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add test for assay samples
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@kdp-cloud
kdp-cloud committed Nov 21, 2023
1 parent 14085e5 commit ae138a6
Showing 1 changed file with 216 additions and 13 deletions.
229 changes: 216 additions & 13 deletions test/functional/single_pages_controller_test.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -100,30 +100,233 @@ def setup
},
contributor: other_user.person)

assay_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
# Create a 'private' assay
FactoryBot.create(:assay, sample_type: assay_sample_type, study: accessible_study, contributor: other_user.person)
# Create a 'private' assay in an assay stream
assay_1_stream_1_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
assay_1_stream_1 = FactoryBot.create(:assay, position: 0, sample_type: assay_1_stream_1_sample_type, study: accessible_study, contributor: current_user.person)
assay_2_stream_1_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, linked_sample_type: assay_1_stream_1_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
assay_2_stream_1 = FactoryBot.create(:assay, position:1, sample_type: assay_2_stream_1_sample_type, study: accessible_study, contributor: other_user.person)

# Create an assay stream with all assays visible
assay_1_stream_2_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
assay_1_stream_2 = FactoryBot.create(:assay, position: 0, sample_type: assay_1_stream_2_sample_type, study: accessible_study, contributor: current_user.person)
assay_2_stream_2_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, linked_sample_type: assay_1_stream_2_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
assay_2_stream_2 = FactoryBot.create(:assay, position:1, sample_type: assay_2_stream_2_sample_type, study: accessible_study, contributor: current_user.person)

# create samples in second assay stream with viewing permission

assay_1_stream_2_sample =
FactoryBot.create(:sample,
title: 'Assay 1 - stream 2 - sample 1',
sample_type: assay_1_stream_2_sample_type,
project_ids: [project.id],
data: {
Input: [study_sample.id],
'Protocol Assay 1': 'Protocol Assay 1',
'Assay 1 parameter value 1': 'Assay 1 parameter value 1',
'Assay 1 parameter value 2': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 1 parameter value 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'Assay 1 parameter value 3': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 1 parameter value 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'Extract Name': 'Extract 1 stream 2',
'other material characteristic 1': 'other material characteristic 1',
'other material characteristic 2': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'other material characteristic 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'other material characteristic 3': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'other material characteristic 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label},
contributor: current_user.person)

assay_1_stream_2_hidden_sample =
FactoryBot.create(:sample,
title: 'Assay 1 - stream 2 - sample 2',
sample_type: assay_1_stream_2_sample_type,
project_ids: [project.id],
data: {
Input: [study_sample.id],
'Protocol Assay 1': 'Protocol Assay 1',
'Assay 1 parameter value 1': 'Assay 1 parameter value 1',
'Assay 1 parameter value 2': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 1 parameter value 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'Assay 1 parameter value 3': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 1 parameter value 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'Extract Name': 'Extract 1 stream 2',
'other material characteristic 1': 'other material characteristic 1',
'other material characteristic 2': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'other material characteristic 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'other material characteristic 3': assay_1_stream_2_sample_type
.sample_attributes
.find_by(title: 'other material characteristic 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label},
contributor: other_user.person)

assay_2_stream_2_sample =
FactoryBot.create(:sample,
title: 'Assay 2 - stream 2 - sample 1',
sample_type: assay_2_stream_2_sample_type,
project_ids: [project.id],
data: {
Input: [assay_1_stream_2_sample.id],
'Protocol Assay 2': 'Protocol Assay 2',
'Assay 2 parameter value 1': 'Assay 2 parameter value 1',
'Assay 2 parameter value 2': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 2 parameter value 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'Assay 2 parameter value 3': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 2 parameter value 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'File Name': 'file 1 stream 2',
'Data file comment 1': 'Data file comment 1',
'Data file comment 2': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Data file comment 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label,
'Data file comment 3': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Data file comment 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.first
.label},
contributor: current_user.person)

assay_2_stream_2_hidden_sample =
FactoryBot.create(:sample,
title: 'Assay 2 - stream 2 - sample 2',
sample_type: assay_2_stream_2_sample_type,
project_ids: [project.id],
data: {
Input: [assay_1_stream_2_sample.id],
'Protocol Assay 2': 'Protocol Assay 2',
'Assay 2 parameter value 1': 'Assay 2 parameter value 1',
'Assay 2 parameter value 2': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 2 parameter value 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'Assay 2 parameter value 3': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Assay 2 parameter value 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'File Name': 'file 1 stream 2',
'Data file comment 1': 'Data file comment 1',
'Data file comment 2': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Data file comment 2')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label,
'Data file comment 3': assay_2_stream_2_sample_type
.sample_attributes
.find_by(title: 'Data file comment 3')
.sample_controlled_vocab
.sample_controlled_vocab_terms
.second
.label},
contributor: other_user.person)


get :export_isa, params: { id: project.id, investigation_id: investigation.id }

assert_response :success
json_investigation = JSON.parse(response.body)
assert json_investigation['studies'].map { |s| s['title'] }.include? accessible_study.title
study_json = json_investigation['studies'].first
assert study_json['assays'].blank?

sample_names = study_json['materials']['samples'].map { |sample| sample['name'] }
# Only one assay should end up in 1 assay stream in the ISA JSON
assert_equal accessible_study.assays.count, 4
assert_equal study_json['assays'].count, 1

sample_ids = study_json['materials']['samples'].map { |sample| sample['@id'] }

# Check whether permitted samples end up in the materials
assert sample_ids.include?("#sample/#{study_sample.id}")
refute sample_ids.include?("#sample/#{hidden_study_sample.id}")

# Check whether permitted study samples end up in the study's processSequence
study_output_ids = []
study_json['processSequence'].map do |process|
process['outputs'].map { |output| study_output_ids.push(output['@id']) }
end

assert study_output_ids.include? "#sample/#{study_sample.id}"
refute study_output_ids.include? "#sample/#{hidden_study_sample.id}"

assay_json = study_json['assays'].first

# Check otherMaterials
other_material_ids = assay_json['materials']['otherMaterials'].map { |om| om['@id'] }
assert other_material_ids.include? "#other_material/#{assay_1_stream_2_sample.id}"
refute other_material_ids.include? "#other_material/#{assay_1_stream_2_hidden_sample.id}"

assert sample_names.include?(study_sample.title)
refute sample_names.include?(hidden_study_sample.title)
# Check dataFiles
data_file_ids = assay_json['dataFiles'].map { |df| df['@id'] }
assert data_file_ids.include? "#data_file/#{assay_2_stream_2_sample.id}"
refute data_file_ids.include? "#data_file/#{assay_2_stream_2_hidden_sample.id}"

study_process_sequence = study_json['processSequence']
output_ids=[]
study_process_samples = study_process_sequence.map do |process|
process['outputs'].map { |output| output_ids.push(output['@id']) }
# Check whether permitted study samples end up in the assay's processSequence
assay_output_ids = []
assay_json['processSequence'].map do |process|
process['outputs'].map { |output| assay_output_ids.push(output['@id']) }
end

assert output_ids.include? "#sample/#{study_sample.id}"
refute output_ids.include? "#sample/#{hidden_study_sample.id}"
assert assay_output_ids.include? "#other_material/#{assay_1_stream_2_sample.id}"
assert assay_output_ids.include? "#data_file/#{assay_2_stream_2_sample.id}"
refute assay_output_ids.include? "#other_material/#{assay_1_stream_2_hidden_sample.id}"
refute assay_output_ids.include? "#data_file/#{assay_2_stream_2_hidden_sample.id}"
end
end

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