Fix workflow execution completion activities (#791)

* starting a migration to remove group activites with workflow keys * checking if workflow completion service was executed by an automation bot before adding activities * starting to add public activity checks within the workflow execution completion service * adding a new test * fixing translations * fixing rubocop error * fixing migration query * fixing load more button on activities page * fixing load more button on activities page
phac-nml · Oct 1, 2024 · d80ff3f · d80ff3f
1 parent 4d54e70
commit d80ff3f
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Showing 15 changed files with 273 additions and 11 deletions.
diff --git a/app/services/workflow_executions/completion_service.rb b/app/services/workflow_executions/completion_service.rb
@@ -155,6 +155,8 @@ def put_output_attachments_onto_samples
     end
 
     def create_activities # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity, Metrics/MethodLength, Metrics/PerceivedComplexity
+      return unless current_user.automation_bot?
+
       @workflow_execution.samples_workflow_executions&.each do |swe|
         next if swe.metadata.nil? && swe.outputs.empty?
 

diff --git a/app/views/groups/activity.turbo_stream.erb b/app/views/groups/activity.turbo_stream.erb
@@ -1,6 +1,6 @@
 <%= turbo_stream.append "activities" do %>
   <% @activities.each do |activity| %>
-    <%= render Activities::ListItemComponent.new(activity: activity, pagy: @pagy) %>
+    <%= render Activities::ListItemComponent.new(activity: activity) %>
   <% end %>
 <% end %>
 

diff --git a/app/views/projects/activity.turbo_stream.erb b/app/views/projects/activity.turbo_stream.erb
@@ -1,6 +1,6 @@
 <%= turbo_stream.append "activities" do %>
   <% @activities.each do |activity| %>
-    <%= render Activities::ListItemComponent.new(activity: activity, pagy: @pagy) %>
+    <%= render Activities::ListItemComponent.new(activity: activity) %>
   <% end %>
 <% end %>
 

diff --git a/config/locales/en.yml b/config/locales/en.yml
@@ -263,13 +263,13 @@ en:
       transfer_html: "%{user} transferred project from namespace <span class='font-medium text-slate-800 dark:text-slate-300'>%{old_namespace}</span> to <span class='font-medium text-slate-800 dark:text-slate-300'>%{new_namespace}</span>"
       update_html: "%{user} updated project attributes"
     workflow_execution:
-      automated_pipeline_completion:
-        metadata_written_html: Project automation bot wrote pipeline %{href} metadata to sample %{sample_href}
-        outputs_and_metadata_written_html: Project automation bot attached pipeline %{href} outputs and wrote metadata to sample %{sample_href}
-        outputs_written_html: Project automation bot attached pipeline %{href} outputs to sample %{sample_href}
       automated_workflow:
         create_html: "%{user} setup automated pipeline %{href} for the project"
         launch_html: Project automation bot launched pipeline %{href} on sample %{sample_href}
+      automated_workflow_completion:
+        metadata_written_html: Project automation bot wrote pipeline %{href} metadata to sample %{sample_href}
+        outputs_and_metadata_written_html: Project automation bot attached pipeline %{href} outputs and wrote metadata to sample %{sample_href}
+        outputs_written_html: Project automation bot attached pipeline %{href} outputs to sample %{sample_href}
   application:
     errors:
       access_denied: Access Denied.

diff --git a/config/locales/fr.yml b/config/locales/fr.yml
@@ -263,13 +263,13 @@ fr:
       transfer_html: "%{user} transferred project from namespace <span class='font-medium text-slate-800 dark:text-slate-300'>%{old_namespace}</span> to <span class='font-medium text-slate-800 dark:text-slate-300'>%{new_namespace}</span>"
       update_html: "%{user} updated project attributes"
     workflow_execution:
-      automated_pipeline_completion:
-        metadata_written_html: Project automation bot wrote pipeline %{href} metadata to sample %{sample_href}
-        outputs_and_metadata_written_html: Project automation bot attached pipeline %{href} outputs and wrote metadata to sample %{sample_href}
-        outputs_written_html: Project automation bot attached pipeline %{href} outputs to sample %{sample_href}
       automated_workflow:
         create_html: "%{user} setup automated pipeline %{href} for the project"
         launch_html: Project automation bot launched pipeline %{href} on sample %{sample_href}
+      automated_workflow_completion:
+        metadata_written_html: Project automation bot wrote pipeline %{href} metadata to sample %{sample_href}
+        outputs_and_metadata_written_html: Project automation bot attached pipeline %{href} outputs and wrote metadata to sample %{sample_href}
+        outputs_written_html: Project automation bot attached pipeline %{href} outputs to sample %{sample_href}
   application:
     errors:
       access_denied: Access Denied.

diff --git a/db/migrate/20240925155747_remove_group_activities_with_workflow_keys.rb b/db/migrate/20240925155747_remove_group_activities_with_workflow_keys.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+# Migration to remove any activities from a group where an automated workflow key exists
+class RemoveGroupActivitiesWithWorkflowKeys < ActiveRecord::Migration[7.2]
+  def change
+    PublicActivity::Activity.where(
+      trackable_id: Group.as_ids,
+      trackable_type: 'Namespace',
+      key: ['workflow_execution.automated_workflow_completion.outputs_and_metadata_written',
+            'workflow_execution.automated_workflow_completion.metadata_written',
+            'workflow_execution.automated_workflow_completion.outputs_written']
+    ).find_each(&:destroy)
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
diff --git a/test/fixtures/files/blob_outputs/normal4/analysis1.txt b/test/fixtures/files/blob_outputs/normal4/analysis1.txt
@@ -0,0 +1 @@
+some text in here
diff --git a/test/fixtures/files/blob_outputs/normal4/analysis2.txt b/test/fixtures/files/blob_outputs/normal4/analysis2.txt
@@ -0,0 +1 @@
+and more in here
diff --git a/test/fixtures/files/blob_outputs/normal4/analysis3.txt b/test/fixtures/files/blob_outputs/normal4/analysis3.txt
@@ -0,0 +1 @@
+even more text here
diff --git a/test/fixtures/files/blob_outputs/normal4/iridanext.output.json b/test/fixtures/files/blob_outputs/normal4/iridanext.output.json
@@ -0,0 +1,58 @@
+{
+    "files": {
+        "global": [
+            {
+                "path": "summary.txt"
+            }
+        ],
+        "samples": {
+            "INXT_SAM_AAAAAAAAA3": [
+                {
+                    "path": "analysis1.txt"
+                },
+                {
+                    "path": "analysis2.txt"
+                }
+            ],
+            "INXT_SAM_AAAAAAAAA4": [
+                {
+                    "path": "analysis3.txt"
+                }
+            ]
+        }
+    },
+    "metadata": {
+        "samples": {
+            "INXT_SAM_AAAAAAAAA3": {
+                "organism": "an organism",
+                "amr": [
+                    {
+                        "gene": "x",
+                        "start": 1234,
+                        "end": 5678
+                    },
+                    {
+                        "gene": "y",
+                        "start": 1,
+                        "end": 2
+                    }
+                ]
+            },
+            "INXT_SAM_AAAAAAAAA4": {
+                "organism": "a different organism",
+                "amr": [
+                    {
+                        "gene": "x",
+                        "start": 2345,
+                        "end": 6789
+                    },
+                    {
+                        "gene": "y",
+                        "start": 2,
+                        "end": 3
+                    }
+                ]
+            }
+        }
+    }
+}
diff --git a/test/fixtures/files/blob_outputs/normal4/summary.txt b/test/fixtures/files/blob_outputs/normal4/summary.txt
@@ -0,0 +1 @@
+This is a text file.
diff --git a/test/fixtures/samples_workflow_executions.yml b/test/fixtures/samples_workflow_executions.yml
@@ -186,6 +186,24 @@ sample42_irida_next_example_completing_f:
     "fastq_2": ""
   }
 
+sampleA_irida_next_example_completing_g:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sampleA, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_g, :uuid) %>
+  samplesheet_params: {
+    "sample": INXT_SAM_AAAAAAAAA3,
+    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
+    "fastq_2": ""
+  }
+
+sampleB_irida_next_example_completing_g:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sampleB, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_g, :uuid) %>
+  samplesheet_params: {
+    "sample": INXT_SAM_AAAAAAAAA4,
+    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
+    "fastq_2": ""
+  }
+
 sample46_irida_next_example_completed_with_output:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample46, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completed_with_output, :uuid) %>

diff --git a/test/fixtures/workflow_executions.yml b/test/fixtures/workflow_executions.yml
@@ -439,6 +439,29 @@ irida_next_example_completing_f:
   email_notification: true
   cleaned: false
 
+irida_next_example_completing_g:
+  <<: *DEFAULTS
+  metadata:
+    {
+      "workflow_name": "phac-nml/iridanextexample",
+      "workflow_version": "1.0.2",
+    }
+  workflow_params:
+    {
+      "input": "/blah/samplesheet.csv",
+      "outdir": "/blah/output",
+    }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
+  run_id: "my_run_id_g"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:projectA_automation_bot, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:projectA_namespace, :uuid) %>
+  state: "completing"
+  blob_run_directory: "not a run dir"
+  update_samples: true
+  email_notification: true
+  cleaned: false
+
 irida_next_example_completed_with_output:
   <<: *DEFAULTS
   metadata: