openbel-api 0.6.2-java → 1.0.0-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gemspec

@@ -34,27 +34,24 @@ Gem::Specification.new do |spec|
   # Dependencies
 
   ## bel.rb
-  spec.add_runtime_dependency 'bel',               '0.6.0'
+  spec.add_runtime_dependency 'bel',               '~> 1.0.0'
 
   ## bel.rb translator dependencies
-  spec.add_runtime_dependency 'json-ld',           '1.99.0'
-  spec.add_runtime_dependency 'rdf-json',          '1.99.0'
-  spec.add_runtime_dependency 'rdf-rdfa',          '1.99.0'
-  spec.add_runtime_dependency 'rdf-rdfxml',        '1.99.0'
-  spec.add_runtime_dependency 'rdf-trig',          '1.99.0.1'
-  spec.add_runtime_dependency 'rdf-trix',          '1.99.0'
-  spec.add_runtime_dependency 'rdf-turtle',        '1.99.0'
+  spec.add_runtime_dependency 'json-ld',           '2.0.0'
+  spec.add_runtime_dependency 'rdf-json',          '2.0.0'
+  spec.add_runtime_dependency 'rdf-rdfa',          '2.0.0'
+  spec.add_runtime_dependency 'rdf-rdfxml',        '2.0.0'
+  spec.add_runtime_dependency 'rdf-trig',          '2.0.0'
+  spec.add_runtime_dependency 'rdf-trix',          '2.0.0'
+  spec.add_runtime_dependency 'rdf-turtle',        '2.0.0'
 
   ## bel.rb plugin - annotation/namespace search
-  spec.add_runtime_dependency 'bel-search-sqlite', '0.4.2'
+  spec.add_runtime_dependency 'bel-search-sqlite', '~> 1.0.0.beta'
 
   ## bel.rb plugin - RDF repository using Apache Jena
-  spec.add_runtime_dependency 'bel-rdf-jena',      '0.4.2'
+  spec.add_runtime_dependency 'bel-rdf-jena',      '~> 1.0.0.beta'
 
-  ## RDF - RDF abstraction
-  spec.add_runtime_dependency 'rdf',               '1.99.1'
-
-  ## Mongo - Faceted search of evidence.
+  ## Mongo - Faceted search of nanopub.
   spec.add_runtime_dependency 'mongo',             '1.12.5'
   spec.add_runtime_dependency 'bson',              '1.12.5'
 

data/CHANGELOG.md

@@ -3,6 +3,10 @@ All notable changes to openbel-api will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [1.0.0][1.0.0] - TBD
+### Added
+- Support JWT authentication via *token* query parameter ([PR #108][108]).
+
 ## [0.6.2][0.6.2] - 2016-03-23
 ### Fixed
 - Missing authorization header reported when header is malformed ([Issue #105][105]).
@@ -13,12 +17,12 @@ This project adheres to [Semantic Versioning][Semantic Versioning].
 
 ## [0.6.0][0.6.0] - 2016-03-16
 ### Added
-- Retrieve evidence in a format supported by BEL translator plugins ([Issue 44][44]).
-- Retrieve dataset evidence in a format supported by BEL translator plugins ([Issue 99][99]).
+- Retrieve nanopub in a format supported by BEL translator plugins ([Issue 44][44]).
+- Retrieve dataset nanopub in a format supported by BEL translator plugins ([Issue 99][99]).
 
 ### Fixed
-- Dataset evidence collection is missing annotation/namespace URIs ([Issue 95][95]).
-- Facets are not created for evidence uploaded through a dataset.
+- Dataset nanopub collection is missing annotation/namespace URIs ([Issue 95][95]).
+- Facets are not created for nanopub uploaded through a dataset.
 
 ### Changed
 - MongoDB version 3.2.0 is now required due to use of `$slice` operator in Aggregation queries.
@@ -32,7 +36,7 @@ Datasets are stored with a URI computed from the scheme and host that is serving
 
 ## [0.5.1][0.5.1] - 2015-12-18
 ### Fixed
-- Authentication error for MongoDB user when faceting on `GET /api/evidence` ([Issue #93][93]).
+- Authentication error for MongoDB user when faceting on `GET /api/nanopub` ([Issue #93][93]).
 
 ### Changed
 - MongoDB version 3.2.0 is now required due to use of `$slice` operator in Aggregation queries ([Issue ?][]).
@@ -56,12 +60,12 @@ Datasets are stored with a URI computed from the scheme and host that is serving
 
 ## 0.4.0 - 2015-12-14
 ### Added
-- Evidence Store
-  - Storage of evidence including creation, retrieval, modification, and deletion actions.
-  - Flexible filtering of stored, evidence based on user's custom data requirements.
-  - Upload a document (e.g. BEL script, XBEL, or Evidence JSON), to the Evidence Store, as a dataset. These can later be retrieved or deleted from the Evidence Store.
-  - Flexible filtering of evidence contained within a dataset.
-  - Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
+- Nanopub Store
+  - Storage of nanopub including creation, retrieval, modification, and deletion actions.
+  - Flexible filtering of stored, nanopub based on user's custom data requirements.
+  - Upload a document (e.g. BEL script, XBEL, or Nanopub JSON), to the Nanopub Store, as a dataset. These can later be retrieved or deleted from the Nanopub Store.
+  - Flexible filtering of nanopub contained within a dataset.
+  - Download a document (e.g. BEL script, XBEL, or Nanopub JSON) from a dataset.
 - BEL Expressions
   - Autocomplete a BEL term expression.
   - Retrieve the structural components of a BEL expression.
@@ -70,13 +74,14 @@ Datasets are stored with a URI computed from the scheme and host that is serving
   - Retrieve equivalent namespace values from the individual.
   - Retrieve orthologous namespace values from the individual.
 
+[1.0.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.0
 [0.6.2]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.1...0.6.2
 [0.6.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.0...0.6.1
 [0.6.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.5.1...0.6.0
 [0.5.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.5.0...0.5.1
 [0.5.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.4.0...0.5.0
 [Semantic Versioning]:         http://semver.org
-[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#mongodb-user-authentication
+[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store#mongodb-user-authentication
 [44]:                          https://github.com/OpenBEL/openbel-api/issues/44
 [91]:                          https://github.com/OpenBEL/openbel-api/issues/91
 [92]:                          https://github.com/OpenBEL/openbel-api/issues/92
@@ -85,3 +90,4 @@ Datasets are stored with a URI computed from the scheme and host that is serving
 [99]:                          https://github.com/OpenBEL/openbel-api/issues/99
 [102]:                         https://github.com/OpenBEL/openbel-api/issues/102
 [105]:                         https://github.com/OpenBEL/openbel-api/issues/105
+[108]:                         https://github.com/OpenBEL/openbel-api/issues/108

data/README.md

@@ -4,12 +4,12 @@ The OpenBEL API provides RESTful API access to your BEL content. It is part of [
 
 ## Features
 
-- Evidence Store
-  - Storage of evidence including creation, retrieval, modification, and deletion actions.
-  - Flexible filtering of stored, evidence based on user's custom data requirements.
-  - Upload a document (e.g. BEL script, XBEL, or Evidence JSON), to the Evidence Store, as a dataset. These can later be retrieved or deleted from the Evidence Store.
-  - Flexible filtering of evidence contained within a dataset.
-  - Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
+- Nanopub Store
+  - Storage of nanopub including creation, retrieval, modification, and deletion actions.
+  - Flexible filtering of stored, nanopub based on user's custom data requirements.
+  - Upload a document (e.g. BEL script, XBEL, or nanopub JSON), to the Nanopub Store, as a dataset. These can later be retrieved or deleted from the nanopub Store.
+  - Flexible filtering of nanopub contained within a dataset.
+  - Download a document (e.g. BEL script, XBEL, or Nanopub JSON) from a dataset.
 - BEL Expressions
    - Autocomplete a BEL term expression.
    - Retrieve the structural components of a BEL expression.
@@ -21,28 +21,28 @@ The OpenBEL API provides RESTful API access to your BEL content. It is part of [
 ## Vocabulary
 
 *Annotation*
-A name/value property that describes an aspect of an *Evidence*. For example *Ncbi Taxonomy*:*Homo sapiens* is an annotation for the Human species.
+A name/value property that describes an aspect of a *nanopub*. For example *Ncbi Taxonomy*:*Homo sapiens* is an annotation for the Human species.
 
 *Namespace*
 A biological identifier that is curated and maintained by an organization. For example the *Gene Ontology* (i.e. *GO*) or *HGNC* (i.e. *HUGO Gene Nomenclature Committee*) database.
 
-*Evidence*
+*nanopub*
 A biological interaction curated from scientific literature. It is comprised of five parts.
 
 - *Citation*: The identification for the scientific literature where the interaction was stated.
 - *BEL Statement*: The biological interaction curated from the *Citation*.
-- *Summary text*: The text (i.e. *quotation*) within the *Citation* that supports the *BEL Statement*.
+- *Support*: The text (i.e. *quotation*) within the *Citation* that supports the *BEL Statement*.
 - *Experiment Context*: The biological context within the experiment where the *BEL Statement* was observed. For example if the experiment sample was a biopsy on Human, Lung tissue then you might provide *Ncbi Taxonomy*: *Homo sapiens* and *Uberon*: *lung epithelium*.
-- *Metadata*: Additional data about this *Evidence* that is not part of the experiment (i.e. in *Experiment Context*). For example the evidence's *Reviewer*, *Create Date*, or *Reviewed Date* would be considered metadata.
+- *Metadata*: Additional data about this *nanopub* that is not part of the experiment (i.e. in *Experiment Context*). For example the nanopub's *Reviewer*, *Create Date*, or *Reviewed Date* would be considered metadata.
 - *References*: The annotation and namespace sources used in the *BEL Statement*, *Experiment Context*, and *Metadata*. For example *Ncbi Taxonomy* may refer to an annotation identified by the URI http://www.openbel.org/bel/namespace/ncbi-taxonomy.
 
-*Document*: A file containing a collection of *Evidence* with document metadata like *Name*, *Description*, and *Version*. The supported document formats are BEL script, XBEL, and JSON Evidence.
+*Document*: A file containing a collection of *nanopub* with document metadata like *Name*, *Description*, and *Version*. The supported document formats are BEL script, XBEL, and JSON Nanopub.
 
-*Dataset*: The representation of a *BEL Document* within the OpenBEL API. This provides access to document metadata as well as the collection of *Evidence* stored in the OpenBEL API that originate from the *BEL Document*.
+*Dataset*: The representation of a *BEL Document* within the OpenBEL API. This provides access to document metadata as well as the collection of *nanopub* stored in the OpenBEL API that originate from the *BEL Document*.
 
 *Expression*: A string encoded in BEL that may represent a parameter (e.g. *AKT1*, *GO:"apoptotic process"*), term (e.g. *bp(GO:"apoptotic process")*), or statement (e.g. *p(HGNC:AKT1) increases bp(GO:"apoptotic process")*).
 
-*Evidence Store*: A database used for *Evidence*. It facilitates storage, filtering, and transformation of *Evidence*.
+*Nanopub Store*: A database used for BEL *nanopubs*. It facilitates storage, filtering, and transformation of *nanopubs*.
 
 ## Technical requirements
 
@@ -57,7 +57,7 @@ The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
 - [MongoDB][MongoDB], version 3.2 or greater
   - Follow [MongoDB download][MongoDB download] page for download and installation instructions.
 - [SQLite][SQLite], version 3.8.0 or greater
-  - Follow [SQLite download][SQLite download] page for download and installation instructions. 
+  - Follow [SQLite download][SQLite download] page for download and installation instructions.
 
 ## Getting up and Running
 
@@ -103,20 +103,7 @@ The OpenBEL API requires a configuration file to set up a few things. You can cr
 openbel-config --file openbel-api-config.yml
 ```
 
-*Configure the Evidence Store*
-The Evidence Store is backed by a [MongoDB][MongoDB] database. You will need to provide the *host*, *port*, and *database* option.
-
-The default configuration is:
-
-```yaml
-evidence_store:
-  mongo:
-    host:     'localhost'
-    port:     27017
-    database: 'openbel'
-```
-
-There are also settings for user authentication. See [MongoDB User Authentication][MongoDB User Authentication] on the wiki.
+[Configuring the Nanopub Store][https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store]
 
 *Resource RDF data*
 Annotations, namespaces, and dataset storage are represented as [RDF][RDF] data. The data is stored in an on-disk database using Apache Jena (Java library included with `openbel-api`).
@@ -150,7 +137,7 @@ resource_search:
 You can obtain the latest Resource Search database (20150611) from the [OpenBEL build server][Resource Search 20150611].
 
 *Token-based authentication*
-The OpenBEL API is equipped to require authentication for specific API paths (e.g. Evidence, Datasets). The implementation uses [Auth0][Auth0] as a single sign-on service.
+The OpenBEL API is equipped to require authentication for specific API paths (e.g. nanopub, Datasets). The implementation uses [Auth0][Auth0] as a single sign-on service.
 
 By default authentication is disabled.
 
@@ -228,11 +215,13 @@ server {
 }
 ```
 
-## API Documentation
+## Upgrading
 
-The REST API is defined by a [RAML][RAML] specification. Th                is published [here][OpenBEL API RAML specification].
+[Upgrading instructions][Upgrading]
+
+## API Documentation
 
-API documentation with *Try it* functionality is available [here][OpenBEL API documentation].
+API documentation with *Try it* functionality is available here [OpenBEL API documentation][OpenBEL API documentation].  You can download the [RAML 0.8][RAML] or Swagger specification files, try it on the webpage or generate curl, httpie, and various language templates for using the API.
 
 -----
 
@@ -241,9 +230,8 @@ Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] communit
 [OpenBEL]: http://www.openbel.org
 [OpenBEL Platform]: https://github.com/OpenBEL/openbel-platform
 [RAML]: http://raml.org/
-[OpenBEL API RAML specification]: http://next.belframework.org/openbel-api.raml
-[OpenBEL API documentation]: http://next.belframework.org/
-[Evidence API documentation]: http://next.belframework.org/#evidence
+[OpenBEL API documentation]: http://openbelapi.api-docs.io/
+[Nanopub API documentation]: http://openbelapi.api-docs.io/0.0.2/models/enWQug5KYcBtXxmPN
 [JRuby]: http://jruby.org
 [JRuby Getting Started]: http://jruby.org/getting-started
 [Java 8]: http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
@@ -251,6 +239,7 @@ Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] communit
 [MongoDB download]: https://www.mongodb.org/downloads#production
 [SQLite]: https://www.sqlite.org
 [SQLite download]: https://www.sqlite.org/download.html
+[Upgrading]: https://github.com/OpenBEL/openbel-api/blob/master/UPGRADING.md
 [RubyGems]: https://rubygems.org
 [RDF]: http://www.w3.org/RDF/
 [Auth0]: https://auth0.com/
@@ -258,4 +247,4 @@ Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] communit
 [Resource RDF 20150611]: http://build.openbel.org/browse/OR-RRD2/latestSuccessful/artifact
 [Resource Search 20150611]: http://build.openbel.org/browse/OR-RSD2/latestSuccessful/artifact
 [Nginx]: http://nginx.org/
-[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#mongodb-user-authentication
+[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store#mongodb-user-authentication

data/VERSION

@@ -1 +1 @@
-0.6.2
+1.0.0

data/app/openbel/api/app.rb

@@ -2,12 +2,12 @@ require 'rubygems'
 
 # TODO This should probably be in app-config.rb.
 require 'jrjackson'
+require 'bel_parser'
 
 require_relative 'util'
 
 require 'rack/cors'
 require 'sinatra/base'
-require "sinatra/reloader"
 require "sinatra/cookies"
 
 require_relative 'version'
@@ -15,12 +15,12 @@ require_relative 'config'
 require_relative 'routes/base'
 require_relative 'routes/root'
 require_relative 'routes/annotations'
-require_relative 'routes/evidence'
+require_relative 'routes/authenticate'
 require_relative 'routes/datasets'
 require_relative 'routes/expressions'
-require_relative 'routes/functions'
+require_relative 'routes/language'
 require_relative 'routes/namespaces'
-require_relative 'routes/authenticate'
+require_relative 'routes/nanopubs'
 require_relative 'routes/version'
 require_relative 'middleware/auth'
 
@@ -28,13 +28,13 @@ module OpenBEL
 
   class Server < Sinatra::Application
 
-    configure :development do
-      register Sinatra::Reloader
-    end
-
     configure do
       config = OpenBEL::Config::load!
       OpenBEL.const_set :Settings, config
+
+      tdbdir = OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
+      BELParser::Resource.default_uri_reader =
+        BELParser::Resource::JenaTDBReader.new(tdbdir)
     end
 
     if OpenBEL::Settings[:auth][:enabled]
@@ -67,19 +67,20 @@ module OpenBEL
 
     # routes not requiring authentication
     use OpenBEL::Routes::Root
-    use OpenBEL::Routes::Version
+    #use OpenBEL::Routes::Version
     use OpenBEL::Routes::Annotations
+    use OpenBEL::Routes::Authenticate
     use OpenBEL::Routes::Expressions
-    use OpenBEL::Routes::Functions
+    use OpenBEL::Routes::Language
     use OpenBEL::Routes::Namespaces
-    use OpenBEL::Routes::Authenticate
+    use OpenBEL::Routes::Version
 
     # routes requiring authentication
     if OpenBEL::Settings[:auth][:enabled]
       use OpenBEL::JWTMiddleware::Authentication
     end
     use OpenBEL::Routes::Datasets
-    use OpenBEL::Routes::Evidence
+    use OpenBEL::Routes::Nanopubs
   end
 end
 # vim: ts=2 sts=2 sw=2

data/app/openbel/api/config.rb

@@ -1,4 +1,5 @@
 require 'dot_hash'
+require 'bel_parser'
 
 module OpenBEL
   module Config
@@ -35,28 +36,69 @@ module OpenBEL
     private
 
     def self.validate(cfg)
-      # validate evidence_store block
-      evidence_store = cfg[:evidence_store]
-      unless evidence_store
+      # validate BEL version
+      bel = cfg[:bel]
+      unless bel
+        return [
+          true, <<-ERR.gsub(/ {12}/, '')
+            The "bel" section has not been configured.
+            You will need to supply a "bel.version" configuration block.
+            #{boilerplate_help}
+          ERR
+        ]
+      end
+      bel_failure = self.validate_bel(bel)
+      return bel_failure if bel_failure
+
+      # validate nanopub_store block
+      nanopub_store = cfg[:nanopub_store]
+      unless nanopub_store
+        return [
+          true, <<-ERR
+            An "nanopub_store" is not configured.
+            #{boilerplate_help}
+          ERR
+        ]
+      end
+      nanopub_failure = self.validate_nanopub_store(cfg[:nanopub_store])
+      return nanopub_failure if nanopub_failure
+
+      nil
+    end
+
+    def self.validate_bel(bel)
+      unless bel[:version]
+        return [
+          true, <<-ERR
+            The "bel.version" setting is not configured. This is required to
+            indicate which BEL version is supported by this OpenBEL API
+            instance.
+            #{boilerplate_help}
+          ERR
+        ]
+      end
+
+      version = bel[:version]
+      unless BELParser::Language.defines_version?(version)
+        defined_versions = BELParser::Language.versions
         return [
           true, <<-ERR
-            An "evidence_store" is not configured.
+            The "bel.version" setting of "#{version}" is not a defined BEL version. Allowed values: #{defined_versions}
             #{boilerplate_help}
           ERR
         ]
+
       end
-      evidence_failure = self.validate_evidence_store(cfg[:evidence_store])
-      return evidence_failure if evidence_failure
 
       nil
     end
 
-    def self.validate_evidence_store(evidence_store)
-      mongo = evidence_store[:mongo]
+    def self.validate_nanopub_store(nanopub_store)
+      mongo = nanopub_store[:mongo]
       unless mongo
         return [
           true, <<-ERR
-            The "evidence_store.mongo" configuration block is not configured.
+            The "nanopub_store.mongo" configuration block is not configured.
             #{boilerplate_help}
           ERR
         ]
@@ -68,7 +110,7 @@ module OpenBEL
         unless mongo[setting]
           return [
             true, <<-ERR
-              The "evidence_store.mongo.#{setting}" setting is not configured.
+              The "nanopub_store.mongo.#{setting}" setting is not configured.
               #{boilerplate_help}
             ERR
           ]
@@ -131,7 +173,7 @@ module OpenBEL
     def self.boilerplate_help
       <<-ERR.gsub(/^\s+/, '')
         Run the "openbel-config" command to see an example configuration.
-        See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store for details on how to configure an Evidence Store.
+        See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store for details on how to configure a Nanopub Store.
       ERR
     end
 

data/app/openbel/api/helpers/{evidence.rb → nanopub.rb}

@@ -5,9 +5,9 @@ require_relative 'translators'
 module OpenBEL
   module Helpers
 
-    def render_evidence_collection(
+    def render_nanopub_collection(
       name, page_results, start, size, filters,
-      filtered_total, collection_total, evidence_api
+      filtered_total, collection_total, nanopub_api
     )
       # see if the user requested a BEL translator (Accept header or ?format)
       translator        = Translators.requested_translator(request, params)
@@ -20,7 +20,7 @@ module OpenBEL
       if wants_default? || !translator
         facets   = page_results[:facets]
         pager    = Pager.new(start, size, filtered_total)
-        evidence = page_results[:cursor].map { |item|
+        nanopub = page_results[:cursor].map { |item|
                      item.delete('facets')
                      item
                    }.to_a
@@ -36,7 +36,7 @@ module OpenBEL
               :total_filtered         => pager.total_size,
               :total_pages            => pager.total_pages,
               :current_page           => pager.current_page,
-              :current_page_size      => evidence.size,
+              :current_page_size      => nanopub.size,
             }
           }
         }
@@ -45,7 +45,7 @@ module OpenBEL
         options[:previous_page] = pager.previous_page
         options[:next_page]     = pager.next_page
 
-        render_collection(evidence, :evidence, options)
+        render_collection(nanopub, :nanopub, options)
       else
         extension = translator_plugin.file_extensions.first
 
@@ -54,18 +54,17 @@ module OpenBEL
         attachment "#{name}.#{extension}"
         stream :keep_open do |response|
           cursor             = page_results[:cursor]
-          dataset_evidence = cursor.lazy.map { |evidence|
-            evidence.delete('facets')
-            evidence.delete('_id')
-            evidence = BEL::Model::Evidence.create(BEL.keys_to_symbols(evidence))
-            evidence.bel_statement = BEL::Model::Evidence.parse_statement(evidence)
-            evidence
+          dataset_nanopub = cursor.lazy.map { |nanopub|
+            nanopub.delete('facets')
+            nanopub.delete('_id')
+            nanopub = BEL::Nanopub::Nanopub.create(BEL.keys_to_symbols(nanopub))
+            nanopub
           }
 
           translator.write(
-            dataset_evidence, response,
-            :annotation_reference_map => evidence_api.find_all_annotation_references,
-            :namespace_reference_map  => evidence_api.find_all_namespace_references
+            dataset_nanopub, response,
+            :annotation_reference_map => nanopub_api.find_all_annotation_references,
+            :namespace_reference_map  => nanopub_api.find_all_namespace_references
           )
         end
       end