Merge branch 'development'

app/assets/javascripts/views/georeferences/geolocate/_geolocate_iframe.js

@@ -1,7 +1,7 @@
 function displayMessage(event) {
   message = undefined;
 
-  if (event.origin !== "http://www.museum.tulane.edu") {
+  if (event.origin !== "http://www.geo-locate.org") {
     message = "iframe url does not have permision to interact with me";
   }
   else {

app/controllers/alternate_values_controller.rb

@@ -15,8 +15,8 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @alternate_values = Queries::AlternateValue::Filter.new(params).all.limit(500)
-          .where(project_id: sessions_current_project_id).order(:id)
+        @alternate_values = Queries::AlternateValue::Filter.new(params).all
+          .where(project_id: sessions_current_project_id).page(param[:page]).per(500)
       }
     end
   end

app/controllers/citations_controller.rb

@@ -42,11 +42,11 @@ def create
     @citation = Citation.new(citation_params)
     respond_to do |format|
       if @citation.save
-        format.html { redirect_to url_for(@citation.citation_object.metamorphosize), notice: 'Citation was successfully created.' }
-        format.json { render :show, status: :created, location: @citation }
+        format.html {redirect_to url_for(@citation.citation_object.metamorphosize), notice: 'Citation was successfully created.'}
+        format.json {render :show, status: :created, location: @citation}
       else
         format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Citation was NOT successfully created.')}
-        format.json { render json: @citation.errors, status: :unprocessable_entity }
+        format.json {render json: @citation.errors, status: :unprocessable_entity}
       end
     end
   end
@@ -56,11 +56,11 @@ def create
   def update
     respond_to do |format|
       if @citation.update(citation_params)
-        format.html { redirect_to url_for(@citation.citation_object.metamorphosize), notice: 'Citation was successfully updated.' }
-        format.json { render :show, location: @citation }
+        format.html {redirect_to url_for(@citation.citation_object.metamorphosize), notice: 'Citation was successfully updated.'}
+        format.json {render :show, location: @citation}
       else
         format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Citation was NOT successfully updated.')}
-        format.json { render json: @citation.errors, status: :unprocessable_entity }
+        format.json {render json: @citation.errors, status: :unprocessable_entity}
       end
     end
   end
@@ -70,8 +70,13 @@ def update
   def destroy
     @citation.destroy
     respond_to do |format|
-      format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Citation was successfully destroyed.')}
-      format.json { head :no_content }
+      if @citation.destroyed?
+        format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Citation was successfully destroyed.')}
+        format.json {head :no_content}
+      else
+        format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Citation was not destroyed, ' + errors.messages)}
+        format.json {render json: @citation.errors, status: :unprocessable_entity}
+      end
     end
   end
 
@@ -112,8 +117,8 @@ def download
 
   def filter_params
     params.permit(
-      :citation_object_type, :citation_object_id, :source_id,
-      Citation.related_foreign_keys.map(&:to_sym)
+        :citation_object_type, :citation_object_id, :source_id,
+        Citation.related_foreign_keys.map(&:to_sym)
     ).merge(project_id: sessions_current_project_id)
   end
 
@@ -123,13 +128,13 @@ def set_citation
 
   def citation_params
     params.require(:citation).permit(
-      :citation_object_type, :citation_object_id, :source_id, :pages, :is_original,
-      :annotated_global_entity,
-      citation_topics_attributes: [
-        :id, :_destroy, :pages, :topic_id,
-        topic_attributes: [:id, :_destroy, :name, :definition]
-      ],
-      topics_attributes: [:name, :definition]
+        :citation_object_type, :citation_object_id, :source_id, :pages, :is_original,
+        :annotated_global_entity,
+        citation_topics_attributes: [
+            :id, :_destroy, :pages, :topic_id,
+            topic_attributes: [:id, :_destroy, :name, :definition]
+        ],
+        topics_attributes: [:name, :definition]
     )
   end
 end

app/controllers/confidences_controller.rb

@@ -13,12 +13,13 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @confidences = Queries::Confidence::Filter.new(params).all.limit(500)
-          .where(project_id: sessions_current_project_id)
+        @confidences = Queries::Confidence::Filter.new(filter_params).all
+          .where(project_id: sessions_current_project_id).page(params[:page]).per(500)
       }
     end
   end
 
+
   # GET /confidences/new
   def new
     @confidence_object = confidence_object
@@ -102,6 +103,13 @@ def set_confidence
     @confidence = Confidence.find(params[:id])
   end
 
+  def filter_params
+    params.permit(
+      :confidence_level_id, :object_global_id, :confidence_object_type, 
+      Confidence.related_foreign_keys.map(&:to_sym)
+    )
+  end
+
   def confidence_params
     params.require(:confidence).permit(
       :annotated_global_entity,

app/controllers/data_attributes_controller.rb

@@ -13,7 +13,7 @@ def index
       }
       format.json {
         @data_attributes = Queries::DataAttribute::Filter.new(params).all
-          .where(project_id: sessions_current_project_id).page(params[:page]).per(500)
+          .where(project_id: sessions_current_project_id).page(params[:page] || 1).per(500)
       }
     end
   end

app/controllers/notes_controller.rb

@@ -13,8 +13,8 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @notes = Queries::Note::Filter.new(params).all.limit(500)
-          .where(project_id: sessions_current_project_id)
+        @notes = Queries::Note::Filter.new(params).all
+        .where(project_id: sessions_current_project_id).page(param[:page]).per(500)
       }
     end
   end

app/controllers/otus_controller.rb

@@ -246,7 +246,8 @@ def filter_params
     params.permit(
       :taxon_name_id, :otu_id,
       biological_association_ids: [], taxon_name_ids: [], otu_ids: [],
-      taxon_name_classification_ids: [], taxon_name_relationship_ids: [], asserted_distribution_ids: []
+      taxon_name_relationship_ids: [],taxon_name_classification_ids: [],
+      asserted_distribution_ids: []
     )
   end
 

app/controllers/sources_controller.rb

@@ -187,16 +187,16 @@ def source_params
       :abstract, :copyright, :language, :stated_year, :verbatim,
       :bibtex_type, :day, :year, :isbn, :issn, :verbatim_contents,
       :verbatim_keywords, :language_id, :translator, :year_suffix, :url, :type,
-      roles_attributes:           [
-                                    :id,
-                                    :_destroy,
-                                    :type,
-                                    :person_id,
-                                    :position,
-                                    person_attributes: [
-                                                         :last_name, :first_name, :suffix, :prefix
-                                                       ]
-                                  ],
+      roles_attributes: [
+        :id,
+        :_destroy,
+        :type,
+        :person_id,
+        :position,
+        person_attributes: [
+          :last_name, :first_name, :suffix, :prefix
+        ]
+      ],
       project_sources_attributes: [:project_id]
     )
   end

app/controllers/tags_controller.rb

@@ -12,8 +12,8 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @tags = Queries::Tag::Filter.new(params).all.limit(500)
-          .where(project_id: sessions_current_project_id)
+        @tags = Queries::Tag::Filter.new(params).all.where(project_id: sessions_current_project_id).
+        page(param[:page]).per(500)
       }
     end
   end

app/controllers/tasks/nomenclature/by_source_controller.rb

@@ -2,13 +2,7 @@ class Tasks::Nomenclature::BySourceController < ApplicationController
   include TaskControllerConfiguration
 
   def index
-
-    if !ProjectSource.where(project_id: sessions_current_project_id).any?
-      flash[:notice] = 'Create or add a source to your project first.'
-      redirect_to sources_path and return
-    end
-
-    @source = Source.find(params[:id]) if !params[:id].blank?
-    @source ||= Project.find(sessions_current_project_id).project_sources.first.source
+    # @source = Source.find(params[:id]) unless params[:id].blank?
+    # @source ||= Project.find(sessions_current_project_id).project_sources.first.source
   end
 end

app/helpers/README.md

@@ -1,6 +1,5 @@
 
 
-
 Helper Descriptions
 ===================
 
@@ -9,6 +8,8 @@ See individual headers at https://github.com/SpeciesFileGroup/taxonworks/tree/ma
 Code Organization
 =================
 
+TODO: Go over patterns, clean up where no longer pertinent.
+
 ```Ruby
 class <Model>Helper 
 
@@ -29,30 +30,40 @@ class <Model>Helper
   # Exemplar data model helper methods 
   #    
 
-  #  Return a single line, ideally wrapped in a content_tag(:span, ... ) naming the instance.
-  def <model_name>_tag(model)
-    return nil if model.nil
-    # return some model.attribute of interpolated string of model attributes
+  #  Return a single line, ideally wrapped in a content_tag(:span, ... ) naming the instance. 
+  #  Often contains html.
+  def <model_name>_tag(object)
+    return nil if object.nil
+    # return some object.attribute of interpolated string of object attributes
   end
 
   #  Return a single line, ideally wrapped in a content_tag(:span, ... ) briefly naming the instance. 
-  def <model_name>_short_tag(model)
+  #  May contain html.
+  def <model_name>_short_tag(object)
   end
 
   #  Return one or more line, ideally wrapped in a content_tag(:div, ... ) detailing the instance.
-  def <model_name>_detailed_tag(model)
+  #  Rarely used at present.  Often contains html.
+  def <model_name>_detailed_tag(object)
   end
 
   # Return a link_to(model_path) using model_tag
-  def <model_name>_link(model)
+  def <model_name>_link(object)
   end
 
   # Return a link_to(model_path) using model_short_tag
-  def model_short_link(model)
+  def model_short_link(mobject)
+  end
+
+  # Return a content_tag(:li, <model>_tag(object))
+  def model_select_item(mobject)
   end
 
-  # Return a content_tag(:li, model_tag(model))
-  def model_select_item(model)
+  # Return a String
+  #  An equivalent to object_tag, but never with HTML!
+  #  Same as
+  #     label_for(object)
+  def label_for_<model>(object)
   end
 
 end

app/helpers/annotations_helper.rb

@@ -14,7 +14,8 @@ def annotations_summary_tag(object)
              data_attribute_list_tag(object), 
              note_list_tag(object), 
              tag_list_tag(object),
-             alternate_values_list_tag(object)
+             alternate_values_list_tag(object),
+             confidence_list_tag(object)
           ].compact.join.html_safe, class: :annotations_summary_list, 'data-annotator-list-object-id' => object.id)
 
         end

app/helpers/confidences_helper.rb

@@ -7,7 +7,22 @@ def confidence_tag(confidence)
 
   def confidence_link(confidence)
     return nil if confidence.nil?
-    link_to(confidence_tag(confidence), confidence)
+    link_to(confidence_tag(confidence), confidence.confidence_object.metamorphosize)
+  end
+
+  # @return [String (html), nil]
+  #    a ul/li of tags for the object
+  def confidence_list_tag(object)
+    return nil unless object.has_confidences? && object.confidences.any?
+    content_tag(:h3, 'Confidences') +
+      content_tag(:ul, class: 'annotations__confidences_list') do
+      object.confidences.collect { |a| content_tag(:li, confidence_tag(a)) }.join.html_safe
+    end
+  end
+
+  def confidence_annotation_confidence(confidence)
+    return nil if confidence.nil?
+    content_tag(:span, controlled_vocabulary_term_tag(confidence.confidence_level), class: [:annotation__confidence])
   end
 
   def confidences_search_form

app/helpers/otus_helper.rb

@@ -21,6 +21,13 @@ def otu_link(otu)
     link_to(otu_tag(otu).html_safe, otu)
   end
 
+  def label_for_otu(otu)
+    return nil if otu.nil?
+    [otu.name, 
+     label_for_taxon_name(otu.taxon_name)
+    ].compact.join(': ')
+  end
+
   def otus_search_form
     render('/otus/quick_search_form')
   end

app/helpers/taxon_names_helper.rb

@@ -8,6 +8,11 @@ def taxon_name_tag(taxon_name)
     taxon_name.cached_html.try(:html_safe) || taxon_name.name
   end
 
+  def label_for_taxon_name(taxon_name)
+    return nil if taxon_name.nil?
+    [taxon_name.cached, taxon_name.cached_author_year].compact.join(' ') 
+  end
+
   def taxon_name_autocomplete_tag(taxon_name, term)
     return nil if taxon_name.nil?
     klass = taxon_name.rank_class ? taxon_name.rank_class.nomenclatural_code : nil

app/helpers/workbench/display_helper.rb

@@ -1,6 +1,10 @@
 # Generic wrappers around AR instances, these should not include link generation, but may call out to other helpers that do generate links. 
+# See /app/helpers/README.md for more.
 #
 module Workbench::DisplayHelper
+
+
+
   # General wrapper around individual <model_name>_tag methods
   #   object_tag(@otu) 
   def object_tag(object)
@@ -31,6 +35,34 @@ def object_tag_method(object)
     end
   end
 
+  # General wrapper around individual <model_name>_tag methods
+  #   label_for(@otu) 
+  def label_for(object)
+    return nil if object.nil?
+    method = label_for_method(object)
+
+    if self.respond_to?(method)
+      string = send(method, object)
+      return string if string
+    else
+      nil 
+    end
+  end
+
+  def label_for_method(object)
+    return nil if object.nil?
+    klass_name = object.class.name
+    method = "label_for_#{klass_name.underscore.gsub('/', '_')}"
+    if ApplicationController.helpers.respond_to?(method)
+      method
+    else
+      klass_name = metamorphosize_if(object).class.name
+      "label_for_#{klass_name.underscore}"
+    end
+  end
+
+
+
   def model_name_title
     controller_name.humanize
   end

app/javascript/packs/application.js

@@ -21,10 +21,10 @@ require('../vue/browse_annotations/main.js')
 require('../vue/tasks/descriptor/main.js')
 require('../vue/tasks/new_matrix/main.js')
 require('../vue/tasks/clipboard/main.js')
-require('../vue/tasks/digitize/main.js')
 require('../vue/tasks/uniquify/people/main.js')
 require('../vue/tasks/uniquify/sources/main.js')
 require('../vue/tasks/single_bibtex_source/main.js')
+require('../vue/tasks/nomenclature/by_source/main.js')
 
 // Styles
 require('../style/application.scss')