Merge pull request #347 from umccr/update-srm-convention

Updated SequenceRunManager with latest convention change request

lib/workload/stateless/stacks/bs-runs-upload-manager/Readme.md

@@ -25,7 +25,7 @@ The two steps of the statemachine are:
 1. Generate a V2 Samplesheet and reupload it
 2. Launch an ICAv1 tes task that runs the bs runs upload command
 
-This statemachine will subscribe to the orcabus.srm events and trigger the statemachine when a new run is detected.
+This statemachine will subscribe to the `orcabus.sequencerunmanager` events and trigger the statemachine when a new run is detected.
 
 ![](images/bs_runs_upload_manager.png)
 

lib/workload/stateless/stacks/bs-runs-upload-manager/deploy/constructs/bs-runs-upload-manager/index.ts

@@ -123,10 +123,10 @@ export class BsRunsUploadManagerConstruct extends Construct {
     const rule = new events.Rule(this, 'bs_runs_upload_event_rule', {
       eventBus: props.eventBusObj,
       eventPattern: {
-        source: ['orcabus.srm'],
+        source: ['orcabus.sequencerunmanager'],
         detailType: ['SequenceRunStateChange'],
         detail: {
-          status: ['succeeded'],
+          status: [{ 'equals-ignore-case': 'SUCCEEDED' }],
         },
       },
     });

lib/workload/stateless/stacks/sequence-run-manager/Makefile

@@ -30,10 +30,10 @@ start: migrate
 	@python manage.py runserver_plus
 
 openapi:
-	@python manage.py generateschema > orcabus.srm.openapi.yaml
+	@python manage.py generateschema > orcabus.sequencerunmanager.openapi.yaml
 
 validate: openapi
-	@python -m openapi_spec_validator orcabus.srm.openapi.yaml
+	@python -m openapi_spec_validator orcabus.sequencerunmanager.openapi.yaml
 
 coverage: install up migrate
 	@echo $$DJANGO_SETTINGS_MODULE

lib/workload/stateless/stacks/sequence-run-manager/README.md

@@ -1,7 +1,7 @@
 # Sequence Run Manager
 
 ```
-Namespace: orcabus.srm
+Namespace: orcabus.sequencerunmanager
 ```
 
 ## CDK
@@ -133,7 +133,7 @@ Or visit in browser:
 #### OpenAPI v3
 
 ```
-python manage.py generateschema > orcabus.srm.openapi.yaml
+python manage.py generateschema > orcabus.sequencerunmanager.openapi.yaml
 ```
 
 ## Testing

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager/migrations/0002_alter_sequence_status.py

@@ -0,0 +1,26 @@
+# Generated by Django 5.0.5 on 2024-06-12 01:28
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("sequence_run_manager", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="sequence",
+            name="status",
+            field=models.CharField(
+                choices=[
+                    ("STARTED", "Started"),
+                    ("FAILED", "Failed"),
+                    ("SUCCEEDED", "Succeeded"),
+                    ("ABORTED", "Aborted"),
+                ],
+                max_length=255,
+            ),
+        ),
+    ]

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager/models/sequence.py

@@ -9,10 +9,11 @@
 
 
 class SequenceStatus(models.TextChoices):
-    STARTED = "started"
-    FAILED = "failed"
-    SUCCEEDED = "succeeded"
-    ABORTED = "aborted"
+    # Convention: status values are to be stored as upper cases
+    STARTED = "STARTED"
+    FAILED = "FAILED"
+    SUCCEEDED = "SUCCEEDED"
+    ABORTED = "ABORTED"
 
     @classmethod
     def from_value(cls, value):

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager/tests/test_models.py

@@ -17,7 +17,7 @@ def build_mock():
         run_volume_name="gds_name",
         run_folder_path="/to/gds/folder/path",
         run_data_uri="gds://gds_name/to/gds/folder/path",
-        status="Complete",
+        status="SUCCEEDED",
         start_time=now(),
         sample_sheet_name="SampleSheet.csv",
         sequence_run_id="r.AAAAAA",
@@ -28,7 +28,7 @@ def build_mock():
         run_volume_name="gds_name",
         run_folder_path="/to/gds/folder/path",
         run_data_uri="gds://gds_name/to/gds/folder/path",
-        status="Fail",
+        status="FAILED",
         start_time=now(),
         sample_sheet_name="SampleSheet.csv",
         sequence_run_id="r.BBBBBB",
@@ -43,28 +43,28 @@ def test_get_sequence(self):
         """
         build_mock()
         logger.info("Test get success sequence table")
-        get_complete_sequence = Sequence.objects.get(status="Complete")
+        get_complete_sequence = Sequence.objects.get(status="SUCCEEDED")
         self.assertEqual(
-            get_complete_sequence.status, "Complete", "Status Complete is expected"
+            get_complete_sequence.status, "SUCCEEDED", "Status SUCCEEDED is expected"
         )
         logger.info(get_complete_sequence)
 
         try:
-            Sequence.objects.get(status="Complete")
+            Sequence.objects.get(status="SUCCEEDED")
         except ObjectDoesNotExist:
             logger.info(f"Raised ObjectDoesNotExist")
 
     def test_from_seq_run_status(self):
         """
         python manage.py test sequence_run_manager.tests.test_models.SequenceTestCase.test_from_seq_run_status
         """
-        sq_status: SequenceStatus = SequenceStatus.from_seq_run_status("running")
+        sq_status: SequenceStatus = SequenceStatus.from_seq_run_status("Running")
         self.assertIs(sq_status, SequenceStatus.STARTED)
 
-        sq_status = SequenceStatus.from_seq_run_status("pendinganalysis")
+        sq_status = SequenceStatus.from_seq_run_status("PendingAnalysis")
         self.assertIs(sq_status, SequenceStatus.SUCCEEDED)
 
-        sq_status = SequenceStatus.from_seq_run_status("failed")
+        sq_status = SequenceStatus.from_seq_run_status("Failed")
         self.assertIs(sq_status, SequenceStatus.FAILED)
 
     def test_from_seq_run_status_stopped(self):

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager_proc/domain/sequence.py

@@ -1,8 +1,6 @@
 import json
 import logging
-import uuid
 from dataclasses import dataclass
-from datetime import datetime, timezone
 
 from libumccr import libjson
 from libumccr.aws import libssm
@@ -23,8 +21,8 @@
 
 @dataclass
 class SequenceDomain:
-    _namespace = "orcabus.srm"
-    _version = "1.0.0"
+    # Convention: https://github.com/umccr/orcabus/tree/main/docs/schemas#namespace
+    _namespace = "orcabus.sequencerunmanager"
     sequence: Sequence
     state_has_changed: bool = False
 
@@ -33,11 +31,6 @@ def namespace(self) -> str:
         """Domain event namespace"""
         return self._namespace
 
-    @property
-    def event_version(self) -> str:
-        """Domain event version"""
-        return self._version
-
     @property
     def event_type(self) -> str:
         """Domain event type in string representation"""

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager_proc/services/sequence_srv.py

@@ -59,7 +59,7 @@ def create_or_update_sequence_from_bssh_event(payload: dict) -> SequenceDomain:
     # --- start mapping to internal Sequence model
 
     # status must exist in payload
-    status = SequenceStatus.from_seq_run_status(payload["status"])
+    status: SequenceStatus = SequenceStatus.from_seq_run_status(payload["status"])
 
     # derive start_time and end_time from date_modified and status
     start_time = date_modified

lib/workload/stateless/stacks/sequence-run-manager/sequence_run_manager_proc/tests/test_sequence_srv.py

@@ -30,16 +30,19 @@ def test_create_or_update_sequence_from_bssh_event(self):
         )
         self.assertIsNotNone(seq_domain)
         logger.info(seq_domain)
-        ses_in_db: Sequence = Sequence.objects.get(
+        seq_in_db: Sequence = Sequence.objects.get(
             instrument_run_id=TestConstant.instrument_run_id.value
         )
         self.assertEqual(
-            seq_domain.sequence.instrument_run_id, ses_in_db.instrument_run_id
+            seq_domain.sequence.instrument_run_id, seq_in_db.instrument_run_id
         )
         self.assertTrue(
             seq_domain.state_has_changed
         )  # assert Sequence Run State has changed True
 
+        # assert status value are stored as upper case
+        self.assertEqual(seq_in_db.status, "STARTED")
+
     def test_create_or_update_sequence_from_bssh_event_skip(self):
         """
         python manage.py test sequence_run_manager_proc.tests.test_sequence_srv.SequenceRunSrvUnitTests.test_create_or_update_sequence_from_bssh_event_skip