Updated biodiversity custom gem

.travis.yml

@@ -28,7 +28,7 @@ jobs:
       bundler_args: --without development production
       addons:
         postgresql: "10"
-        firefox: "79.0"
+        firefox: "latest"
         apt:
           packages:
             - imagemagick

CHANGELOG.md

@@ -7,7 +7,34 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
-\-
+### Added
+- Added `rake tw:maintenance:otus:missplaced_references` [#1439]
+- Spinner for when converting verbatim to bibtex [#1710]
+
+### Changed
+- Methods that write to cached should not fire callbacks, potential for [#1701]
+- Using custom geckodriver-helper for Firefox 80 support
+
+## Fixed
+- Serial multiple updates did not update bibtex author field [#1709]
+- Fix (likely) for pinboard items failing to remove [#1690]
+- Better response for failed collecting event cloning [#1705]
+- Cleaned up deprecated biological associations graph autcomplete [#1707]
+- Colliding `namespace` method for identifiers breaks identifiers list [#1702]
+- Graceful failed serial destroy response [#1703]
+- Restored Show -> edit link [#1699]
+
+
+[#1439]: https://github.com/SpeciesFileGroup/taxonworks/issues/1439
+[#1709]: https://github.com/SpeciesFileGroup/taxonworks/issues/1709
+[#1690]: https://github.com/SpeciesFileGroup/taxonworks/issues/1690
+[#1701]: https://github.com/SpeciesFileGroup/taxonworks/issues/1701
+[#1705]: https://github.com/SpeciesFileGroup/taxonworks/issues/1705
+[#1707]: https://github.com/SpeciesFileGroup/taxonworks/issues/1707
+[#1702]: https://github.com/SpeciesFileGroup/taxonworks/issues/1702
+[#1703]: https://github.com/SpeciesFileGroup/taxonworks/issues/1703
+[#1699]: https://github.com/SpeciesFileGroup/taxonworks/issues/1699
+[#1710]: https://github.com/SpeciesFileGroup/taxonworks/issues/1710
 
 ## [0.12.17] - 2020-02-02
 
@@ -30,7 +57,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Removed limit of download bibtex on filter source [#1683]
 - Disable/enable destroy button from metadata on radial navigator [#1696]
 
-#### Fixed
+### Fixed
 - Non admins not able to destroy shared data [#1098]
 - Pending confirmation: Include original combinations in CoLDP [#1204] 
 - Pending confirmation: Include forma/variety properly in CoLDP [#1203] 

Gemfile

@@ -123,7 +123,7 @@ group :test, :development do
   gem 'byebug', '~> 11.1', {}.merge(ENV['RM_INFO'] ? {require: false} : {})
   gem 'factory_bot_rails', '~> 5.1', '>= 5.1.1'
   gem 'selenium-webdriver', '~> 3.141'
-  gem 'geckodriver-helper', '~> 0.24.0'
+  gem 'geckodriver-helper', github: 'LocoDelAssembly/geckodriver-helper'
   gem 'prawn', '~> 2.2.2'
 end
 

Gemfile.lock

@@ -9,11 +9,18 @@ GIT
 
 GIT
   remote: https://github.com/LocoDelAssembly/biodiversity.git
-  revision: 555d1706f3603f4945b14009e2e0f6f3b57d5c6c
+  revision: 77406b3cf9b40cc08aacb2d5aeecf5997f19abde
   branch: ipc-mode
   specs:
     biodiversity (4.1.0)
 
+GIT
+  remote: https://github.com/LocoDelAssembly/geckodriver-helper.git
+  revision: 8cb32dde4b152250ad053aab7432b151d11dddf9
+  specs:
+    geckodriver-helper (0.27.0)
+      archive-zip (~> 0.7)
+
 GIT
   remote: https://github.com/james2m/seedbank
   revision: 58d19b0c5c2afd139b3d395f2a516dd399eef57b
@@ -182,8 +189,6 @@ GEM
     ffi-geos (2.1.0)
       ffi (>= 1.0.0)
     formatador (0.2.5)
-    geckodriver-helper (0.24.0)
-      archive-zip (~> 0.7)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
     gnfinder (0.11.0)
@@ -589,7 +594,7 @@ DEPENDENCIES
   factory_bot_rails (~> 5.1, >= 5.1.1)
   faker (~> 2.10)
   ffi-geos (~> 2.1.0)
-  geckodriver-helper (~> 0.24.0)
+  geckodriver-helper!
   gnfinder (~> 0.11.0)
   google-protobuf (~> 3.12.0.rc.1)
   gpx (~> 1.0.0)

app/controllers/biological_associations_controller.rb

@@ -20,7 +20,7 @@ def index
       }
     end
   end
- 
+
   # GET /biological_associations/1
   # GET /biological_associations/1.json
   def show
@@ -88,13 +88,13 @@ def search
   end
 
   private
-  
+
   def filter_params
     params.permit(:subject_global_id, :object_global_id, :any_global_id, :biological_relationship_id)
 
     # Shallow resource hack
     if !params[:collection_object_id].blank? && c = CollectionObject.where(project_id: sessions_current_project_id).find(params[:collection_object_id])
-       params[:any_global_id] = c.to_global_id.to_s 
+      params[:any_global_id] = c.to_global_id.to_s
     end
     params
   end

app/controllers/biological_associations_graphs_controller.rb

@@ -76,22 +76,7 @@ def search
       redirect_to biological_association_graph_path(params[:id])
     end
   end
-
-  def autocomplete
-    @biological_associations_graphs = BiologicalAssociationsGraph.find_for_autocomplete(params.merge(project_id: sessions_current_project_id))
-    data = @biological_associations_graphs.collect do |t|
-      {id: t.id,
-       label: ApplicationController.helpers.biological_associations_graph_tag(t),
-       response_values: {
-           params[:method] => t.id
-       },
-       label_html: ApplicationController.helpers.biological_associations_graph_autocomplete_selected_tag(t)
-      }
-    end
-
-    render json: data
-  end
-
+
   private
 
   def set_biological_associations_graph

app/controllers/collecting_events_controller.rb

@@ -50,9 +50,14 @@ def create
   # POST /collecting_events/1/clone.json
   def clone
     @collecting_event = @collecting_event.clone
-    respond_to do |format|
-      format.html { redirect_to edit_collecting_event_path(@collecting_event), notice: 'Clone successful, on new record.' }
-      format.json { render :show }
+    if @collecting_event.persisted?
+      respond_to do |format|
+        format.html { redirect_to edit_collecting_event_path(@collecting_event), notice: 'Clone successful, on new record.' }
+        format.json { render :show }
+      end
+    else
+      format.html { redirect_to edit_collecting_event_path(@collecting_event), notice: 'Failed to clone the collecting event..' }
+      format.json {render json: @collecting_event.errors, status: :unprocessable_entity}
     end
   end
 

app/controllers/hub_controller.rb

@@ -22,6 +22,7 @@ def order_tabs
   end
 
   def update_tab_order
+    # TODO: update_column likely 
     @sessions_current_user.update_attribute(:hub_tab_order, params[:order])
     head :ok
   end
@@ -32,6 +33,7 @@ def handle_bad_tab_order
     # This is preventative only, it should never happen in real data, and may only occur when 
     # we reset tab performance.
     if @sessions_current_user.hub_tab_order.empty?
+      # TODO: update_column likely
       @sessions_current_user.update_attribute(:hub_tab_order, DEFAULT_HUB_TAB_ORDER)
     end
     true

app/controllers/serials_controller.rb

@@ -20,14 +20,6 @@ def index
     end
   end
 
-  def filter_params
-    params.permit(
-        :name, :id,
-        data_attributes_attributes: [ :id, :_destroy, :controlled_vocabulary_term_id, :type, :attribute_subject_id, :attribute_subject_type, :value ]
-    )
-  end
-
-
   def list
     @serials = Serial.order(:id).page(params[:page])
   end
@@ -80,10 +72,15 @@ def update
   # DELETE /serials/1
   # DELETE /serials/1.json
   def destroy
-    @serial.destroy!
+    @serial.destroy
     respond_to do |format|
-      format.html { redirect_to serials_url }
-      format.json { head :no_content }
+      if @serial.destroyed?
+        format.html { redirect_to serials_url }
+        format.json { head :no_content }
+      else
+        format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'Serial was not destroyed, ' + @serial.errors.full_messages.join('; '))}
+        format.json {render json: @serial.errors, status: :unprocessable_entity}
+      end
     end
   end
 
@@ -120,6 +117,19 @@ def download
 
   private
 
+  def filter_params
+    params.permit(
+      :name, :id,
+      data_attributes_attributes: [
+        :id,
+        :_destroy,
+        :controlled_vocabulary_term_id,
+        :type,
+        :attribute_subject_id,
+        :attribute_subject_type,
+        :value ])
+  end
+
   def set_serial
     @serial = Serial.find(params[:id])
     @recent_object = @serial

app/helpers/biological_associations_graphs_helper.rb

@@ -10,8 +10,4 @@ def biological_associations_graph_link(biological_associations_graph)
     link_to(biological_associations_graph_tag(biological_associations_graph).html_safe, biological_associations_graph)
   end
 
-  def biological_associations_graphs_search_form
-    render('/biological_associations_graphs/quick_search_form')
-  end
-
 end

app/helpers/namespaces_helper.rb

@@ -33,14 +33,6 @@ def namespaces_search_form
     render('/namespaces/quick_search_form')
   end
 
-  def namespace_from_identifier_tag(identifier)
-    if identifier.respond_to?(:namespace)
-      namespace_tag(identifier.namespace)
-    else
-      nil
-    end
-  end
-
   def namespace_select_tag(namespace_element)
     select_tag(namespace_element,
                options_for_select(Namespace.pluck(:short_name).uniq),

app/helpers/workbench/navigation_helper.rb

@@ -1,6 +1,10 @@
 # Methods for 1) generating paths; or 2) generating links.
 module Workbench::NavigationHelper
-  NO_NEW_FORMS = %w{Confidence Attribution ObservationMatrixRow ObservationMatrixColumn Note Tag Citation Identifier DataAttribute AlternateValue GeographicArea ContainerItem ProtocolRelationship Download}.freeze
+
+  NO_NEW_FORMS = %w{Confidence Attribution ObservationMatrixRow ObservationMatrixColumn Note Tag
+  Citation Identifier DataAttribute AlternateValue
+  GeographicArea ContainerItem ProtocolRelationship Download}.freeze
+
   NOT_DATA_PATHS = %w{/project /administration /user}.freeze
 
   # Slideout panels

app/javascript/vue/tasks/sources/new_source/app.vue

@@ -110,13 +110,19 @@
     <bibtex-button
       v-if="showBibtex"
       @close="showBibtex = false"/>
+    <spinner-component
+      v-if="settings.isConverting"
+      :full-screen="true"
+      :logo-size="{ width: '100px', height: '100px'}"
+      legend="Converting verbatim to BiBTeX..."/>
   </div>
 </template>
 
 <script>
 
 import SourceType from './components/sourceType'
 import RecentComponent from './components/recent'
+import SpinnerComponent from 'components/spinner'
 
 import CrossRef from './components/crossRef'
 import BibtexButton from './components/bibtex'
@@ -153,7 +159,8 @@ export default {
     BibtexButton,
     AddSource,
     NavBar,
-    RecentComponent
+    RecentComponent,
+    SpinnerComponent
   },
   computed: {
     section () {

app/javascript/vue/tasks/sources/new_source/store/actions/convertToBibtex.js

@@ -4,7 +4,7 @@ import { UpdateSource, LoadSoftValidation } from '../../request/resources'
 import setParam from 'helpers/setParam'
 
 export default ({ state, commit }) => {
-  state.settings.saving = true
+  state.settings.isConverting = true
   if (state.source.id) {
     UpdateSource({ id: state.source.id, convert_to_bibtex: true }).then(response => {
       if (response.body.type === 'Source::Bibtex') {
@@ -13,8 +13,9 @@ export default ({ state, commit }) => {
       } else {
         TW.workbench.alert.create('Source needs to be converted manually', 'error')
       }
+      state.settings.isConverting = false
     }, () => {
-      state.settings.saving = false
+      state.settings.isConverting = false
     })
   }
 

app/javascript/vue/tasks/sources/new_source/store/store.js

@@ -13,6 +13,7 @@ function makeInitialState () {
   return {
     settings: {
       saving: false,
+      isConverting: false,
       loading: false,
       lastSave: 0,
       lastEdit: 0,

app/models/biological_associations_graph.rb

@@ -16,8 +16,4 @@ class BiologicalAssociationsGraph < ApplicationRecord
   has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_associations_graph
   has_many :biological_associations, through: :biological_associations_biological_associations_graphs
 
-  def self.find_for_autocomplete(params)
-    Queries::BiologicalAssociationsGraphAutocompleteQuery.new(params[:term]).all.where(project_id: params[:project_id])
-  end
-
 end

app/models/citation.rb

@@ -119,11 +119,7 @@ def reject_topic(attributed)
 
   def update_related_cached_values
     if citation_object_type == 'TaxonName'
-      t = citation_object
-      if t.id
-        taxon = TaxonName.find(t.id)
-        taxon.update_attribute(:cached_author_year, citation_object.get_author_and_year)
-      end
+      citation_object.update_column(:cached_author_year, citation_object.get_author_and_year)  if citation_object.persisted?
     end
     true
   end

app/models/collecting_event.rb

@@ -1075,7 +1075,8 @@ def cached_level0_name
     cache_geographic_names[:state]
   end
 
-  # @return [CollectingEvent instance]
+  # @return [CollectingEvent]
+  #   the instance may not be valid!
   def clone
     a = dup
     a.verbatim_label = [verbatim_label, "[CLONED FROM #{id}", "at #{Time.now}]"].compact.join(' ')
@@ -1092,11 +1093,7 @@ def clone
       end
     end
 
-    begin
-      a.save!
-    rescue ActiveRecord::RecordInvalid
-      return false
-    end
+    a.save
     a
   end
 

app/models/concerns/shared/is_data.rb

@@ -122,7 +122,7 @@ def is_editable?(user)
   end
 
   def is_in_users_projects?(user)
-    user.projects.where(id: created_by_id).any?
+    user.projects.pluck(:id).include?(project_id)
   end
 
   # @return [Boolean]