Merge branch 'master' into metrics-deliver

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.1.2
+current_version = 54.2.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.1.2"
+__version__ = "54.2.0"

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/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"

cg/meta/report/balsamic.py

@@ -1,7 +1,5 @@
 import logging
 
-from housekeeper.store.models import File, Version
-
 from cg.constants import (
     BALSAMIC_ANALYSIS_TYPE,
     BALSAMIC_REPORT_ACCREDITED_PANELS,
@@ -19,7 +17,7 @@
     REQUIRED_SAMPLE_TIMESTAMP_FIELDS,
     Pipeline,
 )
-from cg.constants.scout_upload import BALSAMIC_CASE_TAGS
+from cg.constants.scout import BALSAMIC_CASE_TAGS
 from cg.meta.report.field_validators import get_million_read_pairs
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI

cg/meta/report/balsamic_umi.py

@@ -1,6 +1,6 @@
 import logging
 
-from cg.constants.scout_upload import BALSAMIC_UMI_CASE_TAGS
+from cg.constants.scout import BALSAMIC_UMI_CASE_TAGS
 from cg.meta.report.balsamic import BalsamicReportAPI
 from cg.meta.workflow.balsamic_umi import BalsamicUmiAnalysisAPI
 from cg.models.cg_config import CGConfig

cg/meta/report/mip_dna.py

@@ -16,7 +16,7 @@
     REQUIRED_SAMPLE_TIMESTAMP_FIELDS,
     Pipeline,
 )
-from cg.constants.scout_upload import MIP_CASE_TAGS
+from cg.constants.scout import MIP_CASE_TAGS
 from cg.meta.report.field_validators import get_million_read_pairs
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI

cg/meta/report/rnafusion.py

@@ -14,8 +14,11 @@
     Pipeline,
 )
 from cg.constants.constants import GenomeVersion
-from cg.constants.scout_upload import RNAFUSION_CASE_TAGS
-from cg.meta.report.field_validators import get_mapped_reads_fraction, get_million_read_pairs
+from cg.constants.scout import RNAFUSION_CASE_TAGS
+from cg.meta.report.field_validators import (
+    get_mapped_reads_fraction,
+    get_million_read_pairs,
+)
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
 from cg.models.analysis import AnalysisModel

cg/meta/upload/scout/balsamic_config_builder.py

@@ -4,7 +4,7 @@
 
 from cg.apps.lims import LimsAPI
 from cg.constants.constants import SampleType
-from cg.constants.scout_upload import BALSAMIC_CASE_TAGS, BALSAMIC_SAMPLE_TAGS
+from cg.constants.scout import BALSAMIC_CASE_TAGS, BALSAMIC_SAMPLE_TAGS
 from cg.constants.subject import PhenotypeStatus
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder

cg/meta/upload/scout/balsamic_umi_config_builder.py

@@ -3,7 +3,7 @@
 from housekeeper.store.models import Version
 
 from cg.apps.lims import LimsAPI
-from cg.constants.scout_upload import BALSAMIC_UMI_CASE_TAGS, BALSAMIC_UMI_SAMPLE_TAGS
+from cg.constants.scout import BALSAMIC_UMI_CASE_TAGS, BALSAMIC_UMI_SAMPLE_TAGS
 from cg.meta.upload.scout.balsamic_config_builder import BalsamicConfigBuilder
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.models.scout.scout_load_config import (

cg/meta/upload/scout/mip_config_builder.py

@@ -6,7 +6,7 @@
 
 from cg.apps.lims import LimsAPI
 from cg.apps.madeline.api import MadelineAPI
-from cg.constants.scout_upload import MIP_CASE_TAGS, MIP_SAMPLE_TAGS
+from cg.constants.scout import MIP_CASE_TAGS, MIP_SAMPLE_TAGS
 from cg.constants.subject import RelationshipStatus
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder

cg/meta/upload/scout/rnafusion_config_builder.py

@@ -4,7 +4,7 @@
 
 from cg.apps.lims import LimsAPI
 from cg.constants.constants import PrepCategory
-from cg.constants.scout_upload import RNAFUSION_CASE_TAGS, RNAFUSION_SAMPLE_TAGS, GenomeBuild
+from cg.constants.scout import RNAFUSION_CASE_TAGS, RNAFUSION_SAMPLE_TAGS, GenomeBuild
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder
 from cg.models.scout.scout_load_config import (

cg/meta/upload/scout/uploadscoutapi.py

@@ -12,7 +12,7 @@
 from cg.apps.scout.scoutapi import ScoutAPI
 from cg.constants import HK_MULTIQC_HTML_TAG, Pipeline
 from cg.constants.constants import FileFormat, PrepCategory
-from cg.constants.scout_upload import ScoutCustomCaseReportTags
+from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.exc import CgDataError, HousekeeperBundleVersionMissingError
 from cg.io.controller import WriteFile
 from cg.meta.upload.scout.balsamic_config_builder import BalsamicConfigBuilder

cg/meta/workflow/analysis.py

@@ -10,9 +10,16 @@
 
 from cg.apps.environ import environ_email
 from cg.constants import EXIT_FAIL, EXIT_SUCCESS, Pipeline, Priority
-from cg.constants.constants import AnalysisType, CaseActions, WorkflowManager
+from cg.constants.constants import (
+    AnalysisType,
+    CaseActions,
+    FileFormat,
+    WorkflowManager,
+)
 from cg.constants.gene_panel import GenePanelCombo
+from cg.constants.scout import ScoutExportFileName
 from cg.exc import AnalysisNotReadyError, BundleAlreadyAddedError, CgDataError, CgError
+from cg.io.controller import WriteFile
 from cg.meta.meta import MetaAPI
 from cg.meta.workflow.fastq import FastqHandler
 from cg.models.analysis import AnalysisModel
@@ -509,10 +516,34 @@ def prepare_fastq_files(self, case_id: str, dry_run: bool) -> None:
         if not self.is_case_ready_for_analysis(case_id):
             raise AnalysisNotReadyError("FASTQ file are not present for the analysis to start")
 
+    @staticmethod
+    def _write_managed_variants(out_dir: Path, content: list[str]) -> None:
+        """Write the managed variants to case dir."""
+        out_dir.mkdir(parents=True, exist_ok=True)
+        WriteFile.write_file_from_content(
+            content="\n".join(content),
+            file_format=FileFormat.TXT,
+            file_path=Path(out_dir, ScoutExportFileName.MANAGED_VARIANTS),
+        )
+
+    @staticmethod
+    def _write_panel(out_dir: Path, content: list[str]) -> None:
+        """Write the managed variants to case dir."""
+        out_dir.mkdir(parents=True, exist_ok=True)
+        WriteFile.write_file_from_content(
+            content="\n".join(content),
+            file_format=FileFormat.TXT,
+            file_path=Path(out_dir, ScoutExportFileName.PANELS),
+        )
+
     def _get_gene_panel(self, case_id: str, genome_build: str) -> list[str]:
         """Create and return the aggregated gene panel file."""
         case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
         all_panels: list[str] = self.get_aggregated_panels(
             customer_id=case.customer.internal_id, default_panels=set(case.panels)
         )
         return self.scout_api.export_panels(build=genome_build, panels=all_panels)
+
+    def _get_managed_variants(self, genome_build: str) -> list[str]:
+        """Create and return the managed variants."""
+        return self.scout_api.export_managed_variants(genome_build=genome_build)

cg/meta/workflow/fluffy.py

@@ -40,7 +40,7 @@ class FluffySampleSheetHeaders(StrEnum):
 
     @classmethod
     def headers(cls) -> list[str]:
-        return list(cls)
+        return list(map(lambda header: header.value, cls))
 
 
 class FluffySample(BaseModel):

cg/meta/workflow/mip.py

@@ -152,13 +152,7 @@ def link_fastq_files(self, case_id: str, dry_run: bool = False) -> None:
 
     def write_panel(self, case_id: str, content: list[str]) -> None:
         """Write the gene panel to case dir."""
-        out_dir = Path(self.root, case_id)
-        out_dir.mkdir(parents=True, exist_ok=True)
-        WriteFile.write_file_from_content(
-            content="\n".join(content),
-            file_format=FileFormat.TXT,
-            file_path=Path(out_dir, f"gene_panels{FileExtensions.BED}"),
-        )
+        self._write_panel(out_dir=Path(self.root, case_id), content=content)
 
     @staticmethod
     def get_aggregated_panels(customer_id: str, default_panels: set[str]) -> list[str]: