openbel-api 0.4.0-java
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- checksums.yaml +7 -0
- data/.gemspec +65 -0
- data/CHANGELOG.md +22 -0
- data/INSTALL.md +19 -0
- data/INSTALL_RUBY.md +107 -0
- data/LICENSE +191 -0
- data/README.md +208 -0
- data/app/openbel/api/app.rb +83 -0
- data/app/openbel/api/config.rb +45 -0
- data/app/openbel/api/config.ru +3 -0
- data/app/openbel/api/helpers/pager.rb +109 -0
- data/app/openbel/api/middleware/auth.rb +112 -0
- data/app/openbel/api/resources/adapters/basic_json.rb +52 -0
- data/app/openbel/api/resources/annotation.rb +141 -0
- data/app/openbel/api/resources/base.rb +16 -0
- data/app/openbel/api/resources/completion.rb +89 -0
- data/app/openbel/api/resources/evidence.rb +115 -0
- data/app/openbel/api/resources/evidence_transform.rb +143 -0
- data/app/openbel/api/resources/function.rb +98 -0
- data/app/openbel/api/resources/match_result.rb +79 -0
- data/app/openbel/api/resources/namespace.rb +174 -0
- data/app/openbel/api/routes/annotations.rb +168 -0
- data/app/openbel/api/routes/authenticate.rb +108 -0
- data/app/openbel/api/routes/base.rb +326 -0
- data/app/openbel/api/routes/datasets.rb +519 -0
- data/app/openbel/api/routes/evidence.rb +330 -0
- data/app/openbel/api/routes/expressions.rb +560 -0
- data/app/openbel/api/routes/functions.rb +41 -0
- data/app/openbel/api/routes/namespaces.rb +382 -0
- data/app/openbel/api/routes/root.rb +39 -0
- data/app/openbel/api/schemas.rb +34 -0
- data/app/openbel/api/schemas/annotation_collection.schema.json +20 -0
- data/app/openbel/api/schemas/annotation_resource.schema.json +36 -0
- data/app/openbel/api/schemas/annotation_value_collection.schema.json +21 -0
- data/app/openbel/api/schemas/annotation_value_resource.schema.json +35 -0
- data/app/openbel/api/schemas/completion_collection.schema.json +21 -0
- data/app/openbel/api/schemas/completion_resource.schema.json +146 -0
- data/app/openbel/api/schemas/evidence.schema.json +198 -0
- data/app/openbel/api/schemas/evidence_collection.schema.json +98 -0
- data/app/openbel/api/schemas/evidence_resource.schema.json +29 -0
- data/app/openbel/api/schemas/namespace_value_collection.schema.json +21 -0
- data/app/openbel/api/schemas/namespace_value_resource.schema.json +43 -0
- data/app/openbel/api/util.rb +11 -0
- data/bin/openbel-api +78 -0
- data/bin/openbel-config +46 -0
- data/config/async_evidence.rb +12 -0
- data/config/async_jena.rb +14 -0
- data/config/config.yml +31 -0
- data/config/server_config.rb +184 -0
- data/lib/openbel/api/cache/cache.rb +30 -0
- data/lib/openbel/api/config/config.rb +33 -0
- data/lib/openbel/api/evidence/api.rb +39 -0
- data/lib/openbel/api/evidence/facet_api.rb +18 -0
- data/lib/openbel/api/evidence/facet_filter.rb +83 -0
- data/lib/openbel/api/evidence/mongo.rb +247 -0
- data/lib/openbel/api/evidence/mongo_facet.rb +105 -0
- data/lib/openbel/api/helpers/dependency_graph.rb +52 -0
- data/lib/openbel/api/model/rdf_resource.rb +74 -0
- data/lib/openbel/api/plugin/cache/kyotocabinet.rb +85 -0
- data/lib/openbel/api/plugin/configure_plugins.rb +97 -0
- data/lib/openbel/api/plugin/evidence/evidence.rb +58 -0
- data/lib/openbel/api/plugin/plugin.rb +99 -0
- data/lib/openbel/api/plugin/plugin_manager.rb +20 -0
- data/lib/openbel/api/plugin/plugin_repository.rb +60 -0
- data/lib/openbel/api/storage/cache_proxy.rb +74 -0
- data/lib/openbel/api/storage/triple_storage.rb +43 -0
- metadata +379 -0
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require 'bel'
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require 'cgi'
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require 'openbel/api/evidence/mongo'
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require 'openbel/api/evidence/facet_filter'
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require_relative '../resources/evidence_transform'
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require_relative '../helpers/pager'
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module OpenBEL
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module Routes
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class Evidence < Base
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include OpenBEL::Evidence::FacetFilter
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include OpenBEL::Resource::Evidence
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include OpenBEL::Helpers
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def initialize(app)
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super
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@api = OpenBEL::Evidence::Evidence.new(
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:host => OpenBEL::Settings[:evidence_store][:mongo][:host],
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:port => OpenBEL::Settings[:evidence_store][:mongo][:port],
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:database => OpenBEL::Settings[:evidence_store][:mongo][:database]
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)
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# RdfRepository using Jena
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@rr = BEL::RdfRepository.plugins[:jena].create_repository(
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:tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
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)
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# Annotations using RdfRepository
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annotations = BEL::Resource::Annotations.new(@rr)
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@annotation_transform = AnnotationTransform.new(annotations)
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@annotation_grouping_transform = AnnotationGroupingTransform.new
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end
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helpers do
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def stream_evidence_objects(cursor)
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stream :keep_open do |response|
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cursor.each do |evidence|
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evidence.delete('facets')
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response << render_resource(
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evidence,
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:evidence,
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:as_array => false,
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:_id => evidence['_id'].to_s
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)
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end
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end
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end
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def stream_evidence_array(cursor)
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stream :keep_open do |response|
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current = 0
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# determine true size of cursor given cursor limit/count
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if cursor.limit.zero?
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total = cursor.total
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else
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total = [cursor.limit, cursor.count].min
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end
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response << '['
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cursor.each do |evidence|
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evidence.delete('facets')
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response << render_resource(
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evidence,
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:evidence,
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:as_array => false,
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:_id => evidence['_id'].to_s
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)
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current += 1
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response << ',' if current < total
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end
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response << ']'
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end
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end
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def keys_to_s_deep(hash)
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hash.inject({}) do |new_hash, (key, value)|
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kstr = key.to_s
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if value.kind_of?(Hash)
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new_hash[kstr] = keys_to_s_deep(value)
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elsif value.kind_of?(Array)
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new_hash[kstr] = value.map do |item|
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item.kind_of?(Hash) ?
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keys_to_s_deep(item) :
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item
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end
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else
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new_hash[kstr] = value
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end
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new_hash
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end
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end
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end
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options '/api/evidence' do
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response.headers['Allow'] = 'OPTIONS,POST,GET'
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status 200
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end
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options '/api/evidence/:id' do
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response.headers['Allow'] = 'OPTIONS,GET,PUT,DELETE'
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status 200
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end
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post '/api/evidence' do
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# Validate JSON Evidence.
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validate_media_type! "application/json"
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evidence_obj = read_json
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schema_validation = validate_schema(keys_to_s_deep(evidence_obj), :evidence)
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unless schema_validation[0]
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halt(
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400,
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{ 'Content-Type' => 'application/json' },
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render_json({ :status => 400, :msg => schema_validation[1].join("\n") })
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)
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end
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evidence = ::BEL::Model::Evidence.create(evidence_obj[:evidence])
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# Standardize annotations.
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@annotation_transform.transform_evidence!(evidence, base_url)
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# Build facets.
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facets = map_evidence_facets(evidence)
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hash = evidence.to_h
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hash[:bel_statement] = hash.fetch(:bel_statement, nil).to_s
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hash[:facets] = facets
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_id = @api.create_evidence(hash)
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# Return Location information (201).
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status 201
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headers "Location" => "#{base_url}/api/evidence/#{_id}"
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end
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get '/api/evidence-stream', provides: 'application/json' do
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start = (params[:start] || 0).to_i
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size = (params[:size] || 0).to_i
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group_as_array = as_bool(params[:group_as_array])
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# check filters
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filters = []
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filter_params = CGI::parse(env["QUERY_STRING"])['filter']
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filter_params.each do |filter|
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filter = read_filter(filter)
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halt 400 unless ['category', 'name', 'value'].all? { |f| filter.include? f}
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if filter['category'] == 'fts' && filter['name'] == 'search'
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halt 400 unless filter['value'].to_s.length > 1
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end
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filters << filter
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end
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cursor = @api.find_evidence(filters, start, size, false)[:cursor]
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if group_as_array
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stream_evidence_array(cursor)
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else
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stream_evidence_objects(cursor)
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end
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end
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get '/api/evidence' do
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start = (params[:start] || 0).to_i
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size = (params[:size] || 0).to_i
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faceted = as_bool(params[:faceted])
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max_values_per_facet = (params[:max_values_per_facet] || 0).to_i
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# check filters
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filters = []
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filter_params = CGI::parse(env["QUERY_STRING"])['filter']
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filter_params.each do |filter|
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filter = read_filter(filter)
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halt 400 unless ['category', 'name', 'value'].all? { |f| filter.include? f}
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if filter['category'] == 'fts' && filter['name'] == 'search'
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halt 400 unless filter['value'].to_s.length > 1
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end
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filters << filter
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end
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collection_total = @api.count_evidence()
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filtered_total = @api.count_evidence(filters)
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page_results = @api.find_evidence(filters, start, size, faceted)
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evidence = page_results[:cursor].map { |item|
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item.delete('facets')
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item
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}.to_a
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facets = page_results[:facets]
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halt 404 if evidence.empty?
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pager = Pager.new(start, size, filtered_total)
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options = {
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:start => start,
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:size => size,
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:filters => filter_params,
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:metadata => {
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:collection_paging => {
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:total => collection_total,
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:total_filtered => pager.total_size,
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:total_pages => pager.total_pages,
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:current_page => pager.current_page,
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:current_page_size => evidence.size,
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}
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}
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}
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if facets
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# group by category/name
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hashed_values = Hash.new { |hash, key| hash[key] = [] }
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facets.each { |facet|
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filter = read_filter(facet['_id'])
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category, name = filter.values_at('category', 'name')
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next if !category || !name
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key = [category.to_sym, name.to_sym]
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facet_obj = {
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:value => filter['value'],
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:filter => facet['_id'],
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:count => facet['count']
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}
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hashed_values[key] << facet_obj
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}
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if max_values_per_facet == 0
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facet_hashes = hashed_values.map { |(category, name), value_objects|
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{
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:category => category,
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:name => name,
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:values => value_objects
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}
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}
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else
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facet_hashes = hashed_values.map { |(category, name), value_objects|
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{
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:category => category,
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:name => name,
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:values => value_objects.take(max_values_per_facet)
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}
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}
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end
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options[:facets] = facet_hashes
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end
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# pager links
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options[:previous_page] = pager.previous_page
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options[:next_page] = pager.next_page
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render_collection(evidence, :evidence, options)
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end
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get '/api/evidence/:id' do
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object_id = params[:id]
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halt 404 unless BSON::ObjectId.legal?(object_id)
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evidence = @api.find_evidence_by_id(object_id)
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halt 404 unless evidence
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evidence.delete('facets')
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# XXX Hack to return single resource wrapped as json array
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# XXX Need to better support evidence resource arrays in base.rb
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render_resource(
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evidence,
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:evidence,
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:as_array => false,
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:_id => object_id
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)
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end
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put '/api/evidence/:id' do
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object_id = params[:id]
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halt 404 unless BSON::ObjectId.legal?(object_id)
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validate_media_type! "application/json"
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ev = @api.find_evidence_by_id(object_id)
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halt 404 unless ev
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evidence_obj = read_json
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schema_validation = validate_schema(keys_to_s_deep(evidence_obj), :evidence)
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unless schema_validation[0]
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halt(
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400,
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{ 'Content-Type' => 'application/json' },
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render_json({ :status => 400, :msg => schema_validation[1].join("\n") })
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)
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end
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# transformation
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evidence = evidence_obj[:evidence]
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evidence_model = ::BEL::Model::Evidence.create(evidence)
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@annotation_transform.transform_evidence!(evidence_model, base_url)
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facets = map_evidence_facets(evidence_model)
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evidence = evidence_model.to_h
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evidence[:bel_statement] = evidence.fetch(:bel_statement, nil).to_s
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evidence[:facets] = facets
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@api.update_evidence_by_id(object_id, evidence)
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status 202
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end
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delete '/api/evidence/:id' do
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object_id = params[:id]
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halt 404 unless BSON::ObjectId.legal?(object_id)
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ev = @api.find_evidence_by_id(object_id)
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halt 404 unless ev
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@api.delete_evidence_by_id(object_id)
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status 202
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end
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end
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end
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end
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# vim: ts=2 sw=2:
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# encoding: utf-8
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@@ -0,0 +1,560 @@
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1
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require 'cgi'
|
2
|
+
require 'bel'
|
3
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+
require 'uri'
|
4
|
+
|
5
|
+
module OpenBEL
|
6
|
+
module Routes
|
7
|
+
|
8
|
+
class Expressions < Base
|
9
|
+
|
10
|
+
def initialize(app)
|
11
|
+
super
|
12
|
+
|
13
|
+
# RdfRepository using Jena.
|
14
|
+
@rr = BEL::RdfRepository.plugins[:jena].create_repository(
|
15
|
+
:tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
|
16
|
+
)
|
17
|
+
|
18
|
+
# Annotations using RdfRepository
|
19
|
+
@annotations = BEL::Resource::Annotations.new(@rr)
|
20
|
+
# Namespaces using RdfRepository
|
21
|
+
@namespaces = BEL::Resource::Namespaces.new(@rr)
|
22
|
+
|
23
|
+
# Resource Search using SQLite.
|
24
|
+
@search = BEL::Resource::Search.plugins[:sqlite].create_search(
|
25
|
+
:database_file => OpenBEL::Settings[:resource_search][:sqlite][:database_file]
|
26
|
+
)
|
27
|
+
|
28
|
+
@sequence_variation = SequenceVariationFunctionHasLocationPredicate.new
|
29
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+
end
|
30
|
+
|
31
|
+
options '/api/expressions/*/completions' do
|
32
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+
response.headers['Allow'] = 'OPTIONS,GET'
|
33
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+
status 200
|
34
|
+
end
|
35
|
+
|
36
|
+
options '/api/expressions/*/components/?' do
|
37
|
+
response.headers['Allow'] = 'OPTIONS,GET'
|
38
|
+
status 200
|
39
|
+
end
|
40
|
+
|
41
|
+
options '/api/expressions/*/components/terms?' do
|
42
|
+
response.headers['Allow'] = 'OPTIONS,GET'
|
43
|
+
status 200
|
44
|
+
end
|
45
|
+
|
46
|
+
options '/api/expressions/*/syntax-validations/?' do
|
47
|
+
response.headers['Allow'] = 'OPTIONS,GET'
|
48
|
+
status 200
|
49
|
+
end
|
50
|
+
|
51
|
+
options '/api/expressions/*/semantic-validations/?' do
|
52
|
+
response.headers['Allow'] = 'OPTIONS,GET'
|
53
|
+
status 200
|
54
|
+
end
|
55
|
+
|
56
|
+
# options '/api/expressions/*/ortholog' do
|
57
|
+
# response.headers['Allow'] = 'OPTIONS,GET'
|
58
|
+
# status 200
|
59
|
+
# end
|
60
|
+
|
61
|
+
# options '/api/expressions/*/ortholog/:species' do
|
62
|
+
# response.headers['Allow'] = 'OPTIONS,GET'
|
63
|
+
# status 200
|
64
|
+
# end
|
65
|
+
|
66
|
+
helpers do
|
67
|
+
|
68
|
+
def normalize_relationship(relationship)
|
69
|
+
return nil unless relationship
|
70
|
+
BEL::Language::RELATIONSHIPS[relationship.to_sym]
|
71
|
+
end
|
72
|
+
|
73
|
+
def statement_components(bel_statement, flatten = false)
|
74
|
+
obj = {}
|
75
|
+
if flatten
|
76
|
+
obj[:subject] = bel_statement.subject ? bel_statement.subject.to_bel : nil
|
77
|
+
obj[:relationship] = normalize_relationship(bel_statement.relationship)
|
78
|
+
obj[:object] = bel_statement.object ? bel_statement.object.to_bel : nil
|
79
|
+
else
|
80
|
+
obj[:subject] = term_components(bel_statement.subject)
|
81
|
+
obj[:relationship] = normalize_relationship(bel_statement.relationship)
|
82
|
+
obj[:object] = term_components(bel_statement.object)
|
83
|
+
end
|
84
|
+
obj
|
85
|
+
end
|
86
|
+
|
87
|
+
def arg_components(bel_argument)
|
88
|
+
if bel_argument.respond_to? :fx
|
89
|
+
term_components(bel_argument)
|
90
|
+
elsif bel_argument.respond_to? :ns
|
91
|
+
parameter_components(bel_argument)
|
92
|
+
else
|
93
|
+
nil
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
def term_components(bel_term)
|
98
|
+
return nil unless bel_term
|
99
|
+
|
100
|
+
{
|
101
|
+
:term => {
|
102
|
+
:fx => bel_term.fx,
|
103
|
+
:arguments => bel_term.arguments.map { |a| arg_components(a) }
|
104
|
+
}
|
105
|
+
}
|
106
|
+
end
|
107
|
+
|
108
|
+
def parameter_components(bel_parameter)
|
109
|
+
return nil unless bel_parameter
|
110
|
+
|
111
|
+
{
|
112
|
+
:parameter => {
|
113
|
+
:ns => bel_parameter.ns ? bel_parameter.ns.prefix : nil,
|
114
|
+
:value => bel_parameter.value.to_s
|
115
|
+
}
|
116
|
+
}
|
117
|
+
end
|
118
|
+
end
|
119
|
+
|
120
|
+
get '/api/expressions/*/completions/?' do
|
121
|
+
bel = params[:splat].first
|
122
|
+
caret_position = (params[:caret_position] || bel.length).to_i
|
123
|
+
halt 400 unless bel and caret_position
|
124
|
+
|
125
|
+
begin
|
126
|
+
completions = BEL::Completion.complete(bel, @search, caret_position)
|
127
|
+
rescue IndexError => ex
|
128
|
+
halt(
|
129
|
+
400,
|
130
|
+
{ 'Content-Type' => 'application/json' },
|
131
|
+
render_json({ :status => 400, :msg => ex.to_s })
|
132
|
+
)
|
133
|
+
end
|
134
|
+
halt 404 if completions.empty?
|
135
|
+
|
136
|
+
render_collection(
|
137
|
+
completions,
|
138
|
+
:completion,
|
139
|
+
:bel => bel,
|
140
|
+
:caret_position => caret_position
|
141
|
+
)
|
142
|
+
end
|
143
|
+
|
144
|
+
get '/api/expressions/*/components/?' do
|
145
|
+
bel = params[:splat].first
|
146
|
+
flatten = as_bool(params[:flatten])
|
147
|
+
|
148
|
+
statement = BEL::Script.parse(bel).find { |obj|
|
149
|
+
obj.is_a? BEL::Model::Statement
|
150
|
+
}
|
151
|
+
halt 404 unless statement
|
152
|
+
|
153
|
+
response.headers['Content-Type'] = 'application/json'
|
154
|
+
MultiJson.dump({
|
155
|
+
:expression_components => statement_components(statement, flatten),
|
156
|
+
:statement_short_form => statement.to_s
|
157
|
+
})
|
158
|
+
end
|
159
|
+
|
160
|
+
get '/api/expressions/*/components/terms?' do
|
161
|
+
bel = params[:splat].first
|
162
|
+
functions = CGI::parse(env["QUERY_STRING"])['function']
|
163
|
+
flatten = as_bool(params[:flatten])
|
164
|
+
inner_terms = as_bool(params[:inner_terms])
|
165
|
+
|
166
|
+
terms = BEL::Script.parse(bel).select { |obj|
|
167
|
+
obj.is_a? BEL::Model::Term
|
168
|
+
}
|
169
|
+
|
170
|
+
if !functions.empty?
|
171
|
+
functions = functions.map(&:to_sym)
|
172
|
+
terms = terms.select { |term|
|
173
|
+
functions.any? { |match|
|
174
|
+
term.fx.short_form == match || term.fx.long_form == match
|
175
|
+
}
|
176
|
+
}
|
177
|
+
end
|
178
|
+
|
179
|
+
if inner_terms
|
180
|
+
terms = terms.flat_map { |term|
|
181
|
+
term.arguments.select { |arg| arg.is_a? BEL::Model::Term }
|
182
|
+
}
|
183
|
+
end
|
184
|
+
|
185
|
+
terms = terms.to_a
|
186
|
+
halt 404 if terms.empty?
|
187
|
+
|
188
|
+
response.headers['Content-Type'] = 'application/json'
|
189
|
+
if flatten
|
190
|
+
MultiJson.dump({
|
191
|
+
:terms => terms.map { |term| term.to_bel }
|
192
|
+
})
|
193
|
+
else
|
194
|
+
MultiJson.dump({
|
195
|
+
:terms => terms.map { |term| term_components(term) }
|
196
|
+
})
|
197
|
+
end
|
198
|
+
end
|
199
|
+
|
200
|
+
# TODO Relies on LibBEL.bel_parse_statement which is not currently supported.
|
201
|
+
# get '/api/expressions/*/ortholog/:species' do
|
202
|
+
# bel = params[:splat].first
|
203
|
+
# species = params[:species]
|
204
|
+
# taxon_annotation = @annotations.find('taxon').first
|
205
|
+
#
|
206
|
+
# unless taxon_annotation
|
207
|
+
# halt(
|
208
|
+
# 404,
|
209
|
+
# { 'Content-Type' => 'application/json' },
|
210
|
+
# render_json({
|
211
|
+
# :status => 404,
|
212
|
+
# :msg => 'Could not find NCBI Taxonomy annotation.'
|
213
|
+
# })
|
214
|
+
# )
|
215
|
+
# end
|
216
|
+
#
|
217
|
+
# species = taxon_annotation.find(species).first
|
218
|
+
#
|
219
|
+
# if species
|
220
|
+
# species = species.identifier.to_s
|
221
|
+
# else
|
222
|
+
# halt(
|
223
|
+
# 400,
|
224
|
+
# { 'Content-Type' => 'application/json' },
|
225
|
+
# render_json({
|
226
|
+
# :status => 400,
|
227
|
+
# :msg => %Q{Could not find species "#{params[:species]}"}
|
228
|
+
# })
|
229
|
+
# )
|
230
|
+
# end
|
231
|
+
#
|
232
|
+
# bel_ast = BEL::Parser.parse(bel)
|
233
|
+
#
|
234
|
+
# if bel_ast.any?([@sequence_variation])
|
235
|
+
# msg = 'Could not orthologize sequence variation terms with location'
|
236
|
+
# halt(
|
237
|
+
# 404,
|
238
|
+
# { 'Content-Type' => 'application/json' },
|
239
|
+
# render_json({
|
240
|
+
# :status => 404,
|
241
|
+
# :msg => msg
|
242
|
+
# })
|
243
|
+
# )
|
244
|
+
# end
|
245
|
+
#
|
246
|
+
# param_transform = ParameterOrthologTransform.new(
|
247
|
+
# @namespaces, @annotations, species
|
248
|
+
# )
|
249
|
+
# transformed_ast = bel_ast.transform_tree([param_transform])
|
250
|
+
#
|
251
|
+
# if !param_transform.parameter_errors.empty?
|
252
|
+
# parameters = param_transform.parameter_errors.map { |p|
|
253
|
+
# p.join(':')
|
254
|
+
# }.join(', ')
|
255
|
+
# halt(
|
256
|
+
# 404,
|
257
|
+
# { 'Content-Type' => 'application/json' },
|
258
|
+
# render_json({
|
259
|
+
# :status => 404,
|
260
|
+
# :msg => "Could not orthologize #{parameters}"
|
261
|
+
# })
|
262
|
+
# )
|
263
|
+
# end
|
264
|
+
#
|
265
|
+
# # serialize AST to BEL
|
266
|
+
# bel_serialization = BELSerializationTransform.new
|
267
|
+
# transformed_ast.transform_tree([bel_serialization])
|
268
|
+
#
|
269
|
+
# # write response
|
270
|
+
# response.headers['Content-Type'] = 'application/json'
|
271
|
+
# MultiJson.dump({
|
272
|
+
# :original => bel,
|
273
|
+
# :species => params[:species],
|
274
|
+
# :orthologized => bel_serialization.bel_string
|
275
|
+
# })
|
276
|
+
# end
|
277
|
+
|
278
|
+
# BEL Syntax Validation
|
279
|
+
# TODO Move out to a separate route.
|
280
|
+
get '/api/expressions/*/syntax-validations/?' do
|
281
|
+
halt 501
|
282
|
+
end
|
283
|
+
|
284
|
+
# BEL Semantic Validations
|
285
|
+
# TODO Move out to a separate route.
|
286
|
+
get '/api/expressions/*/semantic-validations/?' do
|
287
|
+
halt 501
|
288
|
+
end
|
289
|
+
|
290
|
+
class SequenceVariationFunctionHasLocationPredicate
|
291
|
+
include BEL::LibBEL
|
292
|
+
|
293
|
+
SEQUENCE_VARIATION_FX = [
|
294
|
+
'fus', 'fusion',
|
295
|
+
'pmod', 'proteinModification',
|
296
|
+
'sub', 'substitution',
|
297
|
+
'trunc', 'truncation'
|
298
|
+
]
|
299
|
+
|
300
|
+
def call(ast_node)
|
301
|
+
# check if AST node is a TERM
|
302
|
+
if !ast_node.is_a?(BelAstNodeToken) || ast_node.token_type != :BEL_TOKEN_TERM
|
303
|
+
return false
|
304
|
+
end
|
305
|
+
|
306
|
+
# check if AST node is a pmod TERM
|
307
|
+
if !SEQUENCE_VARIATION_FX.include?(ast_node.left.to_typed_node.value)
|
308
|
+
return false
|
309
|
+
end
|
310
|
+
|
311
|
+
# walk arg AST nodes until terminal
|
312
|
+
arg_node = ast_node.right.to_typed_node
|
313
|
+
while !(arg_node.left.pointer.null? && arg_node.right.pointer.null?)
|
314
|
+
# check if NV token child
|
315
|
+
arg_token = arg_node.left.to_typed_node
|
316
|
+
|
317
|
+
if arg_token.token_type == :BEL_TOKEN_NV
|
318
|
+
# true if namespace value is an integer
|
319
|
+
node_value = arg_token.right.to_typed_node.value
|
320
|
+
if integer?(node_value)
|
321
|
+
return true
|
322
|
+
end
|
323
|
+
end
|
324
|
+
|
325
|
+
# advance to the next ARG
|
326
|
+
arg_node = arg_node.right.to_typed_node
|
327
|
+
end
|
328
|
+
|
329
|
+
return false
|
330
|
+
end
|
331
|
+
|
332
|
+
private
|
333
|
+
|
334
|
+
def integer?(value)
|
335
|
+
begin
|
336
|
+
Integer(value)
|
337
|
+
return true
|
338
|
+
rescue ArgumentError
|
339
|
+
return false
|
340
|
+
end
|
341
|
+
end
|
342
|
+
end
|
343
|
+
|
344
|
+
class ParameterOrthologTransform
|
345
|
+
include BEL::LibBEL
|
346
|
+
|
347
|
+
NAMESPACE_PREFERENCE = [
|
348
|
+
"hgnc",
|
349
|
+
"mgi",
|
350
|
+
"rgd",
|
351
|
+
"gocc",
|
352
|
+
"scomp",
|
353
|
+
"meshcs",
|
354
|
+
"sfam",
|
355
|
+
"gobp",
|
356
|
+
"meshpp",
|
357
|
+
"chebi",
|
358
|
+
"schem",
|
359
|
+
"do",
|
360
|
+
"meshd",
|
361
|
+
"sdis",
|
362
|
+
"sp",
|
363
|
+
"affx",
|
364
|
+
"egid",
|
365
|
+
]
|
366
|
+
|
367
|
+
def initialize(namespaces, annotations, species_tax_id)
|
368
|
+
@namespaces = namespaces
|
369
|
+
@orthology = OrthologAdapter.new(
|
370
|
+
namespaces, species_tax_id
|
371
|
+
)
|
372
|
+
@species_tax_id = species_tax_id
|
373
|
+
@parameter_errors = []
|
374
|
+
end
|
375
|
+
|
376
|
+
def parameter_errors
|
377
|
+
@parameter_errors.uniq
|
378
|
+
end
|
379
|
+
|
380
|
+
def call(ast_node)
|
381
|
+
if ast_node.is_a?(BelAstNodeToken) &&
|
382
|
+
ast_node.token_type == :BEL_TOKEN_NV
|
383
|
+
|
384
|
+
ns_value = [
|
385
|
+
ast_node.left.to_typed_node.value,
|
386
|
+
ast_node.right.to_typed_node.value
|
387
|
+
]
|
388
|
+
orthologs = @orthology[ns_value]
|
389
|
+
if !orthologs.empty?
|
390
|
+
orthologs.sort_by! { |ortholog| namespace_preference(ortholog) }
|
391
|
+
ortholog = orthologs.first
|
392
|
+
BEL::LibBEL::bel_free_ast_node(ast_node.left.pointer)
|
393
|
+
ast_node.left = BelAstNode.new(
|
394
|
+
bel_new_ast_node_value(:BEL_VALUE_PFX, ortholog[0].upcase)
|
395
|
+
)
|
396
|
+
|
397
|
+
BEL::LibBEL::bel_free_ast_node(ast_node.right.pointer)
|
398
|
+
ast_node.right = BelAstNode.new(
|
399
|
+
bel_new_ast_node_value(:BEL_VALUE_VAL, ortholog[1])
|
400
|
+
)
|
401
|
+
else
|
402
|
+
# flag as ortholog error if this parameter has a namespace and
|
403
|
+
# the namespace value is either not known or its species differs
|
404
|
+
# from our target
|
405
|
+
if ns_value[0] != nil
|
406
|
+
namespace, value = ns_value
|
407
|
+
namespace = @namespaces.find(namespace).first
|
408
|
+
if namespace
|
409
|
+
value = namespace.find(value).first
|
410
|
+
if !value || value.fromSpecies != @species_tax_id
|
411
|
+
@parameter_errors << value
|
412
|
+
end
|
413
|
+
end
|
414
|
+
end
|
415
|
+
end
|
416
|
+
end
|
417
|
+
end
|
418
|
+
|
419
|
+
private
|
420
|
+
|
421
|
+
def namespace_preference(ortholog)
|
422
|
+
NAMESPACE_PREFERENCE.index(ortholog[0])
|
423
|
+
end
|
424
|
+
end
|
425
|
+
|
426
|
+
class BELSerializationTransform
|
427
|
+
include BEL::LibBEL
|
428
|
+
|
429
|
+
attr_reader :bel_string
|
430
|
+
|
431
|
+
def initialize
|
432
|
+
@bel_string = ""
|
433
|
+
end
|
434
|
+
|
435
|
+
def call(ast_node)
|
436
|
+
if ast_node.is_a?(BelAstNodeToken)
|
437
|
+
case ast_node.token_type
|
438
|
+
when :BEL_TOKEN_STATEMENT
|
439
|
+
when :BEL_TOKEN_SUBJECT
|
440
|
+
when :BEL_TOKEN_OBJECT
|
441
|
+
when :BEL_TOKEN_REL
|
442
|
+
when :BEL_TOKEN_TERM
|
443
|
+
when :BEL_TOKEN_ARG
|
444
|
+
when :BEL_TOKEN_NV
|
445
|
+
end
|
446
|
+
else
|
447
|
+
case ast_node.value_type
|
448
|
+
when :BEL_VALUE_FX
|
449
|
+
function(ast_node.value)
|
450
|
+
when :BEL_VALUE_REL
|
451
|
+
relationship(ast_node.value)
|
452
|
+
when :BEL_VALUE_PFX
|
453
|
+
namespace_prefix(ast_node.value)
|
454
|
+
when :BEL_VALUE_VAL
|
455
|
+
namespace_value(ast_node.value)
|
456
|
+
end
|
457
|
+
end
|
458
|
+
end
|
459
|
+
|
460
|
+
def between(ast_node)
|
461
|
+
if ast_node.is_a?(BelAstNodeToken)
|
462
|
+
case ast_node.token_type
|
463
|
+
when :BEL_TOKEN_STATEMENT
|
464
|
+
when :BEL_TOKEN_SUBJECT
|
465
|
+
when :BEL_TOKEN_OBJECT
|
466
|
+
when :BEL_TOKEN_REL
|
467
|
+
when :BEL_TOKEN_TERM
|
468
|
+
when :BEL_TOKEN_ARG
|
469
|
+
token_arg(ast_node)
|
470
|
+
when :BEL_TOKEN_NV
|
471
|
+
end
|
472
|
+
end
|
473
|
+
end
|
474
|
+
|
475
|
+
def after(ast_node)
|
476
|
+
if ast_node.is_a?(BelAstNodeToken)
|
477
|
+
case ast_node.token_type
|
478
|
+
when :BEL_TOKEN_STATEMENT
|
479
|
+
when :BEL_TOKEN_SUBJECT
|
480
|
+
when :BEL_TOKEN_OBJECT
|
481
|
+
when :BEL_TOKEN_REL
|
482
|
+
when :BEL_TOKEN_TERM
|
483
|
+
@bel_string.concat(')')
|
484
|
+
when :BEL_TOKEN_ARG
|
485
|
+
when :BEL_TOKEN_NV
|
486
|
+
end
|
487
|
+
end
|
488
|
+
end
|
489
|
+
|
490
|
+
private
|
491
|
+
|
492
|
+
def token_arg(ast_node)
|
493
|
+
chained_arg_node = ast_node.right
|
494
|
+
if !chained_arg_node.pointer.null?
|
495
|
+
chained_arg_node = chained_arg_node.to_typed_node
|
496
|
+
if !chained_arg_node.left.pointer.null? ||
|
497
|
+
!chained_arg_node.right.pointer.null?
|
498
|
+
@bel_string.concat(', ')
|
499
|
+
end
|
500
|
+
end
|
501
|
+
end
|
502
|
+
|
503
|
+
def function(fx)
|
504
|
+
@bel_string.concat(fx).concat('(')
|
505
|
+
end
|
506
|
+
|
507
|
+
def relationship(rel)
|
508
|
+
@bel_string.concat(" #{rel} ")
|
509
|
+
end
|
510
|
+
|
511
|
+
def namespace_prefix(prefix)
|
512
|
+
return unless prefix
|
513
|
+
@bel_string.concat(prefix).concat(':')
|
514
|
+
end
|
515
|
+
|
516
|
+
def namespace_value(value)
|
517
|
+
@bel_string.concat(value)
|
518
|
+
end
|
519
|
+
end
|
520
|
+
|
521
|
+
# Hash-like
|
522
|
+
class OrthologAdapter
|
523
|
+
|
524
|
+
EMPTY = [].freeze
|
525
|
+
|
526
|
+
def initialize(namespaces, species_tax_id)
|
527
|
+
@namespaces = namespaces
|
528
|
+
@species_tax_id = species_tax_id
|
529
|
+
end
|
530
|
+
|
531
|
+
def [](key)
|
532
|
+
namespace, value = key
|
533
|
+
|
534
|
+
if value.start_with?('"') && value.end_with?('"')
|
535
|
+
value = value[1...-1]
|
536
|
+
end
|
537
|
+
|
538
|
+
namespace = @namespaces.find(namespace).first
|
539
|
+
return EMPTY unless namespace
|
540
|
+
value = namespace.find(value).first
|
541
|
+
return EMPTY unless value
|
542
|
+
orthologs = value.orthologs.select { |orth|
|
543
|
+
orth.fromSpecies == @species_tax_id
|
544
|
+
}.to_a
|
545
|
+
return EMPTY if orthologs.empty?
|
546
|
+
|
547
|
+
orthologs.map! { |ortholog_value|
|
548
|
+
[
|
549
|
+
ortholog_value.namespace.prefix,
|
550
|
+
ortholog_value.prefLabel
|
551
|
+
]
|
552
|
+
}
|
553
|
+
orthologs
|
554
|
+
end
|
555
|
+
end
|
556
|
+
end
|
557
|
+
end
|
558
|
+
end
|
559
|
+
# vim: ts=2 sw=2:
|
560
|
+
# encoding: utf-8
|