Merge branch 'development'

SpeciesFileGroup · Nov 11, 2021 · 8d889be · 8d889be
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diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml
@@ -0,0 +1,126 @@
+name: Feature request
+description: Open a new issue to describe and request a new feature. 
+title: "[Feature]: "
+labels: ["enhancement"]
+body:
+- type: markdown
+  attributes:
+    value: |
+      A feature could be a function or output or user interface capability for example. Please describe what you would like to see or be able to do. 
+      This issue outlines and proposes a new function, its role, target audience, scope, and brief design [TODO: link to example]. As a way to provide
+      transparency for what is being shown, a new function description should address the statement "*As an X I need Y to answer question Q for audience A*".
+      _Need help filling this out?  Once you have your feature details in hand, contact us and we'll help step you through filling out this issue._
+- type: markdown
+  attributes:
+    value: |
+      # Summary
+      _To understand what you want, as a way to organize and prioritize what we build, please provide a summary in the following form._
+- type: input 
+  id: summary_x
+  attributes:
+    label: Your role 
+    description: Who are you, i.e. in what role are you presenting this feature request? 
+    placeholder: Undergrad ecologist 
+  validations:
+    required: true 
+- type: input 
+  id: summary_y
+  attributes:
+    label: Your needs
+    description: What feature do you need to answer the questions that this feature addresses, a graph, table, map, text?
+    placeholder: A particular table of data and corresponding bar-graph
+  validations:
+    required: true 
+- type: input 
+  id: summary_q
+  attributes:
+    label: Audience question
+    description: What is the question your _audience_ has that you seek to answer using this feature?
+    placeholder:  What names were used for the species and its close relatives originally named Homo sapiens?
+  validations:
+    required: true 
+- type: input 
+  id: summary_a
+  attributes:
+    label: Audience
+    description: Who is your audience? Consider what expertise the person has prior to their engagement with this feature.  
+    placeholder: e.g. Undergraduate, kindergarden child, farmer, taxonomists, policy writer, journalist
+  validations:
+    required: true 
+- type: markdown
+  attributes:
+    value: |
+      # Details
+- type: markdown
+  attributes:
+    value: |
+      ## Interface
+- type: input 
+  id: interface_title
+  attributes:
+    label: Header
+    description: Suggested primary header (title of panel if present)
+    placeholder: Type species 
+  validations:
+    required: false
+- type: textarea 
+  id: interface_napkin_sketch
+  attributes:
+    label: Napkin sketch 
+    description: minimal visual description of feature, can add many iterations. 
+    placeholder: Drag/drop your image here
+  validations:
+    required: false 
+- type: textarea 
+  id: interface_wireframe
+  attributes:
+    label: Wireframe 
+    description: mocked digital description of the feature, can include screenshots
+    placeholder: Drag/drop your image here
+  validations:
+    required: false 
+- type: textarea 
+  id: interface_actions
+  attributes:
+    label: Actions 
+    description: What can the user do with this feature that is "unique" to this part of the TaxonWorks software?  mocked digital description of the feature, can include screenshots.
+    placeholder: Sort table by clicking column headers; filter to show records by year only. 
+  validations:
+    required: false 
+- type: textarea 
+  id: data 
+  attributes:
+    label: Data
+    description: Features might have a corresponding data-object that is accessible to the end user (e.g. by download of CSV, via JSON, GeoJSO, DwC Archive, etc.). What does this look like?
+    placeholder: A CSV file with the DwC headers specificEpithet, family, and year
+  validations:
+    required: true
+- type: textarea 
+  id: citation 
+  attributes:
+    label: Citation 
+    description: What does any citation for the data look like for this section feature? 
+    placeholder: Recommended.  TODO, provide example styles.
+  validations:
+    required: false 
+- type: markdown
+  attributes:
+    value: | 
+      ## Technical details
+      _Largely completed by developers._
+- type: textarea 
+  id: technical_metadata 
+  attributes:
+    label: Metadata 
+    description: What does a citation to the data look like for this section related to this feature? 
+    placeholder: |
+      * General data source (e.g. TaxonWorks, ALA, GBIF, CoL, Globi)
+      * API entry point or offline data-source?
+      * Suitable for offline?
+      * Suitable for print?
+      * GH pages deployable?
+      * Proximity map (What should be rendered close to this panel)
+      * Dependent panels (minimize/eliminate these if possible)? (Reference by issue.)
+      * Panel source code repository
+  validations:
+    required: false
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -96,7 +96,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: spec/fixtures/vcr_cassettes
-        key: ${{ runner.os }}-vcr-${{ steps.datetime.outputs.year_week }}-${{ matrix.worker }}
+        key: ${{ runner.os }}-vcr-rev3-${{ steps.datetime.outputs.year_week }}-${{ matrix.worker }}
 
     - name: Install apt packages
       run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,12 +9,60 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.21.2] - 2021-11-11
+
+### Added
+- Support for DwC terms on body of water depth [#2628]
+- Filter Collection Objects by a specific Loan [#2632]
+
+### Changed
+- Updated ruby gems.
+
+### Fixed
+- Containerized specimens display catalog number in tag correctly [#2623]
+- Improved CrossRef parsing for a new source [#997] [#2620]
+- Container label shows catalog number for loan items [#1275]
+- Determiners are not saved after lock the list in comprehensive form [#2626]
+- Wrong rank for original combinations in DwC checklist importer [#2621]
+- No longer exposing exception data for *failed* records (not to be confused with *errored*) in DwC importer.
+- Smart selector is not working in Browse Annotations
+- Biological associations in OTU radial [#2630]
+- Fix citations on asserted distribution list in OTU radial [#2629]
+- Subsequent combinations are not scoped [#2634]
+- Missing scroll in alternate value annotator [#2635]
+- Smart selectors are not refreshing in New source [#2636]
+- Radial navigation doesn't work on source in New taxon name task [#2633]
+- Determiner is not selectable on Grid Digitizer after "Create and new" [#2637]
+- DwC Dashboard data version counts correct now [#2627]
+- Common statuses are not displayed in New taxon name task [#2642]
+- Nomenclature and OTU (biology) display the same thing on Browse OTU page [#2644]
+- New combination task hangs editing a combination [#2646]
+
+[#2623]: https://github.com/SpeciesFileGroup/taxonworks/issues/2623
+[#2627]: https://github.com/SpeciesFileGroup/taxonworks/issues/2627
+[#1275]: https://github.com/SpeciesFileGroup/taxonworks/issues/1275
+[#2628]: https://github.com/SpeciesFileGroup/taxonworks/issues/2628
+[#2626]: https://github.com/SpeciesFileGroup/taxonworks/issues/2626
+[#2621]: https://github.com/SpeciesFileGroup/taxonworks/pull/2621
+[#2629]: https://github.com/SpeciesFileGroup/taxonworks/issues/2629
+[#2630]: https://github.com/SpeciesFileGroup/taxonworks/issues/2630
+[#2633]: https://github.com/SpeciesFileGroup/taxonworks/issues/2633
+[#2634]: https://github.com/SpeciesFileGroup/taxonworks/issues/2634
+[#2635]: https://github.com/SpeciesFileGroup/taxonworks/issues/2635
+[#2636]: https://github.com/SpeciesFileGroup/taxonworks/issues/2636
+[#2637]: https://github.com/SpeciesFileGroup/taxonworks/issues/2637
+[#2642]: https://github.com/SpeciesFileGroup/taxonworks/issues/2642
+[#2644]: https://github.com/SpeciesFileGroup/taxonworks/issues/2644
+[#2646]: https://github.com/SpeciesFileGroup/taxonworks/issues/2646
+
 ## [0.21.1] - 2021-11-05
 ### Fixed
 - Citations in image viewer
 
 ## [0.21.0] - 2021-11-04
 ### Added
+- Added new handling for plant name author_string.
+- Added new `Combination` section to handle historical protonym combination.
 - Add new task 'Object graph', visualize and navigate your Things via a force-directed-graph (network) [#2587]
 - New combination editing, including support for multiple authors in plant names [#666] [#2407]
 - Add new global identifier class for glbio repositories
@@ -1933,7 +1981,8 @@ 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/v0.21.1...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.21.2...development
+[0.21.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.21.1...v0.21.2
 [0.21.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.21.0...v0.21.1
 [0.21.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.20.1...v0.21.0
 [0.20.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.20.0...v0.20.1

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -300,7 +300,7 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    os (1.1.1)
+    os (1.1.4)
     paper_trail (12.1.0)
       activerecord (>= 5.2)
       request_store (~> 1.1)
@@ -318,7 +318,7 @@ GEM
     parser (3.0.2.0)
       ast (~> 2.4.1)
     parslet (2.0.0)
-    passenger (6.0.11)
+    passenger (6.0.12)
       rack
       rake (>= 0.8.1)
     pdf-core (0.9.0)
@@ -413,7 +413,7 @@ GEM
       rgeo (>= 1.0.0)
     rgeo-geojson (2.1.1)
       rgeo (>= 1.0.0)
-    rgeo-proj4 (3.1.0)
+    rgeo-proj4 (3.1.1)
       rgeo (~> 2.0)
     rmagick (4.2.3)
     roo (2.8.3)
@@ -459,7 +459,7 @@ GEM
       rubocop-ast (>= 1.12.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.12.0)
+    rubocop-ast (1.13.0)
       parser (>= 3.0.1.1)
     rubocop-faker (0.2.0)
       rubocop (>= 0.74)

diff --git a/app/controllers/collection_objects/filter_params.rb b/app/controllers/collection_objects/filter_params.rb
@@ -76,6 +76,7 @@ def collection_object_filter_params
         is_type: [],
         keyword_id_and: [],
         keyword_id_or: [],
+        loan_id: [],
         otu_ids: [],
         preparation_type_id: []
         #  user_id: []
@@ -154,6 +155,7 @@ def collection_object_api_params
         is_type: [],
         keyword_id_and: [],
         keyword_id_or: [],
+        loan_id: [],
         otu_ids: [],
         preparation_type_id: [],
 

diff --git a/app/controllers/dwc_occurrences_controller.rb b/app/controllers/dwc_occurrences_controller.rb
@@ -3,6 +3,13 @@ class DwcOccurrencesController < ApplicationController
 
   before_action :set_object, only: [:status, :create]
 
+  after_action -> { set_pagination_headers(:dwc_occurrences) }, only: [:index], if: :json_request?
+
+  # .json only
+  def index
+    @dwc_occurrences = Queries::DwcOccurrence::Filter.new(filter_params).all.page(params[:page]).per(params[:per] || 1)
+  end
+
   def metadata
     @dwc_occurrences = DwcOccurrence.where(project_id: sessions_current_project_id)
   end
@@ -41,6 +48,16 @@ def create
 
   protected
 
+  def filter_params
+    params.permit(
+      :user_date_end,
+      :user_date_start,
+      dwc_occurrence_object_id: [],
+      dwc_occurrence_object_type: []
+    )
+  end
+
+
   def set_object
     @object = GlobalID::Locator.locate(params[:object_global_id])
 

diff --git a/app/helpers/README.md b/app/helpers/README.md
@@ -67,7 +67,7 @@ class <Model>Helper
   # Return a label to be used in autocomplete dropdown lists
   # May (usually) contain HTML.
   # Note that HTML inputs do not support HTML, so you 
-  # likely want to create <model_name>_label to go with this.
+  # likely want to create label_for_<model> to go with this.
   # Typically used in ../views/../autocomplete.json
   def <model_name>_autocomplete_tag(object)
   end

diff --git a/app/helpers/annotations_helper.rb b/app/helpers/annotations_helper.rb
@@ -1,36 +1,35 @@
 # Helpers that wrap sets of annotations of different types.
-module AnnotationsHelper 
+module AnnotationsHelper
 
   # @return [String]
   # Assumes the context is the object, not a multi-object summary
   def annotations_summary_tag(object)
-    content_tag(:div, class: %w{item panel separate-bottom}) do
-      content_tag(:div, class: [:content]) do
-        content_tag(:div, class: ['information-panel']) do
-          content_tag(:h2, 'Annotations') +
-            content_tag(:div,
-            [citation_list_tag(object),
-             identifier_list_tag(object), 
-             data_attribute_list_tag(object), 
-             note_list_tag(object), 
-             tag_list_tag(object),
-             alternate_values_list_tag(object),
-             confidence_list_tag(object),
-             attribution_list_tag(object)
-          ].compact.join.html_safe, class: :annotations_summary_list, 'data-annotator-list-object-id' => object.id)
-
+    v = [citation_list_tag(object),
+        identifier_list_tag(object),
+        data_attribute_list_tag(object),
+        note_list_tag(object),
+        tag_list_tag(object),
+        alternate_values_list_tag(object),
+        confidence_list_tag(object),
+        attribution_list_tag(object)
+    ].compact
+
+    tag.div(class: %w{item panel separate-bottom}) do
+      tag.div(class: [:content]) do
+        tag.div(class: ['information-panel']) do
+          tag.h2('Annotations') +
+            ( v.count > 0 ?  tag.div(v.join.html_safe, class: :annotations_summary_list, 'data-annotator-list-object-id' => object.id) : tag.em('None'))
         end
       end
     end
 
     # depictions
     # confidences
     # protocols
-
   end
 
   def annotations_exist(object)
-    return (object.has_citations? && object.citations.any?) || 
+    return (object.has_citations? && object.citations.any?) ||
       (object.has_identifiers? && object.identifiers.any?) ||
       (object.has_data_attributes? && object.data_attributes.any?) ||
       (object.has_notes? && object.notes.any?) ||
@@ -49,7 +48,7 @@ def radial_annotator(object, pulse = false, showCount = false)
   end
 
   # @return [Array]
-  #   of { ClassName => human name } 
+  #   of { ClassName => human name }
   def klass_and_labels(klass_names)
     klass_names.collect{|n| [n, n.tableize.humanize]}.to_h
   end

diff --git a/app/helpers/attributions_helper.rb b/app/helpers/attributions_helper.rb
@@ -13,6 +13,33 @@ def attribution_tag(attribution)
     a.compact.join('. ').html_safe
   end
 
+  # @return [String, nil]
+  #   no html in _label
+  # !! if _tag labels add HTML then they must be removed here
+  def label_for_attribution(attribution)
+    return nil if attribution.nil?
+
+    a = [
+      attribution_copyright_label(attribution),
+      attribution_creators_tag(attribution),
+      attribution_editors_tag(attribution),
+      attribution_owners_tag(attribution),
+      attribution.license,
+    ]
+
+    a.compact.join('. ').html_safe
+  end
+
+  # @return [String, nil]
+  def attribution_copyright_label(attribution)
+    a = attribution.copyright_year
+    b = attribution.attribution_copyright_holders
+    return nil unless a or b.any?
+    s = '(c)'
+    s << [a, Utilities::Strings.authorship_sentence(b.collect{|c| c.name})].join(' ')
+    s
+  end
+
   def attribution_copyright_tag(attribution)
     a = attribution.copyright_year
     b = attribution.attribution_copyright_holders