Release 2.3.0

beagle/__init__.py

@@ -1 +1 @@
-__version__ = "2.2.1"
+__version__ = "2.3.0"

beagle/settings.py

@@ -471,8 +471,7 @@
     "IMPACT341,IMPACT+ (341 genes plus custom content),IMPACT468,HemePACT_v4,HemePACT_v3,IMPACT505,IMPACT410",
 ).split(",")
 
-PERMISSION_DENIED_CC = json.loads(os.environ.get("BEAGLE_PERMISSION_DENIED_CC", "{}"))
-PERMISSION_DENIED_EMAILS = json.loads(os.environ.get("BEAGLE_PERMISSION_DENIED_EMAIL", "{}"))
+PERMISSION_DENIED_EMAILS = os.environ.get("BEAGLE_PERMISSION_DENIED_EMAIL", "").split(",")
 JOB_HANGING_ALERT_EMAILS = os.environ.get("BEAGLE_JOB_HANGING_ALERT_EMAILS", "").split(",")
 
 # Tempo

beagle_etl/admin.py

@@ -30,7 +30,8 @@ class SMILEMessagesAdmin(AdminAdvancedFiltersMixin, ModelAdmin):
     list_filter = ("request_id", "topic", "status")
     advanced_filter_fields = ("request_id", "topic", "status")
     ordering = ("-created_date",)
-    list_display = ("created_date", "request_id", "topic", "status")
+    list_display = ("created_date", "request_id", "gene_panel", "topic", "status")
+    search_fields = ("request_id", "gene_panel")
 
 
 class RequestCallbackJobAdmin(ModelAdmin):

beagle_etl/jobs/metadb_jobs.py

@@ -29,10 +29,18 @@
     WESJobFailedEvent,
     VoyagerCantProcessRequestAllNormalsEvent,
     SMILEUpdateEvent,
+    ErrorImportingFilesEvent,
 )
 from notifier.tasks import send_notification
 from notifier.helper import get_emails_to_notify
-from beagle_etl.models import Operator, ETLConfiguration, SMILEMessage, RequestCallbackJob, RequestCallbackJobStatus
+from beagle_etl.models import (
+    Operator,
+    ETLConfiguration,
+    SMILEMessage,
+    RequestCallbackJob,
+    RequestCallbackJobStatus,
+    SmileMessageStatus,
+)
 from file_system.serializers import UpdateFileSerializer
 from file_system.repository.file_repository import FileRepository
 from file_system.models import File
@@ -202,6 +210,7 @@ def new_request(message_id):
 
     # Validate samples and fastqs
     log, status = data.validate_all_samples()
+    logger.info(f"Request validation log for SMILEMessage id:{message_id}: {log}")
     message.add_log(log)
 
     jgn_id = None
@@ -214,6 +223,38 @@ def new_request(message_id):
     study, _ = Study.objects.get_or_create(study_id=StudyObject.generate_study_id(data.labHeadName))
 
     valid_samples = {k for k, v in status.items() if v.status == "COMPLETED"}
+
+    retry_samples = {k for k, v in status.items() if v.status == "RETRY"}
+
+    if retry_samples:
+        sample_status = sorted([sample.to_dict() for sample in status.values()], key=lambda d: d["sample"])
+        message.set_sample_status(sample_status)
+        message.add_log(f"Permission Denied error during import for igoRequestId:{message.request_id} id:{message_id}")
+        logger.error(f"Permission Denied error during import for igoRequestId:{message.request_id} id:{message_id}")
+        message.retry()
+        message.refresh_from_db()
+        if message.status in (SmileMessageStatus.RETRY,):
+            logger.info(
+                f"Retrying import for igoRequestId:{message.request_id} id:{message_id}, "
+                f"attempt {message.retry_count} of 2, next attempt scheduled at {message.scheduled}"
+            )
+        elif message.status in (SmileMessageStatus.FAILED,):
+            logger.error(
+                f"Import failed for igoRequestId:{message.request_id} id:{message_id} "
+                f"after {message.retry_count - 1} retries due to permission errors"
+            )
+        for email in settings.PERMISSION_DENIED_EMAILS:
+            e = ErrorImportingFilesEvent(
+                job_notifier=settings.BEAGLE_NOTIFIER_EMAIL_GROUP,
+                email_to=email,
+                subject=f"VOYAGER: Permission Denied error during import for igoRequestId:{message.request_id} id:{message_id}",
+                email_from=settings.BEAGLE_NOTIFIER_EMAIL_FROM,
+                request_id=message.request_id,
+                msg=f"Samples {', '.join(sorted(retry_samples))} failed to import because fastqs don't have correct permissions",
+            )
+            send_notification.delay(e.to_dict())
+        return
+
     request_metadata = data.request_metadata()
 
     import_status = True

beagle_etl/migrations/0047_add_scheduled_retry_count.py

@@ -0,0 +1,37 @@
+# Generated by Django 6.0.4 on 2026-07-08 20:56
+
+import django.utils.timezone
+from django.db import migrations, models
+
+
+def set_scheduled_to_created_date(apps, schema_editor):
+    SMILEMessage = apps.get_model("beagle_etl", "SMILEMessage")
+    messages = list(SMILEMessage.objects.all())
+    for message in messages:
+        message.scheduled = message.created_date
+    SMILEMessage.objects.bulk_update(messages, ["scheduled"], batch_size=1000)
+
+
+def noop(apps, schema_editor):
+    pass
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("beagle_etl", "0046_delete_skipproject"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="smilemessage",
+            name="retry_count",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AddField(
+            model_name="smilemessage",
+            name="scheduled",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.RunPython(set_scheduled_to_created_date, noop),
+    ]

beagle_etl/models.py

@@ -1,8 +1,10 @@
 import uuid
 import logging
 from enum import IntEnum
+from datetime import timedelta
 from django.db import models
 from django.db.models import JSONField
+from django.utils import timezone
 from django.contrib.postgres.fields import ArrayField
 from notifier.tasks import notifier_start
 from notifier.models import Notifier, JobGroup, JobGroupNotifier
@@ -45,6 +47,7 @@ class SmileMessageStatus(IntEnum):
     COMPLETED = 3
     NOT_SUPPORTED = 4
     FAILED = 5
+    RETRY = 6
 
 
 class SMILEMessage(BaseModel):
@@ -61,14 +64,22 @@ class SMILEMessage(BaseModel):
         default=SmileMessageStatus.PENDING,
         db_index=True,
     )
+    scheduled = models.DateTimeField(default=timezone.now, editable=True)
+    retry_count = models.IntegerField(default=0)
 
     def in_progress(self):
         self.status = SmileMessageStatus.IN_PROGRESS
-        job_group = JobGroup.objects.create()
-        self.job_group = job_group
-        job_group_notifier_id = notifier_start(job_group, self.request_id)
-        job_group_notifier = JobGroupNotifier.objects.get(id=job_group_notifier_id) if job_group_notifier_id else None
-        self.job_group_notifier = job_group_notifier
+        # Retries re-enter in_progress() with a job_group already set from the first
+        # attempt; skip creating another one so retries update the original ticket
+        # instead of opening a new one each pass.
+        if not self.job_group:
+            job_group = JobGroup.objects.create()
+            self.job_group = job_group
+            job_group_notifier_id = notifier_start(job_group, self.request_id)
+            job_group_notifier = (
+                JobGroupNotifier.objects.get(id=job_group_notifier_id) if job_group_notifier_id else None
+            )
+            self.job_group_notifier = job_group_notifier
         self.save(update_fields=["job_group", "job_group_notifier", "status"])
 
     def complete(self, request_metadata=None):
@@ -83,6 +94,17 @@ def failed(self, request_metadata=None):
         if self.job_group_notifier and request_metadata:
             self._generate_description(request_metadata)
 
+    def retry(self):
+        if self.retry_count >= 2:
+            # Fail after 2 retries
+            self.status = SmileMessageStatus.FAILED
+        else:
+            # Retry import after 24 hours
+            self.status = SmileMessageStatus.RETRY
+            self.scheduled = self.scheduled + timedelta(hours=24)
+        self.retry_count += 1
+        self.save(update_fields=["scheduled", "status", "retry_count"])
+
     def not_supported(self):
         self.status = SmileMessageStatus.NOT_SUPPORTED
         self.save(update_fields=["status"])

beagle_etl/smile_message/objects/sample_object.py

@@ -507,9 +507,22 @@ def validate_with_file_checks(self, redelivery: bool = False, log: str = "") ->
             log = self._process_validation_results(validation_results, log, redelivery)
         except Exception as e:
             if isinstance(e, ETLExceptions):
-                sample_status = SampleStatus(
-                    sample_id=self.primaryId, igocomplete=self.igoComplete, code=e.code, status="FAILED", message=str(e)
-                )
+                if isinstance(e, FailedToCopyFilePermissionDeniedException):
+                    sample_status = SampleStatus(
+                        sample_id=self.primaryId,
+                        igocomplete=self.igoComplete,
+                        code=e.code,
+                        status="RETRY",
+                        message=str(e),
+                    )
+                else:
+                    sample_status = SampleStatus(
+                        sample_id=self.primaryId,
+                        igocomplete=self.igoComplete,
+                        code=e.code,
+                        status="FAILED",
+                        message=str(e),
+                    )
             else:
                 sample_status = SampleStatus(
                     sample_id=self.primaryId, igocomplete=self.igoComplete, code=None, status="FAILED", message=str(e)

beagle_etl/tasks.py

@@ -65,12 +65,13 @@ def get_pending_smile_messages():
 
     # Get all pending messages with priority
     pending_messages = SMILEMessage.objects.filter(
-        status=SmileMessageStatus.PENDING,
+        status__in=(SmileMessageStatus.PENDING, SmileMessageStatus.RETRY),
         topic__in=[
             settings.METADB_NATS_NEW_REQUEST,
             settings.METADB_NATS_SAMPLE_UPDATE,
             settings.METADB_NATS_REQUEST_UPDATE,
         ],
+        scheduled__lte=datetime.datetime.now(tz=pytz.UTC),
     ).annotate(
         topic_priority=Case(
             When(topic=settings.METADB_NATS_NEW_REQUEST, then=0),

beagle_etl/tests/jobs/test_metadb.py

@@ -3,9 +3,10 @@
 """
 
 import os
-from mock import patch
 import json
+from mock import patch
 from deepdiff import DeepDiff
+from datetime import timedelta
 from django.conf import settings
 from django.contrib.auth.models import User
 from django.test import TestCase, override_settings
@@ -157,6 +158,46 @@ def test_new_request(
         msg.refresh_from_db()
         self.assertEqual(msg.status, SmileMessageStatus.COMPLETED)
 
+    @patch("os.access")
+    @patch("notifier.tasks.notifier_start")
+    @patch("notifier.tasks.send_notification.delay")
+    @patch("notifier.models.JobGroupNotifier.objects.get")
+    @patch("file_system.tasks.populate_job_group_notifier_metadata.delay")
+    @patch("os.path.exists")
+    @patch("beagle_etl.jobs.helper_jobs.calculate_checksum.delay")
+    @override_settings(IMPORT_FILE_GROUP="1a1b29cf-3bc2-4f6c-b376-d4c5d701166a")
+    def test_retry_permission_denied(
+        self,
+        calculate_checksum,
+        path_exists,
+        populate_job_group_notifier_metadata,
+        job_group_notifier_get,
+        send_notification,
+        notifier_start,
+        access,
+    ):
+        calculate_checksum.return_value = None
+        path_exists.return_value = True
+        populate_job_group_notifier_metadata.return_value = None
+        job_group_notifier_get.return_value = self.job_group_notifier
+        notifier_start.return_value = True
+        send_notification.return_value = True
+        access.return_value = False
+        msg = SMILEMessage.objects.create(
+            topic="new-request", request_id="08944_B", gene_panel="", message=self.new_request_str
+        )
+        scheduled_before_retry = msg.scheduled
+        msg.in_progress()
+        new_request(str(msg.id))
+        msg.refresh_from_db()
+        files = FileRepository.filter(
+            metadata={settings.REQUEST_ID_METADATA_KEY: "08944_B"}, file_group=self.file_group_id
+        )
+        self.assertEqual(files.count(), 0)
+        self.assertEqual(msg.status, SmileMessageStatus.RETRY)
+        self.assertEqual(msg.retry_count, 1)
+        self.assertEqual(msg.scheduled, (scheduled_before_retry + timedelta(hours=24)))
+
     @patch("notifier.models.JobGroupNotifier.objects.get")
     @patch("notifier.tasks.send_notification.delay")
     @patch("file_system.tasks.populate_job_group_notifier_metadata.delay")

runner/operator/argos_operator/v2_3_0/argos_operator.py

@@ -250,7 +250,7 @@ def get_files_for_pairs(self, pairing):
                 tumor_current = tumor.first()
                 bait_set = tumor_current.metadata["baitSet"]
                 preservation_types = tumor_current.metadata["preservation"]
-                sample_origin = tumor_current.metadata["sampleOrigin"]
+                sample_origin = tumor_current.metadata.get("sampleOrigin") or ""
                 pooled_normal_files, bait_set_reformatted, sample_name = get_pooled_normal_files(
                     run_ids, preservation_types, bait_set, sample_origin
                 )

runner/operator/argos_operator/v2_3_0/bin/make_sample.py

@@ -144,7 +144,7 @@ def build_sample(data, ignore_sample_formatting=False):
         bait_set = meta["baitSet"]
         tumor_type = meta["tumorOrNormal"]
         specimen_type = meta[settings.SAMPLE_CLASS_METADATA_KEY]
-        sample_origin = meta["sampleOrigin"]
+        sample_origin = meta.get("sampleOrigin") or ""
         species = meta["species"]
         cmo_sample_name = format_sample_name(
             meta[settings.CMO_SAMPLE_NAME_METADATA_KEY], specimen_type, ignore_sample_formatting

runner/operator/argos_operator/v2_3_0/bin/retrieve_samples_by_query.py

@@ -92,7 +92,7 @@ def get_descriptor(bait_set, pooled_normals, preservation_types, run_ids, sample
 
         # sample_name is FROZENPOOLEDNORMAL unless FFPE is in any of the preservation types
         # in preservation_types; plc = preservations lower case
-        plc = set([x.lower() for x in preservation_types])
+        plc = set([x.lower() for x in preservation_types if x])  # filter out None/empty values
         run_ids_suffix_list = [i for i in run_ids if i]  # remove empty or false string values
         run_ids_suffix = "_".join(set(run_ids_suffix_list))
         sample_name = "FROZENPOOLEDNORMAL_" + run_ids_suffix
@@ -156,8 +156,8 @@ def get_preservation_type(preservation_types, sample_origin):
         - if preservation_type is not empty:
             - return 'ffpe' if is_ffpe(); otherwise 'frozen'
     """
-    plc = set([x.lower() for x in preservation_types])  # preservation lower case
-    solc = set([x.lower() for x in sample_origin])  # sample origin lower case
+    plc = set([x.lower() for x in preservation_types if x])  # preservation lower case
+    solc = set([x.lower() for x in sample_origin if x])  # sample origin lower case
     preservation = ""
 
     if not is_list_empty(plc) and not is_list_empty(solc):
@@ -233,7 +233,7 @@ def build_preservation_query(data):
 
     Main logic: if FFPE in data, return FFPE query; else, return FROZEN query
     """
-    plc = set([x.lower() for x in data])
+    plc = set([x.lower() for x in data if x])  # filter out None/empty values
     value = "FROZEN"
     if "ffpe" in plc:
         value = "FFPE"

runner/serializers.py

@@ -278,13 +278,6 @@ class RestartRunSerializer(serializers.Serializer):
     clean = serializers.BooleanField(default=False)
 
 
-# TODO: Delete this
-class RequestIdOperatorSerializer(serializers.Serializer):
-    request_ids = serializers.ListField(child=serializers.CharField(max_length=30), allow_empty=True)
-    run_ids = serializers.ListField(child=serializers.UUIDField(), allow_empty=True)
-    pipeline_name = serializers.CharField(max_length=100)
-
-
 class RequestIdsOperatorSerializer(serializers.Serializer):
     request_ids = serializers.ListField(child=serializers.CharField(max_length=30), allow_empty=True)
     pipeline = serializers.CharField(max_length=30, allow_null=False, allow_blank=False)