refactoring

ComPlat · Jan 22, 2025 · f83522d · f83522d
1 parent 1344be1
commit f83522d
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Showing 5 changed files with 54 additions and 82 deletions.
diff --git a/...apps/mydb/elements/details/researchPlans/attachmentsTab/ResearchPlanDetailsAttachments.js b/...apps/mydb/elements/details/researchPlans/attachmentsTab/ResearchPlanDetailsAttachments.js
@@ -59,7 +59,7 @@ class ResearchPlanDetailsAttachments extends Component {
     this.confirmAttachmentImport = this.confirmAttachmentImport.bind(this);
     this.showImportConfirm = this.showImportConfirm.bind(this);
     this.hideImportConfirm = this.hideImportConfirm.bind(this);
-    this.checkUserQuota = this.checkUserQuota.bind(this);
+    this.isUserQuotaExceeded = this.isUserQuotaExceeded.bind(this);
   }
 
   componentDidMount() {
@@ -220,7 +220,7 @@ class ResearchPlanDetailsAttachments extends Component {
     this.hideImportConfirm(attachment.id);
   }
 
-  checkUserQuota() {
+  isUserQuotaExceeded() {
     const { filteredAttachments } = this.state;
     const totalSize = filteredAttachments.filter((attachment) => attachment.is_new && !attachment.is_deleted)
       .reduce((acc, attachment) => acc + attachment.filesize, 0);
@@ -369,7 +369,7 @@ class ResearchPlanDetailsAttachments extends Component {
                 )}
               </div>
             ))}
-            <Alert variant="warning" show={this.checkUserQuota()}>
+            <Alert variant="warning" show={this.isUserQuotaExceeded()}>
               Uploading attachments will fail; User quota will be exceeded.
             </Alert>
           </>

diff --git a/app/javascript/src/components/container/ContainerDatasetModalContent.js b/app/javascript/src/components/container/ContainerDatasetModalContent.js
@@ -83,7 +83,7 @@ export class ContainerDatasetModalContent extends Component {
     this.handleAttachmentRemove = this.handleAttachmentRemove.bind(this);
     this.handleAttachmentBackToInbox = this.handleAttachmentBackToInbox.bind(this);
     this.classifyAttachments = this.classifyAttachments.bind(this);
-    this.checkUserQuota = this.checkUserQuota.bind(this);
+    this.isUserQuotaExceeded = this.isUserQuotaExceeded.bind(this);
     this.state.attachmentGroups = this.classifyAttachments(props.datasetContainer.attachments);
   }
 
@@ -468,7 +468,7 @@ export class ContainerDatasetModalContent extends Component {
     );
   }
 
-  checkUserQuota() {
+  isUserQuotaExceeded() {
     const { filteredAttachments } = this.state;
     const totalSize = filteredAttachments.filter((attachment) => attachment.is_new === true && !attachment.is_deleted)
       .reduce((acc, attachment) => acc + attachment.filesize, 0);
@@ -649,7 +649,7 @@ export class ContainerDatasetModalContent extends Component {
                   && renderGroup(attachmentGroups.Processed[groupName], `Processed: ${groupName}`, groupName))}
               {attachmentGroups.Combined.length > 0 && renderGroup(attachmentGroups.Combined, 'Combined')}
             </div>
-            <Alert variant="warning" show={this.checkUserQuota()}>
+            <Alert variant="warning" show={this.isUserQuotaExceeded()}>
               Uploading attachments will fail; User quota will be exceeded.
             </Alert>
           </>

diff --git a/app/models/attachment.rb b/app/models/attachment.rb
@@ -277,7 +277,7 @@ def delete_file_and_thumbnail
     attachment_attacher.destroy
   end
 
-  def check_user_quota
+  def user_quota_exceeded?
     user = User.find(created_for.nil? ? created_by : created_for)
     if (user.used_space + attachment_data['metadata']['size']) > user.available_space &&
        !user.available_space.zero?
@@ -296,7 +296,7 @@ def attach_file
     attachment_attacher.attach(File.open(file_path, binmode: true))
     raise 'File to large' unless valid?
 
-    raise 'User quota exceeded' unless check_user_quota
+    raise 'User quota exceeded' unless user_quota_exceeded?
 
     attachment_attacher.create_derivatives
 

diff --git a/db/functions/calculate_collection_space_v01.sql b/db/functions/calculate_collection_space_v01.sql
@@ -3,42 +3,17 @@ returns bigint
 language plpgsql
 as $function$
 declare
-    used_space_samples bigint default 0;
-    used_space_reactions bigint default 0;
-    used_space_wellplates bigint default 0;
-    used_space_screens bigint default 0;
-    used_space_research_plans bigint default 0;
     used_space bigint default 0;
+    element_types text[] := array['Sample', 'Reaction', 'Wellplate', 'Screen', 'ResearchPlan'];
+    element_table text;
+    element_space bigint;
 begin
-    select sum(calculate_element_space(sample_id, 'Sample')) into used_space_samples
-    from collections_samples
-    where collection_id = collectionId;
-
-    used_space = COALESCE(used_space_samples,0);
-
-    select sum(calculate_element_space(reaction_id, 'Reaction')) into used_space_reactions
-    from collections_reactions
-    where collection_id = collectionId;
-
-    used_space = used_space + COALESCE(used_space_reactions,0);
-
-    select sum(calculate_element_space(wellplate_id, 'Wellplate')) into used_space_wellplates
-    from collections_wellplates
-    where collection_id = collectionId;
-
-    used_space = used_space + COALESCE(used_space_wellplates,0);
-
-    select sum(calculate_element_space(screen_id, 'Screen')) into used_space_screens
-    from collections_screens
-    where collection_id = collectionId;
-
-    used_space = used_space + COALESCE(used_space_screens,0);
-
-    select sum(calculate_element_space(research_plan_id, 'ResearchPlan')) into used_space_research_plans
-    from collections_research_plans
-    where collection_id = collectionId;
-
-    used_space = used_space + COALESCE(used_space_research_plans,0);
-
-    return COALESCE(used_space,0);
-end;$function$;
+    foreach element_table in array element_types loop
+        execute format('select sum(calculate_element_space(id, $1)) from collections_%s where collection_id = $2', lower(element_table))
+        into element_space
+        using element_table, collectionId;
+        used_space := used_space + coalesce(element_space, 0);
+    end loop;
+    return coalesce(used_space, 0);
+end;
+$function$;
diff --git a/db/schema.rb b/db/schema.rb
@@ -147,6 +147,8 @@
     t.datetime "created_at", precision: 6, null: false
     t.datetime "updated_at", precision: 6, null: false
     t.string "short_label"
+    t.string "ancestry"
+    t.index ["ancestry"], name: "index_cellline_samples_on_ancestry"
   end
 
   create_table "channels", id: :serial, force: :cascade do |t|
@@ -2171,6 +2173,23 @@
         END;
       $function$
   SQL
+  create_function :lab_record_layers_changes, sql_definition: <<-'SQL'
+      CREATE OR REPLACE FUNCTION public.lab_record_layers_changes()
+       RETURNS trigger
+       LANGUAGE plpgsql
+      AS $function$
+      BEGIN
+          BEGIN
+              INSERT INTO layer_tracks (name, label, description, properties, identifier, created_by, created_at, updated_by, updated_at, deleted_by, deleted_at)
+              VALUES (OLD.name, OLD.label, OLD.description, OLD.properties, OLD.identifier, OLD.created_by, OLD.created_at, OLD.updated_by, OLD.updated_at, OLD.deleted_by, OLD.deleted_at);
+          EXCEPTION
+              WHEN OTHERS THEN
+                  -- Ensure the main operation still completes successfully
+          END;
+          RETURN NEW;
+      END;
+      $function$
+  SQL
   create_function :calculate_dataset_space, sql_definition: <<-'SQL'
       CREATE OR REPLACE FUNCTION public.calculate_dataset_space(cid integer)
        RETURNS bigint
@@ -2214,45 +2233,20 @@
        LANGUAGE plpgsql
       AS $function$
       declare
-          used_space_samples bigint default 0;
-          used_space_reactions bigint default 0;
-          used_space_wellplates bigint default 0;
-          used_space_screens bigint default 0;
-          used_space_research_plans bigint default 0;
           used_space bigint default 0;
+          element_types text[] := array['Sample', 'Reaction', 'Wellplate', 'Screen', 'ResearchPlan'];
+          element_table text;
+          element_space bigint;
       begin
-          select sum(calculate_element_space(sample_id, 'Sample')) into used_space_samples
-          from collections_samples
-          where collection_id = collectionId;
-
-          used_space = COALESCE(used_space_samples,0);
-          
-          select sum(calculate_element_space(reaction_id, 'Reaction')) into used_space_reactions
-          from collections_reactions
-          where collection_id = collectionId;
-
-          used_space = used_space + COALESCE(used_space_reactions,0);
-
-          select sum(calculate_element_space(wellplate_id, 'Wellplate')) into used_space_wellplates
-          from collections_wellplates
-          where collection_id = collectionId;
-
-          used_space = used_space + COALESCE(used_space_wellplates,0);
-
-          select sum(calculate_element_space(screen_id, 'Screen')) into used_space_screens
-          from collections_screens
-          where collection_id = collectionId;
-
-          used_space = used_space + COALESCE(used_space_screens,0);
-
-          select sum(calculate_element_space(research_plan_id, 'ResearchPlan')) into used_space_research_plans
-          from collections_research_plans
-          where collection_id = collectionId;
-
-          used_space = used_space + COALESCE(used_space_research_plans,0);
-
-          return COALESCE(used_space,0);
-      end;$function$
+          foreach element_table in array element_types loop
+              execute format('select sum(calculate_element_space(id, $1)) from collections_%s where collection_id = $2', lower(element_table))
+              into element_space
+              using element_table, collectionId;
+              used_space := used_space + coalesce(element_space, 0);
+          end loop;
+          return coalesce(used_space, 0);
+      end;
+      $function$
   SQL
   create_function :calculate_used_space, sql_definition: <<-'SQL'
       CREATE OR REPLACE FUNCTION public.calculate_used_space(userid integer)
@@ -2364,6 +2358,9 @@
   create_trigger :logidze_on_wells, sql_definition: <<-SQL
       CREATE TRIGGER logidze_on_wells BEFORE INSERT OR UPDATE ON public.wells FOR EACH ROW WHEN ((COALESCE(current_setting('logidze.disabled'::text, true), ''::text) <> 'on'::text)) EXECUTE FUNCTION logidze_logger('null', 'updated_at')
   SQL
+  create_trigger :lab_trg_layers_changes, sql_definition: <<-SQL
+      CREATE TRIGGER lab_trg_layers_changes AFTER UPDATE ON public.layers FOR EACH ROW EXECUTE FUNCTION lab_record_layers_changes()
+  SQL
 
   create_view "v_samples_collections", sql_definition: <<-SQL
       SELECT cols.id AS cols_id,