings.goo_redis_host}:#{@settings.goo_redis_port}"

connect_goo unless overide_connect_goo
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3 changes: 2 additions & 1 deletion lib/ontologies_linked_data/diff/bubastis_diff.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ def initialize(input_fileOld, input_fileNew)
@input_fileNew = input_fileNew
@output_repo = File.expand_path(@input_fileNew).gsub(File.basename(@input_fileNew),'')
@file_diff_path = nil
@java_heap_size = LinkedData.settings.java_max_heap_size
end

def setup_environment
Expand Down Expand Up @@ -83,7 +84,7 @@ def call_bubastis_java_cmd
end
errors_log = File.join([@output_repo, "bubastis_diff_errors.log"])
File.delete errors_log if File.exist? errors_log
java_cmd = "java -DentityExpansionLimit=1500000 -Xmx5120M -jar #{@bubastis_jar_path} #{options.join(' ')}"
java_cmd = "java -DentityExpansionLimit=1500000 -Xmx#{@java_heap_size} -jar #{@bubastis_jar_path} #{options.join(' ')}"
Diff.logger.info("Java call [#{java_cmd}]")
stdout,stderr,status = Open3.capture3(java_cmd)
if not status.success?
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3 changes: 2 additions & 1 deletion lib/ontologies_linked_data/parser/owlapi.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ def initialize(input_file, output_repo, opts = {})
@file_triples_path = nil
@missing_imports = nil
@reasoning = true
@java_heap_size = LinkedData.settings.java_max_heap_size
end

def setup_environment
Expand Down Expand Up @@ -71,7 +72,7 @@ def call_owlapi_java_command
if File.exist? errors_log
File.delete errors_log
end
command_call = "java -DentityExpansionLimit=2500000 -Xmx10240M -jar #{@owlapi_wrapper_jar_path} #{options}"
command_call = "java -DentityExpansionLimit=2500000 -Xmx#{@java_heap_size} -jar #{@owlapi_wrapper_jar_path} #{options}"
@logger.info("Java call [#{command_call}]")
Open3.popen3(command_call) do |i,o,e,w|
i.close
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