cg 83.15.2__py3-none-any.whl → 83.15.4__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.15.2"
+__version__ = "83.15.4"

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/exc.py

@@ -348,6 +348,13 @@ class CaseNotConfiguredError(CgError):
     """Exception raised when a case is being run without a configuration."""
 
 
+class CaseWorkflowMismatchError(CgError):
+    """
+    Exception raised when a case is being run with a workflow different from the one specified
+    for it in the database.
+    """
+
+
 class MissingConfigFilesError(CgError):
     """Exception raised when a case is being run with missing configuration files."""
 

cg/services/analysis_starter/analysis_starter.py

@@ -4,7 +4,7 @@ from subprocess import CalledProcessError
 from requests import HTTPError
 
 from cg.constants import Workflow
-from cg.exc import AnalysisNotReadyError, SeqeraError
+from cg.exc import AnalysisNotReadyError, CaseWorkflowMismatchError, SeqeraError
 from cg.services.analysis_starter.configurator.abstract_model import CaseConfig
 from cg.services.analysis_starter.configurator.configurator import Configurator
 from cg.services.analysis_starter.input_fetcher.input_fetcher import InputFetcher
@@ -51,6 +51,7 @@ class AnalysisStarter:
     def start(self, case_id: str, **flags) -> None:
         """Fetches raw data, generates configuration files and runs the specified case."""
         LOG.info(f"Starting case {case_id}")
+        self._ensure_case_matches_workflow(case_id)
         self.tracker.ensure_analysis_not_ongoing(case_id)
         self.input_fetcher.ensure_files_are_ready(case_id)
         case_config: CaseConfig = self.configurator.configure(case_id=case_id, **flags)
@@ -58,6 +59,7 @@ class AnalysisStarter:
 
     def run(self, case_id: str, **flags) -> None:
         """Run a case using an assumed existing configuration."""
+        self._ensure_case_matches_workflow(case_id)
         self.tracker.ensure_analysis_not_ongoing(case_id)
         case_config: CaseConfig = self.configurator.get_config(case_id=case_id, **flags)
         self._run_and_track(case_id=case_id, case_config=case_config)
@@ -70,3 +72,11 @@ class AnalysisStarter:
         except (CalledProcessError, HTTPError, SeqeraError) as exception:
             self.tracker.set_case_as_not_running(case_id)
             raise exception
+
+    def _ensure_case_matches_workflow(self, case_id: str) -> None:
+        case: Case = self.store.get_case_by_internal_id_strict(case_id)
+        if case.data_analysis != self.workflow:
+            raise CaseWorkflowMismatchError(
+                f"Case {case_id} is assigned to workflow {case.data_analysis}, "
+                f"not {self.workflow}."
+            )

{cg-83.15.2.dist-info → cg-83.15.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.15.2
+Version: 83.15.4
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.15.2.dist-info → cg-83.15.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=h1_DpaXm14buebvsKjVmxOLYjMT2n5LWfEifGHaVN3I,41
+cg/__init__.py,sha256=Zss8t8-mLeYBlfvs0D6w2a6NyOAEOAHXVKXFmuF5jVw,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
@@ -225,7 +225,7 @@ cg/constants/slurm.py,sha256=_Y_InISKpGKT-oVMnES7k7Csz2G1l52MNtJwBZm0prI,313
 cg/constants/subject.py,sha256=EE26Emu6T3_HWvsWeuI5GRGGIvB0BwCjN53KHrsr18U,577
 cg/constants/symbols.py,sha256=c06D1mYFWstZbVEgiby2lUNriswUPVRU5TnSSy889tY,71
 cg/constants/tb.py,sha256=UJHdsu109oR_zxvQrko9SqFANiSUn_UJTw5BFebWcds,621
-cg/exc.py,sha256=lGr9DFUkOyXzK9y1bF2qxRZT_Tp2Falb5fmAa8fdM94,8553
+cg/exc.py,sha256=Omvtdskjyby9ISEV5mM27Aku82XM77I_eIYbiQaKV1I,8736
 cg/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/io/api.py,sha256=WaiompYmK4bkl94fZkGzP2CTsQPmHaTSvy0oD0SKw4s,1037
 cg/io/controller.py,sha256=4TTHm9fNY7Ti3S0r-uhxB3oycJ-Ni5Y44lFj5Yvl3_I,2978
@@ -515,7 +515,7 @@ cg/server/utils.py,sha256=fL5ZFlr2V-F3bbjPUi3LDxRuFK7UdN8jCp3txDvs0dE,227
 cg/services/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/analysis_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/analysis_service/analysis_service.py,sha256=vqT_f83Bf1hZ69HvfXwbR5FNqjh67nYTndWE0Rlr030,2041
-cg/services/analysis_starter/analysis_starter.py,sha256=r2fH5AXhVW8Pt1zHgAE2x6HegNgcZRPmXc5GpNNL3c8,3010
+cg/services/analysis_starter/analysis_starter.py,sha256=B6ZPOSVorkKDZwm1JZxTUKxwrFf7gns_T_eeMBLwGss,3509
 cg/services/analysis_starter/configurator/abstract_model.py,sha256=S1g5VZJ_cnM8QdDe3AeHlUqq8iO9Fykp8Q80X2_6PvM,374
 cg/services/analysis_starter/configurator/configurator.py,sha256=ZgELQu9dQPt_42EwcEbLNPsvaLP58xOrfAVSXFiTZSA,943
 cg/services/analysis_starter/configurator/extensions/nallo.py,sha256=lsqFyzbdUmOgAuB_OKM-Zeyzq1cNiaekjwD5icY1_Nk,1111
@@ -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-83.15.2.dist-info/METADATA,sha256=auXlXIG1QVGKCp6xq7jKsHnieLTQ406wudFiN1HSVww,4940
-cg-83.15.2.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-cg-83.15.2.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.15.2.dist-info/RECORD,,
+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,,