puree 1.9.1 → 2.0.0

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data/CHANGELOG.md

@@ -2,20 +2,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## Unreleased
-- Metadata: activity?, clipping?, externalPerson?
-
-## 1.9.1 - 2018-04-18
-### Fixed
-- Handle missing created and modified.
-
-## 1.9.0 - 2018-03-09
-### Added
-- Publication - doi.
+## 2.0.0 - 2017-12-19
+### Changed
+- For Pure API 59.
 
-## 1.8.0 - 2018-03-02
 ### Added
-- Publication - Scopus id.
+- Independent modules: REST, Extractor, XMLExtractor
+- Testing against known live data.
 
 ## 1.7.0 - 2017-11-03
 ### Added

data/Gemfile

@@ -1,4 +1,4 @@
 source 'https://rubygems.org'
 
 # Specify your gem's dependencies in puree.gemspec
-gemspec
+gemspec

data/README.md

@@ -5,10 +5,7 @@ Metadata extraction from the Pure Research Information System.
 ## Status
 
 [![Gem Version](https://badge.fury.io/rb/puree.svg)](https://badge.fury.io/rb/puree)
-[![Build Status](https://semaphoreci.com/api/v1/aalbinclark/puree/branches/master/badge.svg)](https://semaphoreci.com/aalbinclark/puree)
-[![Code Climate](https://codeclimate.com/github/lulibrary/puree/badges/gpa.svg)](https://codeclimate.com/github/lulibrary/puree)
-[![Dependency Status](https://www.versioneye.com/user/projects/5899d253a86053003f389e1f/badge.svg?style=flat-square)](https://www.versioneye.com/user/projects/5899d253a86053003f389e1f)
-[![GitPitch](https://gitpitch.com/assets/badge.svg)](https://gitpitch.com/lulibrary/puree)
+[![Maintainability](https://api.codeclimate.com/v1/badges/0a0a8249dcadb444eb9e/maintainability)](https://codeclimate.com/github/lulibrary/puree/maintainability)
 
 ## Installation
 
@@ -24,130 +21,164 @@ Or install it yourself as:
 
     $ gem install puree
 
-
-## Usage
-The following examples are for the Dataset resource type.
-
-### Configuration
-
-Create a hash for passing to an extractor.
-
-```ruby
-# Pure host with authentication.
-config = {
-  url:      ENV['PURE_URL'],
-  username: ENV['PURE_USERNAME'],
-  password: ENV['PURE_PASSWORD']
-}
-```
-
+## Configuration
 ```ruby
-# Pure host without authentication.
+# For Extractor and REST modules.
 config = {
-  url: ENV['PURE_URL']
+  url:      'https://YOUR_HOST/ws/api/59',
+  username: 'YOUR_USERNAME',
+  password: 'YOUR_PASSWORD',
+  api_key:  'YOUR_API_KEY'
 }
 ```
 
-### Resource
-
-Configure an extractor to retrieve data from a Pure host.
+## Extractor module
+Find a resource by identifier and get Ruby objects.
 
 ```ruby
-dataset_extractor = Puree::Extractor::Dataset.new config
+# Configure an extractor
+extractor = Puree::Extractor::Dataset.new config
 ```
 
-Fetch the metadata for a resource with a particular identifier.
-
 ```ruby
-dataset = dataset_extractor.find uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
-# =>
-#<Puree::Model::Dataset:0x987f7a4>
+# Fetch the metadata for a resource with a particular identifier
+dataset = extractor.find 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+#=> #<Puree::Model::Dataset:0x00c0ffee>
 ```
 
-Access specific metadata e.g. an internal person's name.
-
 ```ruby
+# Access specific metadata e.g. an internal person's name
 dataset.persons_internal[0].name
-# =>
-#<Puree::Model::PersonName:0x9add67c @first="Foo", @last="Bar">
+#=> #<Puree::Model::PersonName:0x00c0ffee @first="Foo", @last="Bar">
 ```
 
-Select a formatting style for a person's name.
-
 ```ruby
+# Select a formatting style for a person's name
 dataset.persons_internal[0].name.last_initial
-# =>
-# "Bar, F."
+#=> "Bar, F."
 ```
 
-### Collection
+## XMLExtractor module
+Get Ruby objects from Pure XML.
 
-Configure a collection extractor to retrieve data from a Pure host.
+### Single resource
+```ruby
+xml = '<project> ... </project>'
+```
 
 ```ruby
-collection_extractor = Puree::Extractor::Collection.new config:   config,
-                                                        resource: :dataset
+# Configure an XML extractor
+xml_extractor = Puree::XMLExtractor::Project.new xml
 ```
 
-Fetch a bunch of resources.
+```ruby
+# Get a single piece of metadata
+xml_extractor.title
+#=> "An interesting project title"
+```
 
 ```ruby
-collection_extractor.find limit: 2
-# =>
-#<Puree::Model::Dataset:0xa62fd90>
-#<Puree::Model::Dataset:0xa5e8c24>
+# Get all the metadata together
+xml_extractor.model
+#=> #<Puree::Model::Project:0x00c0ffee>
 ```
 
-Fetch a random resource from the entire collection.
+### Homogeneous resource collection
+```ruby
+xml = '<result>
+        <dataSet> ... </dataSet>
+        <dataSet> ... </dataSet>
+        ...
+      </result>'
+```
 
 ```ruby
-collection_extractor.random_resource
-# =>
-#<Puree::Model::Dataset:0x97998bc>
+# Get an array of datasets
+Puree::XMLExtractor::Collection.datasets xml
+#=> [#<Puree::Model::Dataset:0x00c0ffee>, ...]
 ```
 
-### Query
+### Heterogeneous resource collection
+```ruby
+xml = '<result>
+        <contributionToJournal> ... </contributionToJournal>
+        <contributionToConference> ... </contributionToConference>
+        ...
+      </result>'
+```
 
-Get answers to important questions.
+```ruby
+# Get a hash of research outputs
+Puree::XMLExtractor::Collection.research_outputs xml
+#=> {
+#     journal_articles: [#<Puree::Model::JournalArticle:0x00c0ffee>, ...],
+#     conference_papers: [#<Puree::Model::ConferencePaper:0x00c0ffee>, ...],
+#     theses: [#<Puree::Model::Thesis:0x00c0ffee>, ...],
+#     other: [#<Puree::Model::ResearchOutput:0x00c0ffee>, ...]
+#   }
+```
 
-#### Funding
+## REST module
+Query the Pure REST API.
 
-Configure a funding query to retrieve data from a Pure host.
+### Client
+```ruby
+# Configure a client
+client = Puree::REST::Client.new config
+```
 
 ```ruby
-funding_query = Puree::Query::Funding.new config
+# Find a person
+client.persons.find id: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+#=> #<HTTP::Response:0x00c0ffee>
 ```
 
-Who are the funders (if any) for a project?
+```ruby
+# Find a person, limit the metadata to ORCID and employee start date
+client.persons.find id: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx',
+                    params: {fields: ['orcid', 'employeeStartDate']}
+#=> #<HTTP::Response:0x00c0ffee>
+```
 
 ```ruby
-funding_query.project_funders uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
-# =>
-#<Puree::Model::ExternalOrganisation:0x98986f0>
+# Find five people, response body as JSON
+client.persons.all params: {size: 5}, accept: :json
+#=> #<HTTP::Response:0x00c0ffee>
 ```
 
-Who are the funders (if any) for a publication?
+```ruby
+# Find research outputs for a person
+client.persons.research_outputs id: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+#=> #<HTTP::Response:0x00c0ffee>
+```
 
+### Resource
 ```ruby
-funding_query.publication_funders uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+# Configure a resource
+persons = Puree::REST::Person.new config
 ```
 
-#### Person
+```ruby
+# Find a person
+persons.find id: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+#=> #<HTTP::Response:0x00c0ffee>
+```
 
-Configure a person query to retrieve data from a Pure host.
+## REST module with XMLExtractor module
+Query the Pure REST API and get Ruby objects from Pure XML.
 
 ```ruby
-person_query = Puree::Query::Person.new config
+# Configure a client
+client = Puree::REST::Client.new config
 ```
 
-Get at most ten publications published by a person during the first six months of 2017.
+```ruby
+# Find projects for a person
+response = client.persons.projects id: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
+```
 
 ```ruby
-person_query.publications uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx',
-                          limit: 10,
-                          published_start: '2017-01-01',
-                          published_end: '2017-06-30'
-# =>
-#<Puree::Model::Publication:0x9d2c004>
-#<Puree::Model::Publication:0xa285028>
+# Extract metadata from XML
+Puree::XMLExtractor::Collection.projects response.to_s
+#=> [#<Puree::Model::Project:0x00c0ffee>, ...]
 ```

data/lib/puree/extractor/conference_paper.rb

@@ -3,21 +3,13 @@ module Puree
 
     # Conference paper extractor.
     #
-    class ConferencePaper < Puree::Extractor::PaperBase
+    class ConferencePaper < Puree::Extractor::Paper
 
-      # @option (see Puree::Extractor::Resource#initialize)
-      def initialize(config)
-        set_model_type 'conference_paper'
-        super
-      end
-
-      private
-
-      def combine_metadata
-        super
-
-        @model.event = @extractor.event
-        @model
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :research_output,
+                         xml_extractor_resource_type: :conference_paper
       end
 
     end

data/lib/puree/extractor/dataset.rb

@@ -9,49 +9,13 @@ module Puree
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
         super
-        setup :dataset
       end
 
-      private
-
-      def combine_metadata
-        super
-        @model.access = @extractor.access
-        @model.associated = @extractor.associated
-        @model.available = @extractor.available
-        @model.description = @extractor.description
-        @model.doi = @extractor.doi
-        @model.files = @extractor.files
-        @model.keywords = @extractor.keywords
-        @model.links = @extractor.links
-        @model.legal_conditions = @extractor.legal_conditions
-        @model.organisations = @extractor.organisations
-        @model.owner = @extractor.owner
-        @model.persons_internal = @extractor.persons_internal
-        @model.persons_external = @extractor.persons_external
-        @model.persons_other = @extractor.persons_other
-        @model.projects = @extractor.projects
-        @model.production = @extractor.production
-        @model.publications = @extractor.publications
-        @model.publisher = @extractor.publisher
-        @model.spatial_places = @extractor.spatial_places
-        @model.spatial_point = @extractor.spatial_point
-        @model.temporal = @extractor.temporal
-        @model.title = @extractor.title
-        @model.workflow_state = @extractor.workflow_state
-        @model
-      end
-
-      def configure_api(config)
-        @config = Puree::API::Configuration.new url: config[:url]
-        @config.basic_auth username: config[:username],
-                           password: config[:password]
-
-        @request = Puree::API::PersonRequest.new url: @config.url
-        if @config.basic_auth?
-          @request.basic_auth username: @config.username,
-                              password: @config.password
-        end
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :dataset,
+                         xml_extractor_resource_type: :dataset
       end
 
     end

data/lib/puree/extractor/doctoral_thesis.rb

@@ -7,15 +7,14 @@ module Puree
 
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
-        set_model_type 'doctoral_thesis'
         super
       end
 
-      private
-
-      def combine_metadata
-        super
-        @model.type === 'Doctoral Thesis' ? @model : nil
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :research_output,
+                         xml_extractor_resource_type: :doctoral_thesis
       end
 
     end

data/lib/puree/extractor/event.rb

@@ -9,21 +9,13 @@ module Puree
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
         super
-        setup :event
-      end      
- 
-      private
+      end
 
-      def combine_metadata
-        super
-        @model.city = @extractor.city
-        @model.country = @extractor.country
-        @model.date = @extractor.date
-        @model.description = @extractor.description
-        @model.location = @extractor.location
-        @model.title = @extractor.title
-        @model.type = @extractor.type
-        @model
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :event,
+                         xml_extractor_resource_type: :event
       end
 
     end

data/lib/puree/extractor/external_organisation.rb

@@ -9,16 +9,13 @@ module Puree
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
         super
-        setup :external_organisation
       end
 
-      private
-
-      def combine_metadata
-        super
-        @model.name = @extractor.name
-        @model.type = @extractor.type
-        @model
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :external_organisation,
+                         xml_extractor_resource_type: :external_organisation
       end
 
     end

data/lib/puree/extractor/extractor.rb

@@ -1,3 +1,22 @@
+require 'puree/extractor/resource'
+require 'puree/extractor/dataset'
+require 'puree/extractor/event'
+require 'puree/extractor/external_organisation'
+require 'puree/extractor/journal'
+require 'puree/extractor/organisational_unit'
+require 'puree/extractor/person'
+require 'puree/extractor/project'
+
+require 'puree/extractor/research_output'
+require 'puree/extractor/thesis'
+require 'puree/extractor/doctoral_thesis'
+require 'puree/extractor/masters_thesis'
+require 'puree/extractor/journal_article'
+require 'puree/extractor/paper'
+require 'puree/extractor/conference_paper'
+
+require 'puree/extractor/publisher'
+
 module Puree
 
   # An Extractor manages HTTP requests to Pure and the subsequent

data/lib/puree/extractor/journal.rb

@@ -9,17 +9,13 @@ module Puree
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
         super
-        setup :journal
       end
 
-      private
-
-      def combine_metadata
-        super
-        @model.issn = @extractor.issn
-        @model.publisher = @extractor.publisher
-        @model.title = @extractor.title
-        @model
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :journal,
+                         xml_extractor_resource_type: :journal
       end
 
     end

data/lib/puree/extractor/journal_article.rb

@@ -3,27 +3,18 @@ module Puree
 
     # Journal article extractor.
     #
-    class JournalArticle < Puree::Extractor::Publication
+    class JournalArticle < Puree::Extractor::ResearchOutput
 
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
-        set_model_type 'journal_article'
         super
       end
 
-      private
-
-      def combine_metadata
-        super
-
-        @model.article_number = @extractor.article_number
-        @model.issue = @extractor.issue
-        @model.journal = @extractor.journal
-        @model.pages = @extractor.pages
-        @model.page_range = @extractor.page_range
-        @model.peer_reviewed = @extractor.peer_reviewed
-        @model.volume = @extractor.volume
-        @model
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :research_output,
+                         xml_extractor_resource_type: :journal_article
       end
 
     end

data/lib/puree/extractor/masters_thesis.rb

@@ -7,15 +7,14 @@ module Puree
 
       # @option (see Puree::Extractor::Resource#initialize)
       def initialize(config)
-        set_model_type 'masters_thesis'
         super
       end
 
-      private
-
-      def combine_metadata
-        super
-        @model.type === "Master's Thesis" ? @model : nil
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :research_output,
+                         xml_extractor_resource_type: :masters_thesis
       end
 
     end

data/lib/puree/extractor/organisational_unit.rb

@@ -0,0 +1,25 @@
+module Puree
+
+  module Extractor
+
+    # Organisational unit extractor.
+    #
+    class OrganisationalUnit < Puree::Extractor::Resource
+
+      # @option (see Puree::Extractor::Resource#initialize)
+      def initialize(config)
+        super
+      end
+
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :organisational_unit,
+                         xml_extractor_resource_type: :organisational_unit
+      end
+
+    end
+
+  end
+
+end

data/lib/puree/extractor/paper.rb

@@ -3,18 +3,13 @@ module Puree
 
     # Paper extractor.
     #
-    class Paper < Puree::Extractor::PaperBase
+    class Paper < Puree::Extractor::ResearchOutput
 
-      # @option (see Puree::Extractor::Resource#initialize)
-      def initialize(config)
-        set_model_type 'paper'
-        super
-      end
-
-      private
-
-      def combine_metadata
-        super
+      # @param id [String]
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :research_output,
+                         xml_extractor_resource_type: :paper
       end
 
     end

data/lib/puree/extractor/person.rb

@@ -6,60 +6,11 @@ module Puree
     #
     class Person < Puree::Extractor::Resource
 
-      # @option (see Puree::Extractor::Resource#initialize)
-      def initialize(config)
-        super
-        setup :person
-      end
-
-      # Find a person by identifier.
-      #
-      # @param uuid [String]
       # @param id [String]
-      # @param employee_id [String]
-      # @return [Puree::Model::Person]
-      def find_by_id(uuid: nil, id: nil, employee_id: nil)
-        raise 'Cannot perform a request without a configuration' if @config.nil?
-        @response = @request.get uuid:           uuid,
-                                 id:             id,
-                                 employee_id:    employee_id,
-                                 latest_api:     @latest_api,
-                                 resource_type:  @resource_type
-        set_content @response.body
-      end
-
-      private
-
-      def combine_metadata
-        super
-        @model.affiliations = @extractor.affiliations
-        @model.email_addresses = @extractor.email_addresses
-        @model.employee_id = @extractor.employee_id
-        @model.hesa_id = @extractor.hesa_id
-        @model.image_urls = @extractor.image_urls
-        @model.keywords = @extractor.keywords
-        @model.name = @extractor.name
-        @model.orcid = @extractor.orcid
-        @model.scopus_id = @extractor.scopus_id
-        @model
-      end
-
-      # Configure a Pure host for API access.
-      #
-      # @param config [Hash]
-      # @option config [String] :url The URL of the Pure host.
-      # @option config [String] :username The username of the Pure host account.
-      # @option config [String] :password The password of the Pure host account.
-      def configure_api(config)
-        @config = Puree::API::Configuration.new url: config[:url]
-        @config.basic_auth username: config[:username],
-                           password: config[:password]
-
-        @request = Puree::API::PersonRequest.new url: @config.url
-        if @config.basic_auth?
-          @request.basic_auth username: @config.username,
-                              password: @config.password
-        end
+      def find(id)
+        find_and_extract id: id,
+                         api_resource_type: :person,
+                         xml_extractor_resource_type: :person
       end
 
     end