openbel-api 0.6.2-java → 1.0.0-java

data/app/openbel/api/schemas/annotation_resource.schema.json

@@ -1,7 +1,7 @@
 {
   "$schema": "http://json-schema.org/draft-04/schema",
   "title": "Annotation",
-  "description": "A vocabulary of terms for describing evidence resources.",
+  "description": "A vocabulary of terms for describing nanopub resources.",
   "type": "object",
   "additionalProperties": false,
   "required": [

data/app/openbel/api/schemas/{evidence.schema.json → nanopub.schema.json}

@@ -1,11 +1,11 @@
 {
   "$schema":              "http://json-schema.org/draft-04/schema",
-  "description":          "DESCRIBE EVIDENCE",
+  "description":          "DESCRIBE NANOPUB",
   "type":                 "object",
   "additionalProperties": false,
-  "required":             ["evidence"],
+  "required":             ["nanopub"],
   "properties": {
-    "evidence": {
+    "nanopub": {
       "type":                 "object",
       "additionalProperties": false,
       "required":             ["bel_statement", "citation"],
@@ -92,10 +92,10 @@
             }
           }
         },
-        "summary_text": {
+        "support": {
           "type":        ["string", "null"],
-          "title":       "Summary Text",
-          "description": "Abstract from source text to provide support for this evidence"
+          "title":       "Support",
+          "description": "Abstract from source text to provide support for this nanopub"
         },
         "references": {
           "type":        ["object", "null"],
@@ -112,7 +112,7 @@
                   "keyword": {
                     "type":        "string",
                     "title":       "Keyword",
-                    "description": "Keyword that identifies this annotation resource, but only in the context of this Evidence."
+                    "description": "Keyword that identifies this annotation resource, but only in the context of this Nanopub."
                   },
                   "uri": {
                     "type":        "string",
@@ -134,7 +134,7 @@
                   "keyword": {
                     "type":        "string",
                     "title":       "Keyword",
-                    "description": "Keyword that identifies this namespace resource, but only in the context of this Evidence."
+                    "description": "Keyword that identifies this namespace resource, but only in the context of this Nanopub."
                   },
                   "uri": {
                     "type":        "string",
@@ -150,8 +150,8 @@
         },
         "metadata": {
           "type":        ["array", "null"],
-          "title":       "Evidence resource metadata",
-          "description": "Metadata that describes the evidence resource.",
+          "title":       "Nanopub resource metadata",
+          "description": "Metadata that describes the nanopub resource.",
           "items": {
             "oneOf": [
               {

data/app/openbel/api/schemas/{evidence_collection.schema.json → nanopub_collection.schema.json}

@@ -1,20 +1,20 @@
 {
   "$schema": "http://json-schema.org/draft-04/schema",
-  "description": "DESCRIBE EVIDENCE COLLECTION",
+  "description": "DESCRIBE NANOPUB COLLECTION",
   "type": "object",
   "additionalProperties": false,
   "required": [
-    "evidence_collection",
+    "nanopub_collection",
     "facets"
   ],
   "properties": {
-    "evidence_collection": {
+    "nanopub_collection": {
       "type": "array",
       "minItems": 0,
       "title": "",
       "description": "",
       "items": {
-        "$ref":"evidence_resource.schema.json"
+        "$ref":"nanopub_resource.schema.json"
       }
     },
     "facets": {
@@ -53,7 +53,7 @@
     },
     "metadata": {
       "title": "Metadata",
-      "description": "Data about the evidence collection",
+      "description": "Data about the nanopub collection",
       "type": "object",
       "additionalProperties": true,
       "properties": {

data/app/openbel/api/schemas/{evidence_resource.schema.json → nanopub_resource.schema.json}

@@ -1,16 +1,16 @@
 {
   "$schema": "http://json-schema.org/draft-04/schema",
-  "title": "Evidence Resource",
-  "description": "A single evidence resource.",
+  "title": "Nanopub Resource",
+  "description": "A single nanopub resource.",
   "type": "object",
   "additionalProperties": false,
   "required": [
-    "evidence"
+    "nanopub"
   ],
   "properties": {
     "allOf": [
       {
-        "$ref":"evidence.schema.json"
+        "$ref":"nanopub.schema.json"
       },
       {
         "type": "object",

data/config/config.yml

@@ -1,7 +1,17 @@
 # Configuration template for OpenBEL API
 
-# Storage of evidence through the Mongo database.
-evidence_store:
+# BEL configuration.
+bel:
+  # The BEL version supported by this OpenBEL API instance.
+  # Allowed values:
+  #   1.0
+  #     (BEL version 1.0 specification)
+  #   2.0
+  #     (BEL version 2.0 specification)
+  version: 2.0
+
+# Storage of nanopubs through the Mongo database.
+nanopub_store:
   mongo:
 
     # The MongoDB host to connect to. For example if MongoDB's net.bindIp
@@ -12,9 +22,9 @@ evidence_store:
     # The default MongoDB port. Configured under MongoDB's `net.port` setting.
     port:                     27017
 
-    # The name of your database. We think "openbel-evidence" should be fine,
+    # The name of your database. We think "openbel-nanopubs" should be fine,
     # but it's up to you.
-    database:                 'openbel-evidence'
+    database:                 'openbel-nanopubs'
 
     # MongoDB authentication and role assignment. These settings are necessary
     # if you would like to have a MongoDB user authenticated and authorized to
@@ -23,7 +33,7 @@ evidence_store:
     #First, you will need to create a MongoDB user with the "readWrite" and
     #"dbAdmin" roles for the "database" value set above. This is to allow read,
     #write, and index creation in the OpenBEL API application.
-    #See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#adding-the-openbel-user
+    #See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store#adding-the-openbel-user
     #username:                'openbel-user'
 
     #Second, you will need to set a password for the MongoDB user set above.

data/lib/openbel/api/helpers/uuid_generator.rb

@@ -0,0 +1,22 @@
+module OpenBEL
+  module Helpers
+    # Mixin to provide generation of String UUIDs.
+    #
+    # The {#generate_uuid} instance method is available with a
+    # platform-specific implementation.
+    module UUIDGenerator
+      # Define UUID implementation based on Ruby.
+      if RUBY_ENGINE =~ /^jruby/i
+        java_import 'java.util.UUID'
+        define_method(:generate_uuid) do
+          Java::JavaUtil::UUID.random_uuid.to_s
+        end
+      else
+        require 'uuid'
+        define_method(:generate_uuid) do
+          UUID.generate
+        end
+      end
+    end
+  end
+end

data/lib/openbel/api/{evidence → nanopub}/api.rb

@@ -1,17 +1,17 @@
 module OpenBEL
-  module Evidence
+  module Nanopub
     module API
 
       # single or array
-      def create_evidence(evidence)
+      def create_nanopub(nanopub)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def find_evidence_by_id(id)
+      def find_nanopub_by_id(id)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def find_evidence(filters = [], offset = 0, length = 0, facet = false)
+      def find_nanopub(filters = [], offset = 0, length = 0, facet = false)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
@@ -23,23 +23,23 @@ module OpenBEL
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def count_evidence(filters = [])
+      def count_nanopub(filters = [])
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def update_evidence_by_id(id, evidence_update)
+      def update_nanopub_by_id(id, nanopub_update)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def update_evidence_by_query(query, evidence_update)
+      def update_nanopub_by_query(query, nanopub_update)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def delete_evidence_by_id(id)
+      def delete_nanopub_by_id(id)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 
-      def delete_evidence_by_query(query)
+      def delete_nanopub_by_query(query)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
     end

data/lib/openbel/api/{evidence → nanopub}/facet_api.rb

@@ -1,8 +1,8 @@
 module OpenBEL
-  module Evidence
+  module Nanopub
     module FacetAPI
 
-      def create_facets(evidence)
+      def create_facets(nanopub)
         fail NotImplementedError, "#{__method__} is not implemented"
       end
 

data/lib/openbel/api/{evidence → nanopub}/facet_filter.rb

@@ -1,16 +1,16 @@
 require 'multi_json'
 
 module OpenBEL
-  module Evidence
+  module Nanopub
     module FacetFilter
 
       EMPTY = []
-      EVIDENCE_PARTS = [:citation, :experiment_context, :metadata]
+      NANOPUB_PARTS = [:citation, :experiment_context, :metadata]
 
-      def map_evidence_facets(evidence)
-        EVIDENCE_PARTS.reduce([]) { |facets, evidence_part|
-          part = evidence.send(evidence_part)
-          new_facets = self.send(:"map_#{evidence_part}_facets", part)
+      def map_nanopub_facets(nanopub)
+        NANOPUB_PARTS.reduce([]) { |facets, nanopub_part|
+          part = nanopub.send(nanopub_part)
+          new_facets = self.send(:"map_#{nanopub_part}_facets", part)
           facets.concat(new_facets)
         }
       end

data/lib/openbel/api/{evidence → nanopub}/mongo.rb

@@ -1,13 +1,14 @@
 require 'bel'
-require 'bel/evidence_model/util'
+require 'bel_parser/expression/model'
+require 'bel/nanopub/util'
 require 'mongo'
 require_relative 'api'
 require_relative 'mongo_facet'
 
 module OpenBEL
-  module Evidence
+  module Nanopub
 
-    class Evidence
+    class Nanopub
       include API
       include Mongo
 
@@ -30,42 +31,42 @@ module OpenBEL
           @db.authenticate(username, password, nil, auth_db)
         end
 
-        @collection      = @db[:evidence]
-        @evidence_facets = EvidenceFacets.new(options)
+        @collection      = @db[:nanopub]
+        @nanopub_facets = NanopubFacets.new(options)
 
         # ensure all indexes are created and maintained
         ensure_all_indexes
       end
 
-      def create_evidence(evidence)
-        # insert evidence; acknowledge journal
-        if evidence.respond_to?(:each_pair)
-          _id = @collection.insert(evidence, :w => 1, :j => true)
+      def create_nanopub(nanopub)
+        # insert nanopub; acknowledge journal
+        if nanopub.respond_to?(:each_pair)
+          _id = @collection.insert(nanopub, :w => 1, :j => true)
 
-          # remove evidence_facets after insert to facets
-          remove_evidence_facets(_id)
+          # remove nanopub_facets after insert to facets
+          remove_nanopub_facets(_id)
           _id
-        elsif evidence.respond_to?(:each)
-          @collection.insert(evidence.to_a, :w => 1, :j => true)
+        elsif nanopub.respond_to?(:each)
+          @collection.insert(nanopub.to_a, :w => 1, :j => true)
         else
-          raise "Evidence type #{evidence.class} cannot be inserted into Mongo."
+          raise "nanopub type #{nanopub.class} cannot be inserted into Mongo."
         end
       end
 
-      def find_evidence_by_id(value)
+      def find_nanopub_by_id(value)
         @collection.find_one(to_id(value))
       end
 
-      def find_evidence(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
+      def find_nanopub(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
         if includes_fts_search?(filters)
           text_search = get_fts_search(filters)
-          evidence_aggregate(text_search, filters, offset, length, facet, facet_value_limit)
+          nanopub_aggregate(text_search, filters, offset, length, facet, facet_value_limit)
         else
-          evidence_query(filters, offset, length, facet, facet_value_limit)
+          nanopub_query(filters, offset, length, facet, facet_value_limit)
         end
       end
 
-      def find_dataset_evidence(dataset, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
+      def find_dataset_nanopub(dataset, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
         query_hash = to_query(filters)
         query_hash[:$and] ||= []
         query_hash[:$and].unshift({
@@ -85,7 +86,7 @@ module OpenBEL
           :cursor => @collection.find(query_hash, query_opts)
         }
         if facet
-          facets_cursor = @evidence_facets.find_facets(query_hash, filters, facet_value_limit)
+          facets_cursor = @nanopub_facets.find_facets(query_hash, filters, facet_value_limit)
           results[:facets] = facets_cursor.to_a
         end
 
@@ -103,7 +104,7 @@ module OpenBEL
             {
               :$unwind => "$references.namespaces"
             },
-            {   
+            {
               :$project => {
                 keyword: "$references.namespaces.keyword",
                 uri: "$references.namespaces.uri"
@@ -137,7 +138,7 @@ module OpenBEL
           obj = obj.to_h
           obj[:keyword] = obj.delete("keyword")
           obj[:uri]     = obj.delete("uri")
-          union, new_remap = BEL::Model.union_namespace_references(union, [obj], 'incr')
+          union, new_remap = BEL::Nanopub.union_namespace_references(union, [obj], 'incr')
           remap.merge!(new_remap)
         end
 
@@ -153,7 +154,7 @@ module OpenBEL
             {
               :$unwind => "$references.annotations"
             },
-            {   
+            {
               :$project => {
                 keyword: "$references.annotations.keyword",
                 type:    "$references.annotations.type",
@@ -192,38 +193,39 @@ module OpenBEL
         union = []
         remap = {}
         references.each do |obj|
-          obj = obj.to_h
-          obj[:keyword] = obj.delete("keyword")
-          obj[:type]    = obj.delete("type")
-          obj[:domain]  = obj.delete("domain")
-          union, new_remap = BEL::Model.union_annotation_references(union, [obj], 'incr')
+          annotation =
+            BELParser::Expression::Model::Annotation.new(
+              *obj.values_at('keyword', 'type', 'domain')
+            )
+          union, new_remap =
+            BEL::Nanopub.union_annotation_references(union, [annotation], 'incr')
           remap.merge!(new_remap)
         end
 
         remap
       end
 
-      def count_evidence(filters = [])
+      def count_nanopub(filters = [])
         query_hash = to_query(filters)
         @collection.count(:query => query_hash)
       end
 
-      def update_evidence_by_id(value, evidence)
+      def update_nanopub_by_id(value, nanopub)
         # add ObjectId to update
         _id = BSON::ObjectId(value)
-        evidence_h = evidence.to_h
-        evidence_h[:_id] = _id
+        nanopub_h = nanopub.to_h
+        nanopub_h[:_id] = _id
 
-        # save evidence; acknowledge journal
-        @collection.save(evidence_h, :j => true)
+        # save nanopub; acknowledge journal
+        @collection.save(nanopub_h, :j => true)
 
-        # remove evidence_facets after update to facets
-        remove_evidence_facets(_id)
+        # remove nanopub_facets after update to facets
+        remove_nanopub_facets(_id)
         nil
       end
 
       def delete_facets
-        @evidence_facets.delete_all_facets
+        @nanopub_facets.delete_all_facets
       end
 
       def delete_dataset(identifier)
@@ -231,27 +233,27 @@ module OpenBEL
           { :"_dataset" => identifier },
           :j => true
         )
-        @evidence_facets.delete_all_facets
+        @nanopub_facets.delete_all_facets
       end
 
-      def delete_evidence(value)
+      def delete_nanopub(value)
         if value.respond_to?(:each)
           value.each do |v|
-            delete_evidence_by_id(v)
+            delete_nanopub_by_id(v)
           end
         else
-          delete_evidence_by_id(value)
+          delete_nanopub_by_id(value)
         end
       end
 
-      def delete_evidence_by_query(query)
+      def delete_nanopub_by_query(query)
         @collection.remove(
           query,
           :j => true
         )
       end
 
-      def delete_evidence_by_id(value)
+      def delete_nanopub_by_id(value)
         # convert to ObjectId
         begin
           _id = to_id(value)
@@ -260,10 +262,10 @@ module OpenBEL
           false
         end
 
-        # remove evidence_facets before evidence removal
-        remove_evidence_facets(_id)
+        # remove nanopub_facets before nanopub removal
+        remove_nanopub_facets(_id)
 
-        # remove evidence; returns true
+        # remove nanopub; returns true
         @collection.remove(
           {
               :_id => _id
@@ -297,7 +299,7 @@ module OpenBEL
 
       private
 
-      def evidence_query(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
+      def nanopub_query(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
         query_hash = to_query(filters)
         query_opts = query_options(
           query_hash,
@@ -312,14 +314,14 @@ module OpenBEL
           :cursor => @collection.find(query_hash, query_opts)
         }
         if facet
-          facets_cursor = @evidence_facets.find_facets(query_hash, filters, facet_value_limit)
+          facets_cursor = @nanopub_facets.find_facets(query_hash, filters, facet_value_limit)
           results[:facets] = facets_cursor.to_a
         end
 
         results
       end
 
-      def evidence_aggregate(text_search, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
+      def nanopub_aggregate(text_search, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
         match_filters = filters.select { |filter|
           filter['category'] != 'fts'
         }
@@ -376,7 +378,7 @@ module OpenBEL
         facets =
           if facet
             query_hash = to_query(filters)
-            facets_cursor = @evidence_facets.find_facets(query_hash, filters, facet_value_limit)
+            facets_cursor = @nanopub_facets.find_facets(query_hash, filters, facet_value_limit)
             facets_cursor.to_a
           else
             nil
@@ -498,13 +500,13 @@ module OpenBEL
         BSON::ObjectId(value.to_s)
       end
 
-      def remove_evidence_facets(_id)
+      def remove_nanopub_facets(_id)
         doc = @collection.find_one(_id, {
           :fields => {:_id => 0, :facets => 1}
         })
 
         if doc && doc.has_key?('facets')
-          @evidence_facets.delete_facets(doc['facets'])
+          @nanopub_facets.delete_facets(doc['facets'])
         end
       end
     end