Merge tag 'v0.12.17' into production-debug

CHANGELOG.md

@@ -9,6 +9,51 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.12.17] - 2020-02-02
+
+### Added
+- Successfull source destroy message 
+- Pending - Definition field to BiologicalRelationship model and views [#1672]
+- New button to (attempt to) convert verbatim sources to Bibtex via Crossref
+- Model methods and attribute to change Source Verbatim to Bibtex [#1673]
+- DOMPurify package to sanitize html
+- List all Keyword and Topics in smart selector on filter source [#1675]
+- Added data links tool in markdown editor (Ctrl/Alt-Shift-L) [#1674]
+- Definition field on composer biological relationship task [#1672]
+
+### Changed
+- Unified can_destroy/edit methods
+- Improved Source autocomplete with metadata/markup [#1681]
+- Changed CoLDP download to use Catalog::Nomenclature as name source
+- Replace SimpleMDE for EasyMDE
+- Sort alphabetically bibliography style list on filter source
+- Removed limit of download bibtex on filter source [#1683]
+- Disable/enable destroy button from metadata on radial navigator [#1696]
+
+#### 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] 
+- Docker: Fixed path typo on clean up command
+- Tag button on filter source [#1692]
+- Overflow in taxon names list in new taxon name [#1688]
+- Confidence button overlapped in new combination [#1687]
+
+[#1098]: https://github.com/SpeciesFileGroup/taxonworks/issues/1098 
+[#1672]: https://github.com/SpeciesFileGroup/taxonworks/issues/1672
+[#1673]: https://github.com/SpeciesFileGroup/taxonworks/issues/1673
+[#1674]: https://github.com/SpeciesFileGroup/taxonworks/issues/1674
+[#1681]: https://github.com/SpeciesFileGroup/taxonworks/issues/1681
+[#1203]: https://github.com/SpeciesFileGroup/taxonworks/issues/1203
+[#1204]: https://github.com/SpeciesFileGroup/taxonworks/issues/1204
+[#1672]: https://github.com/SpeciesFileGroup/taxonworks/issues/1672
+[#1675]: https://github.com/SpeciesFileGroup/taxonworks/issues/1675
+[#1683]: https://github.com/SpeciesFileGroup/taxonworks/issues/1683
+[#1687]: https://github.com/SpeciesFileGroup/taxonworks/issues/1687
+[#1688]: https://github.com/SpeciesFileGroup/taxonworks/issues/1688
+[#1692]: https://github.com/SpeciesFileGroup/taxonworks/issues/1692
+[#1696]: https://github.com/SpeciesFileGroup/taxonworks/issues/1696
+
 ## [0.12.16] - 2020-08-24
 
 ### Added
@@ -373,7 +418,8 @@ 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/v0.12.16...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.17...development
+[0.12.17]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.16...v0.12.17
 [0.12.16]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.15...v0.12.16
 [0.12.15]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.14...v0.12.15
 [0.12.14]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.13...v0.12.14

Dockerfile

@@ -28,7 +28,7 @@ RUN apt-get update && \
       nodejs \
       redis-server libhiredis-dev && \
       apt clean && \ 
-      rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/*
+      rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 RUN locale-gen en_US.UTF-8
 

Dockerfile.development

@@ -6,7 +6,7 @@ ARG BUNDLER_WORKERS=1
 RUN apt-get update && \
     apt-get install -y curl software-properties-common apt-transport-https && \
     apt clean && \
-    rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/*
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Update repos
 RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
@@ -28,7 +28,7 @@ RUN apt-get update && \
                        zip \
                        nodejs && \
                        apt clean && \
-                       rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/*
+                       rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Install Firefox (for headless feature tests)
 RUN curl -sL 'https://download.mozilla.org/?product=firefox-latest&lang=en-US&os=linux64' | \

app/assets/stylesheets/base/dimensions.scss

@@ -22,6 +22,10 @@ $viewport_width: 1024px;
   width: 100%;
 }
 
+.width-auto {
+  width: auto !important;
+}
+
 .one_tenth_width {
   width: 10%;
 }

app/controllers/biological_relationships_controller.rb

@@ -103,7 +103,7 @@ def set_biological_relationship
 
   def biological_relationship_params
     params.require(:biological_relationship).permit(
-      :name, :inverted_name, :is_transitive, :is_reflexive, 
+      :name, :inverted_name, :is_transitive, :is_reflexive, :definition,
       biological_relationship_types_attributes: [:id, :_destroy, :type, :biological_property_id],
       origin_citation_attributes: [:id, :_destroy, :source_id, :pages]
     )

app/controllers/sources_controller.rb

@@ -107,7 +107,9 @@ def parse
   def update
     respond_to do |format|
       if @source.update(source_params)
-        @source.reload
+        # We go through this dance to handle changing types from verbatim to other
+        @source = @source.becomes!(@source.type.safe_constantize)
+        @source.reload # necessary to reload the cached value.
         format.html { redirect_to url_for(@source.metamorphosize), notice: 'Source was successfully updated.' }
         format.json { render :show, status: :ok, location: @source.metamorphosize }
       else
@@ -122,20 +124,21 @@ def update
   def destroy
     if @source.destroy
       respond_to do |format|
-        format.html { redirect_to sources_url }
+        format.html { redirect_to sources_url, notice: "Destroyed source #{@source.cached}" }
         format.json { head :no_content }
       end
     else
       respond_to do |format|
-        format.html { render action: :show, notice: 'failed to destroy the source' }
+        format.html { render action: :show, notice: 'failed to destroy the source, there is likely data associated with it' }
         format.json { render json: @source.errors, status: :unprocessable_entity }
       end
     end
   end
 
   def autocomplete
+    @term = params.require(:term) 
     @sources = Queries::Source::Autocomplete.new(
-      params.require(:term),
+      @term,
       autocomplete_params
     ).autocomplete
   end
@@ -282,6 +285,7 @@ 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, :style_id,
+      :convert_to_bibtex,
       roles_attributes: [
         :id,
         :_destroy,

app/helpers/sources_helper.rb

@@ -5,6 +5,27 @@ def source_tag(source)
     source.cached ? sanitize(source.cached, tags: ['i']).html_safe : (source.new_record? ? nil : 'ERROR - Source cache not set, please notify admin.')
   end
 
+  def sources_autocomplete_tag(source, term)
+    return nil if source.nil?
+
+    if term
+      s = source.cached.gsub(/#{Regexp.escape(term)}/i, "<mark>#{term}</mark>") + ' ' # weee bit simpler
+    else
+      s = source.cached + ' '
+    end
+
+    if source.is_in_project?(sessions_current_project_id)
+      s += ' ' + content_tag(:span, 'in', class: [:feedback, 'feedback-primary', 'feedback-thin']) 
+      c = source.citations.where(project_id: sessions_current_project_id).count
+      s += ' ' + ( c > 0 ? content_tag(:span, "#{c.to_s}&nbsp;#{'citations'.pluralize(c)}".html_safe, class: [:feedback, 'feedback-secondary', 'feedback-thin']) : '' )
+      s += ' ' + content_tag(:span, 'doc/pdf', class: [:feedback, 'feedback-success', 'feedback-thin']) if source.documentation.where(project_id: sessions_current_project_id).any?
+    else
+      s += ' ' + content_tag(:span, 'out', class: [:feedback, 'feedback-warning', 'feedback-thin']) 
+    end
+
+    s.html_safe
+  end
+
   def source_author_year_tag(source)
     if source && source.type == 'Source::Bibtex' && source.author_year.present?
       source.author_year

app/helpers/workbench/navigation_helper.rb

@@ -136,6 +136,10 @@ def edit_object_path(object)
     send(edit_object_path_string(object), object)
   end
 
+  # Determine wether an edit or destroy route exists
+  # Custom routes can be added per Class by adding
+  # a corresponding `_string` postfixed method.
+  # @return String
   def edit_object_path_string(object)
     default  = "edit_#{metamorphosize_if(object).class.base_class.name.underscore}_path"
     specific = default + '_string'
@@ -148,39 +152,28 @@ def edit_object_path_string(object)
 
   # return [Boolean]
   #   true if there is a route to edit for the object (some objects are not editable, like Tags)
-  def is_editable?(object)
+  def has_route_for_edit?(object)
     self.respond_to?(edit_object_path_string(object))
   end
 
   # return [Boolean]
-  #  true if the current user has permissions to edit the object in question (does not test whether it is actually editable)
-  def user_can_edit?(object)
-    #  sessions_current_user.is_administrator? || user_is_creator?(object)
-    # TODO review
-    true
-  end
-
-  # return [Boolean]
-  #  true if the current user created this object
-  def user_is_creator?(object)
-    object.created_by_id == sessions_current_user_id
-  end
+  #   true if there is a route to edit for the object (some objects are not editable, like Tags)
 
   # return [A tag, nil]
   #   a link, or disabled link
   def edit_object_link(object)
-    if is_editable?(object) && user_can_edit?(object)
+    if has_route_for_edit?(object) && object.is_editable?(sessions_current_user)
       link_to(content_tag(:span, 'Edit', 'data-icon' => 'edit', class: 'small-icon'), edit_object_path(metamorphosize_if(object)), class: 'navigation-item')
     else
       content_tag(:div, content_tag(:span, 'Edit', 'data-icon' => 'edit', class: 'small-icon'), class: 'navigation-item disable')
     end
   end
 
   def destroy_object_link(object)
-    if (!sessions_current_user.is_administrator?) && (@is_shared_data_model)
-      content_tag(:div, content_tag(:span, 'Destroy', 'data-icon' => 'trash', class: 'small-icon'), class: 'navigation-item disable')
+    if object.is_destroyable?(sessions_current_user)
+      link_to(content_tag(:span, 'Destroy', 'data-icon' => 'trash', class: 'small-icon'), object.metamorphosize, method: :delete, data: {confirm: 'Are you sure?'}, class: 'navigation-item')     
     else
-      link_to(content_tag(:span, 'Destroy', 'data-icon' => 'trash', class: 'small-icon'), object.metamorphosize, method: :delete, data: {confirm: 'Are you sure?'}, class: 'navigation-item')
+      content_tag(:div, content_tag(:span, 'Destroy', 'data-icon' => 'trash', class: 'small-icon'), class: 'navigation-item disable')
     end
   end
 
@@ -224,12 +217,8 @@ def related_data_link_tag(object)
     content_tag(:li, link_to('Related data', send(p, object))) if controller.respond_to?(p)
   end
 
-  def a_to_z_range
-    ('A'..'Z')
-  end
-
   def a_to_z_links(targets = [])
-    letters = targets.empty? ? a_to_z_range : a_to_z_range.to_a & targets
+    letters = targets.empty? ? ('A'..'Z') : ('A'..'Z').to_a & targets
     content_tag(:div, class: 'navigation-bar-left', id: 'alphabet_nav') do
       content_tag(:ul, class: 'left_justified_navbar context-menu') do
         letters.collect{|l| content_tag(:li, link_to("#{l}", "\##{l}")) }.join.html_safe

app/javascript/style/filter.scss

@@ -1,4 +1,4 @@
 .vue-filter-container {
-  width: 360px;
-  max-width: 360px;
+  width: 400px;
+  max-width: 400px;
 }

app/javascript/vue/components/depictions/depictionImage.vue

@@ -113,7 +113,6 @@ export default {
       tabs: Object.values(Tabs),
       config: {
         status: false,
-        toolbar: ['bold', 'italic', 'code', 'heading', '|', 'quote', 'unordered-list', 'ordered-list', '|', 'link', 'table', 'preview'],
         spellChecker: false
       }
     }

app/javascript/vue/components/markdown-editor.vue

@@ -1,16 +1,27 @@
 <template>
-  <div id="markdown-editor">
-    <textarea/>
+  <div>
+    <custom-links
+      v-if="showCustomLinks"
+      @close="showCustomLinks = false"
+      @selected="setCustomLink"/>
+    <div ref="markdown">
+      <textarea/>
+    </div>
   </div>
 </template>
 
 <script>
 
-import SimpleMDE from 'simplemde'
-import 'simplemde/dist/simplemde.min.css'
+import EasyMDE from 'easymde'
+import DOMPurify from 'dompurify'
+import 'easymde/dist/easymde.min.css'
+import CustomLinks from './markdown/customLinks.vue'
+import GetOSKey from 'helpers/getMacKey.js'
 
 export default {
-  template: '',
+  components: {
+    CustomLinks
+  },
   props: {
     value: String,
     previewClass: String,
@@ -29,19 +40,34 @@ export default {
     return {
       clicks: 0,
       timerClicks: undefined,
-      cursorPosition: 0
+      cursorPosition: 0,
+      showCustomLinks: false
     }
   },
   mounted () {
     this.initialize()
   },
   methods: {
     initialize () {
-      const configs = {}
+      const configs = {
+        renderingConfig: {
+          sanitizerFunction: (renderedHTML) => DOMPurify.sanitize(renderedHTML)
+        },
+        toolbar: ['bold', 'italic', 'code', 'heading', '|', 'quote', 'unordered-list', 'ordered-list', '|', 'link', 'table', 'preview', {
+          name: 'width-auto',
+          action: (editor) => {
+            this.openCustomLinks()
+          },
+          icon:'<span class="word-keep-all">Data links</span>',
+          title: 'Data links'
+        }]
+      }
       Object.assign(configs, this.configs)
-      configs.element = configs.element || this.$el.firstElementChild
+      console.log(configs)
+      configs.element = configs.element || this.$refs.markdown.firstElementChild
       configs.initialValue = configs.initialValue || this.value
-      this.simplemde = new SimpleMDE(configs)
+      this.simplemde = new EasyMDE(configs)
+      this.customShortcuts()
       const className = this.previewClass || ''
       this.addPreviewClass(className)
       this.bindingEvents()
@@ -78,6 +104,28 @@ export default {
       wrapper.nextSibling.className += ` ${className}`
       preview.className = `editor-preview ${className}`
       wrapper.appendChild(preview)
+    },
+    setCustomLink (item) {
+      var cm = this.simplemde.codemirror
+      var output = ''
+      var selectedText = cm.getSelection()
+      var text = selectedText || item.label
+
+      output = `[${text}](${item.link})`
+      cm.replaceSelection(output)
+    },
+    customShortcuts () {
+      const codemirror = this.simplemde.codemirror
+      const keys = codemirror.getOption('extraKeys')
+      const key = GetOSKey().charAt(0).toUpperCase() + GetOSKey().slice(1)
+      console.log(key)
+      keys[`Shift-${key}-L`] = () => {
+        this.openCustomLinks()
+      }
+      codemirror.setOption('extraKeys', keys)
+    },
+    openCustomLinks () {
+      this.showCustomLinks = true
     }
   },
   destroyed () {