cg 76.0.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/services/analysis_starter/submitters/seqera_platform/submitter.py

@@ -1,39 +0,0 @@
-from pathlib import Path
-
-from cg.constants.priority import SlurmQos
-from cg.io.yaml import read_yaml, write_yaml_stream
-from cg.services.analysis_starter.configurator.models.nextflow import NextflowCaseConfig
-from cg.services.analysis_starter.submitters.seqera_platform.client import SeqeraPlatformClient
-from cg.services.analysis_starter.submitters.seqera_platform.dtos import (
-    LaunchRequest,
-    WorkflowLaunchRequest,
-)
-from cg.services.analysis_starter.submitters.submitter import Submitter
-
-
-class SeqeraPlatformSubmitter(Submitter):
-
-    def __init__(self, client: SeqeraPlatformClient, compute_environment_ids: dict[SlurmQos, str]):
-        self.client: SeqeraPlatformClient = client
-        self.compute_environment_ids: dict[str, str] = compute_environment_ids
-
-    def submit(self, case_config: NextflowCaseConfig) -> str:
-        """Starts a case and returns the workflow id for the job."""
-        run_request: WorkflowLaunchRequest = self._create_launch_request(case_config)
-        return self.client.run_case(run_request)
-
-    def _create_launch_request(self, case_config: NextflowCaseConfig) -> WorkflowLaunchRequest:
-        parameters: dict = read_yaml(Path(case_config.params_file))
-        parameter_stream: str = write_yaml_stream(parameters)
-        launch_request = LaunchRequest(
-            computeEnvId=self.compute_environment_ids[case_config.case_priority],
-            configProfiles=case_config.config_profiles,
-            configText=f"includeConfig '{case_config.nextflow_config_file}'",
-            paramsText=parameter_stream,
-            pipeline=case_config.pipeline_repository,
-            preRunScript=case_config.pre_run_script,
-            revision=case_config.revision,
-            runName=case_config.case_id,
-            workDir=case_config.work_dir,
-        )
-        return WorkflowLaunchRequest(launch=launch_request)

cg/services/delivery_message/messages/microsalt_mwx_message.py

@@ -1,18 +0,0 @@
-from cg.services.delivery_message.messages.delivery_message import DeliveryMessage
-from cg.services.delivery_message.messages.utils import (
-    REMINDER_TO_DOWNLOAD_MESSAGE,
-    get_caesar_delivery_path,
-)
-from cg.store.models import Case
-
-
-class MicrosaltMwxMessage(DeliveryMessage):
-    def create_message(self, cases: list[Case]) -> str:
-        delivery_path: str = get_caesar_delivery_path(cases[0])
-        return (
-            f"Hello,\n\n"
-            f"The analysis is now complete and the fastq files are being uploaded to:\n\n"
-            f"{delivery_path} \n\n"
-            "The QC report can be found attached. \n\n"
-            f"{REMINDER_TO_DOWNLOAD_MESSAGE}"
-        )