cg 83.15.3__tar.gz → 83.16.0__tar.gz

{cg-83.15.3 → cg-83.16.0}/PKG-INFO

@@ -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-83.16.0/cg/__init__.py

@@ -0,0 +1,2 @@
+__title__ = "cg"
+__version__ = "83.16.0"

{cg-83.15.3 → cg-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-83.15.3 → cg-83.16.0}/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 → cg-83.16.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "cg"
-version = "83.15.3"
+version = "83.16.0"
 description = "Clinical Genomics command center"
 readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"

cg-83.15.3/cg/__init__.py

@@ -1,2 +0,0 @@
-__title__ = "cg"
-__version__ = "83.15.3"