fixing tests testing fixtures

phac-nml · Mar 22, 2024 · 23db32c · 23db32c
1 parent 0edd505
commit 23db32c
Show file tree

Hide file tree

Showing 3 changed files with 78 additions and 55 deletions.
diff --git a/test/fixtures/samples_workflow_executions.yml b/test/fixtures/samples_workflow_executions.yml
@@ -116,7 +116,7 @@ sample1_irida_next_example_new:
 
 sample1_irida_next_example_completed:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
-  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completed_with_samples, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completed_c, :uuid) %>
   samplesheet_params: {
     "sample": <%= "Sample_#{ActiveRecord::FixtureSet.identify(:sample1, :uuid)}" %>,
     "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
@@ -125,7 +125,7 @@ sample1_irida_next_example_completed:
 
 sample2_irida_next_example_completed:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample2, :uuid) %>
-  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completed_with_samples, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completed_c, :uuid) %>
   samplesheet_params: {
     "sample": <%= "Sample_#{ActiveRecord::FixtureSet.identify(:sample2, :uuid)}" %>,
     "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,

diff --git a/test/fixtures/workflow_executions.yml b/test/fixtures/workflow_executions.yml
@@ -109,10 +109,10 @@ irida_next_example_completed:
   state: "completed"
   blob_run_directory: "not a run dir"
 
-irida_next_example_completed2:
+irida_next_example_error:
   metadata:
     {
-      "workflow_name": "irida_next_example_completed",
+      "workflow_name": "irida_next_example_error",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -127,16 +127,15 @@ irida_next_example_completed2:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
-  run_id: "my_run_id_6"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_error"
+  run_id: "my_run_id_7"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "completed"
-  blob_run_directory: "not a run dir"
+  state: "error"
 
-irida_next_example_completed_with_samples:
+irida_next_example_canceling:
   metadata:
     {
-      "workflow_name": "irida_next_example_completed",
+      "workflow_name": "irida_next_example_canceling",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -151,16 +150,15 @@ irida_next_example_completed_with_samples:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
-  run_id: "my_run_id_with_samples"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_canceling"
+  run_id: "my_run_id_8"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "completed"
-  blob_run_directory: "not a run dir"
+  state: "canceling"
 
-irida_next_example_error:
+irida_next_example_canceled:
   metadata:
     {
-      "workflow_name": "irida_next_example_error",
+      "workflow_name": "irida_next_example_canceled",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -175,15 +173,15 @@ irida_next_example_error:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_error"
-  run_id: "my_run_id_7"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_canceled"
+  run_id: "my_run_id_9"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "error"
+  state: "canceled"
 
-irida_next_example_canceling:
+irida_next_example_running:
   metadata:
     {
-      "workflow_name": "irida_next_example_canceling",
+      "workflow_name": "irida_next_example_running",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -198,15 +196,15 @@ irida_next_example_canceling:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_canceling"
-  run_id: "my_run_id_8"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_running"
+  run_id: "my_run_id_10"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "canceling"
+  state: "running"
 
-irida_next_example_canceled:
+irida_next_example_queued:
   metadata:
     {
-      "workflow_name": "irida_next_example_canceled",
+      "workflow_name": "irida_next_example_queued",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -221,15 +219,35 @@ irida_next_example_canceled:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_canceled"
-  run_id: "my_run_id_9"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_queued"
+  run_id: "my_run_id_11"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "canceled"
+  state: "queued"
 
-irida_next_example_running:
+irida_next_example_new:
   metadata:
+    { "workflow_name": "irida_next_example_new", "workflow_version": "1.0dev" }
+  workflow_params:
     {
-      "workflow_name": "irida_next_example_running",
+      "-r": "dev",
+      "--input": "/blah/samplesheet.csv",
+      "--outdir": "/blah/output",
+    }
+  workflow_type: "DSL2"
+  workflow_type_version: "22.10.7"
+  tags: []
+  workflow_engine: "nextflow"
+  workflow_engine_version: ""
+  workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
+  workflow_url: "https://github.com/phac-nml/irida_next_example_new"
+  run_id: "my_run_id_12"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
+  state: "new"
+
+irida_next_example_completed_a:
+  metadata:
+    {
+      "workflow_name": "irida_next_example_completed",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -244,15 +262,16 @@ irida_next_example_running:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_running"
-  run_id: "my_run_id_10"
-  submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "running"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
+  run_id: "my_run_id_a"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:jeff_doe, :uuid) %>
+  state: "completed"
+  blob_run_directory: "not a run dir"
 
-irida_next_example_queued:
+irida_next_example_completed_b:
   metadata:
     {
-      "workflow_name": "irida_next_example_queued",
+      "workflow_name": "irida_next_example_completed",
       "workflow_version": "1.0dev",
     }
   workflow_params:
@@ -267,14 +286,18 @@ irida_next_example_queued:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_queued"
-  run_id: "my_run_id_11"
-  submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "queued"
+  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
+  run_id: "my_run_id_b"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:jeff_doe, :uuid) %>
+  state: "completed"
+  blob_run_directory: "not a run dir"
 
-irida_next_example_new:
+irida_next_example_completed_c:
   metadata:
-    { "workflow_name": "irida_next_example_new", "workflow_version": "1.0dev" }
+    {
+      "workflow_name": "irida_next_example_completed",
+      "workflow_version": "1.0dev",
+    }
   workflow_params:
     {
       "-r": "dev",
@@ -287,11 +310,11 @@ irida_next_example_new:
   workflow_engine: "nextflow"
   workflow_engine_version: ""
   workflow_engine_parameters: { "engine": "nextflow", "execute_loc": "azure" }
-  workflow_url: "https://github.com/phac-nml/irida_next_example_new"
-  run_id: "my_run_id_12"
-  submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
-  state: "new"
-
+  workflow_url: "https://github.com/phac-nml/irida_next_example_completed"
+  run_id: "my_run_id_c"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:jeff_doe, :uuid) %>
+  state: "completed"
+  blob_run_directory: "not a run dir"
 
 <% (1..25).each do |n| %>
 workflow_execution<%= (n) %>:

diff --git a/test/services/workflow_executions/completion_service_test.rb b/test/services/workflow_executions/completion_service_test.rb
@@ -7,7 +7,7 @@ class CompletionServiceTest < ActiveStorageTestCase
     def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
       # normal/
       # get a new secure token for each workflow execution
-      @workflow_execution_completed = workflow_executions(:irida_next_example_completed)
+      @workflow_execution_completed = workflow_executions(:irida_next_example_completed_a)
       blob_run_directory_a = ActiveStorage::Blob.generate_unique_secure_token
       @workflow_execution_completed.blob_run_directory = blob_run_directory_a
 
@@ -23,7 +23,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       # no_files/
       # get a new secure token for each workflow execution
-      @workflow_execution_no_files = workflow_executions(:irida_next_example_completed2)
+      @workflow_execution_no_files = workflow_executions(:irida_next_example_completed_b)
       blob_run_directory_b = ActiveStorage::Blob.generate_unique_secure_token
       @workflow_execution_no_files.blob_run_directory = blob_run_directory_b
 
@@ -35,7 +35,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       # normal2/
       # get a new secure token for each workflow execution
-      @workflow_execution_with_samples = workflow_executions(:irida_next_example_completed_with_samples)
+      @workflow_execution_with_samples = workflow_executions(:irida_next_example_completed_c)
       blob_run_directory_c = ActiveStorage::Blob.generate_unique_secure_token
       @workflow_execution_with_samples.blob_run_directory = blob_run_directory_c
 
@@ -77,7 +77,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       assert WorkflowExecutions::CompletionService.new(workflow_execution, {}).execute
 
-      assert_equal 'my_run_id_6', workflow_execution.run_id
+      assert_equal 'my_run_id_a', workflow_execution.run_id
       assert_equal 1, workflow_execution.outputs.count
       # original file blob should not be the same as the output file blob, but contain the same file
       output_summary_file = workflow_execution.outputs[0]
@@ -106,7 +106,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       assert WorkflowExecutions::CompletionService.new(workflow_execution, {}).execute
 
-      assert_equal 'my_run_id_6', workflow_execution.run_id
+      assert_equal 'my_run_id_b', workflow_execution.run_id
       # no files should be added to the run
       assert_equal 0, workflow_execution.outputs.count
 
@@ -120,7 +120,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       assert WorkflowExecutions::CompletionService.new(workflow_execution, {}).execute
 
-      assert_equal 'my_run_id_with_samples', workflow_execution.run_id
+      assert_equal 'my_run_id_c', workflow_execution.run_id
 
       assert_equal 2, workflow_execution.samples_workflow_executions.count
       assert_equal 'sample1puid', workflow_execution.samples_workflow_executions[0].sample.puid
@@ -155,7 +155,7 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
 
       assert WorkflowExecutions::CompletionService.new(workflow_execution, {}).execute
 
-      assert_equal 'my_run_id_with_samples', workflow_execution.run_id
+      assert_equal 'my_run_id_c', workflow_execution.run_id
 
       metadata1 = { 'amr' => [{ 'end' => 5678, 'gene' => 'x', 'start' => 1234 },
                               { 'end' => 2, 'gene' => 'y', 'start' => 1 }],