Class: TaxonNamesController

Inherits:
ApplicationController show all
Includes:
DataControllerConfiguration::ProjectDataControllerConfiguration
Defined in:
app/controllers/taxon_names_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_catalog ⇒ Object

GET /api/v1/taxon_names/:id/inventory/catalog Contains stats block



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# File 'app/controllers/taxon_names_controller.rb', line 347

def api_catalog
  @data = helpers.recursive_catalog_json(
    taxon_name: @taxon_name,
    target_depth: params[:target_depth] || 0,
    include_distribution: false
  )
  render '/taxon_names/api/v1/catalog'
end

#api_index ⇒ Object

GET /api/v1/taxon_names



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# File 'app/controllers/taxon_names_controller.rb', line 299

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

  respond_to do |format|
    format.json {
      @taxon_names = q.page(params[:page]).per(params[:per])
      render '/taxon_names/api/v1/index'
    }
    format.csv {
      @taxon_names = q
      send_data Export::CSV.generate_csv(
        @taxon_names,
        exclude_columns: %w{updated_by_id created_by_id project_id},
      ), type: 'text', filename: "taxon_names_#{DateTime.now}.tsv"
    }
  end
end

#api_monograph ⇒ Object

GET /api/v1/taxon_names/:id/monograph



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# File 'app/controllers/taxon_names_controller.rb', line 330

def api_monograph
  if helpers.extend_response_with('descendants')
    @descendants_scope = TaxonName
      .with_project_id(sessions_current_project_id)
      .find(params[:id])
      .descendants
      .order('taxon_names.id')
      .page(params[:page])
      .per(params[:per])
  else
    @taxon_name_scope = TaxonName.with_project_id(sessions_current_project_id).where(id: params[:id])
  end
  render '/taxon_names/api/v1/monograph'
end

#api_origin_citation ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 390

def api_origin_citation
  q = ::Queries::TaxonName::Filter.new(params).all
    .where(project_id: sessions_current_project_id)
    .order('taxon_names.id')

  respond_to do |format|
    format.json {
      @taxon_names = q.page(params[:page]).per(params[:per])
      render '/taxon_names/origin_citation'
    }
    format.csv {
      @taxon_names = q
      send_data Export::CSV::TaxonNameOrigin.csv(
        @taxon_names,
      ).read, type: 'text', filename: "taxon_name_origin_citation_#{DateTime.now}.tsv"
    }
  end
end

#api_parse ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 356

def api_parse
  if params[:combination_id]
    @combination = Combination
      .where(project_id: sessions_current_project_id)
      .find(params[:combination_id])
  end
  @result = Vendor::Biodiversity::Result.new(
    query_string: params.require(:query_string),
    project_id: sessions_current_project_id,
    code: :iczn # !! TODO: generalize
  ).result
  render '/taxon_names/api/v1/parse'
end

#api_show ⇒ Object

GET /api/v1/taxon_names/:id



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# File 'app/controllers/taxon_names_controller.rb', line 320

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

#api_summary ⇒ Object

GET /api/v1/taxon_names/:id/inventory/summary



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# File 'app/controllers/taxon_names_controller.rb', line 325

def api_summary
  render '/taxon_names/api/v1/summary'
end

#autocomplete ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 98

def autocomplete
  render json: {} and return if params[:term].blank?
  @taxon_names = ::Queries::TaxonName::Autocomplete.new(
    params[:term],
    exact: 'true',
    **autocomplete_params
  ).autocomplete
end

#autocomplete_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 472

def autocomplete_params
  params.permit(
    :valid, :exact, :no_leaves,
    type: [], parent_id: [], nomenclature_group: []
  ).to_h.symbolize_keys.merge(project_id: sessions_current_project_id)
end

#autoselect ⇒ Object

GET /taxon_names/autoselect



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# File 'app/controllers/taxon_names_controller.rb', line 410

def autoselect
  render json: ::Autoselect::TaxonName::Autoselect.new(
    term: params[:term],
    level: params[:level],
    project_id: sessions_current_project_id,
    user_id: sessions_current_user_id,
    **autoselect_params
  ).response
end

#autoselect_col_create ⇒ Object

POST



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# File 'app/controllers/taxon_names_controller.rb', line 427

def autoselect_col_create
  result = ::Autoselect::TaxonName::CatalogueOfLifeCreator.new(
    rows: autoselect_col_create_params,
    col_code: params[:col_code],
    project_id: sessions_current_project_id,
    user_id: sessions_current_user_id
  ).call
  tn = ::TaxonName.find(result[:taxon_name_id])
  render json: result.merge(global_id: tn.to_global_id.to_s)
rescue ::Autoselect::TaxonName::CatalogueOfLifeCreator::CreationError => e
  render json: {
    error: e.message,
    failed_col_name: e.col_name,
    failed_col_id: e.col_id
  }, status: :unprocessable_entity
end

#autoselect_col_create_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 446

def autoselect_col_create_params
  params.permit(
    rows: [
      :col_name, :col_rank, :col_id, :dataset_id, :taxonworks_id,
      :col_authorship, :col_year, :col_status
    ]
  )
    .fetch(:rows, [])
    .map(&:to_h)
end

#autoselect_col_datasets ⇒ Object

GET /taxon_names/col_datasets?q=...



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# File 'app/controllers/taxon_names_controller.rb', line 421

def autoselect_col_datasets
  results = ::Vendor::Colrapi.datasets(q: params[:q].to_s, limit: 20)
  render json: results
end

#autoselect_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 457

def autoselect_params
  params.permit(
    :valid, :exact, :no_leaves, :dataset_id, :show_info,
    type: [], parent_id: [], nomenclature_group: []
  ).to_h.symbolize_keys
end

#batch_load ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 118

def batch_load
end

#batch_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 510

def batch_params
  params.permit(
    :file,
    :parent_taxon_name_id,
    :nomenclature_code,
    :also_create_otu,
    :import_level).merge(
      user_id: sessions_current_user_id,
      project_id: sessions_current_project_id
    ).to_h.symbolize_keys
end

#batch_update ⇒ Object

PATCH /taxon_names/batch_update.json?taxon_names_query=<>&taxon_name=taxon_name_id=123}



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# File 'app/controllers/taxon_names_controller.rb', line 285

def batch_update
  if r = Protonym.batch_update(
      preview: params[:preview],
      taxon_name: taxon_name_params.merge(by: sessions_current_user_id),
      taxon_name_query: params[:taxon_name_query].merge(by: sessions_current_user_id),
      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

#create ⇒ Object

POST /taxon_names POST /taxon_names.json



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# File 'app/controllers/taxon_names_controller.rb', line 40

def create
  @taxon_name = TaxonName.new(taxon_name_params)
  respond_to do |format|
    if @taxon_name.save
      format.html { redirect_to url_for(@taxon_name.metamorphosize),
                    notice: "Taxon name '#{@taxon_name.name}' was successfully created." }
      format.json { render :show, status: :created, location: @taxon_name.metamorphosize }
    else
      format.html { render action: :new }
      format.json { render json: @taxon_name.errors, status: :unprocessable_content }
    end
  end
end

#create_nomen_batch_load ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 213

def create_nomen_batch_load
  if params[:file] && digested_cookie_exists?(params[:file].tempfile, :nomen_taxon_names_md5)
    @result = BatchLoad::Import::TaxonNames::NomenInterpreter.new(**batch_params)
    if @result.create
      flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} items were created."
      render 'taxon_names/batch_load/nomen/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/taxon_names_controller.rb', line 185

def create_simple_batch_load

  if params[:file] && digested_cookie_exists?(params[:file].tempfile, :simple_taxon_names_md5)
    @result = BatchLoad::Import::TaxonifiToTaxonworks.new(**batch_params)
    if @result.create
      flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} taxon names were created."
      render 'taxon_names/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

#destroy ⇒ Object

DELETE /taxon_names/1 DELETE /taxon_names/1.json



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# File 'app/controllers/taxon_names_controller.rb', line 74

def destroy
  parent_id = @taxon_name.parent_id
  @taxon_name.destroy
  respond_to do |format|
    if @taxon_name.destroyed?
      format.html { destroy_redirect @taxon_name, notice: 'TaxonName was successfully destroyed.' }
      format.json {
        render json: { parent_id: }
      }
    else
      format.html { destroy_redirect @taxon_name, notice: 'TaxonName was not destroyed, ' + @taxon_name.errors.full_messages.join('; ') }
      format.json { render json: @taxon_name.errors, status: :unprocessable_content }
    end
  end
end

#download ⇒ Object

GET /taxon_names/download



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# File 'app/controllers/taxon_names_controller.rb', line 112

def download
  send_data Export::CSV.generate_csv(
    TaxonName.where(project_id: sessions_current_project_id)
  ), type: 'text', filename: "taxon_names_#{DateTime.now}.tsv"
end

#edit ⇒ Object

GET /taxon_names/1/edit



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# File 'app/controllers/taxon_names_controller.rb', line 35

def edit
end

#index ⇒ Object

GET /taxon_names GET /taxon_names.json



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# File 'app/controllers/taxon_names_controller.rb', line 10

def index
  respond_to do |format|
    format.html do
      @recent_objects = TaxonName.recent_from_project_id(sessions_current_project_id).order(updated_at: :desc).limit(10)
      render '/shared/data/all/index'
    end
    format.json {
      @taxon_names = ::Queries::TaxonName::Filter.new(params).all
      .page(params[:page])
      .per(params[:per])
    }
  end
end

#list ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 107

def list
  @taxon_names = TaxonName.with_project_id(sessions_current_project_id).order(:id).page(params[:page])
end

#match ⇒ Object

POST /taxon_names/match.json subgenus_matching - 'with' (default): match names as given; 'without':

if that fails, retry ignoring subgenus; 'both': always try both, so
different taxa matched each way are reported as ambiguous


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# File 'app/controllers/taxon_names_controller.rb', line 250

def match
  names = match_params[:names] || []
  project_id = sessions_current_project_id
  taxon_name_id = match_params[:taxon_name_id]
  subgenus_matching = match_params[:subgenus_matching]

  tn_results = Match::Otu::TaxonName.new(
    names:,
    project_id:,
    levenshtein_distance: match_params[:levenshtein_distance] || 0,
    taxon_name_id:,
    resolve_synonyms: match_params[:resolve_synonyms] == 'true',
    try_without_subgenus: %w{without both}.include?(subgenus_matching),
    try_without_subgenus_after_exact_match: subgenus_matching == 'both'
  ).call

  @result = if match_params[:match_otu_names] == 'true'
    otu_results = Match::Otu::MorphospeciesName.new(
      names:, project_id:, taxon_name_id:
    ).call
    Match::Otu::MergeResults.new(tn_results:, otu_results:).call
  else
    tn_results.map { |r|
      r.merge(match_source: r[:matched] ? 'taxon_name' : nil)
    }
  end

  render :match
end

#match_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 479

def match_params
  params.permit(
    :levenshtein_distance,
    :taxon_name_id,
    :resolve_synonyms,
    :subgenus_matching,
    :match_otu_names,
    names: []
  )
end

#new ⇒ Object

GET /taxon_names/new



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# File 'app/controllers/taxon_names_controller.rb', line 30

def new
  @taxon_name = Protonym.new(source: Source.new)
end

#origin_citation ⇒ Object

GET /api/v1/taxon_names



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# File 'app/controllers/taxon_names_controller.rb', line 371

def origin_citation
  q = ::Queries::TaxonName::Filter.new(params).all
    .where(project_id: sessions_current_project_id)
    .order('taxon_names.id')

  respond_to do |format|
    format.json {
      @taxon_names = q.page(params[:page]).per(params[:per])
      render '/taxon_names/origin_citation'
    }
    format.csv {
      @taxon_names = q
      send_data Export::CSV::TaxonNameOrigin.csv(
        @taxon_names,
      ).read, type: 'text', filename: "taxon_name_origin_citation_#{DateTime.now}.tsv"
    }
  end
end

#original_combination ⇒ Object

GET /taxon_names/1/original_combination



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# File 'app/controllers/taxon_names_controller.rb', line 281

def original_combination
end

#parse ⇒ Object 



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

def parse
  if params[:combination_id]
    @combination = Combination
      .where(project_id: sessions_current_project_id)
      .find(params[:combination_id])
  end
  @result = Vendor::Biodiversity::Result.new(
    query_string: params.require(:query_string),
    project_id: sessions_current_project_id,
    code: :iczn # !! TODO: generalize
  ).result
end

#predicted_rank ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 125

def predicted_rank
  if params[:parent_id]
    p = TaxonName.find_by(id: params[:parent_id])
    if p.nil?
      render json: {predicted_rank: ''}.to_json
    else
      render json: {predicted_rank: p.predicted_child_rank(params[:name]).to_s}.to_json
    end
  else
    render json: {predicted_rank: ''}.to_json
  end
end

#preview_nomen_batch_load ⇒ Object 



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

def preview_nomen_batch_load
  if params[:file]
    @result = BatchLoad::Import::TaxonNames::NomenInterpreter.new(**batch_params)
    digest_cookie(params[:file].tempfile, :nomen_taxon_names_md5)
    render 'taxon_names/batch_load/nomen/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/taxon_names_controller.rb', line 174

def preview_simple_batch_load
  if params[:file]
    @result = BatchLoad::Import::TaxonifiToTaxonworks.new(**batch_params)
    digest_cookie(params[:file].tempfile, :simple_taxon_names_md5)
    render 'taxon_names/batch_load/simple/preview'
  else
    flash[:notice] = 'No file provided!'
    redirect_to action: :batch_load
  end
end

#random ⇒ Object 



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

def random
  redirect_to browse_nomenclature_task_path(
    taxon_name_id: TaxonName.where(project_id: sessions_current_project_id).order('random()').limit(1).pick(:id)
  )
end

#rank_table ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 144

def rank_table
  @query = ::Queries::TaxonName::Tabular.new(
    taxon_name_id: params.require(:taxon_name_id), # this is one of the few places
    ranks: params.require(:ranks),
    fieldsets: params[:fieldsets],
    limit: params[:limit],
    validity: params[:validity],
    combinations: params[:combinations],
    project_id: sessions_current_project_id,
    rank_data: params[:rank_data],
    descriptors_scored_for_otu: params[:descriptors_scored_for_otu],
    otu_observation_count: params[:otu_observation_count],
    otu_observation_depictions: params[:otu_observation_depictions],
    otus: params[:otus]
  )
end

#ranks ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 121

def ranks
  render json: RANKS_JSON.to_json
end

#remove_authors ⇒ Object 



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

def remove_authors
  names = TaxonName.remove_authors(params['names'].first(5000))
  render json: { names: }
end

#search ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 90

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

#select_options ⇒ Object

GET /taxon_names/select_options



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# File 'app/controllers/taxon_names_controller.rb', line 166

def select_options
  @taxon_names = TaxonName.select_optimized(
    sessions_current_user_id,
    sessions_current_project_id,
    target: params[:target]
  )
end

#set_taxon_name ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 464

def set_taxon_name
  @taxon_name = TaxonName
    .with_project_id(sessions_current_project_id)
    .includes(:creator, :updater)
    .find(params[:id])
  @recent_object = @taxon_name
end

#show ⇒ Object

GET /taxon_names/1 GET /taxon_names/1.json



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# File 'app/controllers/taxon_names_controller.rb', line 26

def show
end

#taxon_name_params ⇒ Object (private) 



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# File 'app/controllers/taxon_names_controller.rb', line 490

def taxon_name_params
  params.require(:taxon_name).permit(
    :name,
    :parent_id,
    :year_of_publication,
    :etymology,
    :verbatim_author, :verbatim_name, :rank_class, :type, :masculine_name,
    :feminine_name, :neuter_name, :also_create_otu,
    roles_attributes: [
      :id, :_destroy, :type, :person_id, :position,
      person_attributes: [
        :last_name, :first_name, :suffix, :prefix
      ]
    ],
    family_group_name_form_relationship_attributes: [:id, :_destroy, :object_taxon_name_id],
    origin_citation_attributes: [:id, :_destroy, :source_id, :pages],
    taxon_name_classifications_attributes: [:id, :_destroy, :type]
  )
end

#taxonomy ⇒ Object 



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# File 'app/controllers/taxon_names_controller.rb', line 161

def taxonomy
  @taxon_name = TaxonName.find(params[:id])
end

#update ⇒ Object

PATCH/PUT /taxon_names/1 PATCH/PUT /taxon_names/1.json



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# File 'app/controllers/taxon_names_controller.rb', line 56

def update
  respond_to do |format|
    if @taxon_name.update(taxon_name_params)

      # TODO: WHY?!
      @taxon_name.reload

      format.html { redirect_to url_for(@taxon_name.metamorphosize), notice: 'Taxon name was successfully updated.' }
      format.json { render :show, status: :ok, location: @taxon_name.metamorphosize }
    else
      format.html { render action: :edit }
      format.json { render json: @taxon_name.errors, status: :unprocessable_content }
    end
  end
end