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ISA studies and ISA assays API endpoints #2586

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b72fe5d
Add API actions
kdp-cloud May 19, 2026
49d4a1f
Add serializers
kdp-cloud May 19, 2026
4cf5410
Add API documentation
kdp-cloud May 19, 2026
0c6343c
Add ISA Assays create API test
kdp-cloud May 19, 2026
9043bfb
Add ISA Assays API update test
kdp-cloud May 19, 2026
aacf905
Add ISA studies API test
kdp-cloud May 19, 2026
c1a4029
Add examples
kdp-cloud May 19, 2026
3946ff7
Change meta block
kdp-cloud May 19, 2026
9b0d49b
correct linked sample type
kdp-cloud May 19, 2026
91737df
Add json support for update method
kdp-cloud May 20, 2026
acf376f
Fix validation rules
kdp-cloud May 21, 2026
9ae8d70
Add input ISA tag
kdp-cloud May 21, 2026
6536694
Add rescue statement
kdp-cloud May 21, 2026
dd22e69
Simplify tests
kdp-cloud May 21, 2026
2e8fcbf
Fix double render error
kdp-cloud May 21, 2026
c2e8ca2
Add need for sample type
kdp-cloud May 21, 2026
c4a24be
Change test to include the assay stream
kdp-cloud May 21, 2026
7a17818
Fix isa_studies_controller test
kdp-cloud May 21, 2026
3994a1a
Add input ISA tag
kdp-cloud May 22, 2026
31bad4f
Copilot comments
kdp-cloud May 22, 2026
e9bcb67
Add JSON format
kdp-cloud May 22, 2026
64196b8
Add show methods
kdp-cloud May 22, 2026
0661efe
Add study ID to serializer
kdp-cloud May 22, 2026
c8cfb29
Add rescue for RecordNotFound
kdp-cloud May 22, 2026
5912b7d
Add tests
kdp-cloud May 22, 2026
1e62816
Add samples to serializers
kdp-cloud May 22, 2026
520d567
Add tests
kdp-cloud May 22, 2026
af7c910
Update post and patch responses
kdp-cloud May 22, 2026
09124a5
Copilot comments
kdp-cloud May 22, 2026
937ff5f
Update API documentation
kdp-cloud May 22, 2026
786e141
Copilot review
kdp-cloud May 26, 2026
178e4ed
Copilot review
kdp-cloud May 26, 2026
33eb42d
Add missing attributes
kdp-cloud May 26, 2026
9a15976
Add return statement
kdp-cloud May 26, 2026
262c90e
Add missing attributes
kdp-cloud May 26, 2026
e157bb4
Copilot review
kdp-cloud May 26, 2026
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110 changes: 81 additions & 29 deletions app/controllers/isa_assays_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@ class ISAAssaysController < ApplicationController
include Seek::Publishing::PublishingCommon

before_action :set_up_instance_variable
before_action :find_requested_item, only: %i[edit update]
before_action :find_requested_item_for_edit, only: %i[edit update]
before_action :find_requested_item_for_show, only: :show
before_action :initialize_isa_assay, only: :create
after_action :rearrange_assay_positions_create_isa_assay, only: :create
after_action :fix_assay_linkage_for_new_assays, only: :create
Expand All @@ -12,6 +13,8 @@ class ISAAssaysController < ApplicationController
before_action :old_attributes, only: :update
after_action :update_sample_json_metadata, only: :update

api_actions :create, :update, :show

def new
study = Study.find(params[:study_id])
new_position =
Expand Down Expand Up @@ -66,7 +69,7 @@ def create
redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
item_id: @isa_assay.assay)
end
format.json { render json: @isa_assay, include: [params[:include]] }
format.json { render json: @isa_assay, include: [params[:include]], status: :created }
end
else
respond_to do |format|
Expand All @@ -76,6 +79,17 @@ def create
end
end

def show
respond_to do |format|
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format.json { render json: @isa_assay, include: [params[:include]] }
format.html do
flash[:notice] = "You have been redirected to the #{t('single_page')} view"
redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
item_id: @isa_assay.assay.id)
end
end
end

def edit
respond_to(&:html)
end
Expand All @@ -93,13 +107,18 @@ def update
end

if @isa_assay.save
flash[:notice] = "The #{t('isa_assay')} was successfully updated.<br/>".html_safe
redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
respond_to do |format|
format.html do
flash[:notice] = "The #{t('isa_assay')} was successfully updated"
redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
item_id: @isa_assay.assay.id)
end
format.json { render json: @isa_assay, include: [params[:include]], status: :ok }
end
else
respond_to do |format|
format.html { render action: 'edit', status: :unprocessable_entity }
format.json { render json: @isa_assay.errors, status: :unprocessable_entity }
format.json { render json: json_api_errors(@isa_assay), status: :unprocessable_entity }
end
end
end
Expand Down Expand Up @@ -193,10 +212,10 @@ def sample_type_params(params)
attribute[:sample_attribute_type_id] = attribute[:sample_attribute_type][:id].to_i
elsif attribute[:sample_attribute_type][:title]
attribute[:sample_attribute_type_id] =
SampleAttributeType.where(title: attribute[:sample_attribute_type][:title]).first.id
SampleAttributeType.where(title: attribute[:sample_attribute_type][:title]).first&.id
end
end
attribute[:unit_id] = Unit.where(symbol: attribute[:unit_symbol]).first.id unless attribute[:unit_symbol].nil?
attribute[:unit_id] = Unit.where(symbol: attribute[:unit_symbol]).first&.id unless attribute[:unit_symbol].nil?
params[:sample_type][:sample_attributes_attributes] << attribute
end
end
Expand All @@ -222,7 +241,7 @@ def set_up_instance_variable
end

def old_attributes
return if @isa_assay.assay.is_assay_stream?
return if @isa_assay.assay.is_assay_stream? || @isa_assay.sample_type.nil?

@old_attributes = @isa_assay.sample_type.sample_attributes.map do |attr|
{ id: attr.id, title: attr.title }
Expand All @@ -243,34 +262,67 @@ def update_sample_json_metadata
UpdateSampleMetadataJob.perform_later(@isa_assay.sample_type, @current_user, attribute_changes)
end

def find_requested_item
def respond_with_error(status=:unprocessable_entity)
respond_to do |format|
format.html do
error_messages = @isa_assay.errors.map do |error|
helpers.content_tag(:li) do
"[" + helpers.content_tag(:b, error.attribute.to_s) + "]: #{ERB::Util.html_escape(error.message)}"
end
end
flash[:error] = helpers.content_tag(:ul) do
helpers.safe_join(error_messages)
end.html_safe
path = if @isa_assay.assay.nil?
assays_path
else
single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
item_id: @isa_assay.assay)
end
redirect_to path
end

format.json { render json: json_api_errors(@isa_assay), status: status }
end
end

def find_requested_item_for_show
@isa_assay = ISAAssay.new
@isa_assay.populate(params[:id])

if @isa_assay.assay.nil?
@isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.")
else
@isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay)
@isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.") if @isa_assay.assay.nil?
return respond_with_error(:not_found) if @isa_assay.errors.any?

@isa_assay.errors.add(:assay, "You are not authorized to view this #{t('isa_assay')}.") unless @isa_assay.assay.can_view?
return respond_with_error(:forbidden) if @isa_assay.errors.any?

unless @isa_assay.assay.is_assay_stream?
@isa_assay.errors.add(:sample_type, 'Sample type not found.') if @isa_assay.sample_type.nil?
return respond_with_error(:not_found) if @isa_assay.errors.any?
end
rescue ActiveRecord::RecordNotFound
render json: { errors: [{ title: 'Not Found', detail: "#{t('isa_assay')} with id '#{params[:id]}' was not found." }] },
status: :not_found
end

def find_requested_item_for_edit
@isa_assay = ISAAssay.new
@isa_assay.populate(params[:id])

@isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.") if @isa_assay.assay.nil?
return respond_with_error(:not_found) if @isa_assay.errors.any?

@isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay)
return respond_with_error(:forbidden) if @isa_assay.errors.any?

# Should not deal with sample type if assay has assay_class assay stream
unless @isa_assay.assay&.is_assay_stream?
if @isa_assay.sample_type.nil?
@isa_assay.errors.add(:sample_type, 'Sample type not found.')
elsif @isa_assay.sample_type.locked?
@isa_assay.errors.add(:sample_type, "The #{t('isa_assay')}'s #{t('sample_type')} is locked by a background process and cannot be edited.")
else
@isa_assay.errors.add(:sample_type, "You are not authorized to edit this #{t('isa_assay')}'s #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type)
end
end
unless @isa_assay.assay.is_assay_stream?
@isa_assay.errors.add(:sample_type, 'Sample type not found.') if @isa_assay.sample_type.nil?
return respond_with_error(:not_found) if @isa_assay.errors.any?

if @isa_assay.errors.any?
error_messages = @isa_assay.errors.map do |error|
"<li>[<b>#{error.attribute.to_s}</b>]: #{error.message}</li>"
end.join('')
flash[:error] = "<ul>#{error_messages}</ul>".html_safe
redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
item_id: @isa_assay.assay)
@isa_assay.errors.add(:sample_type, "The #{t('isa_assay')}'s #{t('sample_type')} is locked by a background process and cannot be edited.") if @isa_assay.sample_type.locked?
@isa_assay.errors.add(:sample_type, "You are not authorized to edit this #{t('isa_assay')}'s #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type)
return respond_with_error(:unprocessable_entity) if @isa_assay.errors.any?
end
end
end
104 changes: 84 additions & 20 deletions app/controllers/isa_studies_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,25 @@ class ISAStudiesController < ApplicationController
include Seek::Publishing::PublishingCommon

before_action :set_up_instance_variable
before_action :find_requested_item, only: %i[edit update]
before_action :find_requested_item_for_edit, only: %i[edit update]
before_action :find_requested_item_for_show, only: :show
before_action :old_attributes, only: %i[update]

after_action :update_sample_json_metadata, only: :update

api_actions :create, :update, :show

def show
respond_to do |format|
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format.json { render json: @isa_study, include: [params[:include]] }
format.html do
flash[:notice] = "You have been redirected to the #{t('single_page')} view"
redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study)
end
end
end

def new
@isa_study = ISAStudy.new({ study: { investigation_id: params[:investigation_id] } })
end
Expand All @@ -26,20 +40,20 @@ def create
@isa_study.study.sample_types = [ @isa_study.source, @isa_study.sample_collection ]

if @isa_study.save
flash[:notice] = "The #{t('isa_study')} was succesfully created.<br/>".html_safe
flash[:notice] = "The #{t('isa_study')} was successfully created"

respond_to do |format|
format.html do
redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study)
end
format.json { render json: @isa_study, include: [params[:include]] }
format.json { render json: @isa_study, include: [params[:include]], status: :created }
end

else
respond_to do |format|
format.html { render action: 'new', status: :unprocessable_entity }
format.json { render json: @isa_study.errors, status: :unprocessable_entity }
format.json { render json: json_api_errors(@isa_study), status: :unprocessable_entity }
end
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end
end
Expand Down Expand Up @@ -69,12 +83,20 @@ def update
end

if @isa_study.save
redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study.id)
respond_to do |format|
format.html do
flash[:notice] = "The #{t('isa_study')} was successfully updated"
redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study.id)

end

format.json { render json: @isa_study, include: [params[:include]], status: :ok }
end
else
respond_to do |format|
format.html { render action: 'edit', status: :unprocessable_entity }
format.json { render json: @isa_study.errors, status: :unprocessable_entity }
format.json { render json: json_api_errors(@isa_study), status: :unprocessable_entity }
end
end
end
Expand Down Expand Up @@ -172,27 +194,69 @@ def set_up_instance_variable
@single_page = true
end

def find_requested_item
def respond_with_error(status=:unprocessable_entity)
respond_to do |format|
format.html do
error_messages = @isa_study.errors.map do |error|
helpers.content_tag(:li) do
"[" + helpers.content_tag(:b, error.attribute.to_s) + "]: #{ERB::Util.html_escape(error.message)}"
end
end
flash[:error] = helpers.content_tag(:ul) do
helpers.safe_join(error_messages)
end.html_safe
path = if @isa_study.study.nil?
studies_path
else
single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study)
end
redirect_to path
end
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format.json { render json: json_api_errors(@isa_study), status: status }
end
end

def find_requested_item_for_show
@isa_study = ISAStudy.new
@isa_study.populate(params[:id])

# Check whether base objects exist
@isa_study.errors.add(:study, "The #{t('isa_study')} was not found.") if @isa_study.study.nil?
@isa_study.errors.add(:study, "You are not authorized to edit this #{t('isa_study')}.") unless requested_item_authorized?(@isa_study.study)
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} source' #{t('sample_type')} not found.") if @isa_study.source.nil?
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} sample' #{t('sample_type')} not found.") if @isa_study.sample_collection.nil?
return respond_with_error(:not_found) if @isa_study.errors.any?

# Check authorizations
@isa_study.errors.add(:study, "You are not authorized to view this #{t('isa_study')}.") unless @isa_study.study.can_view?
return respond_with_error(:forbidden) if @isa_study.errors.any?

rescue ActiveRecord::RecordNotFound
render json: { errors: [{ title: 'Not Found', detail: "#{t('isa_study')} with id '#{params[:id]}' was not found." }] },
status: :not_found
return false
end

def find_requested_item_for_edit
@isa_study = ISAStudy.new
@isa_study.populate(params[:id])

# Check whether base objects exist
@isa_study.errors.add(:study, "The #{t('isa_study')} was not found.") if @isa_study.study.nil?
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} source' #{t('sample_type')} not found.") if @isa_study.source.nil?
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} source' #{t('sample_type')} is locked by a background process.") if @isa_study.source.locked?
@isa_study.errors.add(:sample_type, "You are not authorized to edit the '#{t('isa_study')} source' #{t('sample_type')}.") unless requested_item_authorized?(@isa_study.source)
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} sample' #{t('sample_type')} not found.") if @isa_study.sample_collection.nil?
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} sample' #{t('sample_type')} is locked by a background process.") if @isa_study.sample_collection.locked?
return respond_with_error(:not_found) if @isa_study.errors.any?

# Check authorizations
@isa_study.errors.add(:study, "You are not authorized to edit this #{t('isa_study')}.") unless requested_item_authorized?(@isa_study.study)
@isa_study.errors.add(:sample_type, "You are not authorized to edit the '#{t('isa_study')} source' #{t('sample_type')}.") unless requested_item_authorized?(@isa_study.source)
@isa_study.errors.add(:sample_type, "You are not authorized to edit the '#{t('isa_study')} sample collection' #{t('sample_type')}.") unless requested_item_authorized?(@isa_study.sample_collection)
return respond_with_error(:forbidden) if @isa_study.errors.any?

if @isa_study.errors.any?
error_messages = @isa_study.errors.map do |error|
"<li>[<b>#{error.attribute.to_s}</b>]: #{error.message}</li>"
end.join('')
flash[:error] = "<ul>#{error_messages}</ul>".html_safe
redirect_to single_page_path(id: @isa_study.study.projects.first, item_type: 'study',
item_id: @isa_study.study)
end
# Check whether sample types are locked
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} source' #{t('sample_type')} is locked by a background process.") if @isa_study.source&.locked?
@isa_study.errors.add(:sample_type, "'#{t('isa_study')} sample' #{t('sample_type')} is locked by a background process.") if @isa_study.sample_collection&.locked?
return respond_with_error(:unprocessable_entity) if @isa_study.errors.any?
end
end
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