cg 83.15.4__py3-none-any.whl → 83.16.1__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.15.4"
+__version__ = "83.16.1"

cg/services/analysis_starter/factories/starter_factory.py

@@ -3,7 +3,9 @@ import logging
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.constants import Workflow
 from cg.meta.archive.archive import SpringArchiveAPI
+from cg.meta.backup.backup import SpringBackupAPI
 from cg.meta.compress import CompressAPI
+from cg.meta.encryption.encryption import SpringEncryptionAPI
 from cg.models.cg_config import CGConfig
 from cg.services.analysis_starter.analysis_starter import AnalysisStarter
 from cg.services.analysis_starter.configurator.configurator import Configurator
@@ -25,6 +27,7 @@ from cg.services.analysis_starter.tracker.implementations.microsalt import Micro
 from cg.services.analysis_starter.tracker.implementations.mip_dna import MIPDNATracker
 from cg.services.analysis_starter.tracker.implementations.nextflow_tracker import NextflowTracker
 from cg.services.analysis_starter.tracker.tracker import Tracker
+from cg.services.pdc_service.pdc_service import PdcService
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -65,6 +68,13 @@ class AnalysisStarterFactory:
                 data_flow_config=self.cg_config.data_flow,
             )
             compress_api = CompressAPI(
+                backup_api=SpringBackupAPI(
+                    encryption_api=SpringEncryptionAPI(
+                        binary_path=self.cg_config.encryption.binary_path
+                    ),
+                    hk_api=self.cg_config.housekeeper_api,
+                    pdc_service=PdcService(self.cg_config.pdc.binary_path),
+                ),
                 hk_api=self.housekeeper_api,
                 crunchy_api=self.cg_config.crunchy_api,
                 demux_root=self.cg_config.run_instruments.illumina.demultiplexed_runs_dir,

cg/store/models.py

@@ -851,6 +851,13 @@ class Sample(Base, PriorityMixin):
         """Return the sample run metrics for the sample."""
         return self._sample_run_metrics
 
+    @property
+    def device_type(self) -> DeviceType | None:
+        """Return the device type the sample was sequenced on."""
+        if self._sample_run_metrics:
+            return self._sample_run_metrics[0].type
+        return None
+
     def to_dict(self, links: bool = False) -> dict:
         """Represent as dictionary"""
         data = to_dict(model_instance=self)
@@ -858,6 +865,10 @@ class Sample(Base, PriorityMixin):
         data["customer"] = self.customer.to_dict()
         data["application_version"] = self.application_version.to_dict()
         data["application"] = self.application_version.application.to_dict()
+        data["hifi_yield"] = self.hifi_yield
+        data["uses_reads"] = True
+        if self.device_type == DeviceType.PACBIO:
+            data["uses_reads"] = False
         if links:
             data["links"] = [link_obj.to_dict(family=True, parents=True) for link_obj in self.links]
         return data

{cg-83.15.4.dist-info → cg-83.16.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.15.4
+Version: 83.16.1
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.15.4.dist-info → cg-83.16.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=Zss8t8-mLeYBlfvs0D6w2a6NyOAEOAHXVKXFmuF5jVw,41
+cg/__init__.py,sha256=NQd_1VSkCO7eKx0EXRODgO4qNS_gTytb4Ketu8sUyu4,41
 cg/apps/__init__.py,sha256=pYf0vxo4iYQqURzFRYzqpOCdV8Cm9MWx0GHvJOz0EMg,315
 cg/apps/coverage/__init__.py,sha256=dJtsmNf8tODE2-VEomMIoYA7ugLYZAk_upsfOQCZeF8,27
 cg/apps/coverage/api.py,sha256=e_ozC3QeNKoEfpjjMaL-XjeBLtz-JySWccrtw0E9mLM,2940
@@ -554,7 +554,7 @@ cg/services/analysis_starter/configurator/models/mip_dna.py,sha256=-9wiSIPeqp7Mc
 cg/services/analysis_starter/configurator/models/nextflow.py,sha256=Ug-Kj179TW5hnaCBPJFu9rigbBnmFYSfv02kkItmn2o,610
 cg/services/analysis_starter/constants.py,sha256=69R7TyZWXQlDMowpV87faHcY7zpH5KTTjHLViYadeo8,268
 cg/services/analysis_starter/factories/configurator_factory.py,sha256=CB9iyjaH43cEMQb9_Q9JdHGbLvodEwhhXKZatZhkcEI,12295
-cg/services/analysis_starter/factories/starter_factory.py,sha256=hhM-5pRgklJiQ-vZYEyD0bwZ_v1IcybMfVCeKC_ySR8,6138
+cg/services/analysis_starter/factories/starter_factory.py,sha256=bbU8wWsw_CewuyYLVRG2qxiT-m6PonIMDxHUniwLu7s,6660
 cg/services/analysis_starter/input_fetcher/implementations/bam_fetcher.py,sha256=ttpexbRji6VjlxYi_ayevfjNAtgkV25OQbAV7fagKYA,2530
 cg/services/analysis_starter/input_fetcher/implementations/fastq_fetcher.py,sha256=P2NVYgjLNwnmRsebuVVMUA4_ks-1wx2ALfHBxoucmUg,9676
 cg/services/analysis_starter/input_fetcher/input_fetcher.py,sha256=J0LRB-cvkBUi93k2f8gCYNYwGvmUbJlqosM0bLIkYOc,149
@@ -904,7 +904,7 @@ cg/store/filters/status_panel_filters.py,sha256=qMYhIsrF9G3mjCvL9b9O2l_cmD3SfPWh
 cg/store/filters/status_pool_filters.py,sha256=XcYqe2z5k_q09xpp4cleDMQ4Q3o2y7UPCkB0QUkl1ck,4308
 cg/store/filters/status_sample_filters.py,sha256=mRpt_ik7niMjBo9K7pP8cmdfDMdr0B3I6Tt2MWXkLoc,9656
 cg/store/filters/status_user_filters.py,sha256=sMwKeWqgEtqv8gyhbN_Uf5huPUxbOt5qEqMWVu67Zys,1328
-cg/store/models.py,sha256=dSJRWdvqFmgIbYTlQbsZD8utH10BIjbtUKERybnlssI,43915
+cg/store/models.py,sha256=WuTbEtqRdcUsuQpOsSjhUMNovfDQYbPeff3Qo_wjERs,44321
 cg/store/store.py,sha256=mz1TfKPlanH2uQyhZdwe_8VKg0IdFolmromKLu668IY,630
 cg/utils/__init__.py,sha256=gGjdV2l_hfWFCTybU6dwDk_FcItM88EIHNPaX6g1qUk,30
 cg/utils/calculations.py,sha256=zLVJO6nNw6n7AW7fHZI56UnQ23lqJrShB4Hh2ow6-TQ,349
@@ -923,7 +923,7 @@ cg/utils/flask/enum.py,sha256=xwNVtFPkSzoloJctLHu7obRyxcng1GJrhkeYkqwf9tw,1052
 cg/utils/mapping.py,sha256=oZpZW2kgsbtAP2FZ7RtRPELiEE1zZk_nAGisHGtCOUo,491
 cg/utils/time.py,sha256=_VOglhrFEZ5cwHK1U1g36SdwzB7UvV-Nvlt4ymuZUho,1501
 cg/utils/utils.py,sha256=RciI_UhWcnG_pMZrmQZ1ZYb-O1N0DweTYMmhE0SIRgQ,1410
-cg-83.15.4.dist-info/METADATA,sha256=TSXpbbn65reG3IDTqXyiKcvaHwfMll66sS2oVmigzzY,4940
-cg-83.15.4.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-cg-83.15.4.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.15.4.dist-info/RECORD,,
+cg-83.16.1.dist-info/METADATA,sha256=0qPOKTgbs7jLWPvz8c10Uv28QkzMKcGIsnLDPWst4IQ,4940
+cg-83.16.1.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.16.1.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.16.1.dist-info/RECORD,,