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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,69 @@ | ||
| ontologies_linked_data | ||
| ====================== | ||
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| ## TODO | ||
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| DONE: Quand ces champs ne sont pas remplis, faut mettre les valeurs par défaut (skos:prefLabel, skos:altLabel) | ||
| ```ruby | ||
| "prefLabelProperty": null, | ||
| "definitionProperty": null, | ||
| "synonymProperty": null, | ||
| "authorProperty": null, | ||
| "hierarchyProperty": null, | ||
| "obsoleteProperty": null, | ||
| "obsoleteParent": null | ||
| ``` | ||
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| On pourrait aussi peupler seul exampleIdentifier (on prend l'URI d'une classe au pif dans l'ontology) | ||
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| On pourrait générer également useImports avec les URI des owl:imports | ||
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| uriregexpattern: uri de l'ontology (où on vire la fin et on met sous forme de regex) | ||
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| ### Not valid property names | ||
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| Property names with - in it are not valid. | ||
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| Causing the following error: | ||
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| ``` | ||
| NameError - `@bug-database' is not allowed as an instance variable name: | ||
| /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/goo-7bbbb557d9f2/lib/goo/base/resource.rb:203:in `instance_variable_set' | ||
| /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/goo-7bbbb557d9f2/lib/goo/base/resource.rb:203:in `block in bring' | ||
| ``` | ||
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| ## Unit test status | ||
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| Unit test status: | ||
| - master branch: [](https://bmir-jenkins.stanford.edu/job/NCBO_OntLD_MasterTest/) | ||
| - staging branch: [](https://bmir-jenkins.stanford.edu/job/NCBO_OntLD_StagingTest/) | ||
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| Models and serializers for ontologies and related artifacts backed by 4store | ||
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| This is a component of the NCBO [ontologies_api](https://github.com/ncbo/ontologies_api). | ||
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| ## Add a new namespace in GOO for properties | ||
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| To add new namespaces used in the `Goo.vocabulary` go to `lib/ontologies_linked_data/config/config.rb` | ||
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| And use the GOO `add_namespace` method. For example: | ||
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| ```ruby | ||
| Goo.configure do |conf| | ||
| conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#")) | ||
| end | ||
| ``` | ||
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| * To iterate other the namespaces | ||
| ```ruby | ||
| Goo.namespaces.each do |prefix,uri| | ||
| puts "#{prefix}: #{uri}" | ||
| end | ||
| ``` | ||
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| * To resolve a namespace | ||
| ```ruby | ||
| Goo.vocabulary(:omv).to_s | ||
| ``` |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| ./bubastis-1.4.0.jar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,134 @@ | ||
| LinkedData.config do |config| | ||
| config.goo_port = 9000 | ||
| config.goo_host = "localhost" | ||
| config.search_server_url = "http://localhost:8983/solr/term_search_core1" | ||
| config.property_search_server_url = "http://localhost:8983/solr/prop_search_core1" | ||
| 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" | ||
| config.purl_port = 80 | ||
| config.purl_username = "" | ||
| config.purl_password = "" | ||
| config.purl_maintainers = "" | ||
| config.purl_target_url_prefix = "http://bioportal.bioontology.org" | ||
| GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "4store" | ||
| GOO_PATH_QUERY = ENV.include?("GOO_PATH_QUERY") ? ENV["GOO_PATH_QUERY"] : "/sparql/" | ||
| GOO_PATH_DATA = ENV.include?("GOO_PATH_DATA") ? ENV["GOO_PATH_DATA"] : "/data/" | ||
| GOO_PATH_UPDATE = ENV.include?("GOO_PATH_UPDATE") ? ENV["GOO_PATH_UPDATE"] : "/update/" | ||
| GOO_PORT = ENV.include?("GOO_PORT") ? ENV["GOO_PORT"] : 9000 | ||
| GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : "localhost" | ||
| REDIS_HOST = ENV.include?("REDIS_HOST") ? ENV["REDIS_HOST"] : "localhost" | ||
| REDIS_PORT = ENV.include?("REDIS_PORT") ? ENV["REDIS_PORT"] : 6379 | ||
| SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" | ||
| SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" | ||
| GOO_SLICES = ENV["GOO_SLICES"] || 500 | ||
| begin | ||
| LinkedData.config do |config| | ||
| Goo.slice_loading_size = GOO_SLICES.to_i | ||
| config.goo_backend_name = GOO_BACKEND_NAME.to_s | ||
| config.goo_host = GOO_HOST.to_s | ||
| config.goo_port = GOO_PORT.to_i | ||
| config.goo_path_query = GOO_PATH_QUERY.to_s | ||
| config.goo_path_data = GOO_PATH_DATA.to_s | ||
| config.goo_path_update = GOO_PATH_UPDATE.to_s | ||
| config.goo_redis_host = REDIS_HOST.to_s | ||
| config.goo_redis_port = REDIS_PORT.to_i | ||
| config.http_redis_host = REDIS_HOST.to_s | ||
| config.http_redis_port = REDIS_PORT.to_i | ||
| config.ontology_analytics_redis_host = REDIS_HOST.to_s | ||
| config.ontology_analytics_redis_port = REDIS_PORT.to_i | ||
| config.search_server_url = SOLR_TERM_SEARCH_URL.to_s | ||
| config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s | ||
| config.sparql_endpoint_url = "http:://sparql_endpoint.com" | ||
| # config.enable_notifications = false | ||
| # | ||
| config.java_max_heap_size = '20480M' | ||
| config.main_languages = ['en'] | ||
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| # Caches | ||
| config.goo_redis_host = REDIS_HOST.to_s | ||
| config.goo_redis_port = REDIS_PORT.to_i | ||
| config.enable_http_cache = false | ||
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| # Email notifications | ||
| config.enable_notifications = false | ||
| config.email_sender = '[email protected]' # Default sender for emails | ||
| config.email_override = '[email protected]' # all email gets sent here. Disable with email_override_disable. | ||
| config.email_disable_override = true | ||
| config.smtp_host = 'localhost' | ||
| config.smtp_port = 1025 | ||
| config.smtp_auth_type = :plain # :none, :plain, :login, :cram_md5 | ||
| config.smtp_domain = 'lirmm.fr' | ||
| config.smtp_user = 'test' | ||
| config.smtp_password = 'test' | ||
| # Emails of the instance administrators to get mail notifications when new user or new ontology | ||
| # config.admin_emails = ['[email protected]'] | ||
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| # Used to define other bioportal that can be mapped to | ||
| # Example to map to ncbo bioportal : {"ncbo" => {"api" => "http://data.bioontology.org", "ui" => "http://bioportal.bioontology.org", "apikey" => ""} | ||
| # Then create the mapping using the following class in JSON : "http://purl.bioontology.org/ontology/MESH/C585345": "ncbo:MESH" | ||
| # Where "ncbo" is the namespace used as key in the interportal_hash | ||
| config.interportal_hash = { | ||
| 'agroportal' => { | ||
| 'api' => 'http://data.agroportal.lirmm.fr', | ||
| 'ui' => 'http://agroportal.lirmm.fr', | ||
| 'apikey' => '1cfae05f-9e67-486f-820b-b393dec5764b' | ||
| }, | ||
| 'ncbo' => { | ||
| 'api' => 'http://data.bioontology.org', | ||
| 'ui' => 'http://bioportal.bioontology.org', | ||
| 'apikey' => '4a5011ea-75fa-4be6-8e89-f45c8c84844e' | ||
| }, | ||
| 'sifr' => { | ||
| 'api' => 'http://data.bioportal.lirmm.fr', | ||
| 'ui' => 'http://bioportal.lirmm.fr', | ||
| 'apikey' => '1cfae05f-9e67-486f-820b-b393dec5764b' | ||
| } | ||
| } | ||
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| # oauth | ||
| config.oauth_providers = { | ||
| github: { | ||
| check: :access_token, | ||
| link: 'https://api.github.com/user' | ||
| }, | ||
| keycloak: { | ||
| check: :jwt_token, | ||
| cert: 'KEYCLOAK_SECRET_KEY' | ||
| }, | ||
| orcid: { | ||
| check: :access_token, | ||
| link: 'https://pub.orcid.org/v3.0/me' | ||
| }, | ||
| google: { | ||
| check: :access_token, | ||
| link: 'https://www.googleapis.com/oauth2/v3/userinfo' | ||
| } | ||
| } | ||
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| config.ui_name = 'Bioportal' | ||
| config.title = 'NCBO BioPortal' | ||
| config.description = "The world's most comprehensive repository of biomedical ontologies" | ||
| config.color = '#234979' | ||
| config.logo = '' | ||
| config.fundedBy = [ | ||
| { | ||
| img_src: 'https://identity.stanford.edu/wp-content/uploads/sites/3/2020/07/block-s-right.png', | ||
| url: 'https://www.stanford.edu', | ||
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| }, | ||
| { | ||
| img_src: 'https://ontoportal.org/images/logo.png', | ||
| url: 'https://ontoportal.org/', | ||
| } | ||
| ] | ||
| config.federated_portals = { | ||
| 'agroportal' => { | ||
| api: 'http://data.agroportal.lirmm.fr', | ||
| ui: 'http://agroportal.lirmm.fr', | ||
| apikey: '1cfae05f-9e67-486f-820b-b393dec5764b', | ||
| color: '#1e2251' | ||
| }, | ||
| 'bioportal' => { | ||
| api: 'http://data.bioontology.org', | ||
| ui: 'http://bioportal.bioontology.org', | ||
| apikey: '4a5011ea-75fa-4be6-8e89-f45c8c84844e', | ||
| color: '#234979' | ||
| }, | ||
|
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| } | ||
| end | ||
| rescue NameError => e | ||
| binding.pry | ||
| # puts '(CNFG) >> LinkedData not available, cannot load config' | ||
| end | ||
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| #sometimes tmp by default cannot allocate large files | ||
| $TMP_SORT_FOLDER = "SOME TMP FOLDER" | ||
| # sometimes tmp by default cannot allocate large files | ||
| $TMP_SORT_FOLDER = 'SOME TMP FOLDER' |
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