Class: CollectionObjectsController

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

Instance Method Summary collapse

Methods included from DataControllerConfiguration::ProjectDataControllerConfiguration

#annotator_params

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

#autocompleteObject


153
154
155
156
157
158
159
# File 'app/controllers/collection_objects_controller.rb', line 153

def autocomplete
  @collection_objects =
    Queries::CollectionObject::Autocomplete.new(
      params[:term],
      project_id: sessions_current_project_id
  ).autocomplete
end

#batch_loadObject

GET collection_objects/batch_load


167
168
# File 'app/controllers/collection_objects_controller.rb', line 167

def batch_load
end

#batch_paramsObject (private)


298
299
300
301
# File 'app/controllers/collection_objects_controller.rb', line 298

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

#by_identifierObject

GET /collection_objects/by_identifier/ABCD

Raises:

  • (ActiveRecord::RecordNotFound)

74
75
76
77
78
79
80
# File 'app/controllers/collection_objects_controller.rb', line 74

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_paramsObject (private)


284
285
286
287
288
289
290
291
292
293
294
295
296
# File 'app/controllers/collection_objects_controller.rb', line 284

def collection_object_params
  params.require(:collection_object).permit(
    :total, :preparation_type_id, :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,
    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],
    identifiers_attributes: [:id, :_destroy, :identifier, :namespace_id, :type]
  )
end

#containerizeObject


198
199
200
# File 'app/controllers/collection_objects_controller.rb', line 198

def containerize
  @container_item = ContainerItem.new(contained_object: @collection_object)
end

#createObject

POST /collection_objects POST /collection_objects.json


93
94
95
96
97
98
99
100
101
102
103
104
105
# File 'app/controllers/collection_objects_controller.rb', line 93

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_loadObject


239
240
241
242
243
244
245
246
247
248
249
250
251
252
# File 'app/controllers/collection_objects_controller.rb', line 239

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_loadObject


213
214
215
216
217
218
219
220
221
222
223
224
225
226
# File 'app/controllers/collection_objects_controller.rb', line 213

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_loadObject


181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
# File 'app/controllers/collection_objects_controller.rb', line 181

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

#depictionsObject

GET /collection_objects/depictions/1 GET /collection_objects/depictions/1.json


54
55
# File 'app/controllers/collection_objects_controller.rb', line 54

def depictions
end

#destroyObject

DELETE /collection_objects/1 DELETE /collection_objects/1.json


124
125
126
127
128
129
130
131
132
133
134
135
# File 'app/controllers/collection_objects_controller.rb', line 124

def destroy
  @collection_object.destroy
  respond_to do |format|
    if @collection_object.destroyed?
      format.html { redirect_to destroy_redirect, notice: 'CollectionObject was successfully destroyed.'}
      format.json { head :no_content }
    else
      format.html {redirect_back(fallback_location: (request.referer || root_path), notice: 'CollectionObject was not destroyed, ' + @collection_object.errors.full_messages.join('; '))}
      format.json {render json: @collection_object.errors, status: :unprocessable_entity}
    end
  end
end

#destroy_redirectObject (private)


260
261
262
263
264
265
266
267
268
269
270
# File 'app/controllers/collection_objects_controller.rb', line 260

def destroy_redirect
  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

#downloadObject

GET /collection_objects/download


162
163
164
# File 'app/controllers/collection_objects_controller.rb', line 162

def download
  send_data Export::Download.generate_csv(CollectionObject.where(project_id: sessions_current_project_id), header_converters: []), type: 'text', filename: "collection_objects_#{DateTime.now}.csv"
end

#dwcObject


38
39
40
41
42
43
44
45
# File 'app/controllers/collection_objects_controller.rb', line 38

def dwc
  o = nil
  ActiveRecord::Base.connection_pool.with_connection do
    o = CollectionObject.find(params[:id])
    o.get_dwc_occurrence
  end
  render json: o.dwc_occurrence_attribute_values
end

#dwc_indexObject


32
33
34
35
36
# File 'app/controllers/collection_objects_controller.rb', line 32

def dwc_index
  @objects = filtered_collection_objects.includes(:dwc_occurrence).all.pluck( ::CollectionObject.dwc_attribute_vector  )
  @klass = ::CollectionObject
  render '/dwc_occurrences/dwc_index'
end

#dwcaObject

DEPRECATED GET /collection_objects/dwca/123 # SHOULD BE dwc


27
28
29
30
# File 'app/controllers/collection_objects_controller.rb', line 27

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

#editObject

GET /collection_objects/1/edit


88
89
# File 'app/controllers/collection_objects_controller.rb', line 88

def edit
end

#filter_paramsObject (private)


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
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
# File 'app/controllers/collection_objects_controller.rb', line 317

def filter_params
  a = params.permit(
    :recent,
    Queries::CollectingEvent::Filter::ATTRIBUTES,
    :in_labels,
    :md5_verbatim_label,
    :in_verbatim_locality,
    :geo_json,
    :wkt,
    :radius,
    :start_date,
    :end_date,
    :partial_overlap_dates,
    :ancestor_id, 
    :current_determinations,
    :validity,
    :user_id,
    :user_target,
    :user_date_start,
    :user_date_end,
    :identifier,
    :identifier_start,
    :identifier_end,
    :identifier_exact,
    :namespace_id,
    :never_loaned,
    :loaned,
    :on_loan,
    :type_specimen_taxon_name_id,
    :spatial_geographic_areas,
    otu_ids: [],
    keyword_ids: [],
    collecting_event_ids: [],
    geographic_area_ids: [],
    biocuration_class_ids: [],
    biological_relationship_ids: []
    
    #  collecting_event: {
    #   :recent,
    #   keyword_ids: []
    # }
  )

  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

#filtered_collection_objectsObject (private)


272
273
274
275
276
277
# File 'app/controllers/collection_objects_controller.rb', line 272

def filtered_collection_objects
  Queries::CollectionObject::Filter.
    new(filter_params).all.where(project_id: sessions_current_project_id).
    page(params[:page]).per(params[:per] || 500).
    order('collection_objects.id')
end

#geo_jsonObject

GET /collection_objects/1/geo_json GET /collection_objects/1/geo_json.json


68
69
70
71
# File 'app/controllers/collection_objects_controller.rb', line 68

def geo_json
  ce = @collection_object.collecting_event
  @geo_json = ce.nil? ? nil : ce.to_geo_json_feature
end

#imagesObject

GET /collection_objects/1/images GET /collection_objects/1/images.json


62
63
64
# File 'app/controllers/collection_objects_controller.rb', line 62

def images
  @images = @collection_object.images
end

#indexObject

GET /collecting_events GET /collecting_events.json


10
11
12
13
14
15
16
17
18
19
20
21
22
23
# File 'app/controllers/collection_objects_controller.rb', line 10

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 {
      @collection_objects = filtered_collection_objects
    }
  end
end

#listObject

GET /collection_objects/list


138
139
140
141
142
# File 'app/controllers/collection_objects_controller.rb', line 138

def list
  @collection_objects = CollectionObject.with_project_id(sessions_current_project_id)
    .order(:id)
    .page(params[:page]) #.per(10) #.per(3)
end

#metadata_badgeObject


57
58
# File 'app/controllers/collection_objects_controller.rb', line 57

def 
end

#newObject

GET /collection_objects/new


83
84
85
# File 'app/controllers/collection_objects_controller.rb', line 83

def new
  @collection_object = CollectionObject.new
end

#preview_buffered_batch_loadObject


228
229
230
231
232
233
234
235
236
237
# File 'app/controllers/collection_objects_controller.rb', line 228

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_loadObject


202
203
204
205
206
207
208
209
210
211
# File 'app/controllers/collection_objects_controller.rb', line 202

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_loadObject


170
171
172
173
174
175
176
177
178
179
# File 'app/controllers/collection_objects_controller.rb', line 170

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

#searchObject

GET /collection_object/search


145
146
147
148
149
150
151
# File 'app/controllers/collection_objects_controller.rb', line 145

def search
  if params[:id].blank?
    redirect_to collection_object_path, notice: '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_optionsObject


254
255
256
# File 'app/controllers/collection_objects_controller.rb', line 254

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

#set_collection_objectObject (private)


279
280
281
282
# File 'app/controllers/collection_objects_controller.rb', line 279

def set_collection_object
  @collection_object = CollectionObject.with_project_id(sessions_current_project_id).find(params[:id])
  @recent_object = @collection_object
end

#showObject

GET /collection_objects/1 GET /collection_objects/1.json


49
50
# File 'app/controllers/collection_objects_controller.rb', line 49

def show
end

#updateObject

PATCH/PUT /collection_objects/1 PATCH/PUT /collection_objects/1.json


109
110
111
112
113
114
115
116
117
118
119
120
# File 'app/controllers/collection_objects_controller.rb', line 109

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_mapObject (private)

TODO: not used?


304
305
306
307
308
309
310
311
312
313
314
315
# File 'app/controllers/collection_objects_controller.rb', line 304

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