Class: CollectionObjectsController
- Inherits:
-
ApplicationController
- Object
- ActionController::Base
- ApplicationController
- CollectionObjectsController
- Defined in:
- app/controllers/collection_objects_controller.rb
Constant Summary
Constants included from ProjectsHelper
ProjectsHelper::CLASSIFIER, ProjectsHelper::CLASSIFIER_ANNOTATION
Instance Method Summary collapse
-
#add_includes_to_filter_result(collection_objects) ⇒ Object
private
An experiment to balance query/rendering times vs.
- #after_destroy_path ⇒ Object private
- #api_autocomplete ⇒ Object
-
#api_dwc ⇒ Object
GET /api/v1/collection_objects/123/dwc.
-
#api_index ⇒ Object
GET /api/v1/collection_objects.
-
#api_show ⇒ Object
GET /api/v1/collection_objects/:id.
- #autocomplete ⇒ Object
-
#batch_load ⇒ Object
GET collection_objects/batch_load.
- #batch_params ⇒ Object private
-
#batch_update ⇒ Object
PATCH /collection_object/batch_update.json?collection_object_query=<>&collection_object={}.
-
#batch_update_dwc_occurrence ⇒ Object
PATCH /collection_object/batch_update_dwc_occurrence.json?<collection object query params>.
- #biocuration_classifications ⇒ Object
-
#by_identifier ⇒ Object
GET /collection_objects/by_identifier/ABCD TODO: remove for filter.
- #collection_object_params ⇒ Object private
- #containerize ⇒ Object
-
#create ⇒ Object
POST /collection_objects POST /collection_objects.json.
- #create_buffered_batch_load ⇒ Object
- #create_castor_batch_load ⇒ Object
- #create_simple_batch_load ⇒ Object
-
#depictions ⇒ Object
GET /collection_objects/depictions/1 GET /collection_objects/depictions/1.html This is.
-
#destroy ⇒ Object
DELETE /collection_objects/1 DELETE /collection_objects/1.json.
-
#download ⇒ Object
GET /collection_objects/download.
-
#dwc ⇒ Object
TODO: Not used in Vue GET /collection_objects/123/dwc !! Returns a keyless Array of data compatible with combining multiple rows.
-
#dwc_compact ⇒ Object
GET /collection_objects/123/dwc_compact !! Never recalculates !!.
-
#dwc_index ⇒ Object
Render DWC fields only.
-
#dwc_verbose ⇒ Object
GET /collection_objects/123/dwc_verbose.
-
#dwca ⇒ Object
DEPRECATED GET /collection_objects/dwca/123 # SHOULD BE dwc.
-
#edit ⇒ Object
GET /collection_objects/1/edit.
-
#geo_json ⇒ Object
TODO: render in view GET /collection_objects/1/geo_json GET /collection_objects/1/geo_json.json.
-
#images ⇒ Object
GET /collection_objects/1/inventory/images.html GET /collection_objects/1/images.json.
-
#index ⇒ Object
GET /collecting_events GET /collecting_events.json.
-
#index_metadata ⇒ Object
/collection_objects/index_metadata/.json.
-
#list ⇒ Object
GET /collection_objects/list.
- #metadata_badge ⇒ Object
-
#metadata_index(models = {}) ⇒ Object
TODO: probably some deep clean TODO: Move.
- #navigation ⇒ Object
-
#new ⇒ Object
GET /collection_objects/new.
-
#preview ⇒ Object
/collection_objects/preview?<filter params>.
- #preview_buffered_batch_load ⇒ Object
- #preview_castor_batch_load ⇒ Object
- #preview_simple_batch_load ⇒ Object
-
#report ⇒ Object
Intent is DWC fields + quick summary fields for reports !! As currently implemented rebuilds DWC all.
-
#search ⇒ Object
GET /collection_object/search.
- #select_options ⇒ Object
- #set_collection_object ⇒ Object private
-
#show ⇒ Object
GET /collection_objects/1 GET /collection_objects/1.json.
-
#timeline ⇒ Object
GET /collection_objects/1/timeline.json.
-
#update ⇒ Object
PATCH/PUT /collection_objects/1 PATCH/PUT /collection_objects/1.json.
-
#user_map ⇒ Object
private
TODO: not used?.
Methods included from DataControllerConfiguration::ProjectDataControllerConfiguration
Methods included from RedirectHelper
Methods included from RequestType
Methods included from LogRecent
Methods included from Cookies
#digest_cookie, #digested_cookie_exists?
Methods included from Whitelist
Methods included from ProjectsHelper
#cumulative_gb_per_year, #document_cumulative_gb_per_year, #document_gb_per_year, #gb_per_year, #image_cumulative_gb_per_year, #image_gb_per_year, #invalid_object, #project_classification, #project_link, #project_matches, #project_tag, #projects_list, #projects_search_form, #taxonworks_classification, #week_in_review_graphs
Methods included from Api::Intercept
Methods included from TokenAuthentication
#intercept_project, #intercept_user, #intercept_user_or_project, #project_token_authenticate, #token_authenticate
Instance Method Details
#add_includes_to_filter_result(collection_objects) ⇒ Object (private)
An experiment to balance query/rendering times vs. extend[] requests Likely suggests we need some fundamental changes.
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# File 'app/controllers/collection_objects_controller.rb', line 503 def add_includes_to_filter_result(collection_objects) a = %i(identifiers dwc_occurrence repository current_repository) x = [] a.each do |e| if helpers.extend_response_with(e.to_s) x.push e end end if x.any? collection_objects = collection_objects.includes(*x) end if helpers.extend_response_with('collecting_event') collection_objects = collection_objects.includes(collecting_event: [:identifiers]) end if helpers.extend_response_with('taxon_determinations') collection_objects = collection_objects.includes(taxon_determinations: [:otu, roles: [:person]]) end collection_objects end |
#after_destroy_path ⇒ Object (private)
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# File 'app/controllers/collection_objects_controller.rb', line 427 def after_destroy_path if request.referer =~ /tasks\/collection_objects\/browse/ if o = @collection_object.next_by_identifier browse_collection_objects_path(collection_object_id: o.id) else browse_collection_objects_path end else collection_objects_path end end |
#api_autocomplete ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 390 def api_autocomplete render json: {} and return if params[:term].blank? @collection_objects = ::Queries::CollectionObject::Autocomplete.new(params[:term], project_id: sessions_current_project_id).autocomplete render '/collection_objects/api/v1/autocomplete' end |
#api_dwc ⇒ Object
GET /api/v1/collection_objects/123/dwc
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# File 'app/controllers/collection_objects_controller.rb', line 397 def api_dwc ActiveRecord::Base.connection_pool.with_connection do @collection_object.get_dwc_occurrence render json: @collection_object.dwc_occurrence_attributes end end |
#api_index ⇒ Object
GET /api/v1/collection_objects
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# File 'app/controllers/collection_objects_controller.rb', line 377 def api_index @collection_objects = ::Queries::CollectionObject::Filter.new(params.merge!(api: true)).all .where(project_id: sessions_current_project_id) .order('collection_objects.id') .page(params[:page]).per(params[:per]) render '/collection_objects/api/v1/index' end |
#api_show ⇒ Object
GET /api/v1/collection_objects/:id
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# File 'app/controllers/collection_objects_controller.rb', line 386 def api_show render '/collection_objects/api/v1/show' end |
#autocomplete ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 368 def autocomplete @collection_objects = ::Queries::CollectionObject::Autocomplete.new( params[:term], project_id: sessions_current_project_id ).autocomplete end |
#batch_load ⇒ Object
GET collection_objects/batch_load
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# File 'app/controllers/collection_objects_controller.rb', line 277 def batch_load end |
#batch_params ⇒ Object (private)
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# File 'app/controllers/collection_objects_controller.rb', line 481 def batch_params params.permit(:file, :import_level, :source_id, :otu_id) .merge(user_id: sessions_current_user_id, project_id: sessions_current_project_id).to_h.symbolize_keys end |
#batch_update ⇒ Object
PATCH /collection_object/batch_update.json?collection_object_query=<>&collection_object={}
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# File 'app/controllers/collection_objects_controller.rb', line 414 def batch_update if c = CollectionObject.batch_update( preview: params[:preview], collection_object: collection_object_params.merge(by: sessions_current_user_id), collection_object_query: params[:collection_object_query]) render json: c.to_json, status: :ok else render json: {}, status: :unprocessable_entity end end |
#batch_update_dwc_occurrence ⇒ Object
PATCH /collection_object/batch_update_dwc_occurrence.json?<collection object query params>
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# File 'app/controllers/collection_objects_controller.rb', line 405 def batch_update_dwc_occurrence if c = CollectionObject.batch_update_dwc_occurrence(params) render json: c.to_json, status: :ok else render json: {}, status: :unprocessable_entity end end |
#biocuration_classifications ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 74 def biocuration_classifications @biocuration_classifications = @collection_object.biocuration_classifications render '/biocuration_classifications/index' end |
#by_identifier ⇒ Object
GET /collection_objects/by_identifier/ABCD TODO: remove for filter
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# File 'app/controllers/collection_objects_controller.rb', line 192 def by_identifier @identifier = params.require(:identifier) @request_project_id = sessions_current_project_id @collection_objects = CollectionObject.with_identifier(@identifier).where(project_id: @request_project_id).all raise ActiveRecord::RecordNotFound if @collection_objects.empty? end |
#collection_object_params ⇒ Object (private)
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# File 'app/controllers/collection_objects_controller.rb', line 444 def collection_object_params params.require(:collection_object).permit( :total, :preparation_type_id, :repository_id, :current_repository_id, :ranged_lot_category_id, :collecting_event_id, :buffered_collecting_event, :buffered_determinations, :buffered_other_labels, :accessioned_at, :deaccessioned_at, :deaccession_reason, :contained_in, :taxon_determination_id, collecting_event_attributes: [], # needs to be filled out! data_attributes_attributes: [ :id, :_destroy, :controlled_vocabulary_term_id, :type, :value ], tags_attributes: [:id, :_destroy, :keyword_id], depictions_attributes: [:id, :_destroy, :svg_clip, :svg_view_box, :position, :caption, :figure_label, :image_id], identifiers_attributes: [ :id, :_destroy, :identifier, :namespace_id, :type, labels_attributes: [ :text, :type, :text_method, :total ] ], taxon_determinations_attributes: [ :id, :_destroy, :otu_id, :year_made, :month_made, :day_made, :position, roles_attributes: [:id, :_destroy, :type, :organization_id, :person_id, :position, person_attributes: [:last_name, :first_name, :suffix, :prefix]], otu_attributes: [:id, :_destroy, :name, :taxon_name_id] ], biocuration_classifications_attributes: [ :id, :_destroy, :biocuration_class_id ] ) end |
#containerize ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 308 def containerize @container_item = ContainerItem.new(contained_object: @collection_object) end |
#create ⇒ Object
POST /collection_objects POST /collection_objects.json
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# File 'app/controllers/collection_objects_controller.rb', line 211 def create @collection_object = CollectionObject.new(collection_object_params) respond_to do |format| if @collection_object.save format.html { redirect_to url_for(@collection_object.), notice: 'Collection object was successfully created.' } format.json { render action: 'show', status: :created, location: @collection_object. } else format.html { render action: 'new' } format.json { render json: @collection_object.errors, status: :unprocessable_entity } end end end |
#create_buffered_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 349 def create_buffered_batch_load if params[:file] && (params[:file].tempfile, :Buffered_collection_objects_md5) @result = BatchLoad::Import::CollectionObjects::BufferedInterpreter.new(**batch_params) if @result.create flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} items were created." render 'collection_objects/batch_load/buffered/create' and return else flash[:alert] = 'Batch import failed.' end else flash[:alert] = 'File to batch upload must be supplied.' end render :batch_load end |
#create_castor_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 323 def create_castor_batch_load if params[:file] && (params[:file].tempfile, :Castor_collection_objects_md5) @result = BatchLoad::Import::CollectionObjects::CastorInterpreter.new(**batch_params) if @result.create flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} items were created." render 'collection_objects/batch_load/castor/create' and return else flash[:alert] = 'Batch import failed.' end else flash[:alert] = 'File to batch upload must be supplied.' end render :batch_load end |
#create_simple_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 291 def create_simple_batch_load if params[:file] && ( params[:file].tempfile, :batch_collection_objects_md5) @result = BatchLoad::Import::CollectionObjects.new(**batch_params.merge(user_map)) if @result.create flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} collection object-related object-sets were created." render 'collection_objects/batch_load/simple/create' and return else flash[:alert] = 'Batch import failed.' end else flash[:alert] = 'File to batch upload must be supplied.' end render :batch_load end |
#depictions ⇒ Object
GET /collection_objects/depictions/1 GET /collection_objects/depictions/1.html This is
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# File 'app/controllers/collection_objects_controller.rb', line 159 def depictions end |
#destroy ⇒ Object
DELETE /collection_objects/1 DELETE /collection_objects/1.json
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# File 'app/controllers/collection_objects_controller.rb', line 242 def destroy @collection_object.destroy respond_to do |format| if @collection_object.destroyed? format.html { redirect_to after_destroy_path, notice: 'CollectionObject was successfully destroyed.' } format.json { head :no_content } else format.html { destroy_redirect @collection_object, notice: 'CollectionObject was not destroyed, ' + @collection_object.errors..join('; ') } format.json { render json: @collection_object.errors, status: :unprocessable_entity } end end end |
#download ⇒ Object
GET /collection_objects/download
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# File 'app/controllers/collection_objects_controller.rb', line 272 def download send_data Export::CSV.generate_csv(CollectionObject.where(project_id: sessions_current_project_id), header_converters: []), type: 'text', filename: "collection_objects_#{DateTime.now}.tsv" end |
#dwc ⇒ Object
TODO: Not used in Vue GET /collection_objects/123/dwc
!! Returns a keyless Array of data compatible with combining multiple rows
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# File 'app/controllers/collection_objects_controller.rb', line 104 def dwc o = nil ActiveRecord::Base.connection_pool.with_connection do o = CollectionObject.find(params[:id]) if params[:rebuild] == 'true' o.set_dwc_occurrence else o.get_dwc_occurrence end # Default to *exclude* some fields that include large text, like geospatial mode = params[:mode] || :view render json: o.dwc_occurrence_attribute_values(mode) end end |
#dwc_compact ⇒ Object
GET /collection_objects/123/dwc_compact !! Never recalculates !!
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# File 'app/controllers/collection_objects_controller.rb', line 141 def dwc_compact render json: @collection_object.dwc_occurrence.dwc_json end |
#dwc_index ⇒ Object
Render DWC fields only
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# File 'app/controllers/collection_objects_controller.rb', line 90 def dwc_index objects = ::Queries::CollectionObject::Filter.new(params).all.order('collection_objects.id').includes(:dwc_occurrence).page(params[:page]).per(params[:per]).all assign_pagination(objects) # Default to *exclude* some big fields, like geo-spatial wkt mode = params[:mode] || :view @objects = objects.pluck(*::CollectionObject.dwc_attribute_vector(mode)) @headers = ::CollectionObject.dwc_attribute_vector_names(mode) render '/dwc_occurrences/dwc_index' end |
#dwc_verbose ⇒ Object
GET /collection_objects/123/dwc_verbose
!! Always calculates values, never reads from !! Allways returns all values
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# File 'app/controllers/collection_objects_controller.rb', line 125 def dwc_verbose o = nil ActiveRecord::Base.connection_pool.with_connection do o = CollectionObject.find(params[:id]) if params[:rebuild] == 'true' o.set_dwc_occurrence else o.get_dwc_occurrence end end render json: o.dwc_occurrence_attributes end |
#dwca ⇒ Object
DEPRECATED GET /collection_objects/dwca/123 # SHOULD BE dwc
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# File 'app/controllers/collection_objects_controller.rb', line 84 def dwca @dwc_occurrence = CollectionObject.includes(:dwc_occurrence).find(params[:id]).get_dwc_occurrence # find or compute for render json: @dwc_occurrence.to_json end |
#edit ⇒ Object
GET /collection_objects/1/edit
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# File 'app/controllers/collection_objects_controller.rb', line 206 def edit end |
#geo_json ⇒ Object
TODO: render in view GET /collection_objects/1/geo_json GET /collection_objects/1/geo_json.json
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# File 'app/controllers/collection_objects_controller.rb', line 185 def geo_json ce = @collection_object.collecting_event @geo_json = ce.nil? ? nil : ce.to_geo_json_feature end |
#images ⇒ Object
GET /collection_objects/1/inventory/images.html GET /collection_objects/1/images.json
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# File 'app/controllers/collection_objects_controller.rb', line 167 def images @images = ::Queries::Image::Filter.new( collection_object_id: [ params.require(:id)], collection_object_scope: [:all] ) respond_to do |format| format.html { @images = @images.all } format.json do # rendered as Depictions for now @depictions = @iamges.derived_depictions render '/depictions/index' and return end end end |
#index ⇒ Object
GET /collecting_events GET /collecting_events.json
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# File 'app/controllers/collection_objects_controller.rb', line 15 def index respond_to do |format| format.html do @recent_objects = CollectionObject.recent_from_project_id(sessions_current_project_id) .order(updated_at: :desc) .includes(:identifiers, :taxon_determinations) .limit(10) render '/shared/data/all/index' end format.json do collection_objects = ::Queries::CollectionObject::Filter.new(params).all @collection_objects = add_includes_to_filter_result(collection_objects) @collection_objects = @collection_objects .page(params[:page]) .per(params[:per]) end end end |
#index_metadata ⇒ Object
/collection_objects/index_metadata/.json
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# File 'app/controllers/collection_objects_controller.rb', line 37 def render json: ( { repository: Repository, current_respository: Repository, collecting_event: CollectingEvent, taxon_determinations: TaxonDetermination }) .merge( dwc_occurrence: DwcOccurrence.target_columns.inject({}){|hsh,p| hsh[p] = nil; hsh}.delete_if{|k,v| k =~ /(_id|_type)\z/} ) .merge( CollectionObject.core_attributes.inject({}){|hsh,p| hsh[p] = nil; hsh}) .merge( identifiers: nil, object_tag: nil, object_label: nil, ).delete_if{|k,v| k =~ /(_id|_type)\z/} end |
#list ⇒ Object
GET /collection_objects/list
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# File 'app/controllers/collection_objects_controller.rb', line 256 def list @collection_objects = CollectionObject.with_project_id(sessions_current_project_id) .order(:id) .page(params[:page]) #.per(10) #.per(3) end |
#metadata_badge ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 162 def end |
#metadata_index(models = {}) ⇒ Object
TODO: probably some deep clean TODO: Move
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# File 'app/controllers/collection_objects_controller.rb', line 54 def (models = {}) h = {} models.each do |l, m| h.merge!( l => m.core_attributes.inject({}){|hsh,p| hsh[p] = nil; hsh} ) end h end |
#navigation ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 79 def end |
#new ⇒ Object
GET /collection_objects/new
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# File 'app/controllers/collection_objects_controller.rb', line 201 def new @collection_object = CollectionObject.new end |
#preview ⇒ Object
/collection_objects/preview?<filter params>
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# File 'app/controllers/collection_objects_controller.rb', line 152 def preview @collection_objects = ::Queries::CollectionObject::Filter.new(params).all.order('collection_objects.id').includes(:dwc_occurrence).page(params[:page]).per(params[:per] || 500) end |
#preview_buffered_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 338 def preview_buffered_batch_load if params[:file] @result = BatchLoad::Import::CollectionObjects::BufferedInterpreter.new(**batch_params) (params[:file].tempfile, :Buffered_collection_objects_md5) render 'collection_objects/batch_load/buffered/preview' else flash[:notice] = 'No file provided!' redirect_to action: :batch_load end end |
#preview_castor_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 312 def preview_castor_batch_load if params[:file] @result = BatchLoad::Import::CollectionObjects::CastorInterpreter.new(**batch_params) (params[:file].tempfile, :Castor_collection_objects_md5) render 'collection_objects/batch_load/castor/preview' else flash[:notice] = 'No file provided!' redirect_to action: :batch_load end end |
#preview_simple_batch_load ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 280 def preview_simple_batch_load if params[:file] @result = BatchLoad::Import::CollectionObjects.new(**batch_params.merge(user_map)) (params[:file].tempfile, :batch_collection_objects_md5) render 'collection_objects/batch_load/simple/preview' else flash[:notice] = 'No file provided!' redirect_to action: :batch_load end end |
#report ⇒ Object
Intent is DWC fields + quick summary fields for reports !! As currently implemented rebuilds DWC all
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# File 'app/controllers/collection_objects_controller.rb', line 147 def report @collection_objects = ::Queries::CollectionObject::Filter.new(params).all.order('collection_objects.id').includes(:dwc_occurrence).page(params[:page]).per(params[:per] || 500) end |
#search ⇒ Object
GET /collection_object/search
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# File 'app/controllers/collection_objects_controller.rb', line 263 def search if params[:id].blank? redirect_to collection_object_path, alert: 'You must select an item from the list with a click or tab press before clicking show.' else redirect_to collection_object_path(params[:id]) end end |
#select_options ⇒ Object
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# File 'app/controllers/collection_objects_controller.rb', line 364 def @collection_objects = CollectionObject.select_optimized(sessions_current_user_id, sessions_current_project_id, params[:target]) end |
#set_collection_object ⇒ Object (private)
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# File 'app/controllers/collection_objects_controller.rb', line 439 def set_collection_object @collection_object = CollectionObject.with_project_id(sessions_current_project_id).find(params[:id]) @recent_object = @collection_object end |
#show ⇒ Object
GET /collection_objects/1 GET /collection_objects/1.json
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# File 'app/controllers/collection_objects_controller.rb', line 66 def show end |
#timeline ⇒ Object
GET /collection_objects/1/timeline.json
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# File 'app/controllers/collection_objects_controller.rb', line 70 def timeline @data = ::Catalog::CollectionObject.data_for(@collection_object) end |
#update ⇒ Object
PATCH/PUT /collection_objects/1 PATCH/PUT /collection_objects/1.json
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# File 'app/controllers/collection_objects_controller.rb', line 227 def update respond_to do |format| if @collection_object.update(collection_object_params) @collection_object = @collection_object. format.html { redirect_to url_for(@collection_object), notice: 'Collection object was successfully updated.' } format.json { render :show, status: :ok, location: @collection_object } else format.html { render action: 'edit' } format.json { render json: @collection_object.errors, status: :unprocessable_entity } end end end |
#user_map ⇒ Object (private)
TODO: not used?
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# File 'app/controllers/collection_objects_controller.rb', line 487 def user_map { user_header_map: { 'otu' => 'otu_name', 'start_day' => 'start_date_day', 'start_month' => 'start_date_month', 'start_year' => 'start_date_year', 'end_day' => 'end_date_day', 'end_month' => 'end_date_month', 'end_year' => 'end_date_year'} } end |