Move metrics-deliver to command.py for taxprofiler and rnafusion

cg/cli/workflow/commands.py

@@ -9,7 +9,7 @@
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.constants import EXIT_FAIL, EXIT_SUCCESS
 from cg.constants.observations import LOQUSDB_SUPPORTED_PIPELINES
-from cg.exc import FlowCellsNeededError
+from cg.exc import FlowCellsNeededError, CgError
 from cg.meta.rsync import RsyncAPI
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
@@ -22,6 +22,8 @@
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
 from cg.meta.workflow.mutant import MutantAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
+from cg.meta.workflow.taxprofiler import TaxprofilerAnalysisAPI
+from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.store import Store
 
@@ -89,6 +91,29 @@ def link(context: CGConfig, case_id: str, dry_run: bool):
     analysis_api.link_fastq_files(case_id=case_id)
 
 
+@click.command("metrics-deliver")
+@ARGUMENT_CASE_ID
+@OPTION_DRY
+@click.pass_obj
+def metrics_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """Create and validate a metrics deliverables file for given case id.
+    If QC metrics are met it sets the status in Trailblazer to complete.
+    If failed, it sets it as failed and adds a comment with information of the failed metrics."""
+
+    analysis_api: RnafusionAnalysisAPI | TaxprofilerAnalysisAPI = context.meta_apis["analysis_api"]
+
+    try:
+        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
+    except CgError as error:
+        raise click.Abort() from error
+
+    analysis_api.write_metrics_deliverables(case_id=case_id, dry_run=dry_run)
+    try:
+        analysis_api.validate_qc_metrics(case_id=case_id, dry_run=dry_run)
+    except CgError as error:
+        raise click.Abort() from error
+
+
 @click.command("store")
 @ARGUMENT_CASE_ID
 @OPTION_DRY

cg/cli/workflow/rnafusion/base.py

@@ -7,7 +7,7 @@
 from pydantic.v1 import ValidationError
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
-from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression
+from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression, metrics_deliver
 from cg.cli.workflow.nf_analysis import (
     OPTION_COMPUTE_ENV,
     OPTION_CONFIG,
@@ -222,27 +222,7 @@ def start_available(context: click.Context, dry_run: bool = False) -> None:
         raise click.Abort
 
 
-@rnafusion.command("metrics-deliver")
-@ARGUMENT_CASE_ID
-@DRY_RUN
-@click.pass_obj
-def metrics_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Create and validate a metrics deliverables file for given case id.
-    If QC metrics are met it sets the status in Trailblazer to complete.
-    If failed, it sets it as failed and adds a comment with information of the failed metrics."""
-
-    analysis_api: RnafusionAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-
-    try:
-        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-    except CgError as error:
-        raise click.Abort() from error
-
-    analysis_api.write_metrics_deliverables(case_id=case_id, dry_run=dry_run)
-    try:
-        analysis_api.validate_qc_metrics(case_id=case_id, dry_run=dry_run)
-    except CgError as error:
-        raise click.Abort() from error
+rnafusion.add_command(metrics_deliver)
 
 
 @rnafusion.command("report-deliver")

cg/cli/workflow/taxprofiler/base.py

@@ -5,7 +5,7 @@
 import click
 from pydantic.v1 import ValidationError
 
-from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression
+from cg.cli.workflow.commands import ARGUMENT_CASE_ID, resolve_compression, metrics_deliver
 from cg.cli.workflow.nf_analysis import (
     OPTION_COMPUTE_ENV,
     OPTION_CONFIG,
@@ -211,24 +211,4 @@ def start_available(context: click.Context, dry_run: bool = False) -> None:
         raise click.Abort
 
 
-@taxprofiler.command("metrics-deliver")
-@ARGUMENT_CASE_ID
-@DRY_RUN
-@click.pass_obj
-def metrics_deliver(context: CGConfig, case_id: str, dry_run: bool) -> None:
-    """Create and validate a metrics deliverables file for given case id.
-    If QC metrics are met it sets the status in Trailblazer to complete.
-    If failed, it sets it as failed and adds a comment with information of the failed metrics."""
-
-    analysis_api: TaxprofilerAnalysisAPI = context.meta_apis[MetaApis.ANALYSIS_API]
-
-    try:
-        analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
-    except CgError as error:
-        raise click.Abort() from error
-
-    analysis_api.write_metrics_deliverables(case_id=case_id, dry_run=dry_run)
-    try:
-        analysis_api.validate_qc_metrics(case_id=case_id, dry_run=dry_run)
-    except CgError as error:
-        raise click.Abort() from error
+taxprofiler.add_command(metrics_deliver)

cg/meta/workflow/nf_analysis.py

@@ -125,6 +125,10 @@ def create_case_directory(self, case_id: str, dry_run: bool = False) -> None:
         if not dry_run:
             Path(self.get_case_path(case_id=case_id)).mkdir(parents=True, exist_ok=True)
 
+    def write_metrics_deliverables(self, case_id: str, dry_run: bool = False) -> None:
+        """Write <case>_metrics_deliverables.yaml file."""
+        raise NotImplementedError
+
     def get_log_path(self, case_id: str, pipeline: str, log: str = None) -> Path:
         """Path to NF log."""
         if log: