Merge branch 'development'

SpeciesFileGroup · Oct 11, 2022 · e1c859e · e1c859e
2 parents cab796c + f27b57a
commit e1c859e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,19 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.29.5] - 2022-10-10
+
+### Changed
+- Changed author labels on Filter source [#3134]
+- Minor changes to plots on administration activity dashboard 
+- Parallelize some indexing rake tasks
+
+### Fixed
+- Recent and Quick list are empty on Citation annotator [#3133]
+
+[#3133]: https://github.com/SpeciesFileGroup/taxonworks/issues/3133
+[#3134]: https://github.com/SpeciesFileGroup/taxonworks/issues/3134
+
 ## [0.29.4] - 2022-10-07
 ### Added
 - Distribution, Material Examined sections, and zip download for paper catalog [#3098]
@@ -16,7 +29,6 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Previous and next links in Matrix row coder [#3107]
 - Match identifiers facet to Filter extract task  [#3089]
 - `Clone previous citation` to citation panels [#3097]
-- Populate column button for Matrix Column Coder [#3117]
 - `scientificName` is now implied in `typeStatus` when only the type of type is specified in DwC occurrences importer
 - Additional DwC classification terms [#3118]
 
@@ -2966,7 +2978,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.4...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...development
+[0.29.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.4...v0.29.5
 [0.29.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.3...v0.29.4
 [0.29.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.2...v0.29.3
 [0.29.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.1...v0.29.2

diff --git a/Gemfile b/Gemfile
@@ -134,6 +134,10 @@ gem 'asciidoctor', '~> 2.0'
 # www
 gem 'wikidata-client', '~> 0.1.0.pre.rc1', require: 'wikidata'
 
+# Maintenance
+gem 'parallel', '~> 1.22'
+gem 'ruby-progressbar', '~> 1.11'
+
 group :test, :development do
   gem 'faker', '~> 2.10'
   gem 'rspec-rails', '~> 5.0'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -696,6 +696,7 @@ DEPENDENCIES
   paper_trail (~> 12.0)
   paperclip!
   paperclip-meta (~> 3.0)
+  parallel (~> 1.22)
   parallel_tests
   passenger (~> 6.0.2)
   pdf-reader (~> 2.2)
@@ -733,6 +734,7 @@ DEPENDENCIES
   rubocop-rspec (~> 2.6)
   ruby-graphviz (~> 1.2.5)
   ruby-prof (~> 1.2)
+  ruby-progressbar (~> 1.11)
   ruby-units (~> 2.3.0)
   rubyzip (~> 2.3.0)
   sassc-rails (~> 2.1.0)

diff --git a/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue b/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue
@@ -2,6 +2,7 @@
   <div class="citation_annotator">
     <FormCitation
       v-model="citation"
+      :klass="objectType"
       :submit-button="{
         label: 'Save',
         color: 'create'

diff --git a/app/javascript/vue/tasks/sources/filter/components/filters/authors.vue b/app/javascript/vue/tasks/sources/filter/components/filters/authors.vue
@@ -2,7 +2,7 @@
   <div>
     <h3>Authors</h3>
     <div class="field label-above">
-      <label>Author</label>
+      <label>Author as text string</label>
       <input
         type="text"
         class="full_width"
@@ -15,7 +15,7 @@
       </label>
     </div>
     <fieldset>
-      <legend>Authors</legend>
+      <legend>Author as role</legend>
       <smart-selector
         model="people"
         target="Author"

diff --git a/app/models/taxon_name_relationship/iczn/invalidating/homonym/secondary/secondary_1961.rb b/app/models/taxon_name_relationship/iczn/invalidating/homonym/secondary/secondary_1961.rb
@@ -54,4 +54,8 @@ def sv_specific_relationship
     true
   end
 
+  def sv_not_specific_relationship
+    true
+  end
+
 end
diff --git a/app/views/administration/_users_past_day.html.erb b/app/views/administration/_users_past_day.html.erb
@@ -0,0 +1,66 @@
+<div class="panel content">
+  <h2> Activity of past 24 hours</h2>
+
+  <% d = User.where('last_seen_at > ?', 1.day.ago).group_by_hour_of_day(:last_seen_at, format: "%H").count.sort.collect{|a,b| b} %><br>
+
+  <div style="height: 280px; width: 420px;">
+    <canvas id="myChart"></canvas>
+  </div>
+</div>
+
+<script>
+  const ctx = document.getElementById('myChart');
+  const myChart = new Chart(ctx, {
+    type: 'polarArea',
+
+    data:  {
+      labels: [<%= (1..24).collect{|t| ('"' + t.to_s + '"').html_safe}.join(', ').html_safe %>],
+      datasets: [{
+        label: 'Users in past 24 hours',
+        data: <%= d %> ,
+        backgroundColor: [
+          'rgb(250, 250, 110)',
+          'rgb(228, 245, 112)',
+          'rgb(207, 239, 114)',
+          'rgb(187, 234, 118)',
+          'rgb(167, 227, 121)',
+          'rgb(148, 220, 125)',
+          'rgb(130, 213, 129)',
+          'rgb(112, 206, 133)',
+          'rgb(94, 198, 136)',
+          'rgb(77, 190, 139)',
+          'rgb(61, 182, 141)',
+          'rgb(44, 174, 143)',
+          'rgb(26, 165, 143)',
+          'rgb(2, 157, 143)',
+          'rgb(0, 148, 142)',
+          'rgb(0, 140, 139)',
+          'rgb(0, 131, 136)',
+          'rgb(0, 122, 132)',
+          'rgb(10, 114, 126)',
+          'rgb(22, 105, 120)',
+          'rgb(30, 97, 113)',
+          'rgb(36, 88, 105)',
+          'rgb(40, 80, 97)',
+          'rgb(42, 72, 88)']
+      }]
+    },
+    options: {
+      responsibe: true,
+      maintainAspectRatio: false,
+      plugins: {
+        legend: {
+          position: 'left',
+          title: {
+            text: 'Hours ago',
+            display: true,
+          }
+        },
+        title: {
+          display: false,
+        }
+      }
+    },
+  });
+</script>
+
diff --git a/app/views/administration/user_activity.html.erb b/app/views/administration/user_activity.html.erb
@@ -6,8 +6,9 @@
 
 <%= link_to 'Back', administration_path() %>
 
-<div class="flexbox">
-  <div class="item item1">
+<div class="flexbox separate-bottom">
+
+  <div class="panel content separate-left">
     <h2> Last 20 logins </h2>
     <ol>
       <% User.limit(20).order(current_sign_in_at: :desc).where('current_sign_in_at IS NOT NULL').each do |u| -%>
@@ -16,7 +17,7 @@
     </ol>
   </div>
 
-  <div class="item item2">
+  <div class="panel content separate-left">
     <h2> Recently seen </h2>
     <ol>
       <% User.limit(20).order(last_seen_at: :desc).where('last_seen_at IS NOT NULL').each do |u| -%>
@@ -25,7 +26,8 @@
     </ol>
   </div>
 
-  <div class="item item3">
+
+  <div class="panel content separate-left">
     <h2> Most active </h2>
     <p> Estimate. If sequential requests are less than 5 minutes appart time between requests is summed to total. <p>
     <ol>
@@ -38,41 +40,39 @@
 </div>
 
 <div class="simple_flexbox">
-  <div>
-    <h2> Activity today by hour</h2>
-    <p> For the past 24 hrs. Hours are UTC.</p>
-    <%= pie_chart User.where('last_seen_at > ?', 1.day.ago).group_by_hour(:last_seen_at, format: "%H").count.sort, discrete: true %>
+  <% days = ['Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat', 'Sun'] %>
+
+  <div class="panel content">
+    <h2> Active users in past </h2>
+    <ul>
+      <li> 24 hours: <%= tag.strong User.where('last_seen_at > ?', 24.hours.ago).count %></li>
+      <li> Week: <%= tag.strong User.where('last_seen_at > ?', 1.week.ago).count %></li>
+      <li> Month: <%= tag.strong User.where('last_seen_at > ?', 1.month.ago).count %></li>
+      <li> Half year: <%= tag.strong User.where('last_seen_at > ?', 6.months.ago).count %></li>
+      <li> Year: <%= tag.strong User.where('last_seen_at > ?', 1.year.ago).count %></li>
+      <li> 3 Years: <%= tag.strong User.where('last_seen_at > ?', 3.years.ago).count %></li>
+      <li> All time: <%= tag.strong User.where('last_seen_at > ?', 1000.years.ago).count %></li>
+    </ul>
   </div>
 
-  <div>
+  <%= render partial: 'users_past_day' %>
+
+  <div class="panel content">
     <h2> Last seen - past week </h2>
-    <% data = User.where('last_seen_at > ?', 1.week.ago).group_by_day_of_week(:last_seen_at, format: "%a").count %>
+    <% data = User.where('last_seen_at > ?', 1.week.ago).group_by_day_of_week(:last_seen_at, format: "%a").count  %>
     <p><%= data.values.sum %> users were seen last week.</p>
-    <%= column_chart data, discrete: true, ytitle: 'Count', xtitle: 'Last seen day', width: '400px' %>
-  </div>
-
-  <div>
-    <h2> All time user activity activity by last seen at per week </h2>
-    <p> This describes when all users were <em>last</em> active across all time. </p>
-    <%= column_chart User.group_by_day(:last_seen_at, format: "%a").count, xtitle: 'Day', ytitle: 'Number of users', width: '400px' %>
+    <%= column_chart data.to_a.sort{|a,b| days.index(a[0]) <=> days.index(b[0]) }, discrete: true, ytitle: 'Count', xtitle: 'Last seen day', width: '400px' %>
   </div>
 </div>
 
-<div class="flexbox">
-  <div class="item item1">
+  <div class="panel content separate-top">
     <h2> Users per project</h2>
     <%= column_chart Project.joins(:users).group(:id).count.to_a.collect{|a,b| [Project.find(a).name, b] }.sort_by(&:second).reverse!, xtitle: 'Project', ytitle: 'Number of users', discrete: true, height: '400px' %>
   </div>
-</div>
 
-<div class="flexbox">
-  <div class="item item1">
+  <div class="panel content separate-top">
     <h2> Estimated activity per project </h2>
     <p>Important: this plot is an estimate based on user activity.  Active users in multiple projects will skew this estimate as their toal activity throughout is added to both projects. </p>
     <%= column_chart Project.joins(:users).where('last_seen_at > ?', 1.week.ago).group(:id).sum(:time_active).to_a.collect{|a,b| [Project.find(a).name, (b.to_f / 3600.0).round(0) ]}.sort_by(&:second).reverse!, xtitle: 'Project', ytitle: 'Time active (hours)', discrete: true, height: '400px' %>
-  </div>
 </div>
 
-
-
-
diff --git a/lib/tasks/maintenance/collecting_events.rake b/lib/tasks/maintenance/collecting_events.rake
@@ -2,6 +2,40 @@ namespace :tw do
   namespace :maintenance do
     namespace :collecting_events do
 
+      #  # Removed from CollectingEvent
+      #  # @return [Boolean] always true
+      #  #   A development method only. Attempts to create a verbatim georeference for every
+      #  #   collecting event record that doesn't have one.
+      #  #   TODO: this needs to be in a curate rake task or somewhere else
+      #  def self.update_verbatim_georeferences
+      #    if Rails.env == 'production'
+      #      puts "You can't run this in #{Rails.env} mode."
+      #      exit
+      #    end
+
+      #    passed = 0
+      #    failed = 0
+      #    attempted = 0
+
+      #    CollectingEvent.includes(:georeferences).where(georeferences: {id: nil}).each do |c|
+      #      next if c.verbatim_latitude.blank? || c.verbatim_longitude.blank?
+      #      attempted += 1
+      #      g = c.generate_verbatim_data_georeference(true)
+      #      if g.errors.empty?
+      #        passed += 1
+      #        puts "created for #{c.id}"
+      #      else
+      #        failed += 1
+      #        puts "failed for #{c.id}, #{g.errors.full_messages.join('; ')}"
+      #      end
+      #    end
+      #    puts "passed: #{passed}"
+      #    puts "failed: #{failed}"
+      #    puts "attempted: #{attempted}"
+      #    true
+      #  end
+
+      # export PARALLEL_PROCESSOR_COUNT=2 && rake tw:maintenance:collecting_events:tested_reindex_geographic_name_cached_values
       desc 'check cached geographic names and re-indx where ncessary'
       task tested_reindex_geographic_name_cached_values: [:environment] do |t|
         updated = 0
-Original file line number
+Diff line change
@@ Expand Up / @@ -54,4 +54,8 @@ def sv_specific_relationship @@
         true
       end
+      def sv_not_specific_relationship
+        true
+      end
     end