Class: TaxonNamesController

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

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

#invalid_object, #project_link, #project_matches, #project_tag, #projects_list, #projects_search_form

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_indexObject

GET /api/v1/taxon_names



226
227
228
229
230
231
232
# File 'app/controllers/taxon_names_controller.rb', line 226

def api_index
  @taxon_names = Queries::TaxonName::Filter.new(api_params).all
    .where(project_id: sessions_current_project_id)
    .order('taxon_names.id')
    .page(params[:page]).per(params[:per])
  render '/taxon_names/api/v1/index'
end

#api_paramsObject (private)



348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
# File 'app/controllers/taxon_names_controller.rb', line 348

def api_params
  params.permit(
    :ancestors,
    :author,
    :authors,
    :citations,
    :data_attribute_exact_value,
    :data_attributes,
    :descendants,
    :descendants_max_depth,
    :etymology,
    :exact,
    :leaves,
    :name,
    :nomenclature_code,
    :nomenclature_group, # !! different than autocomplete
    :not_specified,
    :otus,
    :taxon_name_type,
    :type_metadata,
    :updated_since,
    :validity,
    :year,
#     :page, # TODO: yes or no?
#     :per,
    combination_taxon_name_id: [],
    data_attribute_predicate_id: [], # DataAttributes concern
    data_attribute_value: [],        # DataAttributes concern
    keyword_id_and: [],
    keyword_id_or: [],
    parent_id: [],
    taxon_name_classification: [],
    taxon_name_id: [],
    taxon_name_relationship: [],
    taxon_name_relationship_type: [],
    type: []
  ).to_h.symbolize_keys.merge(project_id: sessions_current_project_id)

  # TODO: see config in collection objects controller
  # a[:user_id] = params[:user_id] if params[:user_id] && is_project_member_by_id(params[:user_id], sessions_current_project_id) # double check vs. setting project_id from API
  # a
end

#api_parseObject



244
245
246
247
248
249
250
251
252
# File 'app/controllers/taxon_names_controller.rb', line 244

def api_parse
  @combination = Combination.where(project_id: sessions_current_project_id).find(params[:combination_id]) if params[:combination_id]
  @result = TaxonWorks::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_showObject

GET /api/v1/taxon_names/:id



235
236
237
# File 'app/controllers/taxon_names_controller.rb', line 235

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

#api_summaryObject

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



240
241
242
# File 'app/controllers/taxon_names_controller.rb', line 240

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

#autocompleteObject



93
94
95
96
97
98
99
# File 'app/controllers/taxon_names_controller.rb', line 93

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

#autocomplete_paramsObject (private)



261
262
263
264
265
266
# File 'app/controllers/taxon_names_controller.rb', line 261

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

#batch_loadObject



112
113
# File 'app/controllers/taxon_names_controller.rb', line 112

def batch_load
end

#batch_paramsObject (private)



287
288
289
290
291
292
293
294
295
296
297
# File 'app/controllers/taxon_names_controller.rb', line 287

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

#createObject

POST /taxon_names POST /taxon_names.json



38
39
40
41
42
43
44
45
46
47
48
49
50
# File 'app/controllers/taxon_names_controller.rb', line 38

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_entity }
    end
  end
end

#create_castor_batch_loadObject



197
198
199
200
201
202
203
204
205
206
207
208
209
210
# File 'app/controllers/taxon_names_controller.rb', line 197

def create_castor_batch_load
  if params[:file] && digested_cookie_exists?(params[:file].tempfile, :Castor_taxon_names_md5)
    @result = BatchLoad::Import::TaxonNames::CastorInterpreter.new(**batch_params)
    if @result.create
      flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} items were created."
      render 'taxon_names/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_loadObject



171
172
173
174
175
176
177
178
179
180
181
182
183
184
# File 'app/controllers/taxon_names_controller.rb', line 171

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

#destroyObject

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



72
73
74
75
76
77
78
79
80
81
82
83
# File 'app/controllers/taxon_names_controller.rb', line 72

def destroy
  @taxon_name.destroy
  respond_to do |format|
    if @taxon_name.destroyed?
      format.html { destroy_redirect @taxon_name, notice: 'TaxonName was successfully destroyed.' }
      format.json { head :no_content }
    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_entity }
    end
  end
end

#downloadObject

GET /taxon_names/download



106
107
108
109
110
# File 'app/controllers/taxon_names_controller.rb', line 106

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

#editObject

GET /taxon_names/1/edit



32
33
34
# File 'app/controllers/taxon_names_controller.rb', line 32

def edit
  @taxon_name.source = Source.new if !@taxon_name.source
end

#filter_paramsObject (private)



299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
# File 'app/controllers/taxon_names_controller.rb', line 299

def filter_params
  params.permit(
    :ancestors,
    :author,
    :authors,
    :citations,
    :data_attribute_exact_value,
    :data_attributes,
    :descendants,
    :descendants_max_depth,
    :etymology,
    :exact,
    :leaves,
    :name,
    :nomenclature_code,
    :nomenclature_group, # !! different than autocomplete
    :not_specified,
    :note_exact, # Notes concern
    :note_text,
    :notes,
    :otus,
    :page,
    :per,
    :taxon_name_author_ids_or,
    :taxon_name_type,
    :type_metadata,
    :updated_since,
    :user_date_end,
    :user_date_start,
    :user_id,
    :user_target,
    :validity,
    :year,
    combination_taxon_name_id: [],
    data_attribute_predicate_id: [], # DataAttributes concern
    data_attribute_value: [],        # DataAttributes concern
    keyword_id_and: [],
    keyword_id_or: [],
    parent_id: [],
    taxon_name_author_ids: [],
    taxon_name_classification: [],
    taxon_name_id: [],
    taxon_name_relationship: [],
    taxon_name_relationship_type: [],
    type: [],
    # user_id: []
  ).to_h.symbolize_keys.merge(project_id: sessions_current_project_id)
end

#indexObject

GET /taxon_names GET /taxon_names.json



9
10
11
12
13
14
15
16
17
18
19
# File 'app/controllers/taxon_names_controller.rb', line 9

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(filter_params).all.page(params[:page]).per(params[:per] || 50)
    }
  end
end

#listObject



101
102
103
# File 'app/controllers/taxon_names_controller.rb', line 101

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

#newObject

GET /taxon_names/new



27
28
29
# File 'app/controllers/taxon_names_controller.rb', line 27

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

#original_combinationObject

GET /taxon_names/1/original_combination



222
223
# File 'app/controllers/taxon_names_controller.rb', line 222

def original_combination
end

#parseObject



212
213
214
215
216
217
218
219
# File 'app/controllers/taxon_names_controller.rb', line 212

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

#predicted_rankObject



119
120
121
122
123
124
125
126
127
128
129
130
# File 'app/controllers/taxon_names_controller.rb', line 119

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_castor_batch_loadObject



186
187
188
189
190
191
192
193
194
195
# File 'app/controllers/taxon_names_controller.rb', line 186

def preview_castor_batch_load
  if params[:file]
    @result = BatchLoad::Import::TaxonNames::CastorInterpreter.new(**batch_params)
    digest_cookie(params[:file].tempfile, :Castor_taxon_names_md5)
    render 'taxon_names/batch_load/castor/preview'
  else
    flash[:notice] = 'No file provided!'
    redirect_to action: :batch_load
  end
end

#preview_simple_batch_loadObject



160
161
162
163
164
165
166
167
168
169
# File 'app/controllers/taxon_names_controller.rb', line 160

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

#randomObject



132
133
134
135
136
# File 'app/controllers/taxon_names_controller.rb', line 132

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

#rank_tableObject



138
139
140
141
142
143
144
145
146
147
148
149
# File 'app/controllers/taxon_names_controller.rb', line 138

def rank_table
  @query = Queries::TaxonName::Tabular.new(
    ancestor_id: params.require(:ancestor_id),
    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]
  )
end

#ranksObject



115
116
117
# File 'app/controllers/taxon_names_controller.rb', line 115

def ranks
  render json: RANKS_JSON.to_json
end

#searchObject



85
86
87
88
89
90
91
# File 'app/controllers/taxon_names_controller.rb', line 85

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_optionsObject

GET /taxon_names/select_options



152
153
154
155
156
157
158
# File 'app/controllers/taxon_names_controller.rb', line 152

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

#set_taxon_nameObject (private)



256
257
258
259
# File 'app/controllers/taxon_names_controller.rb', line 256

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

#showObject

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



23
24
# File 'app/controllers/taxon_names_controller.rb', line 23

def show
end

#taxon_name_paramsObject (private)



268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
# File 'app/controllers/taxon_names_controller.rb', line 268

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
      ]
    ],
    origin_citation_attributes: [:id, :_destroy, :source_id, :pages],
    taxon_name_classifications_attributes: [:id, :_destroy, :type]
  )
end

#updateObject

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



54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
# File 'app/controllers/taxon_names_controller.rb', line 54

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_entity }
    end
  end
end