Merge branch 'master' into archiving-delete-files

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.0.0
+current_version = 54.2.1
 commit = True
 tag = True
 tag_name = v{new_version}

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: isort
         name: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.289
+    rev: v0.1.7
     hooks:
       - id: ruff
 

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.0.0"
+__version__ = "54.2.1"

cg/apps/scout/scoutapi.py

@@ -7,7 +7,7 @@
 from cg.apps.scout.scout_export import ScoutExportCase, Variant
 from cg.constants.constants import FileFormat
 from cg.constants.gene_panel import GENOME_BUILD_37
-from cg.constants.scout_upload import ScoutCustomCaseReportTags
+from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.exc import ScoutUploadError
 from cg.io.controller import ReadFile, ReadStream
 from cg.models.scout.scout_load_config import ScoutLoadConfig
@@ -69,6 +69,20 @@ def export_panels(self, panels: list[str], build: str = GENOME_BUILD_37) -> list
 
         return list(self.process.stdout_lines())
 
+    def export_managed_variants(self, genome_build: str = GENOME_BUILD_37) -> list[str]:
+        """Export a list of managed variants."""
+        export_command = ["export", "managed"]
+        if genome_build:
+            export_command.extend(["--build", genome_build])
+        try:
+            self.process.run_command(export_command)
+            if not self.process.stdout:
+                return []
+        except CalledProcessError:
+            LOG.info("Could not export managed variants")
+            return []
+        return list(self.process.stdout_lines())
+
     def get_genes(self, panel_id: str, build: str = None) -> list[dict]:
         """Return panel genes."""
         export_panel_command = ["export", "panel", panel_id]

cg/cli/demultiplex/base.py

@@ -7,7 +7,6 @@
     confirm_flow_cell_sync,
     copy_novaseqx_flow_cells,
     create_manifest_files,
-    delete_flow_cell,
     demultiplex_all,
     demultiplex_flow_cell,
 )
@@ -27,7 +26,6 @@ def demultiplex_cmd_group():
 for sub_cmd in [
     create_manifest_files,
     confirm_flow_cell_sync,
-    delete_flow_cell,
     demultiplex_flow_cell,
     demultiplex_all,
     finish_group,

cg/cli/demultiplex/demux.py

@@ -13,7 +13,6 @@
 )
 from cg.constants.demultiplexing import OPTION_BCL_CONVERTER, DemultiplexingDirsAndFiles
 from cg.exc import FlowCellError
-from cg.meta.demultiplex.delete_demultiplex_api import DeleteDemuxAPI
 from cg.meta.demultiplex.utils import (
     create_manifest_file,
     is_flow_cell_sync_confirmed,
@@ -121,66 +120,6 @@ def demultiplex_flow_cell(
         )
 
 
-@click.command(name="delete-flow-cell")
-@click.option(
-    "-f",
-    "--flow-cell-name",
-    required=True,
-    help="The name of the flow cell you want to delete, e.g. HVKJCDRXX",
-)
-@click.option(
-    "--demultiplexing-dir", is_flag=True, help="Delete flow cell demultiplexed dir on file system"
-)
-@click.option("--housekeeper", is_flag=True, help="Delete flow cell in housekeeper")
-@click.option("--init-files", is_flag=True, help="Delete flow cell init-files")
-@click.option("--run-dir", is_flag=True, help="Delete flow cell run on file system")
-@click.option(
-    "--sample-lane-sequencing-metrics",
-    is_flag=True,
-    help="Delete flow cell in sample lane sequencing metrics",
-)
-@click.option(
-    "--status-db",
-    is_flag=True,
-    help="Delete flow cell in status-db, if passed all other entries are also deleted",
-)
-@click.option("--yes", is_flag=True, help="Pass yes to click confirm")
-@DRY_RUN
-@click.pass_obj
-def delete_flow_cell(
-    context: CGConfig,
-    dry_run: bool,
-    demultiplexing_dir: bool,
-    housekeeper: bool,
-    init_files: bool,
-    run_dir: bool,
-    sample_lane_sequencing_metrics: bool,
-    status_db: bool,
-    yes: bool,
-    flow_cell_name: str,
-):
-    """Delete a flow cell. If --status-db is passed then all other options will be treated as True."""
-
-    delete_demux_api: DeleteDemuxAPI = DeleteDemuxAPI(
-        config=context, dry_run=dry_run, flow_cell_name=flow_cell_name
-    )
-
-    if yes or click.confirm(
-        f"Are you sure you want to delete the flow cell from the following databases:\n"
-        f"Housekeeper={True if status_db else housekeeper}\nInit_files={True if status_db else init_files}\n"
-        f"Run-dir={True if status_db else run_dir}\nStatusdb={status_db}\n"
-        f"\nSample-lane-sequencing-metrics={True if sample_lane_sequencing_metrics else sample_lane_sequencing_metrics}"
-    ):
-        delete_demux_api.delete_flow_cell(
-            demultiplexing_dir=demultiplexing_dir,
-            housekeeper=housekeeper,
-            init_files=init_files,
-            sample_lane_sequencing_metrics=sample_lane_sequencing_metrics,
-            run_dir=run_dir,
-            status_db=status_db,
-        )
-
-
 @click.command(name="copy-completed-flow-cell")
 @click.pass_obj
 def copy_novaseqx_flow_cells(context: CGConfig):

cg/cli/upload/scout.py

@@ -10,7 +10,7 @@
 from cg.cli.upload.utils import suggest_cases_to_upload
 from cg.constants import Pipeline
 from cg.constants.constants import FileFormat
-from cg.constants.scout_upload import ScoutCustomCaseReportTags
+from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.io.controller import WriteStream
 from cg.meta.upload.scout.uploadscoutapi import UploadScoutAPI
 from cg.meta.upload.upload_api import UploadAPI

cg/cli/utils.py

@@ -0,0 +1,6 @@
+import click
+
+
+def echo_lines(lines: list[str]) -> None:
+    for line in lines:
+        click.echo(line)

cg/cli/workflow/mip/base.py

@@ -4,6 +4,7 @@
 import click
 
 from cg.apps.environ import environ_email
+from cg.cli.utils import echo_lines
 from cg.cli.workflow.commands import link
 from cg.cli.workflow.mip.options import (
     ARGUMENT_CASE_ID,
@@ -59,12 +60,27 @@ def panel(context: CGConfig, case_id: str, dry_run: bool) -> None:
 
     bed_lines: list[str] = analysis_api.get_gene_panel(case_id=case_id)
     if dry_run:
-        for bed_line in bed_lines:
-            click.echo(bed_line)
+        echo_lines(lines=bed_lines)
         return
     analysis_api.write_panel(case_id, bed_lines)
 
 
+@click.command()
+@OPTION_DRY
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def managed_variants(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """Write managed variants file exported from Scout."""
+
+    analysis_api: MipAnalysisAPI = context.meta_apis["analysis_api"]
+    analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
+    vcf_lines: list[str] = analysis_api.get_managed_variants()
+    if dry_run:
+        echo_lines(lines=vcf_lines)
+        return
+    analysis_api.write_managed_variants(case_id=case_id, content=vcf_lines)
+
+
 @click.command()
 @QOS_OPTION
 @EMAIL_OPTION
@@ -164,6 +180,7 @@ def start(
     analysis_api.prepare_fastq_files(case_id=case_id, dry_run=dry_run)
     context.invoke(link, case_id=case_id, dry_run=dry_run)
     context.invoke(panel, case_id=case_id, dry_run=dry_run)
+    context.invoke(managed_variants, case_id=case_id, dry_run=dry_run)
     context.invoke(config_case, case_id=case_id, panel_bed=panel_bed, dry_run=dry_run)
     context.invoke(
         run,

cg/cli/workflow/mip_dna/base.py

@@ -11,7 +11,14 @@
     store,
     store_available,
 )
-from cg.cli.workflow.mip.base import config_case, panel, run, start, start_available
+from cg.cli.workflow.mip.base import (
+    config_case,
+    managed_variants,
+    panel,
+    run,
+    start,
+    start_available,
+)
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 
@@ -33,6 +40,7 @@ def mip_dna(
     config_case,
     ensure_flow_cells_on_disk,
     link,
+    managed_variants,
     panel,
     resolve_compression,
     run,

cg/cli/workflow/raredisease/base.py

@@ -4,6 +4,7 @@
 
 import click
 
+from cg.cli.utils import echo_lines
 from cg.cli.workflow.commands import ARGUMENT_CASE_ID, OPTION_DRY
 from cg.constants.constants import MetaApis
 from cg.meta.workflow.analysis import AnalysisAPI
@@ -35,7 +36,23 @@ def panel(context: CGConfig, case_id: str, dry_run: bool) -> None:
 
     bed_lines: list[str] = analysis_api.get_gene_panel(case_id=case_id)
     if dry_run:
-        for bed_line in bed_lines:
-            click.echo(bed_line)
+        echo_lines(lines=bed_lines)
         return
     analysis_api.write_panel(case_id=case_id, content=bed_lines)
+
+
+@raredisease.command("managed-variants")
+@OPTION_DRY
+@ARGUMENT_CASE_ID
+@click.pass_obj
+def managed_variants(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """Write managed variants file exported from Scout."""
+
+    analysis_api: RarediseaseAnalysisAPI = context.meta_apis["analysis_api"]
+    analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
+
+    vcf_lines: list[str] = analysis_api.get_managed_variants()
+    if dry_run:
+        echo_lines(lines=vcf_lines)
+        return
+    analysis_api.write_managed_variants(case_id=case_id, content=vcf_lines)

cg/constants/constants.py

@@ -40,7 +40,7 @@ class CaseActions(StrEnum):
 
     @classmethod
     def actions(cls) -> list[str]:
-        return list(cls)
+        return list(map(lambda action: action.value, cls))
 
 
 CONTAINER_OPTIONS = ("Tube", "96 well plate", "No container")
@@ -71,7 +71,7 @@ class FlowCellStatus(StrEnum):
 
     @classmethod
     def statuses(cls) -> list[str]:
-        return list(cls)
+        return list(map(lambda status: status.value, cls))
 
 
 class AnalysisType(StrEnum):

cg/constants/gene_panel.py

@@ -45,7 +45,7 @@ class GenePanelMasterList(StrEnum):
     @classmethod
     def get_panel_names(cls, panels=None) -> list[str]:
         """Return requested panel names from the Master list, or all panels if none are specified."""
-        return list(panels) if panels else list(cls)
+        return list(panels) if panels else list(map(lambda panel: panel.value, cls))
 
     @staticmethod
     def collaborators() -> set[str]:

cg/constants/housekeeper_tags.py

@@ -18,7 +18,7 @@ class AlignmentFileTag(StrEnum):
 
     @classmethod
     def file_tags(cls) -> list[str]:
-        return list(cls)
+        return list(map(lambda tag: tag.value, cls))
 
 
 class ArchiveTag(StrEnum):

cg/constants/scout_upload.py → cg/constants/scout.py

@@ -1,5 +1,6 @@
 from enum import StrEnum
 
+from cg.constants import FileExtensions
 from cg.constants.housekeeper_tags import AlignmentFileTag
 
 
@@ -8,6 +9,11 @@ class GenomeBuild(StrEnum):
     hg38: str = "38"
 
 
+class ScoutExportFileName(StrEnum):
+    MANAGED_VARIANTS: str = f"managed_variants{FileExtensions.VCF}"
+    PANELS: str = f"gene_panels{FileExtensions.BED}"
+
+
 class ScoutCustomCaseReportTags(StrEnum):
     DELIVERY: str = "delivery_report"
     CNV: str = "cnv_report"