cg 80.1.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/server/endpoints/sequencing_run/dtos.py

@@ -3,7 +3,7 @@ from datetime import datetime
 from pydantic import BaseModel
 
 
-class PacbioSequencingRunDTO(BaseModel):
+class PacbioSmrtCellMetricsDTO(BaseModel):
     barcoded_hifi_mean_read_length: int
     barcoded_hifi_reads: int
     barcoded_hifi_reads_percentage: float
@@ -24,5 +24,23 @@ class PacbioSequencingRunDTO(BaseModel):
     well: str
 
 
-class PacbioSequencingRunsResponse(BaseModel):
-    runs: list[PacbioSequencingRunDTO]
+class PacbioSmrtCellMetricsResponse(BaseModel):
+    runs: list[PacbioSmrtCellMetricsDTO]
+
+
+class PacbioSequencingRunDTO(BaseModel):
+    id: int
+    run_name: str
+    comment: str
+    processed: bool
+
+
+class PacbioSequencingRunResponse(BaseModel):
+    pacbio_sequencing_runs: list[PacbioSequencingRunDTO]
+    total_count: int
+
+
+class PacbioSequencingRunUpdateRequest(BaseModel):
+    id: int
+    comment: str | None = None
+    processed: bool | None = None

cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py

@@ -1,20 +1,39 @@
-from flask import Blueprint, jsonify
+from http import HTTPStatus
+
+from flask import Blueprint, Response, jsonify, request
+from pydantic import ValidationError
 
 from cg.server.endpoints.error_handler import handle_missing_entries
-from cg.server.endpoints.sequencing_run.dtos import PacbioSequencingRunsResponse
+from cg.server.endpoints.sequencing_run.dtos import (
+    PacbioSequencingRunResponse,
+    PacbioSequencingRunUpdateRequest,
+)
 from cg.server.endpoints.utils import before_request
 from cg.server.ext import pacbio_sequencing_runs_service
 
-PACBIO_SEQUENCING_RUN_BLUEPRINT = Blueprint(
-    "pacbio_sequencing_run", __name__, url_prefix="/api/v1/pacbio_sequencing_run"
+PACBIO_SEQUENCING_RUNS_BLUEPRINT = Blueprint(
+    "pacbio_sequencing_runs", __name__, url_prefix="/api/v1/"
 )
-PACBIO_SEQUENCING_RUN_BLUEPRINT.before_request(before_request)
+PACBIO_SEQUENCING_RUNS_BLUEPRINT.before_request(before_request)
 
 
-@PACBIO_SEQUENCING_RUN_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@PACBIO_SEQUENCING_RUNS_BLUEPRINT.route("/pacbio_sequencing_runs", methods=["GET"])
 @handle_missing_entries
-def get_sequencing_runs(run_name: str):
-    response: PacbioSequencingRunsResponse = (
-        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+def get_sequencing_runs():
+    page: int = int(request.args.get("page", "0"))
+    page_size: int = int(request.args.get("pageSize", "0"))
+    sequencing_runs: PacbioSequencingRunResponse = (
+        pacbio_sequencing_runs_service.get_sequencing_runs(page=page, page_size=page_size)
     )
-    return jsonify(response.model_dump())
+    return jsonify(sequencing_runs.model_dump())
+
+
+@PACBIO_SEQUENCING_RUNS_BLUEPRINT.route("/pacbio_sequencing_runs/<id>", methods=["PATCH"])
+@handle_missing_entries
+def update_sequencing_run(id: str):
+    try:
+        update_request = PacbioSequencingRunUpdateRequest(id=id, **request.json)
+    except ValidationError:
+        return Response(status=HTTPStatus.UNPROCESSABLE_ENTITY)
+    pacbio_sequencing_runs_service.update_sequencing_run(update_request=update_request)
+    return Response(status=HTTPStatus.NO_CONTENT)

cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py

@@ -0,0 +1,20 @@
+from flask import Blueprint, jsonify
+
+from cg.server.endpoints.error_handler import handle_missing_entries
+from cg.server.endpoints.sequencing_run.dtos import PacbioSmrtCellMetricsResponse
+from cg.server.endpoints.utils import before_request
+from cg.server.ext import pacbio_sequencing_runs_service
+
+PACBIO_SMRT_CELL_METRICS_BLUEPRINT = Blueprint(
+    "pacbio_smrt_cell_metrics", __name__, url_prefix="/api/v1/pacbio_smrt_cell_metrics"
+)
+PACBIO_SMRT_CELL_METRICS_BLUEPRINT.before_request(before_request)
+
+
+@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@handle_missing_entries
+def get_smrt_cell_metrics(run_name: str):
+    response: PacbioSmrtCellMetricsResponse = (
+        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+    )
+    return jsonify(response.model_dump())

cg/services/analysis_starter/configurator/configurator.py

@@ -20,7 +20,7 @@ class Configurator(ABC):
     @staticmethod
     def _set_flags(config: SpecificCaseConfig, **flags) -> SpecificCaseConfig:
         curated_flags: dict = {key: value for key, value in flags.items() if value is not None}
-        return config.model_copy(update=curated_flags)
+        return config.model_validate(config.model_dump(by_alias=True) | curated_flags)
 
     @abstractmethod
     def _ensure_required_config_files_exist(self, **kwargs) -> None:

cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/models.py

@@ -1,6 +1,21 @@
 from pathlib import Path
 
-from cg.models.nf_analysis import WorkflowParameters
+from pydantic import BaseModel, field_validator
+
+from cg.constants.constants import GenomeVersion
+from cg.constants.sample_sources import SourceType
+from cg.utils.utils import replace_non_alphanumeric
+
+
+class WorkflowParameters(BaseModel):
+    input: Path
+    outdir: Path
+
+
+class NalloParameters(WorkflowParameters):
+    """Model for Nallo parameters."""
+
+    filter_variants_hgnc_ids: str
 
 
 class RarediseaseParameters(WorkflowParameters):
@@ -20,3 +35,27 @@ class RNAFusionParameters(WorkflowParameters):
 
 class TaxprofilerParameters(WorkflowParameters):
     """Taxprofiler parameters."""
+
+
+class TomteParameters(WorkflowParameters):
+    """Model for Tomte parameters."""
+
+    gene_panel_clinical_filter: Path
+    tissue: str
+    genome: str = GenomeVersion.HG38
+
+    @field_validator("tissue", mode="before")
+    @classmethod
+    def restrict_tissue_values(cls, tissue: str | None) -> str:
+        if tissue:
+            return replace_non_alphanumeric(string=tissue)
+        else:
+            return SourceType.UNKNOWN
+
+    @field_validator("genome", mode="before")
+    @classmethod
+    def restrict_genome_values(cls, genome: str) -> str:
+        if genome == GenomeVersion.HG38:
+            return GenomeVersion.GRCh38.value
+        elif genome == GenomeVersion.HG19:
+            return GenomeVersion.GRCh37.value

cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/nallo.py

@@ -4,10 +4,12 @@ from typing import Any
 
 from cg.constants.scout import ScoutExportFileName
 from cg.io.yaml import read_yaml, write_yaml_nextflow_style
-from cg.models.nallo.nallo import NalloParameters
 from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.abstract import (
     ParamsFileCreator,
 )
+from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.models import (
+    NalloParameters,
+)
 from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.utils import (
     replace_values_in_params_file,
 )

cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/tomte_params_file_creator.py

@@ -6,10 +6,12 @@ from cg.constants.constants import GenomeVersion
 from cg.constants.scout import ScoutExportFileName
 from cg.exc import CgError
 from cg.io.yaml import read_yaml, write_yaml_nextflow_style
-from cg.models.tomte.tomte import TomteParameters
 from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.abstract import (
     ParamsFileCreator,
 )
+from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.models import (
+    TomteParameters,
+)
 from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.utils import (
     replace_values_in_params_file,
 )

cg/services/analysis_starter/factories/configurator_factory.py

@@ -47,19 +47,19 @@ from cg.services.analysis_starter.configurator.file_creators.nextflow.params_fil
 from cg.services.analysis_starter.configurator.file_creators.nextflow.params_file.tomte_params_file_creator import (
     TomteParamsFileCreator,
 )
-from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.nallo import (
+from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.nallo_sample_sheet_creator import (
     NalloSampleSheetCreator,
 )
 from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.protocol import (
     SampleSheetCreator,
 )
-from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.raredisease import (
+from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.raredisease_sample_sheet_creator import (
     RarediseaseSampleSheetCreator,
 )
-from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.rnafusion import (
+from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.rnafusion_sample_sheet_creator import (
     RNAFusionSampleSheetCreator,
 )
-from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.taxprofiler import (
+from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.taxprofiler_sample_sheet_creator import (
     TaxprofilerSampleSheetCreator,
 )
 from cg.services.analysis_starter.configurator.file_creators.nextflow.sample_sheet.tomte_sample_sheet_creator import (

cg/services/analysis_starter/tracker/implementations/balsamic.py

@@ -12,7 +12,10 @@ class BalsamicTracker(Tracker):
         return WorkflowManager.Slurm
 
     def _get_job_ids_path(self, case_id: str) -> Path:
-        return Path(self.workflow_root, case_id, "analysis", "slurm_jobids.yaml")
+        return Path(self._get_out_dir_path(case_id), "slurm_jobids.yaml")
+
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return Path(self.workflow_root, case_id, "analysis")
 
     def _get_workflow_version(self, case_config: BalsamicCaseConfig) -> str:
         config_data: dict = read_json(case_config.sample_config)

cg/services/analysis_starter/tracker/implementations/microsalt.py

@@ -27,13 +27,13 @@ class MicrosaltTracker(Tracker):
     def _get_job_ids_path(self, case_id: str) -> Path:
         project_id: str = self._get_file_name_start(case_id)
         return Path(
-            self.workflow_root,
-            "results",
-            "reports",
-            "trailblazer",
+            self._get_out_dir_path(case_id),
             f"{project_id}_slurm_ids{FileExtensions.YAML}",
         )
 
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return Path(self.workflow_root, "results", "reports", "trailblazer")
+
     def _get_file_name_start(self, case_id: str) -> str:
         """Returns the LIMS project id if the case contains multiple samples, else the sample id."""
         case: Case = self.store.get_case_by_internal_id(case_id)

cg/services/analysis_starter/tracker/implementations/mip_dna.py

@@ -12,7 +12,10 @@ class MIPDNATracker(Tracker):
         return WorkflowManager.Slurm
 
     def _get_job_ids_path(self, case_id: str) -> Path:
-        return Path(self.workflow_root, case_id, "analysis", "slurm_job_ids.yaml")
+        return Path(self._get_out_dir_path(case_id), "slurm_job_ids.yaml")
+
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return Path(self.workflow_root, case_id, "analysis")
 
     def _get_sample_info_path(self, case_id: str) -> Path:
         return Path(self.workflow_root, case_id, "analysis", f"{case_id}_qc_sample_info.yaml")

cg/services/analysis_starter/tracker/implementations/nextflow_tracker.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from cg.constants.constants import FileExtensions, WorkflowManager
+from cg.constants.constants import WorkflowManager
 from cg.services.analysis_starter.configurator.models.nextflow import NextflowCaseConfig
 from cg.services.analysis_starter.tracker.tracker import Tracker
 
@@ -9,9 +9,11 @@ class NextflowTracker(Tracker):
     def _workflow_manager(self) -> WorkflowManager:
         return WorkflowManager.Tower
 
-    def _get_job_ids_path(self, case_id: str) -> Path:
-        """Return the path to a Trailblazer config file containing Tower IDs."""
-        return Path(self.workflow_root, case_id, "tower_ids").with_suffix(FileExtensions.YAML)
+    def _get_job_ids_path(self, case_id: str) -> Path | None:
+        return None
+
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return Path(self.workflow_root, case_id)
 
     def _get_workflow_version(self, case_config: NextflowCaseConfig) -> str:
         return case_config.revision

cg/services/analysis_starter/tracker/tracker.py

@@ -6,7 +6,7 @@ from pathlib import Path
 from cg.apps.environ import environ_email
 from cg.apps.tb import TrailblazerAPI
 from cg.apps.tb.models import TrailblazerAnalysis
-from cg.constants.constants import CaseActions, CustomerId, Workflow
+from cg.constants.constants import CaseActions, CustomerId, Workflow, WorkflowManager
 from cg.constants.priority import TrailblazerPriority
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.constants.tb import AnalysisType
@@ -61,17 +61,17 @@ class Tracker(ABC):
         self, case_id: str, tower_workflow_id: str | None
     ) -> TrailblazerAnalysis:
         analysis_type: str = self._get_analysis_type(case_id)
-        config_path: Path = self._get_job_ids_path(case_id)
+        config_path: Path | None = self._get_job_ids_path(case_id)
         email: str = environ_email()
         order_id: int = self.store.get_case_by_internal_id_strict(case_id).latest_order.id
-        out_dir: str = config_path.parent.as_posix()
+        out_dir: str = self._get_out_dir_path(case_id).as_posix()
         priority: TrailblazerPriority = self._get_trailblazer_priority(case_id)
         ticket: str = self.store.get_latest_ticket_from_case(case_id)
         is_case_for_development: bool = self._is_case_for_development(case_id)
         return self.trailblazer_api.add_pending_analysis(
             analysis_type=analysis_type,
             case_id=case_id,
-            config_path=config_path.as_posix(),
+            config_path=config_path.as_posix() if config_path else None,
             email=email,
             order_id=order_id,
             out_dir=out_dir,
@@ -133,11 +133,15 @@ class Tracker(ABC):
         return case.customer.internal_id == CustomerId.CG_INTERNAL_CUSTOMER
 
     @abstractmethod
-    def _workflow_manager(self):
+    def _workflow_manager(self) -> WorkflowManager:
         pass
 
     @abstractmethod
-    def _get_job_ids_path(self, case_id: str):
+    def _get_job_ids_path(self, case_id: str) -> Path | None:
+        pass
+
+    @abstractmethod
+    def _get_out_dir_path(self, case_id: str) -> Path:
         pass
 
     @abstractmethod

cg/services/illumina/backup/backup_service.py

@@ -114,7 +114,10 @@ class IlluminaBackupService:
         """Process a flow cell from backup. Return elapsed time."""
         start_time: float = get_start_time()
         run_dir = Path(self.sequencing_runs_dir)
-        sequencing_run_output_dir = Path(run_dir, archived_run.name.split(".")[0])
+        is_current: bool = self._is_archiving_directory_current(archived_run)
+        sequencing_run_output_dir: Path = self._get_sequencing_run_output_dir(
+            archived_run=archived_run, is_current=is_current
+        )
         self.retrieve_archived_key(
             archived_key=archived_key, sequencing_run=sequencing_run, run_dir=run_dir
         )
@@ -128,9 +131,12 @@ class IlluminaBackupService:
                 encryption_key,
                 retrieved_run,
                 retrieved_key,
-            ) = self.decrypt_sequencing_run(archived_run, archived_key, run_dir)
-
-            self.extract_sequencing_run(decrypted_run, run_dir)
+            ) = self.decrypt_sequencing_run(
+                archived_run=archived_run, archived_key=archived_key, run_dir=run_dir
+            )
+            self.extract_sequencing_run(
+                decrypted_run=decrypted_run, is_current=is_current, run_dir=run_dir
+            )
             self.create_rta_complete(sequencing_run_output_dir)
             self.create_copy_complete(sequencing_run_output_dir)
             self.unlink_files(decrypted_run, encryption_key, retrieved_run, retrieved_key)
@@ -145,6 +151,20 @@ class IlluminaBackupService:
 
         return get_elapsed_time(start_time=start_time)
 
+    def _get_sequencing_run_output_dir(self, archived_run: Path, is_current: bool) -> Path:
+        """Return the path to the sequencing run based on the archived run path."""
+        if is_current:
+            run_full_name: str = archived_run.parent.name
+        else:
+            run_full_name: str = archived_run.name.split(".")[0]
+        return Path(self.sequencing_runs_dir, run_full_name)
+
+    def _is_archiving_directory_current(self, archived_run: Path) -> bool:
+        """Check if the archived run is in the current archiving directory."""
+        return archived_run.as_posix().startswith(
+            Path(self.pdc_archiving_directory.current).parent.as_posix()
+        )
+
     def unlink_files(
         self,
         decrypted_run: Path,
@@ -184,10 +204,12 @@ class IlluminaBackupService:
         """Create a CopyComplete.txt file in the flow cell run directory."""
         Path(flow_cell_directory, DemultiplexingDirsAndFiles.COPY_COMPLETE).touch()
 
-    def extract_sequencing_run(self, decrypted_run, run_dir):
+    def extract_sequencing_run(self, decrypted_run: Path, is_current: bool, run_dir: Path) -> None:
         """Extract the sequencing run tar archive."""
-        extraction_command = self.tar_api.get_extract_file_command(
-            input_file=decrypted_run, output_dir=run_dir
+        extraction_command: list[str] = self.tar_api.get_extract_file_command(
+            input_file=decrypted_run,
+            output_dir=run_dir,
+            is_current=is_current,
         )
         LOG.debug(f"Extract sequencing run command: {extraction_command}")
         self.tar_api.run_tar_command(extraction_command)

cg/services/orders/validation/constants.py

@@ -30,6 +30,7 @@ class ExtractionMethod(StrEnum):
 
 
 class IndexEnum(StrEnum):
+    ARCHER_SET_B = "Archer Set B"
     AVIDA_INDEX_PLATE = "Avida Index plate"
     AVIDA_INDEX_STRIP = "Avida Index strip"
     IDT_DS_B = "IDT DupSeq 10 bp Set B"
@@ -37,6 +38,7 @@ class IndexEnum(StrEnum):
     IDT_XGEN_UDI = "IDT xGen UDI Adapters"
     IDT10_UDI_NIPT = "IDT10 UDI NIPT"
     KAPA_UDI_NIPT = "KAPA UDI NIPT"
+    NEBNEXT_LV_Unique_Dual_2A = "NEBNext LV Unique Dual Index Primers Set 2A"
     NEXTERA_XT = "Nextera XT Dual"
     NEXTFLEX_UDI_96 = "NEXTflex® Unique Dual Index Barcodes 1 - 96"
     NEXTFLEX_V2_UDI_96 = "NEXTflex® v2 UDI Barcodes 1 - 96"
@@ -46,4 +48,5 @@ class IndexEnum(StrEnum):
     TWIST_UDI_B = "TWIST UDI Set B"
     TWIST_UDI_C = "TWIST UDI Set C"
     TRUSEQ_DNA_HT = "TruSeq DNA HT Dual-index (D7-D5)"
+    XGEN_UDI_10_1_4 = "xGen UDI 10nt Primer Plates 1-4"
     NO_INDEX = "NoIndex"