umlaut 3.2.0 → 3.3.0

data/app/service_adaptors/scopus2.rb

@@ -0,0 +1,330 @@
+# Service adapter plug-in.
+#
+# 
+# PURPOSE: Includes "cited by", "similar articles" and "more by these authors"
+# links from scopus. 
+#
+# LIMTATIONS: You must be a Scopus customer for these links generated to work
+# for your users at all! Off-campus users should be probably going through ezproxy, see
+# the EZProxy plug-in.
+# Must find a match in scopus, naturally. "cited by" will only
+# be included if Scopus has non-0 "cited by" links. But there's no good way
+# to precheck similar/more-by for this, so they are provided blind and may
+# result in 0 hits.  You can turn them off if you like, with @include_similar,
+# and @include_more_by_authors. 
+# Abstracts are not used because it seems to violate Scopus terms of service
+# to use them. 
+#
+# REGISTERING:  Register for a Scopus API key at: 
+# http://www.developers.elsevier.com/action/devprojects?pageOrigin=cmsPage&zone=topNavBar
+# Look for "Register a new site" button at the bottom right of the page. 
+#
+# For the second Scopus API, you theoretically need a Scopus "PartnerID" and
+# corresponding "release number", in @partner_id and @scopus_release
+# There's no real easy way to get one. Scopus says:
+#    "To obtain a partner ID or release number, contact your nearest regional
+#    Scopus office. A list of Scopus contacts is available at
+#    http://www.info.scopus.com/contactus/index.shtml"
+# Bah! But fortunately, using the "partnerID" assigned to the Scopus Json
+# API, 65, _seems_ to work, and is coded here as the default. You could try
+# going with that. When you register a partnerID, you also get a 'salt key',
+# which is currently not used by this code, but @link_salt_key is reserved
+# for it in case added functionality does later. 
+#
+# SCOPUS USEFUL URLS:
+#
+# api key register: http://www.developers.elsevier.com/action/devprojects?pageOrigin=cmsPage&zone=topNavBar 
+#
+# 'content policies' terms of use: http://www.developers.elsevier.com/cms/content-apis 
+#
+# API overview docs: http://www.developers.elsevier.com/cms/content-apis 
+#
+# Various other api docs? Confused myself as to organization here. 
+#
+# * http://www.developers.elsevier.com/devcms/content-api-search-request
+# * http://www.developers.elsevier.com/devcms/content/search-fields-overview
+# * http://api.elsevier.com/content/search/#d0n14606
+#
+# Some API recommendations for federated search: http://www.developers.elsevier.com/cms/restful-api-federated-search
+#
+class Scopus2 < Service
+  require 'umlaut_http'
+  require 'nokogiri'
+  
+  include ActionView::Helpers::SanitizeHelper
+  
+  include MetadataHelper
+  include UmlautHttp
+  
+  required_config_params :api_key
+
+  attr_accessor :scopus_search_base
+
+  def service_types_generated
+    types = []
+    types.push( ServiceTypeValue[:cited_by] ) if @include_cited_by
+    types.push( ServiceTypeValue[:abstract] ) if @include_abstract
+    types.push( ServiceTypeValue[:similar] ) if @include_similar
+    types.push( ServiceTypeValue[@more_by_authors_type] ) if @include_more_by_authors
+
+    return types
+  end
+
+  def initialize(config)
+    #defaults
+    @display_name = "Scopus"
+    @registered_referer
+    @scopus_search_base = 'http://api.elsevier.com/content/search/index:SCOPUS'
+    
+    @include_cited_by = true
+    @include_similar = true
+    @include_more_by_authors = true
+    @more_by_authors_type = "similar"
+
+    @inward_cited_by_url = "http://www.scopus.com/scopus/inward/citedby.url"
+    #@partner_id = "E5wmcMWC"
+    @partner_id = 65
+    @link_salt_key = nil
+    @scopus_release = "R6.0.0"
+
+    # Scopus offers two algorithms for finding similar items.
+    # This variable can be:
+    # "key" => keyword based similarity 
+    # "ref" => reference based similiarity (cites similar refs?) Seems to offer 0 hits quite often, so we use keyword instead. 
+    # "aut" => author. More docs by same authors. Incorporated as seperate link usually. 
+    @more_like_this_type = "key"
+    @inward_more_like_url = "http://www.scopus.com/scopus/inward/mlt.url"
+    
+    @credits = {
+      @display_name => "http://www.scopus.com/home.url"
+    }
+    
+    super(config)
+  end
+
+  def xml_namespaces
+    @xml_namespaces ||= 
+      { "atom"        => "http://www.w3.org/2005/Atom",
+        "dc"          => "http://purl.org/dc/elements/1.1/",
+        "opensearch"  => "http://a9.com/-/spec/opensearch/1.1/",
+        "prism"       => "http://prismstandard.org/namespaces/basic/2.0/"
+      }
+  end
+
+  def handle(request)
+    scopus_query = scopus_query(request)
+
+    # we can't make a good query, nevermind. 
+    return request.dispatched(self, true) if scopus_query.blank? 
+    
+    url = scopus_url(scopus_query)
+    
+    
+    # Make the call.
+    headers = {"Accept" => "application/xml"}
+    headers["Referer"] = @registered_referer if @registered_referer 
+
+    response = http_fetch(url, :headers => headers, :raise_on_http_error_code => false)
+
+    unless response.kind_of? Net::HTTPSuccess
+      # error, sometimes we have info in XML <service-error>
+      xml = begin
+        Nokogiri::XML(response.body)
+      rescue Exception
+        nil
+      end
+    
+      code, message = nil, nil
+      if xml && error = xml.at_xpath("./service-error")
+        code    = error.at_xpath("./status/statusCode")
+        message = error.at_xpath("./status/statusText")
+      end
+      e = StandardError.new("Scopus returned error: #{code}: #{message}: scopus query: #{url}")
+      return request.dispatched(self, DispatchedService::FailedFatal, e)
+    end
+
+    xml      = Nokogiri::XML(response.body)
+    
+    # Take the first hit from scopus's results, hope they relevancy ranked it
+    # well. For DOI/pmid search, there should ordinarly be only one hit!    
+    first_hit = xml.at_xpath("//atom:entry[1]", xml_namespaces)
+
+    # Weirdly, a zero-hit result has one <atom:entry> containing an
+    # <atom:error> (Sic). Could other kinds of errors be reported that
+    # way too? Maybe. Better check just in case, ugh. 
+    if first_hit && (error = first_hit.at_xpath("./atom:error", xml_namespaces))      
+        scopus_message = error.text
+
+        if scopus_message == "Result set was empty"
+          # Just zero hits, no big deal, but nothing to do. 
+          return request.dispatched(self, true)
+        else
+          # real error, log it. 
+          e = StandardError.new("Scopus returned error: #{error.text}: scopus query: #{url}")
+          return request.dispatched(self, DispatchedService::FailedFatal, e)
+        end
+    end 
+
+    if first_hit
+      if first_hit && (error = first_hit.at_xpath("./atom:error", xml_namespaces))      
+        e = StandardError.new("Scopus returned error: #{error.text}")
+        return request.dispatched(self, DispatchedService::FailedFatal, e)
+      end 
+    
+      if (@include_cited_by)
+        try_add_cited_by_response(first_hit, request)
+      end
+  
+      if (@include_similar)
+        url = more_like_this_url(first_hit)
+        # Pre-checking for actual hits not currently working, disabled.
+        if (true || ( hits = check_for_hits(url) ) > 0 )
+          request.add_service_response( 
+            :service=>self, 
+            :display_text => "#{hits} #{ServiceTypeValue[:similar].display_name_pluralize.downcase.capitalize}", 
+            :url => url, 
+            :service_type_value => :similar)          
+        end                
+      end
+
+      if ( @include_more_by_authors)
+        url = more_like_this_url(first_hit, :type => "aut")
+        # Pre-checking for actual hits not currently working, disabled. 
+        if (true || ( hits = check_for_hits(url) ) > 0 )
+          request.add_service_response( 
+            :service=>self, 
+            :display_text => "#{hits} More from these authors", 
+            :url => url, 
+            :service_type_value => :similar)          
+        end        
+      end
+
+    end
+
+    return request.dispatched(self, true)
+  end
+
+  
+  # Returns a scopus advanced search query intended to find the exact
+  # known item identified by this citation.
+  #
+  # NOT uri-escaped yet, make sure to uri-escape before putting it in a uri
+  # param! 
+  #
+  # Will try to use DOI or PMID if available. Otherwise
+  # will use issn/year/vol/iss/start page if available.
+  # In some cases may resort to author/title. 
+  def scopus_query(request)
+    
+    if (doi = get_doi(request.referent))
+      return "DOI(#{phrase(doi)})"
+    elsif (pmid = get_pmid(request.referent))
+      return "PMID(#{phrase(pmid)})"
+    elsif (isbn = get_isbn(request.referent))
+      # I don't think scopus has a lot of ISBN-holding citations, but
+      # it allows search so we might as well try. 
+      return "ISBN(#{phrase(isbn)})"
+    else            
+      # Okay, we're going to try to do it on issn/vol/issue/page.
+      # If we don't have issn, we'll reluctantly use journal title
+      # (damn you google scholar).
+      metadata = request.referent.metadata
+      issn = request.referent.issn
+      if ( (issn || ! metadata['jtitle'].blank? ) &&
+           ! metadata['volume'].blank? &&
+           ! metadata['issue'].blank? &&
+           ! metadata['spage'].blank? )
+        query = "VOLUME(#{phrase(metadata['volume'])}) AND ISSUE(#{phrase(metadata['issue'])}) AND PAGEFIRST(#{phrase(metadata['spage'])}) "
+        if ( issn )
+          query += " AND (ISSN(#{phrase(issn)}) OR EISSN(#{phrase(issn)}))"
+        else
+          query += " AND EXACTSRCTITLE(#{phrase(metadata['jtitle'])})"
+        end
+        return query
+      end      
+    end
+    return nil
+  end
+
+  def scopus_url(query)
+    "#{@scopus_search_base}?apiKey=#{CGI.escape @api_key}&query=#{CGI.escape query}"
+  end
+  
+  # backslash escapes any double quotes, and embeds string in scopus
+  # phrase search double quotes. Does NOT uri-escape. 
+  def phrase(str)
+    '"' + str.gsub('"', '\\"') + '"'
+  end
+
+  # Input is a ruby hash that came from the scopus JSON, representing
+  # a single hit. We're going to add this as a result. 
+  def try_add_cited_by_response(result, request)
+    # While scopus provides an "inwardurl" in the results, this just takes
+    # us to the record detail page. We actually want to go RIGHT to the
+    # list of cited-by items. So we create our own, based on Scopus's
+    # reversed engineered predictable URLs. 
+
+    count_str = result.at_xpath("atom:citedby-count/text()", xml_namespaces).to_s
+    count_i   = count_str.to_i
+
+    return if count_i < 1
+    
+    label = ServiceTypeValue[:cited_by].display_name_pluralize.downcase.capitalize    
+      if count_i == 1
+        label = ServiceTypeValue[:cited_by].display_name.downcase.capitalize
+      end
+    cited_by_url = cited_by_url( result )
+    
+    request.add_service_response(:service=>self, 
+      :display_text => "#{count_str} #{label}", 
+      :count=> count_i, 
+      :url => cited_by_url, 
+      :service_type_value => :cited_by)
+  end
+
+  def eid_from_hit(result)
+    result.at_xpath("atom:eid/text()", xml_namespaces).to_s
+  end
+
+  def cited_by_url(result)
+    eid = CGI.escape( eid_from_hit(result) )    
+    #return "#{@scopus_cited_by_base}?eid=#{eid}&src=s&origin=recordpage"
+    # Use the new scopus direct link format!
+    return "#{@inward_cited_by_url}?partnerID=#{@partner_id}&rel=#{@scopus_release}&eid=#{eid}"
+    return 
+  end
+
+  def more_like_this_url(result, options = {})
+    options[:type] ||= @more_like_this_type
+    eid = CGI.escape eid_from_hit(result)
+
+    return "#{@inward_more_like_url}?partnerID=#{@partner_id}&rel=#{@scopus_release}&eid=#{eid}&mltType=#{options[:type]}"
+  end
+
+  # NOT currently working. Scopus doesn't make this easy. 
+  # Takes a scopus direct url for which we're not sure if there will be results
+  # or not, and requests it and html screen-scrapes to get hit count. (We
+  # can conveniently find this just in the html <title> at least).
+  # Works for cited_by and more_like_this searches at present. 
+  # May break if Scopus changes their html title!
+  def check_for_hits(url)
+  
+    response = http_fetch(url).body
+
+    response_html = Nokogiri::HTML(response)
+
+    title = response_xml.at('title').inner_text
+    # title is "X documents" (or 'Documents') if there are hits.
+    # It's annoyingly "Search Error" if there are either 0 hits, or
+    # if there was an actual error. So we can't easily log actual
+    # errors, sorry.
+    title.downcase =~ /^\s*(\d+)?\s+document/
+    if ( hits = $1)
+      return hits.to_i
+    else
+      return 0
+    end    
+  end
+
+    
+end

data/app/views/feedback/_resolve_section.html.erb

@@ -0,0 +1,16 @@
+<div class="help-text-icon">?</div>
+<%= render 'section_heading', :presenter => renderer, :force_render => true %>
+
+<ul class="response_list umlaut-help-list">
+<% umlaut_config.feedback.contacts.each_pair do |key, config| %>
+    <li>
+        <% if config[:link_out] %>
+            <%# simply link out to somewhere outside of umlaut %>
+            <%= link_to config[:label], config[:link_out] %>
+        <% else %>
+            <%# link to our feedback form %>
+            <%= link_to config[:label], feedback_path(umlaut_request.id, :contact_id => key) %>
+        <% end %>
+    </li>
+<% end %>
+</ul>

data/app/views/feedback/new.html.erb

@@ -0,0 +1,33 @@
+<h1>Contact Us <small>Send us questions, problems, or comments</small></h1>
+
+<%= form_tag(feedback_path(params[:request_id], :contact_id => params[:contact_id]) , :method => :post, :class => "feedback-form form-horizontal") do %>
+    
+    <div class="control-group">
+        <label class="control-label" for="name">Your Name</label>
+        <div class="controls">
+          <input type="text" id="name" name="name">
+        </div>
+    </div>
+
+    <div class="control-group">
+        <label class="control-label" for="email">Your Email</label>
+        <div class="controls">
+          <input type="text" id="email" name="email">
+        </div>
+    </div>
+
+    <div class="control-group">
+        <label class="control-label" for="feedback">Question or Comment</label>
+        <div class="controls">
+          <textarea id="feedback" name="feedback" class="input-xxlarge" rows=6></textarea>
+        </div>
+    </div>
+
+
+    <div class="control-group">
+        <div class="controls">
+          <button type="submit" class="btn">Send</button>
+        </div>
+    </div>
+    
+<% end %>

data/app/views/feedback_mailer/feedback.text.erb

@@ -0,0 +1,23 @@
+** User **
+
+<%= @name %> <<%= @email %>>
+
+** User Comments **
+
+<%= @feedback %>
+
+** Citation **
+
+<%- if @umlaut_request -%>
+<%= brief_citation(@umlaut_request, :include_labels => true) %>
+<%= citation_identifiers(@umlaut_request) %>
+<%- if @umlaut_request.referent.permalinks.present? -%>
+Permalink: <%= url_for(:controller=>"store",        
+        :id=> @umlaut_request.referent.permalinks.first.id,
+        :only_path => false, :host => @host) %>
+
+Original Source: <%= @umlaut_request.referrer_id %>
+<%- end -%>
+<%- else -%>
+No citation supplied.
+<%- end -%>

data/app/views/layouts/umlaut.html.erb

@@ -14,6 +14,8 @@
       <%= render :partial => "umlaut/header" %>
 
       <div class="umlaut-main-container-fluid container-fluid <%= "umlaut-#{params[:controller]}-container" %>">
+        <%= render :partial => "umlaut/alerts" %>
+        
         <%= yield %>
       </div>
 

data/app/views/umlaut/_alerts.html.erb

@@ -0,0 +1,14 @@
+<%- 
+    text, css_class = nil, nil
+    [:alert_success, :alert_info, :alert_error].each do |key|
+        if flash[key]
+            text = flash[key]
+            css_class = key.to_s.parameterize
+        end
+    end
+-%>
+<% if text %>
+    <div class="alert <%= css_class %>">
+        <%= text %>
+    </div>
+<% end %>

data/lib/generators/templates/umlaut_services.yml

@@ -29,7 +29,14 @@ default:
         disabled: true
         display_name: Find It       
         base_url: YOUR_SFX_BASE_URL
-        priority: 3      
+        priority: 3
+
+      # blind link to price comparison site AllBooks.com. 
+      # just a blind link with no API pre-check, will be near
+      # instantaneous to calculate. 
+      AllBooksDotCom:
+        type: AllBooksDotCom
+        priority: 3
       
         
       # First half of Amazon, run in foreground, get metadata and cover images.
@@ -134,13 +141,6 @@ default:
         type: UlrichsLink
         priority: d
         
-      IsbnDb:
-        display_name: isbndb.com
-        disabled: true
-        type: IsbnDb
-        priority: d
-        access_key: YOUR_ISBNDB_ACCESS_KEY
-                
       EmailExport:
         type: EmailExport
         priority: d

data/lib/umlaut/routes.rb

@@ -31,7 +31,7 @@ module Umlaut
     end
 
     def default_route_sets
-      [:root, :permalinks, :a_z, :resolve, :open_search, :link_router, :export_email, :resources, :search, :javascript]
+      [:root, :permalinks, :a_z, :resolve, :open_search, :link_router, :export_email, :resources, :search, :javascript, :feedback]
     end
 
     module RouteSets
@@ -151,6 +151,13 @@ module Umlaut
           match 'images/spinner.gif' => redirect("/assets/spinner.gif")
         end
       end
+
+      def feedback
+        add_routes do |options|
+          get 'feedback(/:request_id)', :to => "feedback#new", :as => "feedback"
+          post 'feedback(/:request_id)' => 'feedback#create'
+        end
+      end
       
       def admin
         add_routes do |options|

data/lib/umlaut/version.rb

@@ -1,3 +1,3 @@
 module Umlaut
-  VERSION = "3.2.0"
+  VERSION = "3.3.0"
 end

data/test/functional/feedback_controller_test.rb

@@ -0,0 +1,59 @@
+require 'test_helper'
+ 
+class FeedbackControllerTest < ActionController::TestCase
+  setup do 
+    @umlaut_request = fake_umlaut_request("/resolve?sid=google&auinit=S&aulast=Madsbad&atitle=Mechanisms+of+changes+in+glucose+metabolism+and+bodyweight+after+bariatric+surgery&id=doi:10.1016/S2213-8587(13)70218-3&title=The+Lancet+Diabetes+%26+Endocrinology&volume=2&issue=2&date=2014&spage=152&issn=2213-8587")    
+    @umlaut_request.save!
+
+    FeedbackController.umlaut_config.feedback ||= Confstruct::Configuration.new
+    FeedbackController.umlaut_config.feedback.contacts ||= Confstruct::Configuration.new
+    FeedbackController.umlaut_config.feedback.contacts[:example] = Confstruct::Configuration.new(
+      :email_address => "librarian@example.org",
+      :label => "Librarian"
+    )
+  end
+
+  test "display feedback form" do
+    get :new, :contact_id => "example"
+    assert_response :success
+    assert_template "feedback/new"
+  end
+
+  test "send feedback" do
+    assert_difference 'ActionMailer::Base.deliveries.size', +1 do
+      post :create, :contact_id => 'example', :name => "Joe Example", :email => "joe@example.org", :feedback => "Some feedback", :request_id => @umlaut_request.id
+    end
+    email = ActionMailer::Base.deliveries.last
+
+    assert_equal ["librarian@example.org"], email.to
+    assert_equal ["joe@example.org"], email.reply_to
+    assert_include email.body, "Some feedback"
+
+    assert_present flash[:alert_success]
+
+    assert_redirected_to(:controller => "resolve", :action => "index", :'umlaut.request_id' => @umlaut_request.id)
+  end
+
+  test "#create raises error on missing contact_id email" do
+    assert_raise(FeedbackController::NoFeedbackEmailFoundException) do
+      post :create, :name => "Joe Example", :email => "joe@example.org", :feedback => "Some feedback", :request_id => @umlaut_request.id
+    end
+
+    assert_raise(FeedbackController::NoFeedbackEmailFoundException) do
+      post :create, :contact_id => "NO_SUCH_ID", :name => "Joe Example", :email => "joe@example.org", :feedback => "Some feedback", :request_id => @umlaut_request.id
+    end    
+  end
+
+  test "#new raises error on missing contact_id email" do
+    assert_raise(FeedbackController::NoFeedbackEmailFoundException) do
+      get :new
+    end
+
+    assert_raise(FeedbackController::NoFeedbackEmailFoundException) do
+      get :new, :contact_id => "NO_SUCH_ID"
+    end    
+  end
+  
+
+
+end

data/test/test_helper.rb

@@ -95,3 +95,16 @@ end
 def assert_length(size, list)
   assert_equal size, list.length, "Expected size of #{size} for #{list}"
 end
+
+
+# Methods you can use to make a mocked up Rails Request and corersponding Umlaut Request
+# Pass in a URL, absolute or partial, eg "/resolve?isbn=X"
+def fake_rails_request(umlaut_url)  
+  # hard to figure out how to mock a request, this seems to work
+  ActionController::TestRequest.new(Rack::MockRequest.env_for(umlaut_url))    
+end
+
+def fake_umlaut_request(umlaut_url)
+  rails_request = fake_rails_request(umlaut_url)
+  Request.find_or_create(rails_request.params, {}, rails_request)
+end

data/test/unit/feedback_mailer_test.rb

@@ -0,0 +1,57 @@
+
+
+require 'test_helper'
+ 
+class FeedbackMailerTest < ActionMailer::TestCase
+  setup do 
+    ActionMailer::Base.deliveries.clear
+
+    @host       = "umlaut.example.org"
+    @to_email   = "librarian@example.org"
+  end
+
+  test "feedback" do
+    umlaut_request = fake_umlaut_request("/resolve?sid=google&auinit=S&aulast=Madsbad&atitle=Mechanisms+of+changes+in+glucose+metabolism+and+bodyweight+after+bariatric+surgery&id=doi:10.1016/S2213-8587(13)70218-3&title=The+Lancet+Diabetes+%26+Endocrinology&volume=2&issue=2&date=2014&spage=152&issn=2213-8587")
+
+    feedback_name  = "Joe Example"
+    feedback_email = "joe@example.org"
+    feedback_text = "This is my feedback, yes it is"
+
+    email = FeedbackMailer.feedback(@host, @to_email, :umlaut_request => umlaut_request, :name => feedback_name, :email => feedback_email, :feedback => feedback_text).deliver
+
+    assert ActionMailer::Base.deliveries.present?
+    assert_equal [UmlautController.umlaut_config.from_email_addr], email.from
+    assert_equal [feedback_email],           email.reply_to
+    assert_equal [@to_email],       email.to
+    assert_equal "#{UmlautController.umlaut_config.app_name} Feedback: #{feedback_name}", email.subject
+
+    assert_includes email.body, feedback_text
+
+    assert_includes email.body, "#{feedback_name} <#{feedback_email}>"
+    # citation
+    assert_includes email.body, "Mechanisms of changes in glucose metabolism and bodyweight"
+    assert_includes email.body, "Madsbad"
+    assert_includes email.body, "The Lancet Diabetes & Endocrinology"
+    assert_includes email.body, "Published: 2014  Vol: 2  Iss: 2  p. 152"
+    assert_includes email.body, "ISSN: 22138587"
+    assert_includes email.body, "10.1016/S2213-8587(13)70218-3" # doi
+
+    assert_includes email.body, "Original Source: #{umlaut_request.referrer_id}"
+
+    # Permalink properly generated and included
+    assert_present umlaut_request.referent.permalinks
+    assert_includes email.body, "Permalink: http"
+  end
+
+  test "feedback with no umlaut_request" do
+    feedback_name  = "Joe Example"
+    feedback_email = "joe@example.org"
+    feedback_text = "This is my feedback, yes it is"
+
+    email = FeedbackMailer.feedback(@host, @to_email, :name => feedback_name, :email => feedback_email, :feedback => feedback_text).deliver
+    # just no raise is good enough for this test for now, mostly
+
+    assert_includes email.body, "No citation supplied"
+  end
+
+end