Merge branch 'master' into add-nallo-metrics-deliver

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 66.0.2
+current_version = 67.0.2
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "66.0.2"
+__version__ = "67.0.2"

cg/apps/hermes/hermes_api.py

@@ -18,6 +18,7 @@ def __init__(self, config: dict):
         self.process = Process(
             binary=config["hermes"]["binary_path"],
         )
+        self.container_path: str = config["hermes"]["container_path"]
         self.container_mount_volume = config["hermes"]["container_mount_volume"]
 
     def convert_deliverables(
@@ -33,7 +34,7 @@ def convert_deliverables(
             "run",
             "--bind",
             self.container_mount_volume,
-            "/home/proj/stage/singularity_containers/hermes_latest.sif",
+            self.container_path,
             "convert",
             "deliverables",
             "--workflow",

cg/apps/orderform/excel_orderform_parser.py

@@ -12,8 +12,8 @@
 from cg.constants import DataDelivery
 from cg.constants.orderforms import Orderform
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.excel_sample import ExcelSample
-from cg.models.orders.order import OrderType
 
 LOG = logging.getLogger(__name__)
 

cg/apps/orderform/json_orderform_parser.py

@@ -1,8 +1,8 @@
 from cg.apps.orderform.orderform_parser import OrderformParser
 from cg.constants import DataDelivery, Workflow
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.json_sample import JsonSample
-from cg.models.orders.order import OrderType
 
 
 class JsonOrderformParser(OrderformParser):

cg/apps/orderform/orderform_parser.py

@@ -7,7 +7,7 @@
 from cg.apps.orderform.utils import ORDER_TYPES_WITH_CASES
 from cg.constants import DataDelivery
 from cg.exc import OrderFormError
-from cg.models.orders.order import OrderType
+from cg.models.orders.constants import OrderType
 from cg.models.orders.orderform_schema import OrderCase, Orderform, OrderPool
 from cg.models.orders.sample_base import OrderSample
 from cg.store.models import Customer

cg/constants/orderforms.py

@@ -1,19 +1,11 @@
 from enum import StrEnum
 
 from cg.constants import ANALYSIS_SOURCES, METAGENOME_SOURCES
-from cg.models.orders.order import OrderType
 
 SEX_MAP = {"male": "M", "female": "F", "unknown": "unknown"}
 REV_SEX_MAP = {value: key for key, value in SEX_MAP.items()}
-CONTAINER_TYPES = ["Tube", "96 well plate"]
 SOURCE_TYPES = set().union(METAGENOME_SOURCES, ANALYSIS_SOURCES)
 
-CASE_PROJECT_TYPES = [
-    OrderType.MIP_DNA,
-    OrderType.BALSAMIC,
-    OrderType.MIP_RNA,
-]
-
 
 class Orderform(StrEnum):
     BALSAMIC: str = "1508"
@@ -79,4 +71,5 @@ def get_current_orderform_version(order_form: str) -> str:
     "LaboratorieMedicinskt Centrum Gotland": "621 84 Visby",
     "Unilabs Eskilstuna Laboratorium": "631 88 Eskilstuna",
     "Norrland University Hospital": "901 85 Umeå",
+    "Länssjukhuset Sundsvall": "856 43 Sundsvall",
 }

cg/exc.py

@@ -174,6 +174,12 @@ class OrderError(CgError):
     """
 
 
+class OrderSubmissionError(CgError):
+    """
+    Exception related to order submission.
+    """
+
+
 class OrderFormError(CgError):
     """
     Exception related to the order form.

cg/models/cg_config.py

@@ -27,9 +27,7 @@
 from cg.meta.delivery.delivery import DeliveryAPI
 from cg.services.analysis_service.analysis_service import AnalysisService
 from cg.services.decompression_service.decompressor import Decompressor
-from cg.services.deliver_files.factory import (
-    DeliveryServiceFactory,
-)
+from cg.services.deliver_files.factory import DeliveryServiceFactory
 from cg.services.deliver_files.rsync.models import RsyncDeliveryConfig
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
@@ -147,6 +145,10 @@ class CommonAppConfig(BaseModel):
     container_mount_volume: str | None = None
 
 
+class HermesConfig(CommonAppConfig):
+    container_path: str
+
+
 class FluffyUploadConfig(BaseModel):
     user: str
     password: str
@@ -425,7 +427,7 @@ class CGConfig(BaseModel):
     genotype_api_: GenotypeAPI = None
     gens: CommonAppConfig = None
     gens_api_: GensAPI = None
-    hermes: CommonAppConfig = None
+    hermes: HermesConfig = None
     hermes_api_: HermesApi = None
     janus: ClientConfig | None = None
     janus_api_: JanusAPIClient | None = None