Merge pull request #912 from mskcc/release/1.54.0

Release 1.54.0
mskcc · Aug 5, 2021 · f605614 · f605614
2 parents b5dc110 + c2b6f86
commit f605614
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Showing 5 changed files with 42 additions and 20 deletions.
diff --git a/beagle/__init__.py b/beagle/__init__.py
@@ -1 +1 @@
-__version__ = "1.53.0"
+__version__ = "1.54.0"
diff --git a/beagle_etl/jobs/lims_etl_jobs.py b/beagle_etl/jobs/lims_etl_jobs.py
@@ -237,6 +237,27 @@ def fetch_samples(request_id, import_pooled_normals=True, import_samples=True, j
             raise FailedToFetchSampleException("No samples reported for requestId: %s" % request_id)
 
         for sample in sample_ids.get('samples', []):
+            sampleMetadata = LIMSClient.get_sample_manifest(sample['igoSampleId'])
+            try:
+                data = sampleMetadata[0]
+            except Exception as e:
+                pass
+            patient_id = format_patient_id(data.get('cmoPatientId'))
+
+            if not Patient.objects.filter(patient_id=patient_id):
+                Patient.objects.create(patient_id=patient_id)
+
+            sample_name = data.get('cmoSampleName', None)
+            specimen_type = data.get('specimenType', None)
+            cmo_sample_name = format_sample_name(sample_name, specimen_type)
+
+            if not Sample.objects.filter(sample_id=sample['igoSampleId'],
+                                         sample_name=sample_name,
+                                         cmo_sample_name=cmo_sample_name):
+                Sample.objects.create(sample_id=sample['igoSampleId'],
+                                      sample_name=sample_name,
+                                      cmo_sample_name=cmo_sample_name)
+
             job = create_sample_job(sample['igoSampleId'],
                                     sample['igocomplete'],
                                     request_id,
@@ -393,29 +414,12 @@ def fetch_sample_metadata(sample_id, igocomplete, request_id, request_metadata,
         raise FailedToFetchSampleException(
             "Failed to fetch SampleManifest for sampleId:%s. Invalid response" % sample_id)
     if data['igoId'] != sample_id:
-        # logger.info(data)
         logger.info("Failed to fetch SampleManifest for sampleId:%s. LIMS returned %s " % (sample_id, data['igoId']))
         raise FailedToFetchSampleException(
             "Failed to fetch SampleManifest for sampleId:%s. LIMS returned %s " % (sample_id, data['igoId']))
 
     validate_sample(sample_id, data.get('libraries', []), igocomplete, redelivery)
 
-    patient_id = format_patient_id(data.get('cmoPatientId'))
-
-    if not Patient.objects.filter(patient_id=patient_id):
-        Patient.objects.create(patient_id=patient_id)
-
-    sample_name = data.get('cmoSampleName', None)
-    specimen_type = data.get('specimenType', None)
-    cmo_sample_name = format_sample_name(sample_name, specimen_type)
-
-    if not Sample.objects.filter(sample_id=sample_id,
-                                 sample_name=sample_name,
-                                 cmo_sample_name=cmo_sample_name):
-        Sample.objects.create(sample_id=sample_id,
-                              sample_name=sample_name,
-                              cmo_sample_name=cmo_sample_name)
-
     libraries = data.pop('libraries')
     for library in libraries:
         logger.info("Processing library %s" % library)

diff --git a/file_system/migrations/0027_auto_20210804_1508.py b/file_system/migrations/0027_auto_20210804_1508.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.24 on 2021-08-04 19:08
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('file_system', '0026_auto_20210729_0917'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='sample',
+            name='sample_id',
+            field=models.CharField(max_length=32, unique=True),
+        ),
+    ]
diff --git a/file_system/models.py b/file_system/models.py
@@ -47,7 +47,7 @@ class Request(BaseModel):
 
 
 class Sample(BaseModel):
-    sample_id = models.CharField(max_length=32, unique=False, null=False, blank=False)
+    sample_id = models.CharField(max_length=32, unique=True, null=False, blank=False)
     sample_name = models.CharField(max_length=100, null=True, blank=True)
     cmo_sample_name = models.CharField(max_length=100, null=True, blank=True)
     redact = models.BooleanField(default=False, null=False)

diff --git a/runner/operator/argos_operator/v1_1_3/bin/retrieve_samples_by_query.py b/runner/operator/argos_operator/v1_1_3/bin/retrieve_samples_by_query.py
@@ -127,7 +127,7 @@ def get_descriptor(bait_set, pooled_normals, preservation_types, run_ids):
 
 def get_sequencer_type(run_ids_list):
     hiseq_machines = ['jax', 'pitt']
-    novaseq_machines = ['diana', 'michelle', 'aa00227']
+    novaseq_machines = ['diana', 'michelle', 'aa00227', 'ruth']
     run_ids_lower = [ i.lower() for i in run_ids_list if i ]
     for machine in hiseq_machines:
         is_hiseq = find_substr(machine, run_ids_lower)