Merge branch 'master' into improve-order-flow-main

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 66.0.2
+current_version = 66.1.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "66.0.2"
+__version__ = "66.1.0"

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/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

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "cg"
-version = "66.0.2"
+version = "66.1.0"
 description = "Clinical Genomics command center"
 readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"

tests/conftest.py

@@ -1229,6 +1229,7 @@ def hermes_api(hermes_process: ProcessMock) -> HermesApi:
         "hermes": {
             "binary_path": "/bin/true",
             "container_mount_volume": "a_str",
+            "container_path": "/singularity_cache",
         }
     }
     hermes_api = HermesApi(config=hermes_config)
@@ -2053,7 +2054,7 @@ def context_config(
             "upload_password": "pass",
             "submitter": "s.submitter",
         },
-        "hermes": {"binary_path": "hermes"},
+        "hermes": {"binary_path": "hermes", "container_path": "/singularity_cache"},
         "housekeeper": {"database": hk_uri, "root": str(housekeeper_dir)},
         "lims": {
             "host": "https://lims.scilifelab.se",