app/controllers/descriptors_controller.rb
class DescriptorsController < ApplicationController
include DataControllerConfiguration::ProjectDataControllerConfiguration
before_action :set_descriptor, only: [:show, :edit, :update, :destroy, :annotations]
after_action -> { set_pagination_headers(:descriptors) }, only: [:index], if: :json_request?
# GET /descriptors
# GET /descriptors.json
def index
respond_to do |format|
format.html do
@recent_objects = Descriptor.recent_from_project_id(sessions_current_project_id)
.order(updated_at: :desc).limit(10)
render '/shared/data/all/index'
end
format.json {
@descriptors = ::Queries::Descriptor::Filter.new(params).all
.page(params[:page])
.per(params[:per])
.order('descriptors.name')
}
end
end
# GET /descriptors/1
# GET /descriptors/1.json
def show
end
def list
@descriptor = Descriptor.with_project_id(sessions_current_project_id).page(params[:page])
end
# GET /descriptors/new
def new
@descriptor = Descriptor.new
redirect_to new_descriptor_task_path(), notice: 'Using task interface.'
end
# GET /descriptors/1/edit
def edit
redirect_to new_descriptor_task_path(descriptor_id: @descriptor.id), notice: 'Editing in new interface.'
end
# POST /descriptors
# POST /descriptors.json
def create
@descriptor = Descriptor.new(descriptor_params)
respond_to do |format|
if @descriptor.save
format.html { redirect_to url_for(@descriptor.metamorphosize),
notice: 'Descriptor was successfully created.' }
format.json { render :show, status: :created, location: @descriptor.metamorphosize }
else
format.html { render :new }
format.json { render json: @descriptor.metamorphosize.errors, status: :unprocessable_entity }
end
end
end
# PATCH/PUT /descriptors/1
# PATCH/PUT /descriptors/1.json
def update
respond_to do |format|
begin
if @descriptor.update(descriptor_params)
format.html { redirect_to url_for(@descriptor.metamorphosize),
notice: 'Descriptor was successfully updated.' }
format.json { render :show, status: :ok, location: @descriptor.metamorphosize }
else
format.html { render :edit }
format.json { render json: @descriptor.metamorphosize.errors, status: :unprocessable_entity }
end
# Can not cascade destroy Observations
rescue ActiveRecord::RecordNotDestroyed
format.html { render :edit }
format.json { render json: 'Could not destroy, do observations still exist?', status: :unprocessable_entity }
end
end
end
# DELETE /descriptors/1
# DELETE /descriptors/1.json
def destroy
@descriptor.destroy
respond_to do |format|
if @descriptor.destroyed?
format.html { destroy_redirect @descriptor, notice: 'Descriptor was successfully destroyed.' }
format.json { head :no_content }
else
format.html { destroy_redirect @descriptor, notice: 'Descriptor was not destroyed, ' + @descriptor.errors.full_messages.join('; ') }
format.json { render json: @descriptor.errors, status: :unprocessable_entity }
end
end
end
def autocomplete
@term = params[:term]
@descriptors = Queries::Descriptor::Autocomplete.new(params.require(:term), project_id: sessions_current_project_id).all
end
def search
if params[:id].blank?
redirect_to descriptors_path, notice: 'You must select an item from the list with a click or ' \
'tab press before clicking show.'
else
redirect_to descriptor_path(params[:id])
end
end
# TODO: remove for shared end point
# GET /annotations
def annotations
@object = @descriptor
render '/shared/data/all/annotations'
end
def batch_load
end
def preview_modify_gene_descriptor_batch_load
if params[:file]
@result = BatchLoad::Import::Descriptors::ModifyGeneDescriptorInterpreter.new(**batch_params)
digest_cookie(params[:file].tempfile, :modify_gene_descriptor_batch_load_descriptors_md5)
render 'descriptors/batch_load/modify_gene_descriptor/preview'
else
flash[:notice] = 'No file provided!'
redirect_to action: :batch_load
end
end
def preview_qualitative_descriptor_batch_load
if params[:file]
@result = BatchLoad::Import::Descriptors::QualitativeInterpreter.new(**batch_params)
digest_cookie(params[:file].tempfile, :qualitative_descriptors_batch_load_md5)
render 'descriptors/batch_load/qualitative_descriptor/preview'
else
flash[:notice] = 'No file provided!'
redirect_to action: :batch_load
end
end
def create_modify_gene_descriptor_batch_load
if params[:file] && digested_cookie_exists?(
params[:file].tempfile,
:modify_gene_descriptor_batch_load_descriptors_md5)
@result = BatchLoad::Import::Descriptors::ModifyGeneDescriptorInterpreter.new(**batch_params)
if @result.create
flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} " \
'Gene Descriptors were modified.'
render 'descriptors/batch_load/modify_gene_descriptor/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
def create_qualitative_descriptor_batch_load
if params[:file] && digested_cookie_exists?(
params[:file].tempfile,
:qualitative_descriptors_batch_load_md5)
@result = BatchLoad::Import::Descriptors::QualitativeInterpreter.new(**batch_params)
if @result.create
flash[:notice] = "Successfully proccessed file, #{@result.total_records_created}."
render 'descriptors/batch_load/qualitative_descriptor/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
def units
render json: UNITS
end
private
def set_descriptor
@descriptor = Descriptor.where(project_id: sessions_current_project_id).find(params[:id])
end
def descriptor_params
params.require(:descriptor).permit(
:name, :short_name, :key_name, :description_name,
:description, :position, :type, :gene_attribute_logic, :default_unit, :weight,
character_states_attributes: [:id, :descriptor_id, :_destroy, :label, :name, :position, :description_name, :key_name],
gene_attributes_attributes: [:id, :_destroy, :sequence_id, :sequence_relationship_type, :controlled_vocabulary_term_id, :position ]
)
end
def batch_params
params.permit(:file).merge(
user_id: sessions_current_user_id,
project_id: sessions_current_project_id).to_h.symbolize_keys
end
end