Merge pull request #1420 from sanger/develop

Develop to master

.release-version

@@ -1 +1 @@
-3.37.1
+3.38.0

Gemfile.lock

@@ -225,7 +225,7 @@ GEM
       digest
       net-protocol
       timeout
-    nio4r (2.5.8)
+    nio4r (2.5.9)
     nokogiri (1.15.2)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
@@ -244,7 +244,7 @@ GEM
       byebug (~> 11.0)
       pry (~> 0.13.0)
     public_suffix (4.0.7)
-    puma (5.6.4)
+    puma (5.6.7)
       nio4r (~> 2.0)
     racc (1.6.2)
     rack (2.2.7)

app/models/labware_creators/multi_stamp_tubes.rb

@@ -111,11 +111,11 @@ def request_hash(transfer, child_plate)
       }
     end
 
-    def submission_options_from_config
-      @submission_options_from_config ||= purpose_config.submission_options
-    end
-
-    def create_submission_from_parent_tubes
+    # Retrieves the submission parameters
+    #
+    # Returns: a hash containing the submission parameters
+    # Adds: errors if there is more than one submission specified
+    def configured_params
       submission_options_from_config = purpose_config.submission_options
 
       # if there's more than one appropriate submission, we can't know which one to choose,
@@ -126,25 +126,45 @@ def create_submission_from_parent_tubes
       end
 
       # otherwise, create a submission with params specified in the config
-      configured_params = submission_options_from_config.values.first
+      submission_options_from_config.values.first
+    end
 
-      create_submission(configured_params)
+    # Returns a list of parent tube uuids
+    def asset_uuids
+      parent_tubes.map { |tube| tube.receptacle.uuid }
     end
 
-    # Project and Study are specified on the Submission Template (submission_parameters field)
-    # It's important that autodetect_studies_projects is false here,
-    # to make sure the Study is set explicitly, since it controls data access
-    def create_submission(configured_params)
-      asset_uuids = parent_tubes.map { |tube| tube.receptacle.uuid }
+    # Autodetection looks at the Study and Project already linked to the aliquots and uses that.
+    #
+    # Otherwise, Project and Study can be specified explicitly on the Submission Template
+    # (submission_parameters field) if autodetection is not appropriate (for instance in Cardinal,
+    # where one tube will contain samples from multiple different studies).
+    def autodetect_studies_project
+      configured_params[:autodetect_studies_project] || false
+    end
 
+    # Creates a submission in Sequencescape based on the parent tubes
+    def create_submission_from_parent_tubes
       sequencescape_submission_parameters = {
         template_name: configured_params[:template_name],
         request_options: configured_params[:request_options],
-        asset_groups: [{ assets: asset_uuids, autodetect_studies_projects: false }],
+        asset_groups: [{ assets: asset_uuids, autodetect_studies_projects: autodetect_studies_project }],
         api: api,
         user: user_uuid
       }
 
+      create_submission(sequencescape_submission_parameters)
+    end
+
+    # Creates a submission in Sequencescape
+    #
+    # Parameters:
+    # - sequencescape_submission_parameters: a hash containing the parameters for the submission
+    #
+    # Returns: true if submission created, false otherwise
+    # Sets: @submission_uuid if submission created
+    # Adds: errors if submission not created
+    def create_submission(sequencescape_submission_parameters)
       ss = SequencescapeSubmission.new(sequencescape_submission_parameters)
       submission_created = ss.save