Class: CollectionObjectsController

Inherits:
ApplicationController show all
Includes:
DataControllerConfiguration::ProjectDataControllerConfiguration
Defined in:
app/controllers/collection_objects_controller.rb

Constant Summary

Constants included from ProjectsHelper

ProjectsHelper::CLASSIFIER, ProjectsHelper::CLASSIFIER_ANNOTATION

Instance Method Summary collapse

Methods included from DataControllerConfiguration::ProjectDataControllerConfiguration

#annotator_params

Methods included from RedirectHelper

#destroy_redirect

Methods included from RequestType

#json_request?

Methods included from LogRecent

#log_user_recent_route

Methods included from Cookies

#digest_cookie, #digested_cookie_exists?

Methods included from Whitelist

#whitelist_constantize

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

#intercept_api

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.

Parameters:

  • CollectionObject::Filter.new() —

    instance



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# File 'app/controllers/collection_objects_controller.rb', line 504

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 428

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 391

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 398

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 378

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 387

def api_show
  render '/collection_objects/api/v1/show'
end

#autocomplete ⇒ Object 



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# File 'app/controllers/collection_objects_controller.rb', line 369

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 278

def batch_load
end

#batch_params ⇒ Object (private) 



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# File 'app/controllers/collection_objects_controller.rb', line 482

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 415

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 406

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

Raises:

  • (ActiveRecord::RecordNotFound) 


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# File 'app/controllers/collection_objects_controller.rb', line 193

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 445

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 309

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 212

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.metamorphosize), notice: 'Collection object was successfully created.' }
      format.json { render action: 'show', status: :created, location: @collection_object.metamorphosize }
    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 350

def create_buffered_batch_load
  if params[:file] && digested_cookie_exists?(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 324

def create_castor_batch_load
  if params[:file] && digested_cookie_exists?(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 292

def create_simple_batch_load
  if params[:file] && digested_cookie_exists?(
      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 160

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 243

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.full_messages.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 273

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

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 103

def dwc
  o = nil
  ActiveRecord::Base.connection_pool.with_connection do
    o = CollectionObject.find(params[:id])
    if params[:rebuild] == 'true'
      # get does not rebuild, but does set if it doesn't exist
      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 142

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'
      # get does not rebuild
      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 207

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 186

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 168

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 index_metadata
  render json: metadata_index( {
    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 257

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 163

def metadata_badge
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 metadata_index(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 navigation
end

#new ⇒ Object

GET /collection_objects/new



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# File 'app/controllers/collection_objects_controller.rb', line 202

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 153

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 339

def preview_buffered_batch_load
  if params[:file]
    @result = BatchLoad::Import::CollectionObjects::BufferedInterpreter.new(**batch_params)
    digest_cookie(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 313

def preview_castor_batch_load
  if params[:file]
    @result = BatchLoad::Import::CollectionObjects::CastorInterpreter.new(**batch_params)
    digest_cookie(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 281

def preview_simple_batch_load
  if params[:file]
    @result = BatchLoad::Import::CollectionObjects.new(**batch_params.merge(user_map))
    digest_cookie(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 148

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 264

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 365

def select_options
  @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 440

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 228

def update
  respond_to do |format|
    if @collection_object.update(collection_object_params)
      @collection_object = @collection_object.metamorphosize
      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 488

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