cg 83.15.3__py3-none-any.whl → 83.16.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.15.3"
+__version__ = "83.16.0"

cg/cli/base.py

@@ -1,4 +1,4 @@
-""" Start of CLI """
+"""Start of CLI"""
 
 import logging
 import sys
@@ -28,16 +28,10 @@ from cg.cli.transfer import transfer_group
 from cg.cli.upload.base import upload
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.cli.workflow.base import workflow as workflow_cmd
-from cg.constants.cli_options import FORCE
 from cg.constants.constants import FileFormat
 from cg.io.controller import ReadFile
 from cg.models.cg_config import CGConfig
-from cg.store.database import (
-    create_all_tables,
-    drop_all_tables,
-    get_scoped_session_registry,
-    get_tables,
-)
+from cg.store.database import get_scoped_session_registry
 
 LOG = logging.getLogger(__name__)
 LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR"]
@@ -82,26 +76,6 @@ def base(
     context.call_on_close(teardown_session)
 
 
-@base.command()
-@click.option("--reset", is_flag=True, help="Reset database before setting up tables")
-@FORCE
-@click.pass_obj
-def init(context: CGConfig, reset: bool, force: bool):
-    """Setup the database."""
-    existing_tables: list[str] = get_tables()
-    if force or reset:
-        if existing_tables and not force:
-            message = f"Delete existing tables? [{', '.join(existing_tables)}]"
-            click.confirm(click.style(message, fg="yellow"), abort=True)
-        drop_all_tables()
-    elif existing_tables:
-        LOG.error("Database already exists, use '--reset'")
-        raise click.Abort
-
-    create_all_tables()
-    LOG.info(f"Success! New tables: {', '.join(get_tables())}")
-
-
 def find_commands(group, query: str) -> list[str]:
     """Recursively find commands in a group that match the query.
     Args:

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-83.15.3.dist-info → cg-83.16.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.15.3
+Version: 83.16.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.15.3.dist-info → cg-83.16.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=wv-WioAcstp0tI-e4BA-fOP5yyUjNNdpVHMGeppa8R0,41
+cg/__init__.py,sha256=VGXZH8PBR91D3KpgHWvDCflZAEo93QE2i1onU6Ey7cY,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
@@ -72,7 +72,7 @@ cg/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/cli/add.py,sha256=hNW79Nrr7kbmv5DNDjZh_JsAGxZSQp_cLFh1gT8qAe0,11935
 cg/cli/archive.py,sha256=0P1KCMDHSHQIm-z3ONkF7JkmHvx0cziUJodYG-Z-pN8,4411
 cg/cli/backup.py,sha256=TBLF3yLstEI_bcrGoCo79CcClBqa2-Lk-54rofmo57I,11229
-cg/cli/base.py,sha256=j5og_6HL_Ef4WzqsGqBD0Bfi-RGGf82gvD8YnT_TQzs,5105
+cg/cli/base.py,sha256=x0dWVQrY5HnTjMEXMQIP4mmoo7wHCR1tfalAGFkEUdo,4287
 cg/cli/clean.py,sha256=uKpRYl9__VIrFQ5sFJeV8QwxkBBMLUZ3nB0vnsArlFU,7854
 cg/cli/compress/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/cli/compress/base.py,sha256=GSBDojXXz4yn6LzXj3RvmosIg3z1bjcPsv3r2ubQpWU,2344
@@ -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-83.15.3.dist-info/METADATA,sha256=K9yyPr_YAzs94GM0SsE9un_FRwjmtkggZjBGalpq_r4,4940
-cg-83.15.3.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-cg-83.15.3.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.15.3.dist-info/RECORD,,
+cg-83.16.0.dist-info/METADATA,sha256=HzX6a5Bovk5Z1Qn2joM4a-pO_C_CFO6sIJx9jdv9uCs,4940
+cg-83.16.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.16.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.16.0.dist-info/RECORD,,