fix: attached research_plans in screens not being imported from colle…

…ction * fix: attached research_plans in screens not being imported from collection wellplates not being imported from collection * style: rubocop --------- Co-authored-by: Tasnim Mehzabin <[email protected]> Refs: #1671
ComPlat · Dec 21, 2023 · b44edaa · b44edaa
1 parent a08e6a1
commit b44edaa
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Showing 2 changed files with 26 additions and 15 deletions.
diff --git a/lib/export/export_collections.rb b/lib/export/export_collections.rb
@@ -12,8 +12,8 @@ def initialize(export_id, collection_ids, format = 'zip', nested = false, gate =
       @nested = nested
       @gt = gate
 
-      @file_path = Rails.public_path.join( format, "#{export_id}.#{format}")
-      @schema_file_path = Rails.public_path.join( 'json', 'schema.json')
+      @file_path = Rails.public_path.join(format, "#{export_id}.#{format}")
+      @schema_file_path = Rails.public_path.join('json', 'schema.json')
 
       @data = {}
       @uuids = {}
@@ -122,8 +122,8 @@ def prepare_data
       collections.each do |collection|
         # fetch collection
         fetch_one(collection, {
-          'user_id' => 'User'
-        })
+                    'user_id' => 'User',
+                  })
         fetch_samples collection
         fetch_chemicals collection
         fetch_reactions collection
@@ -154,11 +154,11 @@ def fetch_samples(collection)
                    'fingerprint_id' => 'Fingerprint',
                    'created_by' => 'User',
                    'user_id' => 'User',
-      })
+                 })
       fetch_many(collection.collections_samples, {
                    'collection_id' => 'Collection',
                    'sample_id' => 'Sample',
-      })
+                 })
 
       # loop over samples and fetch sample properties
       samples.each do |sample|
@@ -167,10 +167,10 @@ def fetch_samples(collection)
         fetch_one(sample.molecule_name, {
                     'molecule_id' => 'Molecule',
                     'user_id' => 'User',
-        })
+                  })
         fetch_many(sample.residues, {
                      'sample_id' => 'Sample',
-        })
+                   })
 
         segment, @attachments = Labimotion::Export.fetch_segments(sample, @attachments, &method(:fetch_one))
         @segments += segment if segment.present?
@@ -224,7 +224,9 @@ def fetch_reactions(collection)
     end
 
     def fetch_elements(collection)
-      @segments, @attachments = Labimotion::Export.fetch_elements(collection, @segments, @attachments, method(:fetch_many), method(:fetch_one), method(:fetch_containers))
+      @segments, @attachments = Labimotion::Export.fetch_elements(collection, @segments, @attachments,
+                                                                  method(:fetch_many), method(:fetch_one),
+                                                                  method(:fetch_containers))
     end
 
     def fetch_wellplates(collection)
@@ -263,6 +265,11 @@ def fetch_screens(collection)
                      'wellplate_id' => 'Wellplate',
                    })
 
+        fetch_many(screen.research_plans_screens, {
+                     'screen_id' => 'Screen',
+                     'research_plan_id' => 'ResearchPlan',
+                   })
+
         segment, @attachments = Labimotion::Export.fetch_segments(screen, @attachments, &method(:fetch_one))
         @segments += segment if segment.present?
 
@@ -339,7 +346,9 @@ def fetch_containers(containable)
                         'containable_id' => containable_type,
                         'parent_id' => 'Container',
                       })
-            @datasets += Labimotion::Export.fetch_datasets(attachment_container.dataset, &method(:fetch_one) ) if attachment_container.dataset.present?
+            if attachment_container.dataset.present?
+              @datasets += Labimotion::Export.fetch_datasets(attachment_container.dataset, &method(:fetch_one))
+            end
             fetch_many(attachment_container.attachments, {
                          'attachable_id' => 'Container',
                          'created_by' => 'User',

diff --git a/lib/import/import_collections.rb b/lib/import/import_collections.rb
@@ -92,12 +92,12 @@ def import
         import_residues
         import_reactions
         import_reactions_samples
- #       import_elements if @gt == false
- #       import_elements_samples if @gt == false
+        # import_elements if @gt == false
+        # import_elements_samples if @gt == false
         import_wellplates if @gt == false
         import_wells if @gt == false
-        import_screens if @gt == false
         import_research_plans if @gt == false
+        import_screens if @gt == false
         import_containers
         import_segments
         import_datasets
@@ -397,7 +397,6 @@ def import_reactions_samples
       end
     end
 
-
     def import_elements
       Labimotion::Import.import_elements(@data, @instances, @gt, @current_user_id, method(:fetch_many), &method(:update_instances!))
     end
@@ -442,7 +441,7 @@ def import_wells
           'updated_at',
         ).merge(
           wellplate: @instances.fetch('Wellplate').fetch(fields.fetch('wellplate_id')),
-          sample: @instances.fetch('Sample').fetch(fields.fetch('sample_id'), nil),
+          sample: @instances.fetch('Sample', nil)&.fetch(fields.fetch('sample_id'), nil),
         ))
 
         # add reaction to the @instances map
@@ -470,6 +469,9 @@ def import_screens
           wellplates: fetch_many(
             'Wellplate', 'ScreensWellplate', 'screen_id', 'wellplate_id', uuid
           ),
+          research_plans: fetch_many(
+            'ResearchPlan', 'ResearchPlansScreen', 'screen_id', 'research_plan_id', uuid
+          ),
         ))
 
         # create the root container like with samples