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

cg/constants/nf_analysis.py

@@ -17,7 +17,6 @@ class NfTowerStatus(StrEnum):
 
 NALLO_GENERAL_METRIC_CONDITIONS: dict[str, dict[str, Any]] = {
     "median_coverage": {"norm": "gt", "threshold": 20},
-    "predicted_sex_sex_check": {"norm": "eq", "threshold": None},
 }
 
 NALLO_PARENT_PEDDY_METRIC_CONDITION: dict[str, dict[str, Any]] = {

cg/constants/observations.py

@@ -14,10 +14,14 @@ LOQUSDB_SUPPORTED_WORKFLOWS = [
 ]
 LOQUSDB_RARE_DISEASE_CUSTOMERS = [CustomerId.CUST002, CustomerId.CUST003, CustomerId.CUST004]
 LOQUSDB_CANCER_CUSTOMERS = [
+    CustomerId.CUST002,
+    CustomerId.CUST087,
     CustomerId.CUST110,
     CustomerId.CUST127,
     CustomerId.CUST143,
     CustomerId.CUST147,
+    CustomerId.CUST175,
+    CustomerId.CUST185,
 ]
 LOQUSDB_LONG_READ_CUSTOMERS = [
     CustomerId.CUST002,
@@ -35,9 +39,18 @@ LOQUSDB_RARE_DISEASE_SEQUENCING_METHODS = [
 LOQUSDB_CANCER_SEQUENCING_METHODS = [
     CancerAnalysisType.TUMOR_WGS,
     CancerAnalysisType.TUMOR_NORMAL_WGS,
+    CancerAnalysisType.TUMOR_PANEL,
 ]
 
 
+class BalsamicObservationPanel(StrEnum):
+    """Group of panels which have associated LoqusDB instances."""
+
+    EXOME = "Twist Exome Comprehensive"
+    LYMPHOID = "GMSlymphoid"
+    MYELOID = "GMSmyeloid"
+
+
 class BalsamicLoadParameters(Enum):
     """Cancer Loqusdb load command parameters."""
 
@@ -57,11 +70,14 @@ class BalsamicObservationsAnalysisTag(StrEnum):
 class LoqusdbInstance(StrEnum):
     """Observations instances."""
 
-    LWP: str = "loqusdb-lwp"
-    WGS: str = "loqusdb"
-    WES: str = "loqusdb-wes"
-    SOMATIC: str = "loqusdb-somatic"
-    TUMOR: str = "loqusdb-tumor"
+    LWP = "loqusdb-lwp"
+    WGS = "loqusdb"
+    WES = "loqusdb-wes"
+    SOMATIC = "loqusdb-somatic"
+    TUMOR = "loqusdb-tumor"
+    SOMATIC_LYMPHOID = "loqusdb-somatic-lymphoid"
+    SOMATIC_MYELOID = "loqusdb-somatic-myeloid"
+    SOMATIC_EXOME = "loqusdb-somatic-exome"
 
 
 class MipDNALoadParameters(Enum):

cg/constants/orderforms.py

@@ -31,11 +31,11 @@ class Orderform(StrEnum):
         """Returns the current version of the given order form."""
         current_order_form_versions = {
             Orderform.MIP_DNA: "35",
-            Orderform.RML: "20",
-            Orderform.MICROSALT: "11",
+            Orderform.RML: "21",
+            Orderform.MICROSALT: "12",
             Orderform.NALLO: "1",
             Orderform.SARS_COV_2: "10",
-            Orderform.MICROBIAL_FASTQ: "2",
+            Orderform.MICROBIAL_FASTQ: "3",
             Orderform.PACBIO_LONG_READ: "2",
         }
         return current_order_form_versions[order_form]

cg/constants/pacbio.py

@@ -64,6 +64,7 @@ class SmrtLinkDatabasesAliases:
     BIO_SAMPLE_NAME: str = "bioSampleName"
     CELL_ID: str = "cellId"
     CELL_INDEX: str = "cellIndex"
+    INSTRUMENT_NAME: str = "instrumentName"
     MOVIE_NAME: str = "metadataContextId"
     PATH: str = "path"
     RUN_COMPLETED_AT = "createdAt"

cg/constants/priority.py

@@ -34,7 +34,7 @@ class Priority(IntEnum):
     express = 4
 
     @classmethod
-    def priority_to_slurm_qos(cls) -> dict[int, str]:
+    def priority_to_slurm_qos(cls) -> dict["Priority", SlurmQos]:
         return {
             Priority.research: SlurmQos.LOW,
             Priority.standard: SlurmQos.NORMAL,

cg/constants/report.py

@@ -209,6 +209,7 @@ REQUIRED_SAMPLE_METADATA_NALLO_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIE
 _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
     "mean_insert_size",
     "fold_80",
+    "predicted_sex",
 ]
 
 REQUIRED_SAMPLE_METADATA_BALSAMIC_TARGETED_FIELDS: list[str] = (

cg/constants/scout.py

@@ -12,14 +12,14 @@ class GenomeBuild(StrEnum):
 
 
 class ScoutExportFileName(StrEnum):
-    MANAGED_VARIANTS: str = f"managed_variants{FileExtensions.VCF}"
-    PANELS: str = f"gene_panels{FileExtensions.BED}"
-    PANELS_TSV: str = f"gene_panels{FileExtensions.TSV}"
+    MANAGED_VARIANTS = f"managed_variants{FileExtensions.VCF}"
+    PANELS = f"gene_panels{FileExtensions.BED}"
+    PANELS_TSV = f"gene_panels{FileExtensions.TSV}"
 
 
 class UploadTrack(StrEnum):
-    RARE_DISEASE: str = "rare"
-    CANCER: str = "cancer"
+    RARE_DISEASE = "rare"
+    CANCER = "cancer"
 
 
 class ScoutCustomCaseReportTags(StrEnum):
@@ -66,12 +66,12 @@ NALLO_CASE_TAGS = dict(
     multiqc={"multiqc-html"},
     peddy_check={"ped-check", "peddy"},
     peddy_ped={"ped", "peddy"},
-    peddy_sex={"sex-check", "peddy"},
-    vcf_snv_research={"vcf-snv-research"},
+    somalier_samples={"somalier", "relate-samples"},
     vcf_snv={"vcf-snv-clinical"},
-    vcf_sv_research={"vcf-sv-research"},
-    vcf_sv={"vcf-sv-clinical"},
+    vcf_snv_research={"vcf-snv-research"},
     vcf_str={"vcf-str"},
+    vcf_sv={"vcf-sv-clinical"},
+    vcf_sv_research={"vcf-sv-research"},
 )
 
 MIP_CASE_TAGS: dict[str, set[str]] = dict(
@@ -138,9 +138,12 @@ RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict(
 NALLO_SAMPLE_TAGS: dict[str, set[str]] = dict(
     alignment_path={AlignmentFileTag.BAM, "haplotags"},
     assembly_alignment_path={AlignmentFileTag.BAM, "assembly"},
+    chromograph_autozyg={"chromograph", "autozyg"},
+    chromograph_coverage={"chromograph", "tcov"},
     d4_file={"coverage", "d4"},
     hificnv_coverage={"hificnv", "bigwig"},
     paraphase_alignment_path={AlignmentFileTag.BAM, NalloAnalysisTag.PARAPHASE},
+    phase_blocks={"whatshap", "gtf"},
     reviewer_alignment={"repeats", "spanning", "bam"},
     reviewer_alignment_index={"repeats", "spanning", "bam-index"},
     reviewer_vcf={"repeats", "sorted", "vcf"},

cg/constants/sequencing.py

@@ -60,8 +60,8 @@ class RecordType(StrEnum):
 
 
 class SequencingPlatform(StrEnum):
-    ILLUMINA: str = "ILLUMINA"
-    OXFORD_NANOPORE: str = "OXFORD_NANOPORE"
+    ILLUMINA = "ILLUMINA"
+    OXFORD_NANOPORE = "OXFORD_NANOPORE"
 
 
 class SeqLibraryPrepCategory(StrEnum):

cg/constants/tb.py

@@ -15,8 +15,8 @@ class AnalysisStatus:
 
 
 class AnalysisType(StrEnum):
-    OTHER: str = "other"
-    TGS: str = SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING
-    WES: str = SeqLibraryPrepCategory.WHOLE_EXOME_SEQUENCING
-    WGS: str = SeqLibraryPrepCategory.WHOLE_GENOME_SEQUENCING
-    WTS: str = SeqLibraryPrepCategory.WHOLE_TRANSCRIPTOME_SEQUENCING
+    OTHER = "other"
+    TGS = SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING
+    WES = SeqLibraryPrepCategory.WHOLE_EXOME_SEQUENCING
+    WGS = SeqLibraryPrepCategory.WHOLE_GENOME_SEQUENCING
+    WTS = SeqLibraryPrepCategory.WHOLE_TRANSCRIPTOME_SEQUENCING

cg/exc.py

@@ -1,5 +1,5 @@
 """
-    Cg Exceptions.
+Cg Exceptions.
 """
 
 
@@ -36,6 +36,12 @@ class AnalysisNotReadyError(CgError):
     """
 
 
+class AnalysisAlreadyCompletedError(CgError):
+    """
+    Exception raised when the latest analysis is already completed.
+    """
+
+
 class AnalysisNotCompletedError(CgError):
     """
     Exception raised when an analysis has not completed.
@@ -144,6 +150,14 @@ class IlluminaRunAlreadyBackedUpError(CgError):
     """Raised when a flow cell is already backed-up."""
 
 
+class PacbioSequencingRunAlreadyExistsError(CgError):
+    """Raised when a PacBio sequencing run already exists."""
+
+
+class PacbioSequencingRunNotFoundError(CgError):
+    """Raised when a PacBio sequencing run is not found."""
+
+
 class HousekeeperFileMissingError(CgError):
     """
     Exception raised when a file is missing in Housekeeper.
@@ -210,10 +224,6 @@ class RunParametersError(CgError):
     """Raised when something is wrong with the run parameters file."""
 
 
-class NfSampleSheetError(CgError):
-    """Raised when something is wrong with the sample sheet."""
-
-
 class SampleSheetContentError(CgError):
     """Raised when something is wrong with the sample sheet content."""
 
@@ -334,5 +344,17 @@ class Chanjo2ResponseError(Chanjo2APIClientError):
     """Exception raised when the response from Chanjo2 API client fails validation."""
 
 
+class CaseNotConfiguredError(CgError):
+    """Exception raised when a case is being run without a configuration."""
+
+
 class MissingConfigFilesError(CgError):
     """Exception raised when a case is being run with missing configuration files."""
+
+
+class SeqeraError(CgError):
+    """Exception raised when receiving an unexpected response from Seqera platform"""
+
+
+class ApplicationDoesNotHaveHiFiYieldError(CgError):
+    """Exception raised when application does not have HiFi yield set."""

cg/meta/compress/compress.py

@@ -96,8 +96,13 @@ class CompressAPI:
     def decompress_case(self, case: Case) -> None:
         """Decompresses all Spring files tied to the case.
         Raises:
-            DecompressionFailedToStartError if no sample could start decompressing."""
-        if not any(self.decompress_spring(sample.internal_id) for sample in case.samples):
+            DecompressionCouldNotStartError if no sample could start decompressing.
+        """
+        success = False
+        for sample in case.samples:
+            if self.decompress_spring(sample.internal_id):
+                success = True
+        if not success:
             raise DecompressionCouldNotStartError(
                 f"No sample could be decompressed for {case.internal_id}"
             )

cg/meta/delivery_report/balsamic.py

@@ -89,6 +89,7 @@ class BalsamicDeliveryReportAPI(DeliveryReportAPI):
             million_read_pairs=million_read_pairs,
             pct_250x=sample_metrics.pct_target_bases_250x if sample_metrics else None,
             pct_500x=sample_metrics.pct_target_bases_500x if sample_metrics else None,
+            predicted_sex=sample_metrics.compare_predicted_to_given_sex if sample_metrics else None,
         )
 
     @staticmethod
@@ -103,13 +104,14 @@ class BalsamicDeliveryReportAPI(DeliveryReportAPI):
             fold_80=sample_metrics.fold_80_base_penalty if sample_metrics else None,
             initial_qc=passed_initial_qc,
             mean_insert_size=sample_metrics.mean_insert_size if sample_metrics else None,
-            median_coverage=sample_metrics.median_coverage if sample_metrics else None,
+            median_coverage=sample_metrics.median_target_coverage if sample_metrics else None,
             million_read_pairs=million_read_pairs,
             pct_15x=sample_metrics.pct_15x if sample_metrics else None,
             pct_60x=sample_metrics.pct_60x if sample_metrics else None,
             pct_reads_improper_pairs=(
                 sample_metrics.pct_pf_reads_improper_pairs if sample_metrics else None
             ),
+            predicted_sex=sample_metrics.compare_predicted_to_given_sex if sample_metrics else None,
         )
 
     def is_report_accredited(

cg/meta/delivery_report/delivery_report_api.py

@@ -23,6 +23,7 @@ from cg.meta.delivery.delivery import DeliveryAPI
 from cg.meta.delivery_report.data_validators import get_empty_report_data, get_missing_report_data
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.models.analysis import AnalysisModel
+from cg.models.delivery.delivery import DeliveryFile
 from cg.models.delivery_report.metadata import SampleMetadataModel
 from cg.models.delivery_report.report import (
     CaseModel,
@@ -250,14 +251,14 @@ class DeliveryReportAPI:
         for case_sample in case_samples:
             sample: Sample = case_sample.sample
             lims_sample: dict[str, Any] = self.lims_api.sample(sample.internal_id)
-            delivered_files: list[File] | None = (
+            delivered_files: list[DeliveryFile] | None = (
                 self.delivery_api.get_analysis_sample_delivery_files_by_sample(
                     case=case, sample=sample
                 )
                 if self.delivery_api.is_analysis_delivery(case.data_delivery)
                 else None
             )
-            delivered_fastq_files: list[File] | None = (
+            delivered_fastq_files: list[DeliveryFile] | None = (
                 self.delivery_api.get_fastq_delivery_files_by_sample(case=case, sample=sample)
                 if self.delivery_api.is_fastq_delivery(case.data_delivery)
                 else None
@@ -332,7 +333,7 @@ class DeliveryReportAPI:
 
     def get_case_analysis_data(self, case: Case, analysis: Analysis) -> DataAnalysisModel:
         """Return workflow attributes used for data analysis."""
-        delivered_files: list[File] | None = (
+        delivered_files: list[DeliveryFile] | None = (
             self.delivery_api.get_analysis_case_delivery_files(case)
             if self.delivery_api.is_analysis_delivery(case.data_delivery)
             else None

cg/meta/delivery_report/nallo.py

@@ -1,7 +1,9 @@
 """Nallo Delivery Report API."""
 
+from typing import cast
+
 from cg.clients.chanjo2.models import CoverageMetrics
-from cg.constants.housekeeper_tags import AnalysisTag, HermesFileTag
+from cg.constants.housekeeper_tags import AnalysisTag
 from cg.constants.report import (
     REQUIRED_APPLICATION_FIELDS,
     REQUIRED_CASE_FIELDS,
@@ -13,8 +15,6 @@ from cg.constants.report import (
     REQUIRED_SAMPLE_NALLO_FIELDS,
     REQUIRED_SAMPLE_TIMESTAMP_FIELDS,
 )
-from cg.constants.scout import ScoutUploadKey
-from cg.constants.subject import PlinkSex
 from cg.meta.delivery_report.data_validators import get_million_read_pairs
 from cg.meta.delivery_report.delivery_report_api import DeliveryReportAPI
 from cg.meta.workflow.nallo import NalloAnalysisAPI
@@ -36,7 +36,9 @@ class NalloDeliveryReportAPI(DeliveryReportAPI):
         self, case: Case, sample: Sample, analysis_metadata: NextflowAnalysis
     ) -> NalloSampleMetadataModel:
         """Return Nallo sample metadata to include in the report."""
-        sample_metrics: NalloQCMetrics = analysis_metadata.sample_metrics[sample.internal_id]
+        sample_metrics: NalloQCMetrics = cast(
+            NalloQCMetrics, analysis_metadata.sample_metrics[sample.internal_id]
+        )
         gene_ids: list[int] = self.analysis_api.get_gene_ids_from_scout(case.panels)
         coverage_metrics: CoverageMetrics | None = self.analysis_api.get_sample_coverage(
             case_id=case.internal_id, sample_id=sample.internal_id, gene_ids=gene_ids
@@ -50,7 +52,7 @@ class NalloDeliveryReportAPI(DeliveryReportAPI):
             median_coverage=sample_metrics.median_coverage,
             million_read_pairs=get_million_read_pairs(sample.reads),
             pct_10x=coverage_metrics.coverage_completeness_percent if coverage_metrics else None,
-            sex=sample_metrics.predicted_sex_sex_check,
+            sex=sample_metrics.predicted_sex,
         )
 
     def is_report_accredited(
@@ -65,23 +67,21 @@ class NalloDeliveryReportAPI(DeliveryReportAPI):
     def get_scout_variants_files(self, case_id: str) -> ScoutVariantsFiles:
         """Return Nallo files that will be uploaded to Scout."""
         return ScoutVariantsFiles(
-            snv_vcf=self.housekeeper_api.get_latest_file(
+            snv_vcf=self.housekeeper_api.get_latest_file_strict(
                 bundle=case_id,
                 tags=[
                     AnalysisTag.VCF_SNV_CLINICAL,
                 ],
             ).full_path,
-            sv_vcf=self.housekeeper_api.get_latest_file(
+            sv_vcf=self.housekeeper_api.get_latest_file_strict(
                 bundle=case_id,
                 tags=[
                     AnalysisTag.VCF_SV_CLINICAL,
                 ],
             ).full_path,
-            vcf_str=self.housekeeper_api.get_latest_file(
+            vcf_str=self.housekeeper_api.get_latest_file_strict(
                 bundle=case_id,
-                tags=[
-                    AnalysisTag.VCF_STR,
-                ],
+                tags=[AnalysisTag.VCF_STR],
             ).full_path,
         )
 

cg/meta/delivery_report/raredisease.py

@@ -1,6 +1,9 @@
 """Raredisease Delivery Report API."""
 
+from housekeeper.store.models import File
+
 from cg.clients.chanjo2.models import CoverageMetrics
+from cg.constants.housekeeper_tags import AnalysisTag
 from cg.constants.report import (
     REQUIRED_APPLICATION_FIELDS,
     REQUIRED_CASE_FIELDS,
@@ -43,7 +46,7 @@ class RarediseaseDeliveryReportAPI(DeliveryReportAPI):
         )
         return RarediseaseSampleMetadataModel(
             bait_set=self.lims_api.capture_kit(sample.internal_id),
-            duplicates=sample_metrics.percent_duplicates,
+            duplicates=round(sample_metrics.percent_duplication * 100, 2),
             initial_qc=self.lims_api.has_sample_passed_initial_qc(sample.internal_id),
             mapped_reads=round((sample_metrics.mapped_reads / sample_metrics.total_reads) * 100, 2),
             mean_target_coverage=coverage_metrics.mean_coverage if coverage_metrics else None,
@@ -69,9 +72,10 @@ class RarediseaseDeliveryReportAPI(DeliveryReportAPI):
         sv_vcf: str | None = self.get_scout_uploaded_file_from_hk(
             case_id=case_id, scout_key=ScoutUploadKey.VCF_SV
         )
-        vcf_str: str | None = self.get_scout_uploaded_file_from_hk(
-            case_id=case_id, scout_key=ScoutUploadKey.VCF_STR
+        vcf_str_file: File | None = self.housekeeper_api.get_latest_file(
+            bundle=case_id, tags=[AnalysisTag.VCF_STR, case_id]
         )
+        vcf_str: str | None = vcf_str_file.full_path if vcf_str_file else None
         smn_tsv: str | None = self.get_scout_uploaded_file_from_hk(
             case_id=case_id, scout_key=ScoutUploadKey.SMN_TSV
         )

cg/meta/delivery_report/templates/macros/data_analysis/qc_metrics/balsamic_qc_metrics.html

@@ -3,6 +3,7 @@
 {% macro balsamic_qc_metrics(samples, analysis_type) %}
   {% set
     metrics = [
+      {"name": "Kön",                         "key": "predicted_sex",      "description": "Kön beräknat genom bioinformatisk analys."},
       {"name": "Läspar [M]",                  "key": "million_read_pairs", "description": "Antal sekvenseringsläsningar i miljoner läspar."},
       {"name": "Duplikat [%]",                "key": "duplicates",         "description": "Sekvenseringsläsningar som är i duplikat och därmed ej unika sekvenser. Hög mängd duplikat kan tyda på dålig komplexitet av sekvenserat bibliotek eller djup sekvensering."},
       {"name": "Medelfragmentlängd [baspar]", "key": "mean_insert_size",   "description": "Medelstorlek av provbiblioteken som laddats på sekvenseringsinstrument."},

cg/meta/delivery_report/templates/macros/ticket_system.html

@@ -2,7 +2,7 @@
   <div class="container">
     <div class="alert alert-info" role="alert">
       All kommunikation gällande ordern, såsom tillägg, avvikelser eller ev undantag i metoden från
-      Clinical Genomics, finns tillgänglig i SupportSystem och är länkad till ärendets ticket:
+      Clinical Genomics, finns tillgänglig i Freshdesk och är länkad till ärendets ticket:
       <a class="alert-link">#{{ ticket_id }}</a>. En stängd ticket kan närsomhelst öppnas upp igen för frågor.
     </div>
   </div>

cg/meta/observations/balsamic_observations_api.py

@@ -12,19 +12,27 @@ from cg.constants.observations import (
     LOQUSDB_CANCER_SEQUENCING_METHODS,
     LOQUSDB_ID,
     BalsamicLoadParameters,
+    BalsamicObservationPanel,
     BalsamicObservationsAnalysisTag,
     LoqusdbInstance,
 )
-from cg.exc import CaseNotFoundError, LoqusdbDuplicateRecordError
+from cg.constants.sequencing import SeqLibraryPrepCategory
+from cg.exc import CaseNotFoundError, LoqusdbDeleteCaseError, LoqusdbDuplicateRecordError
 from cg.meta.observations.observations_api import ObservationsAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.models.observations.input_files import BalsamicObservationsInputFiles
-from cg.store.models import Case
+from cg.store.models import BedVersion, Case, Sample
 from cg.utils.dict import get_full_path_dictionary
 
 LOG = logging.getLogger(__name__)
 
+PANEL_TO_LOQUSDB_INSTANCE_MAP: dict = {
+    BalsamicObservationPanel.LYMPHOID: LoqusdbInstance.SOMATIC_LYMPHOID,
+    BalsamicObservationPanel.MYELOID: LoqusdbInstance.SOMATIC_MYELOID,
+    BalsamicObservationPanel.EXOME: LoqusdbInstance.SOMATIC_EXOME,
+}
+
 
 class BalsamicObservationsAPI(ObservationsAPI):
     """API to manage Balsamic observations."""
@@ -32,6 +40,7 @@ class BalsamicObservationsAPI(ObservationsAPI):
     def __init__(self, config: CGConfig):
         self.analysis_api = BalsamicAnalysisAPI(config)
         super().__init__(config=config, analysis_api=self.analysis_api)
+        self.lims_api = config.lims_api
         self.loqusdb_somatic_api: LoqusdbAPI = self.get_loqusdb_api(LoqusdbInstance.SOMATIC)
         self.loqusdb_tumor_api: LoqusdbAPI = self.get_loqusdb_api(LoqusdbInstance.TUMOR)
 
@@ -45,43 +54,122 @@ class BalsamicObservationsAPI(ObservationsAPI):
         """Return sequencing methods that are eligible for cancer Loqusdb uploads."""
         return LOQUSDB_CANCER_SEQUENCING_METHODS
 
-    def is_analysis_type_eligible_for_observations_upload(self, case_id) -> bool:
+    def is_analysis_type_eligible_for_observations_upload(self, case: Case) -> bool:
         """Return whether the cancer analysis type is eligible for cancer Loqusdb uploads."""
-        if self.analysis_api.is_analysis_normal_only(case_id):
-            LOG.error(f"Normal only analysis {case_id} is not supported for Loqusdb uploads")
+        if self.analysis_api.is_analysis_normal_only(case.internal_id):
+            LOG.error(
+                f"Normal only analysis {case.internal_id} is not supported for Loqusdb uploads"
+            )
+            return False
+        prep_category: str = case.samples[0].prep_category
+        if prep_category in [
+            SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING,
+            SeqLibraryPrepCategory.WHOLE_EXOME_SEQUENCING,
+        ] and self._is_paired_analysis(case):
+            LOG.error(
+                f"Paired analysis {case.internal_id} is not supported for TGS Loqusdb uploads"
+            )
             return False
         return True
 
+    @staticmethod
+    def _is_paired_analysis(case: Case) -> bool:
+        return len(case.samples) > 1
+
     def is_case_eligible_for_observations_upload(self, case: Case) -> bool:
         """Return whether a cancer case is eligible for observations upload."""
         return all(
             [
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
-                self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
-                self.is_analysis_type_eligible_for_observations_upload(case.internal_id),
-                self.is_sample_source_eligible_for_observations_upload(case.internal_id),
+                self.is_analysis_type_eligible_for_observations_upload(case),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
+                self.is_panel_allowed_for_observations_upload(case),
             ]
         )
 
+    def is_panel_allowed_for_observations_upload(self, case: Case) -> bool:
+        """
+        True if WGS.
+        If TGS/WES, True for panels with LoqusDB instances.
+        This assumes that all samples in the case have the same prep-category.
+        """
+        if self._is_panel_upload(case):
+            sample: Sample = case.samples[0]
+            panel_short_name: str | None = self.lims_api.capture_kit(sample.internal_id)
+            bed_version: BedVersion | None = self.store.get_bed_version_by_short_name(
+                panel_short_name
+            )
+            if not bed_version:
+                LOG.warning(
+                    f"No bed version found for LIMS panel {panel_short_name} for sample "
+                    f"{sample.internal_id} in case {case.internal_id}"
+                )
+                return False
+            if bed_version.bed.name not in list(BalsamicObservationPanel):
+                return False
+        return True
+
     def load_observations(self, case: Case) -> None:
         """
-        Load observation counts to Loqusdb for a Balsamic case.
+        Upload observation counts to Loqusdb for a Balsamic case.
 
         Raises:
             LoqusdbDuplicateRecordError: If case has already been uploaded.
         """
-        loqusdb_upload_apis: list[LoqusdbAPI] = [self.loqusdb_somatic_api, self.loqusdb_tumor_api]
+        if self._is_panel_upload(case):
+            self._upload_panel_case(case)
+        else:
+            self._upload_wgs_case(case)
+
+    @staticmethod
+    def _is_panel_upload(case: Case) -> bool:
+        sample: Sample = case.samples[0]
+        return sample.prep_category in [
+            SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING,
+            SeqLibraryPrepCategory.WHOLE_EXOME_SEQUENCING,
+        ]
+
+    def _upload_panel_case(self, case: Case) -> None:
+        """
+        Uploads the case to one of the somatic panel LoqusDB instances. The case is known to have
+        a panel with a known LoqusDB instance.
+        """
+        loqusdb_api: LoqusdbAPI = self._get_panel_loqusdb_api(case)
+        if self.is_duplicate(case=case, loqusdb_api=loqusdb_api):
+            LOG.error(f"Case {case.internal_id} has already been uploaded to Loqusdb")
+            raise LoqusdbDuplicateRecordError
+        input_files: BalsamicObservationsInputFiles = self.get_observations_input_files(case)
+        loqusdb_api.load(
+            case_id=case.internal_id,
+            snv_vcf_path=input_files.snv_vcf_path,
+        )
+        loqusdb_id: str = str(loqusdb_api.get_case(case_id=case.internal_id)[LOQUSDB_ID])
+        self.update_statusdb_loqusdb_id(samples=case.samples, loqusdb_id=loqusdb_id)
+
+    def _get_panel_loqusdb_api(self, case: Case) -> LoqusdbAPI:
+        sample: Sample = case.samples[0]
+        bed_short_name: str = self.lims_api.capture_kit(sample.internal_id)
+        bed_version: BedVersion = self.store.get_bed_version_by_short_name_strict(bed_short_name)
+        panel: str = bed_version.bed.name
+        loqusdb_instance: LoqusdbInstance = PANEL_TO_LOQUSDB_INSTANCE_MAP[
+            BalsamicObservationPanel(panel)
+        ]
+        return self.get_loqusdb_api(loqusdb_instance)
+
+    def _upload_wgs_case(self, case: Case) -> None:
+        loqusdb_upload_apis: list[LoqusdbAPI] = [
+            self.loqusdb_somatic_api,
+            self.loqusdb_tumor_api,
+        ]
         for loqusdb_api in loqusdb_upload_apis:
             if self.is_duplicate(case=case, loqusdb_api=loqusdb_api):
                 LOG.error(f"Case {case.internal_id} has already been uploaded to Loqusdb")
                 raise LoqusdbDuplicateRecordError
-
         input_files: BalsamicObservationsInputFiles = self.get_observations_input_files(case)
         for loqusdb_api in loqusdb_upload_apis:
             self.load_cancer_observations(
                 case=case, input_files=input_files, loqusdb_api=loqusdb_api
             )
-
         # Update Statusdb with a germline Loqusdb ID
         loqusdb_id: str = str(self.loqusdb_tumor_api.get_case(case_id=case.internal_id)[LOQUSDB_ID])
         self.update_statusdb_loqusdb_id(samples=case.samples, loqusdb_id=loqusdb_id)
@@ -137,12 +225,12 @@ class BalsamicObservationsAPI(ObservationsAPI):
                 version=hk_version.id, tags=[BalsamicObservationsAnalysisTag.SV_VCF]
             ).first(),
         }
-        return BalsamicObservationsInputFiles(**get_full_path_dictionary(input_files))
+        return BalsamicObservationsInputFiles.model_validate(get_full_path_dictionary(input_files))
 
     def delete_case(self, case_id: str) -> None:
         """Delete cancer case observations from Loqusdb."""
         case: Case = self.store.get_case_by_internal_id(internal_id=case_id)
-        loqusdb_apis: list[LoqusdbAPI] = [self.loqusdb_somatic_api, self.loqusdb_tumor_api]
+        loqusdb_apis: list[LoqusdbAPI] = self._get_relevant_loqusdb_apis(case)
         for loqusdb_api in loqusdb_apis:
             if not loqusdb_api.get_case(case_id):
                 LOG.error(f"Case {case_id} could not be found in Loqusdb. Skipping case deletion.")
@@ -151,3 +239,11 @@ class BalsamicObservationsAPI(ObservationsAPI):
             loqusdb_api.delete_case(case_id)
         self.update_statusdb_loqusdb_id(samples=case.samples, loqusdb_id=None)
         LOG.info(f"Removed observations for case {case_id} from Loqusdb")
+
+    def _get_relevant_loqusdb_apis(self, case: Case) -> list[LoqusdbAPI]:
+        if not self._is_panel_upload(case):
+            return [self.loqusdb_somatic_api, self.loqusdb_tumor_api]
+        try:
+            return [self._get_panel_loqusdb_api(case)]
+        except ValueError as error:
+            raise LoqusdbDeleteCaseError from error

cg/meta/observations/mip_dna_observations_api.py

@@ -58,7 +58,7 @@ class MipDNAObservationsAPI(ObservationsAPI):
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
                 self.is_sample_type_eligible_for_observations_upload(case),
-                self.is_sample_source_eligible_for_observations_upload(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
             ]
         )
 

cg/meta/observations/nallo_observations_api.py

@@ -59,7 +59,7 @@ class NalloObservationsAPI(ObservationsAPI):
                 self.is_customer_eligible_for_observations_upload(case.customer.internal_id),
                 self.is_sequencing_method_eligible_for_observations_upload(case.internal_id),
                 self.is_sample_type_eligible_for_observations_upload(case),
-                self.is_sample_source_eligible_for_observations_upload(case.internal_id),
+                self.is_sample_source_type_not_ffpe(case.internal_id),
             ]
         )