Merge pull request #1442 from mskcc/release/1.94.0

Release 1.94.0

Author: sivkovic

beagle/__init__.py

@@ -1 +1 @@
-__version__ = "1.93.2"
+__version__ = "1.94.0"

beagle/settings.py

@@ -508,3 +508,57 @@
 
 MISSING_FILES_REPORT_PATH = os.environ.get("BEAGLE_MISSING_FILES_REPORT_PATH")
 MISSING_FILES_REPORT_COUNT = int(os.environ.get("BEAGLE_MISSING_FILES_REPORT_COUNT", 10))
+
+GENE_PANEL_TABLE = {
+    "IMPACT341": {
+        None: "UNKNOWN",
+        "IMPACT341": "IMPACT341",
+        "IMPACT_341_CV2_BAITS": "IMPACT341",
+        "OID42050_HG19_11nov2014_BAITS": "UNKNOWN",
+    },
+    "IMPACT+ (341 genes plus custom content)": {"OID42050_HG19_11nov2014_BAITS": "UNKNOWN"},
+    "IMPACT468": {
+        None: "UNKNOWN",
+        "": "UNKNOWN",
+        "Agilent_v4_51MB_Human_hg19_BAITS": "UNKNOWN",
+        "HemePACT_v4_BAITS": "UNKNOWN",
+        "IDT_Exome_V1_IMPACT468_BAITS": "UNKNOWN",
+        "IMPACT468_BAITS": "IMPACT468",
+        "OID42050_HG19_11nov2014_BAITS": "UNKNOWN",
+        "SureSelect-All-Exon-V4-hg19": "UNKNOWN",
+    },
+    "HemePACT_v4": {
+        "HemePACT_v4_b38": "HemePACT_v4",
+        "HemePACT_v4_BAITS": "HemePACT_v4",
+        "IMPACT-Heme_v2_BAITS": "UNKNOWN",
+        "OCCC_316_primary_targets": "UNKNOWN",
+    },
+    "HemePACT_v3": {None: "", "HemePACT_v3_BAIT": "", "HemePACT_v4_BAITS": ""},
+    "IMPACT505": {
+        None: "UNKNOWN",
+        "null": "UNKNOWN",
+        "08390-IMPACT505-MC1R": "IMPACT505+",
+        "08390-IMPACT505-MC1R-BAITS": "IMPACT505+",
+        "HemePACT_v4_BAITS": "UNKNOWN",
+        "IMPACT-505-BAITS": "IMPACT505",
+        "IMPACT505_BAITS": "IMPACT505",
+        "IMPACT505_GRCh38_BAITS": "IMPACT505",
+    },
+    "IMPACT410": {
+        "None": "UNKNOWN",
+        "CYSLTR2": "UNKNOWN",
+        "IMPACT410": "IMPACT410",
+        "IMPACT410_BAITS": "IMPACT410",
+        "IMPACT410_custom": "IMPACT410",
+        "IMPACT468_BAITS": "IMPACT410",
+        "Impact_modified_bed_BAIT_40bp": "UNKNOWN",
+        "OID42050_HG19_11nov2014_BAITS": "UNKNOWN",
+        "OID42050_HG19_11nov2014_capture_targets": "UNKNOWN",
+        "papaemme_IWG_OID43089_hg19_MHC_RNA_max10_20oct2015_BAITS": "UNKNOWN",
+        "SureSelect-All-Exon-V4-hg19": "UNKNOWN",
+        "VENTURA_V1_designed-probe-coords-SORTED": "UNKNOWN",
+    },
+    "08390_Hg19": {"08390-IMPACT505-MC1R-BAITS": "IMPACT505+"},
+    "IMPACT-Heme": {"IMPACT-Heme_v2_BAITS": "IMPACT-Heme_v2"},
+    "HC_IMPACT": {None: "UNKNOWN", "null": "UNKNOWN", "IMPACT505_BAITS": "IMPACT505"},
+}

beagle_etl/fixtures/beagle_etl.operator.json

@@ -262,5 +262,16 @@
       "version": "v2.1.0",
       "slug": "CopyOutputsOperator_v2.1.0"
     }
+  },
+  {
+    "model": "beagle_etl.operator",
+    "pk": 26,
+    "fields": {
+      "active": true,
+      "recipes": "[\"None\"]",
+      "class_name": "runner.operator.copy_outputs_operator.v2_2_0.copy_outputs_operator.CopyOutputsOperator",
+      "version": "v2.2.0",
+      "slug": "CopyOutputsOperator_v2.2.0"
+    }
   }
 ]

beagle_etl/nats_client/nats_client.py

@@ -21,7 +21,7 @@ def persist_message(topic, message):
         elif topic == settings.METADB_NATS_REQUEST_UPDATE:
             msg.request_id = request_message[0].get(settings.REQUEST_ID_METADATA_KEY)
         elif topic == settings.METADB_NATS_SAMPLE_UPDATE:
-            msg.request_id = request_message[0].get(settings.SAMPLE_ID_METADATA_KEY)
+            msg.request_id = request_message["latestSampleMetadata"][settings.SAMPLE_ID_METADATA_KEY]
         msg.save()
     except Exception as e:
         logger.error(e)