Class: BiologicalAssociationsController

Inherits:
ApplicationController show all
Includes:
DataControllerConfiguration::ProjectDataControllerConfiguration
Defined in:
app/controllers/biological_associations_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 inherited from ApplicationController

#set_time_zone

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, #cumulative_projects_created_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_initials, #project_link, #project_login_link, #project_matches, #project_tag, #projects_list, #projects_search_form, #sound_cumulative_gb_per_year, #sound_gb_per_year, #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

#api_globi ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 138

def api_globi
  render json:  @biological_association.globi_extension_json, status: :ok
end

#api_index ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 146

def api_index
  q = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true)).all
    .where(project_id: sessions_current_project_id)
    .order('biological_associations.id')

  respond_to do |format|
    format.json {
      @biological_associations = q.page(params[:page]).per(params[:per])
      render '/biological_associations/api/v1/index'
    }

    format.csv {
      @biological_associations = q
      send_data Export::CSV.generate_csv(
        @biological_associations,
        exclude_columns: %w{updated_by_id created_by_id project_id},
      ), type: 'text',
     filename: "biological_associations_#{DateTime.now}.tsv"
    }

    format.globi {
      if q.page(params[:page]).per(params[:per]).count < 1001
        send_data Export::CSV::Globi.csv(q.page(params[:page]).per(params[:per])),
          type: 'text',
          filename: "biological_associations_globi_#{DateTime.now}.tsv"
      else
        render json: { msg: 'At present this format is only allowed for 1000 or less records.' }, status: :unprocessable_content
      end
    }
  end
end

#api_index_basic ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 214

def api_index_basic
  @biological_associations = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true))
    .all
    .where(project_id: sessions_current_project_id)
    .select('biological_associations.id')
    .includes(:biological_association_index)
    .order('biological_associations.id')
    .page(params[:page])
    .per(params[:per])

  render '/biological_associations/api/v1/basic'
end

#api_index_extended ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 196

def api_index_extended
  @biological_associations = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true))
    .all
    .where(project_id: sessions_current_project_id)
    .order('biological_associations.id')
    .page(params[:page])
    .per(params[:per])

  respond_to do |format|
    format.json  { render '/biological_associations/api/v1/extended' and return }
    format.csv {
      send_data Export::CSV::BiologicalAssociations::Extended.csv(@biological_associations),
      type: 'text',
      filename: "biological_associations_extended_#{DateTime.now}.tsv"
    }
  end
end

#api_index_simple ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 178

def api_index_simple
  @biological_associations = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true))
    .all
    .where(project_id: sessions_current_project_id)
    .order('biological_associations.id')
    .page(params[:page])
    .per(params[:per])

  respond_to do |format|
    format.json  { render '/biological_associations/api/v1/simple' and return }
    format.csv {
      send_data Export::CSV::BiologicalAssociations::Simple.csv(@biological_associations),
      type: 'text',
      filename: "biological_associations_simple_#{DateTime.now}.tsv"
    }
  end
end

#api_resource_relationship ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 142

def api_resource_relationship
  render json:  @biological_association.globi_extension_json, status: :ok
end

#api_show ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 134

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

#autocomplete ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 241

def autocomplete
  @biological_associations =
    ::Queries::BiologicalAssociation::Autocomplete.new(
      params.require(:term),
      project_id: sessions_current_project_id,
    ).autocomplete
end

#batch_update ⇒ Object

PATCH /biological_associations/batch_update.json?biological_association_query=<>&biological_association={}



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# File 'app/controllers/biological_associations_controller.rb', line 228

def batch_update
  if r = BiologicalAssociation.batch_update(
      preview: params[:preview],
      biological_association: biological_association_params.merge(by: sessions_current_user_id),
      biological_association_query: params[:biological_association_query],
      user_id: sessions_current_user_id,
      project_id: sessions_current_project_id)
    render json: r.to_json, status: :ok
  else
    render json: {}, status: :unprocessable_content
  end
end

#biological_association_params ⇒ Object (private) 



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# File 'app/controllers/biological_associations_controller.rb', line 302

def biological_association_params
  params.require(:biological_association).permit(
    :biological_relationship_id, :biological_association_subject_id, :biological_association_subject_type,
    :biological_association_object_id, :biological_association_object_type,
    :subject_global_id,
    :object_global_id,
    :rotate,
    subject_anatomical_part_attributes: [:name, :uri, :uri_label, :is_material, :preparation_type_id],
    object_anatomical_part_attributes: [:name, :uri, :uri_label, :is_material, :preparation_type_id],
    subject_taxon_determination_attributes: [:otu_id],
    object_taxon_determination_attributes: [:otu_id],
    origin_citation_attributes: [:id, :_destroy, :source_id, :pages],
    citations_attributes: [:id, :is_original, :_destroy, :source_id, :pages, :citation_object_id, :citation_object_type],
  )
end

#create ⇒ Object

POST /biological_associations POST /biological_associations.json



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# File 'app/controllers/biological_associations_controller.rb', line 78

def create
  if create_with_anatomical_parts?
    @biological_association = ::BiologicalAssociations::CreateWithAnatomicalParts.new(biological_association_params).call
  else
    @biological_association = BiologicalAssociation.new(biological_association_params)
    @biological_association.save
  end

  respond_to do |format|
    if @biological_association.persisted?
      format.html { redirect_to @biological_association, notice: 'Biological association was successfully created.' }
      format.json { render :show, status: :created, location: @biological_association }
    else
      format.html { render :new }
      format.json { render json: { errors: @biological_association.errors.full_messages }, status: :unprocessable_content }
    end
  end
end

#create_with_anatomical_parts? ⇒ Boolean (private)

Returns:

  • (Boolean) 


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# File 'app/controllers/biological_associations_controller.rb', line 318

def create_with_anatomical_parts?
  p = biological_association_params
  p[:subject_anatomical_part_attributes].present? || p[:object_anatomical_part_attributes].present?
end

#destroy ⇒ Object

DELETE /biological_associations/1 DELETE /biological_associations/1.json



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# File 'app/controllers/biological_associations_controller.rb', line 113

def destroy
  @biological_association.destroy
  respond_to do |format|
    if @biological_association.destroyed?
      format.html { redirect_to biological_associations_url, notice: 'Biological association was successfully destroyed.' }
      format.json { head :no_content }
    else
      format.html { destroy_redirect @biological_association, notice: 'Biological association was not destroyed: ' + @biological_association.errors.full_messages.join('; ') }
      format.json { render json: @biological_association.errors, status: :unprocessable_content }
    end
  end
end

#edit ⇒ Object

GET /biological_associations/1/edit



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# File 'app/controllers/biological_associations_controller.rb', line 69

def edit
end

#index ⇒ Object

GET /biological_associations GET /biological_associations.json



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# File 'app/controllers/biological_associations_controller.rb', line 11

def index
  respond_to do |format|
    format.html {
      @recent_objects = BiologicalAssociation.recent_from_project_id(sessions_current_project_id).order(updated_at: :desc).limit(10)
      render '/shared/data/all/index'
    }
    format.json {
      @biological_associations = Queries::BiologicalAssociation::Filter.new(params)
        .all
        .where(project_id: sessions_current_project_id)
        .includes(
          citations: [:source, :topics, { citation_topics: :topic }],
          biological_relationship: :biological_relationship_types
        )
        .preload(:biological_association_subject, :biological_association_object)
        .page(params[:page])
        .per(params[:per])
        .load

      # TODO: this isn't good, make it better.
      co_fo_subjects = @biological_associations
        .filter_map { |ba| ba.biological_association_subject if ['CollectionObject', 'FieldOccurrence'].include?(ba.biological_association_subject_type) }
      ActiveRecord::Associations::Preloader.new(records: co_fo_subjects, associations: [:taxon_determinations, :identifiers]).call unless co_fo_subjects.empty?

      co_fo_objects = @biological_associations
        .filter_map { |ba| ba.biological_association_object if ['CollectionObject', 'FieldOccurrence'].include?(ba.biological_association_object_type) }
      ActiveRecord::Associations::Preloader.new(records: co_fo_objects, associations: [:taxon_determinations, :identifiers]).call unless co_fo_objects.empty?

      otu_subjects = @biological_associations
        .filter_map { |ba| ba.biological_association_subject if ba.biological_association_subject_type == 'Otu' }
      ActiveRecord::Associations::Preloader.new(records: otu_subjects, associations: [:taxon_name]).call unless otu_subjects.empty?

      otu_objects = @biological_associations
        .filter_map { |ba| ba.biological_association_object if ba.biological_association_object_type == 'Otu' }
      ActiveRecord::Associations::Preloader.new(records: otu_objects, associations: [:taxon_name]).call unless otu_objects.empty?

      ap_subjects = @biological_associations
        .filter_map { |ba| ba.biological_association_subject if ba.biological_association_subject_type == 'AnatomicalPart' }
      ActiveRecord::Associations::Preloader.new(records: ap_subjects, associations: [:inbound_origin_relationship]).call unless ap_subjects.empty?

      ap_objects = @biological_associations
        .filter_map { |ba| ba.biological_association_object if ba.biological_association_object_type == 'AnatomicalPart' }
      ActiveRecord::Associations::Preloader.new(records: ap_objects, associations: [:inbound_origin_relationship]).call unless ap_objects.empty?
    }
  end
end

#list ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 72

def list
  @biological_associations = BiologicalAssociation.with_project_id(sessions_current_project_id).order(:id).page(params[:page]) #.per(10)
end

#navigation ⇒ Object

GET /biological_associations/1/navigation.json



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# File 'app/controllers/biological_associations_controller.rb', line 259

def navigation
end

#new ⇒ Object

GET /biological_associations/new



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# File 'app/controllers/biological_associations_controller.rb', line 64

def new
  redirect_to new_biological_association_task_path
end

#origin_subject_index ⇒ Object

GET /biological_associations/origin_subject_index.json?origin_object_id=1&origin_object_type=Otu Returns BiologicalAssociations whose subject is an AnatomicalPart originated from the base object.



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# File 'app/controllers/biological_associations_controller.rb', line 277

def origin_subject_index
  object_id = params.require(:origin_object_id).to_i
  object_type = params.require(:origin_object_type).to_s

  @biological_associations = BiologicalAssociation
    .joins("INNER JOIN origin_relationships ap_origin_relationships ON ap_origin_relationships.new_object_id = biological_associations.biological_association_subject_id")
    .where(project_id: sessions_current_project_id)
    .where(biological_association_subject_type: 'AnatomicalPart')
    .where("ap_origin_relationships.new_object_type = 'AnatomicalPart'")
    .where(
      'ap_origin_relationships.old_object_id = ? AND ap_origin_relationships.old_object_type = ?',
      object_id,
      object_type
    )
    .order('biological_associations.updated_at DESC')

  render '/biological_associations/index'
end

#search ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 126

def search
  if params[:id].blank?
    redirect_to biological_associations_path, alert: 'You must select an item from the list with a click or tab press before clicking show.'
  else
    redirect_to biological_association_path(params[:id])
  end
end

#select_options ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 262

def select_options
  @biological_associations = BiologicalAssociation.select_optimized(sessions_current_user_id, sessions_current_project_id, params.require(:target))
end

#set_biological_association ⇒ Object (private) 



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# File 'app/controllers/biological_associations_controller.rb', line 298

def set_biological_association
  @biological_association = BiologicalAssociation.where(project_id: sessions_current_project_id).find(params[:id])
end

#show ⇒ Object

GET /biological_associations/1 GET /biological_associations/1.json



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# File 'app/controllers/biological_associations_controller.rb', line 60

def show
end

#subject_object_types ⇒ Object 



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# File 'app/controllers/biological_associations_controller.rb', line 266

def subject_object_types
  hash = BIOLOGICALLY_RELATABLE_TYPES.reduce({}) do |h, val|
    h[val] = val.tableize
     h
  end
  render json: hash
end

#update ⇒ Object

PATCH/PUT /biological_associations/1 PATCH/PUT /biological_associations/1.json



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# File 'app/controllers/biological_associations_controller.rb', line 99

def update
  respond_to do |format|
    if @biological_association.update(biological_association_params)
      format.html { redirect_to @biological_association, notice: 'Biological association was successfully updated.' }
      format.json { render :show, status: :ok, location: @biological_association }
    else
      format.html { render :edit }
      format.json { render json: @biological_association.errors, status: :unprocessable_content }
    end
  end
end