diff --git a/app/assets/javascripts/sample_types.js b/app/assets/javascripts/sample_types.js
index 2f832bed9f..1d933fd260 100644
--- a/app/assets/javascripts/sample_types.js
+++ b/app/assets/javascripts/sample_types.js
@@ -72,12 +72,10 @@ var SampleTypes = {
attributeTypeChanged: function (e, resetSelection=true) {
//check if it is a controlled vocab, and change the state of the controlled vocab selector if need be
var use_cv = $j(this).find(':selected').data('use-cv');
- var is_ontology = $j(this).find(':selected').data('is-ontology');
var cv_element = $j(this).siblings('.controlled-vocab-block');
if (use_cv) {
var cv_selection = cv_element.find('.controlled-vocab-selection');
cv_selection.find('option').show();
- cv_selection.find(`option[data-is-ontology="${!is_ontology}"]`).hide();
if (resetSelection) cv_selection.find('option:selected').prop("selected", false);
cv_element.show();
}
diff --git a/app/models/sample_attribute.rb b/app/models/sample_attribute.rb
index e64e732a70..bf117fe9cc 100644
--- a/app/models/sample_attribute.rb
+++ b/app/models/sample_attribute.rb
@@ -22,6 +22,9 @@ class SampleAttribute < ApplicationRecord
# sample type exists
attr_reader :deferred_link_to_self
+ # whether this attribute is tied to a controlled vocab which is based on an ontology
+ delegate :ontology_based?, to: :sample_controlled_vocab, allow_nil: true
+
def title=(title)
super
store_accessor_name
diff --git a/app/models/sample_attribute_type.rb b/app/models/sample_attribute_type.rb
index d53e3191f0..f4cac9e336 100644
--- a/app/models/sample_attribute_type.rb
+++ b/app/models/sample_attribute_type.rb
@@ -5,6 +5,7 @@ class SampleAttributeType < ApplicationRecord
has_many :sample_attributes, inverse_of: :sample_attribute_type
has_many :extended_metadata_attributes, inverse_of: :sample_attribute_type
+ has_many :isa_template_attributes, class_name: 'TemplateAttribute', inverse_of: :sample_attribute_type
before_save :set_defaults_attributes
after_initialize :set_defaults_attributes
@@ -108,10 +109,6 @@ def seek_data_file?
base_type == Seek::Samples::BaseType::SEEK_DATA_FILE
end
- def ontology?
- controlled_vocab? && title == 'Ontology'
- end
-
def base_type_handler(additional_options = {})
Seek::Samples::AttributeTypeHandlers::AttributeTypeHandlerFactory.instance.for_base_type(base_type, additional_options)
end
diff --git a/app/views/sample_types/_sample_attribute_form.html.erb b/app/views/sample_types/_sample_attribute_form.html.erb
index 4f01e78e1a..a641b022c3 100644
--- a/app/views/sample_types/_sample_attribute_form.html.erb
+++ b/app/views/sample_types/_sample_attribute_form.html.erb
@@ -55,13 +55,15 @@
|
<%= select_tag "#{field_name_prefix}[sample_attribute_type_id]",
- options_for_select(displayed_sample_attribute_types.sort_by(&:title).sort_by { |t| t.default? ? 0 : 1 }.map { |t| [t.title, t.id,{'data-use-cv'=>t.controlled_vocab? || t.seek_cv_list?,'data-is-ontology'=>t.ontology?, 'data-is-seek-sample'=>t.seek_sample? || t.seek_sample_multi? }] }, attribute_type_id),
+ options_for_select(displayed_sample_attribute_types.sort_by(&:title).sort_by { |t| t.default? ? 0 : 1 }.map do |t|
+ [t.title, t.id,{'data-use-cv': t.controlled_vocab? || t.seek_cv_list?, 'data-is-seek-sample': t.seek_sample? || t.seek_sample_multi? }]
+ end , attribute_type_id),
class: 'form-control sample-type-attribute-type',
disabled: !allow_type_change, data: { attr: "type" } %>
<%= select_tag "#{field_name_prefix}[sample_controlled_vocab_id]",
- options_for_select(SampleControlledVocab.all.map { |scv| [scv.title, scv.id, {'data-editable'=>scv.can_edit?, 'data-is-ontology'=>scv.custom_input?}] },
+ options_for_select(SampleControlledVocab.all.map { |scv| [scv.title, scv.id, {'data-editable': scv.can_edit?}] },
sample_controlled_vocab_id),
include_blank: true,
class: 'form-control controlled-vocab-selection',
diff --git a/app/views/templates/_template_attribute_form.html.erb b/app/views/templates/_template_attribute_form.html.erb
index 0f9a37f8a5..e5a7d3b6ec 100644
--- a/app/views/templates/_template_attribute_form.html.erb
+++ b/app/views/templates/_template_attribute_form.html.erb
@@ -44,13 +44,15 @@
|
<%= select_tag "#{field_name_prefix}[sample_attribute_type_id]",
- options_for_select(SampleAttributeType.all.sort_by(&:title).sort_by { |t| t.default? ? 0 : 1 }.map { |t| [t.title, t.id,{'data-is-cv'=>t.controlled_vocab?,'data-is-ontology'=>t.ontology?, 'data-is-seek-sample'=>t.seek_sample? || t.seek_sample_multi? }] }, attribute_type_id),
+ options_for_select(SampleAttributeType.all.sort_by(&:title).sort_by { |t| t.default? ? 0 : 1 }.map do |t|
+ [t.title, t.id,{'data-is-cv': t.controlled_vocab?,'data-is-seek-sample': t.seek_sample? || t.seek_sample_multi? }]
+ end, attribute_type_id),
class: 'form-control sample-type-attribute-type', data: {attr: "type"} %>
<%= select_tag "#{field_name_prefix}[sample_controlled_vocab_id]",
- options_for_select(SampleControlledVocab.all.map { |scv| [scv.title, scv.id, {'data-editable'=>scv.can_edit?, 'data-is-ontology'=>scv.custom_input?}] },
+ options_for_select(SampleControlledVocab.all.map { |scv| [scv.title, scv.id, {'data-editable': scv.can_edit?}] },
sample_controlled_vocab_id),include_blank: true,
class: 'form-control controlled-vocab-selection', data: {attr: "cv_id"} %>
diff --git a/db/seeds/007_sample_attribute_types.seeds.rb b/db/seeds/007_sample_attribute_types.seeds.rb
index c352b635c5..bf742410f2 100644
--- a/db/seeds/007_sample_attribute_types.seeds.rb
+++ b/db/seeds/007_sample_attribute_types.seeds.rb
@@ -61,12 +61,15 @@
seek_sample_type = SampleAttributeType.find_or_initialize_by(title:'Registered Sample')
seek_sample_type.update(base_type: Seek::Samples::BaseType::SEEK_SAMPLE)
-seek_sample_multi_type = SampleAttributeType.find_or_initialize_by(title:'Registered Sample (multiple)')
+seek_sample_multi_type = SampleAttributeType.find_or_initialize_by(title:'Registered Sample List')
seek_sample_multi_type.update(base_type: Seek::Samples::BaseType::SEEK_SAMPLE_MULTI)
cv_type = SampleAttributeType.find_or_initialize_by(title:'Controlled Vocabulary')
cv_type.update(base_type: Seek::Samples::BaseType::CV)
+cv_list_type = SampleAttributeType.find_or_initialize_by(title:'Controlled Vocabulary List')
+cv_list_type.update(base_type: Seek::Samples::BaseType::CV_LIST)
+
uri_type = SampleAttributeType.find_or_initialize_by(title:'URI')
uri_type.update(base_type: Seek::Samples::BaseType::STRING, regexp: URI.regexp.to_s, placeholder: 'http://www.example.com/123', resolution:'\\0')
@@ -79,12 +82,6 @@
data_file_type = SampleAttributeType.find_or_initialize_by(title: 'Registered Data file')
data_file_type.update(base_type: Seek::Samples::BaseType::SEEK_DATA_FILE)
-ontology_type = SampleAttributeType.find_or_initialize_by(title:'Ontology')
-ontology_type.update(base_type: Seek::Samples::BaseType::CV)
-
-cv_list_type = SampleAttributeType.find_or_initialize_by(title:'Controlled Vocabulary List')
-cv_list_type.update(base_type: Seek::Samples::BaseType::CV_LIST)
-
linked_extended_metadata_type = SampleAttributeType.find_or_initialize_by(title:'Linked Extended Metadata')
linked_extended_metadata_type.update(base_type: Seek::Samples::BaseType::LINKED_EXTENDED_METADATA)
diff --git a/lib/isa_exporter.rb b/lib/isa_exporter.rb
index 8f550f57de..5971017cbe 100644
--- a/lib/isa_exporter.rb
+++ b/lib/isa_exporter.rb
@@ -173,7 +173,7 @@ def convert_ontologies
sample_types = @investigation.studies.map(&:sample_types) + @investigation.assays.map(&:sample_type)
sample_types.flatten.each do |sa|
sa.sample_attributes.each do |atr|
- source_ontologies << atr.sample_controlled_vocab.source_ontology if atr.sample_attribute_type.ontology?
+ source_ontologies << atr.sample_controlled_vocab.source_ontology if atr.ontology_based?
end
end
source_ontologies.uniq.map { |s| { name: s, file: '', version: '', description: '' } }
@@ -487,7 +487,7 @@ def extract_sample_ids(obj, type)
end
def get_ontology_details(sample_attribute, label, vocab_term)
- is_ontology = sample_attribute.sample_attribute_type.ontology?
+ is_ontology = sample_attribute.ontology_based?
iri = ''
if is_ontology
iri =
diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 8386449354..e1dc6476f5 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -12,6 +12,8 @@ namespace :seek do
decouple_extracted_samples_projects
link_sample_datafile_attributes
strip_sample_attribute_pids
+ rename_registered_sample_multiple_attribute_type
+ remove_ontology_attribute_type
]
# these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -48,8 +50,16 @@ namespace :seek do
end
end
+ task(rename_registered_sample_multiple_attribute_type: [:environment]) do
+ attr = SampleAttributeType.find_by(title:'Registered Sample (multiple)')
+ if attr
+ puts "..... Renaming sample attribute type 'Registered Sample (multiple)' to 'Registered Sample List'."
+ attr.update_column(:title, 'Registered Sample List')
+ end
+ end
+
task(strip_sample_attribute_pids: [:environment]) do
- puts '... Stripping Sample Attribute PIds ...'
+ puts '..... Stripping Sample Attribute PIds ...'
n = 0
SampleAttribute.where('pid is NOT NULL AND pid !=?','').each do |attribute|
new_pid = attribute.pid.strip
@@ -58,7 +68,33 @@ namespace :seek do
n += 1
end
end
- puts "... Finished stripping #{n} Sample Attribute PIds."
+ puts "..... Finished stripping #{n} Sample Attribute PIds."
+ end
+
+ task(remove_ontology_attribute_type: [:environment]) do
+ ontology_attr_type = SampleAttributeType.find_by(title:'Ontology')
+ cv_attr_type = SampleAttributeType.find_by(title:'Controlled Vocabulary')
+ if ontology_attr_type
+ puts '..... Removing the Ontology sample attribute type ...'
+ if cv_attr_type
+ if ontology_attr_type.sample_attributes.any?
+ puts "..... Moving #{ontology_attr_type.sample_attributes.count} sample attributes to Controlled Vocabulary"
+ ontology_attr_type.sample_attributes.each do |attr_type|
+ attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id)
+ end
+ end
+ if ontology_attr_type.isa_template_attributes.any?
+ puts "..... Moving #{ontology_attr_type.isa_template_attributes.count} template attributes to Controlled Vocabulary"
+ ontology_attr_type.isa_template_attributes.each do |attr_type|
+ attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id)
+ end
+ end
+
+ ontology_attr_type.destroy
+ else
+ puts '..... Target Controlled Vocabulary attribute type not found'
+ end
+ end
end
task(decouple_extracted_samples_policies: [:environment]) do
diff --git a/test/unit/sample_attribute_test.rb b/test/unit/sample_attribute_test.rb
index 48085edd73..4270b2e7b8 100644
--- a/test/unit/sample_attribute_test.rb
+++ b/test/unit/sample_attribute_test.rb
@@ -330,6 +330,22 @@ class SampleAttributeTest < ActiveSupport::TestCase
assert_equal '', attribute.short_pid
end
+ test 'ontology_based?' do
+ attribute = FactoryBot.create(:sample_sample_attribute, sample_type: FactoryBot.create(:simple_sample_type))
+ refute attribute.ontology_based?
+
+ attribute = FactoryBot.create(:simple_string_sample_attribute, sample_type: FactoryBot.create(:simple_sample_type))
+ refute attribute.ontology_based?
+
+ attribute = FactoryBot.create(:apples_controlled_vocab_attribute, sample_type: FactoryBot.create(:simple_sample_type))
+ refute attribute.sample_controlled_vocab.ontology_based?
+ refute attribute.ontology_based?
+
+ attribute.sample_controlled_vocab = FactoryBot.create(:topics_controlled_vocab)
+ assert attribute.sample_controlled_vocab.ontology_based?
+ assert attribute.ontology_based?
+ end
+
private
def valid_value?(attribute, value)
diff --git a/test/unit/sample_attribute_type_test.rb b/test/unit/sample_attribute_type_test.rb
index 1ecdc5e6d7..eee6d509ad 100644
--- a/test/unit/sample_attribute_type_test.rb
+++ b/test/unit/sample_attribute_type_test.rb
@@ -247,4 +247,22 @@ class SampleAttributeTypeTest < ActiveSupport::TestCase
type = FactoryBot.create(:controlled_vocab_attribute_type)
refute type.seek_data_file?
end
+
+ test 'isa_template_attributes' do
+ type = FactoryBot.create(:age_sample_attribute_type)
+ type2 = FactoryBot.create(:weight_sample_attribute_type)
+
+ ta1 = FactoryBot.create(:template_attribute, sample_attribute_type: type)
+ ta2 = FactoryBot.create(:template_attribute, sample_attribute_type: type)
+ ta3 = FactoryBot.create(:template_attribute, sample_attribute_type: type)
+ ta4 = FactoryBot.create(:template_attribute, sample_attribute_type: type2)
+
+ type.reload
+ template_attributes = type.isa_template_attributes
+ assert_equal 3, template_attributes.count
+ assert_includes template_attributes, ta1
+ assert_includes template_attributes, ta2
+ assert_includes template_attributes, ta3
+ assert_not_includes template_attributes, ta4
+ end
end
|