Make delivery report mandatory for Scout uploads (#2704)

### Changed
* Delivery report mandatory for Scout uploads
* Renamed function get_report_accreditation to is_report_accredited

cg/constants/scout.py

@@ -14,6 +14,11 @@ class ScoutExportFileName(StrEnum):
     PANELS: str = f"gene_panels{FileExtensions.BED}"
 
 
+class UploadTrack(StrEnum):
+    RARE_DISEASE: str = "rare"
+    CANCER: str = "cancer"
+
+
 class ScoutCustomCaseReportTags(StrEnum):
     DELIVERY: str = "delivery_report"
     CNV: str = "cnv_report"

cg/meta/report/balsamic.py

@@ -156,10 +156,10 @@ def get_variant_caller_version(var_caller_name: str, var_caller_versions: dict)
                 return versions[0]
         return None
 
-    def get_report_accreditation(
+    def is_report_accredited(
         self, samples: list[SampleModel], analysis_metadata: BalsamicAnalysis
     ) -> bool:
-        """Checks if the report is accredited or not."""
+        """Check if the Balsamic report is accredited."""
         if analysis_metadata.config.analysis.sequencing_type == "targeted" and next(
             (
                 panel

cg/meta/report/mip_dna.py

@@ -79,10 +79,10 @@ def get_genome_build(self, analysis_metadata: MipAnalysis) -> str:
         """Return build version of the genome reference of a specific case."""
         return analysis_metadata.genome_build
 
-    def get_report_accreditation(
+    def is_report_accredited(
         self, samples: list[SampleModel], analysis_metadata: MipAnalysis = None
     ) -> bool:
-        """Checks if the report is accredited or not by evaluating each of the sample process accreditations."""
+        """Check if the MIP-DNA report is accredited by evaluating each of the sample process accreditations."""
         for sample in samples:
             if not sample.application.accredited:
                 return False

cg/meta/report/report_api.py

@@ -174,7 +174,7 @@ def get_report_data(self, case_id: str, analysis_date: datetime) -> ReportModel:
             version=self.get_report_version(analysis=analysis),
             date=datetime.today(),
             case=case_model,
-            accredited=self.get_report_accreditation(
+            accredited=self.is_report_accredited(
                 samples=case_model.samples, analysis_metadata=analysis_metadata
             ),
         )
@@ -407,10 +407,10 @@ def get_variant_callers(self, _analysis_metadata: AnalysisModel) -> list:
         """Return list of variant-calling filters used during analysis."""
         return []
 
-    def get_report_accreditation(
+    def is_report_accredited(
         self, samples: list[SampleModel], analysis_metadata: AnalysisModel
     ) -> bool:
-        """Checks if the report is accredited or not."""
+        """Check if the report is accredited."""
         raise NotImplementedError
 
     def get_required_fields(self, case: CaseModel) -> dict:

cg/meta/report/rnafusion.py

@@ -79,10 +79,10 @@ def get_genome_build(self, analysis_metadata: AnalysisModel) -> str:
         """Return build version of the genome reference of a specific case."""
         return GenomeVersion.hg38.value
 
-    def get_report_accreditation(
+    def is_report_accredited(
         self, samples: list[SampleModel], analysis_metadata: AnalysisModel
     ) -> bool:
-        """Checks if the report is accredited or not. Rnafusion is an accredited workflow."""
+        """Check if the report is accredited. Rnafusion is an accredited workflow."""
         return True
 
     def get_template_name(self) -> str:

cg/meta/upload/scout/balsamic_config_builder.py

@@ -4,7 +4,8 @@
 
 from cg.apps.lims import LimsAPI
 from cg.constants.constants import SampleType
-from cg.constants.scout import BALSAMIC_CASE_TAGS, BALSAMIC_SAMPLE_TAGS
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
+from cg.constants.scout import BALSAMIC_CASE_TAGS, BALSAMIC_SAMPLE_TAGS, UploadTrack
 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
@@ -22,7 +23,10 @@ def __init__(self, hk_version_obj: Version, analysis_obj: Analysis, lims_api: Li
         )
         self.case_tags: CaseTags = CaseTags(**BALSAMIC_CASE_TAGS)
         self.sample_tags: SampleTags = SampleTags(**BALSAMIC_SAMPLE_TAGS)
-        self.load_config: BalsamicLoadConfig = BalsamicLoadConfig(track="cancer")
+        self.load_config: BalsamicLoadConfig = BalsamicLoadConfig(
+            track=UploadTrack.CANCER.value,
+            delivery_report=self.get_file_from_hk({HK_DELIVERY_REPORT_TAG}),
+        )
 
     def include_case_files(self):
         LOG.info("Including BALSAMIC specific case level files")
@@ -34,7 +38,6 @@ def include_case_files(self):
         )
         self.include_cnv_report()
         self.include_multiqc_report()
-        self.include_delivery_report()
 
     def include_sample_files(self, config_sample: ScoutCancerIndividual) -> None:
         LOG.info("Including BALSAMIC specific sample level files.")

cg/meta/upload/scout/balsamic_umi_config_builder.py

@@ -3,13 +3,11 @@
 from housekeeper.store.models import Version
 
 from cg.apps.lims import LimsAPI
-from cg.constants.scout import BALSAMIC_UMI_CASE_TAGS, BALSAMIC_UMI_SAMPLE_TAGS
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
+from cg.constants.scout import BALSAMIC_UMI_CASE_TAGS, BALSAMIC_UMI_SAMPLE_TAGS, UploadTrack
 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 (
-    BalsamicUmiLoadConfig,
-    ScoutCancerIndividual,
-)
+from cg.models.scout.scout_load_config import BalsamicUmiLoadConfig, ScoutCancerIndividual
 from cg.store.models import Analysis, Sample
 
 LOG = logging.getLogger(__name__)
@@ -22,12 +20,14 @@ def __init__(self, hk_version_obj: Version, analysis_obj: Analysis, lims_api: Li
         )
         self.case_tags: CaseTags = CaseTags(**BALSAMIC_UMI_CASE_TAGS)
         self.sample_tags: SampleTags = SampleTags(**BALSAMIC_UMI_SAMPLE_TAGS)
-        self.load_config: BalsamicUmiLoadConfig = BalsamicUmiLoadConfig(track="cancer")
+        self.load_config: BalsamicUmiLoadConfig = BalsamicUmiLoadConfig(
+            track=UploadTrack.CANCER.value,
+            delivery_report=self.get_file_from_hk({HK_DELIVERY_REPORT_TAG}),
+        )
 
     def include_sample_files(self, config_sample: ScoutCancerIndividual) -> None:
         LOG.info("Including BALSAMIC specific sample level files")
 
     def get_balsamic_analysis_type(self, sample: Sample) -> str:
-        """Returns a formatted balsamic analysis type"""
-
+        """Returns a formatted balsamic analysis type."""
         return "panel-umi"

cg/meta/upload/scout/mip_config_builder.py

@@ -6,17 +6,14 @@
 
 from cg.apps.lims import LimsAPI
 from cg.apps.madeline.api import MadelineAPI
-from cg.constants.scout import MIP_CASE_TAGS, MIP_SAMPLE_TAGS
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
+from cg.constants.scout import MIP_CASE_TAGS, MIP_SAMPLE_TAGS, UploadTrack
 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
 from cg.meta.workflow.mip import MipAnalysisAPI
 from cg.models.mip.mip_analysis import MipAnalysis
-from cg.models.scout.scout_load_config import (
-    MipLoadConfig,
-    ScoutLoadConfig,
-    ScoutMipIndividual,
-)
+from cg.models.scout.scout_load_config import MipLoadConfig, ScoutLoadConfig, ScoutMipIndividual
 from cg.store.models import Analysis, Case, CaseSample
 
 LOG = logging.getLogger(__name__)
@@ -36,7 +33,10 @@ def __init__(
         )
         self.case_tags: CaseTags = CaseTags(**MIP_CASE_TAGS)
         self.sample_tags: SampleTags = SampleTags(**MIP_SAMPLE_TAGS)
-        self.load_config: MipLoadConfig = MipLoadConfig(track="rare")
+        self.load_config: MipLoadConfig = MipLoadConfig(
+            track=UploadTrack.RARE_DISEASE.value,
+            delivery_report=self.get_file_from_hk({HK_DELIVERY_REPORT_TAG}),
+        )
         self.mip_analysis_api: MipAnalysisAPI = mip_analysis_api
         self.lims_api: LimsAPI = lims_api
         self.madeline_api: MadelineAPI = madeline_api
@@ -116,7 +116,6 @@ def include_case_files(self):
         self.load_config.vcf_sv = self.get_file_from_hk(self.case_tags.sv_vcf)
         self.load_config.vcf_sv_research = self.get_file_from_hk(self.case_tags.sv_research_vcf)
         self.include_multiqc_report()
-        self.include_delivery_report()
 
     def include_sample_files(self, config_sample: ScoutMipIndividual) -> None:
         """Include sample level files that are optional for mip samples"""

cg/meta/upload/scout/rnafusion_config_builder.py

@@ -4,7 +4,8 @@
 
 from cg.apps.lims import LimsAPI
 from cg.constants.constants import PrepCategory
-from cg.constants.scout import RNAFUSION_CASE_TAGS, RNAFUSION_SAMPLE_TAGS, GenomeBuild
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
+from cg.constants.scout import RNAFUSION_CASE_TAGS, RNAFUSION_SAMPLE_TAGS, GenomeBuild, UploadTrack
 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 (
@@ -26,7 +27,10 @@ def __init__(self, hk_version_obj: Version, analysis_obj: Analysis, lims_api: Li
         )
         self.case_tags: CaseTags = CaseTags(**RNAFUSION_CASE_TAGS)
         self.sample_tags: SampleTags = SampleTags(**RNAFUSION_SAMPLE_TAGS)
-        self.load_config: RnafusionLoadConfig = RnafusionLoadConfig(track="cancer")
+        self.load_config: RnafusionLoadConfig = RnafusionLoadConfig(
+            track=UploadTrack.CANCER.value,
+            delivery_report=self.get_file_from_hk({HK_DELIVERY_REPORT_TAG}),
+        )
 
     def build_load_config(self) -> None:
         """Build a rnafusion-specific load config for uploading a case to scout."""

cg/meta/upload/scout/scout_config_builder.py

@@ -6,12 +6,14 @@
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.lims import LimsAPI
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.models.scout.scout_load_config import ScoutIndividual, ScoutLoadConfig
 from cg.store.models import Analysis, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
+
 # Maps keys that are used in scout load config on tags that are used in scout
 
 
@@ -24,7 +26,9 @@ def __init__(self, hk_version_obj: Version, analysis_obj: Analysis, lims_api: Li
         self.lims_api: LimsAPI = lims_api
         self.case_tags: CaseTags
         self.sample_tags: SampleTags
-        self.load_config: ScoutLoadConfig = ScoutLoadConfig()
+        self.load_config: ScoutLoadConfig = ScoutLoadConfig(
+            delivery_report=self.get_file_from_hk({HK_DELIVERY_REPORT_TAG})
+        )
 
     def add_common_info_to_load_config(self) -> None:
         """Add the mandatory common information to a scout load config object"""
@@ -137,12 +141,6 @@ def include_multiqc_report(self) -> None:
             hk_tags=self.case_tags.multiqc_report, latest=True
         )
 
-    def include_delivery_report(self) -> None:
-        LOG.info("Include delivery report to case")
-        self.load_config.delivery_report = self.get_file_from_hk(
-            hk_tags=self.case_tags.delivery_report, latest=True
-        )
-
     def include_sample_alignment_file(self, config_sample: ScoutIndividual) -> None:
         """Include the alignment file for a sample
 

cg/models/scout/scout_load_config.py

@@ -5,6 +5,7 @@
 from pydantic import BaseModel, BeforeValidator, ConfigDict
 from typing_extensions import Annotated, Literal
 
+from cg.constants.scout import UploadTrack
 from cg.models.scout.validators import field_not_none
 
 
@@ -91,12 +92,13 @@ class ScoutLoadConfig(BaseModel):
     sv_rank_model_version: str | None = None
     analysis_date: datetime | None = None
     samples: list[ScoutIndividual] = []
-
-    delivery_report: str | None = None
+    delivery_report: str
     coverage_qc_report: str | None = None
     cnv_report: str | None = None
     multiqc: str | None = None
-    track: Literal["rare", "cancer"] = "rare"
+    track: Literal[
+        UploadTrack.RARE_DISEASE.value, UploadTrack.CANCER.value
+    ] = UploadTrack.RARE_DISEASE.value
 
     model_config = ConfigDict(validate_assignment=True)
 

tests/apps/scout/test_scout_load_config.py

@@ -1,4 +1,5 @@
-"""Tests for the models in scout load config"""
+"""Tests for the models in Scout load config."""
+from pathlib import Path
 from typing import Any
 
 import pytest
@@ -11,35 +12,40 @@
 
 @pytest.mark.parametrize("key, value", list(SCOUT_INDIVIDUAL.items()))
 def test_validate_scout_individual_attributes(scout_individual: dict, key: str, value: Any):
-    """Test to validate that all attributes of a ScoutMipIndividual are correctly set."""
+    """Test that all attributes of a ScoutMipIndividual are correctly set."""
+
     # GIVEN some sample information
+
     # WHEN instantiating a ScoutMipIndividual
     ind_obj: ScoutMipIndividual = scout_load_config.ScoutMipIndividual(**scout_individual)
 
     # THEN assert that the attribute is set correctly
     assert getattr(ind_obj, key) == value
 
 
-def test_instantiate_empty_mip_config():
-    """Tests whether a MipLoadConfig can be instantiate without arguments."""
-    # GIVEN nothing
+def test_instantiate_empty_mip_config(delivery_report_html: Path):
+    """Tests whether a MipLoadConfig can be instantiated only with mandatory arguments."""
+
+    # GIVEN a delivery report file
 
-    # WHEN instantiating a empty mip load config
-    config: MipLoadConfig = scout_load_config.MipLoadConfig()
+    # WHEN instantiating an empty MIP load config
+    config: MipLoadConfig = scout_load_config.MipLoadConfig(
+        delivery_report=delivery_report_html.as_posix()
+    )
 
-    # THEN assert it is possible to instantiate without any information
+    # THEN assert it is possible to instantiate without any not mandatory information
     assert isinstance(config, scout_load_config.ScoutLoadConfig)
 
 
-def test_set_mandatory_to_none():
-    """The scout load config object should validate fields as they are set.
+def test_set_mandatory_to_none(delivery_report_html: Path):
+    """Test that a value error is raised when a mandatory field is set to None."""
 
-    This test will check that a value error is raised when a mandatory field is set to None.
-    """
     # GIVEN a load config object
-    config: MipLoadConfig = scout_load_config.MipLoadConfig()
+    config: MipLoadConfig = scout_load_config.MipLoadConfig(
+        delivery_report=delivery_report_html.as_posix()
+    )
 
     # WHEN setting a mandatory field to None
     with pytest.raises(ValidationError):
-        # THEN assert a validation error was raised
+        # THEN a validation error should be raised
         config.vcf_snv = None

tests/cli/upload/conftest.py

@@ -28,12 +28,6 @@
 from cg.models.scout.scout_load_config import ScoutLoadConfig
 from cg.store import Store
 from cg.store.models import Analysis
-from tests.cli.workflow.mip.conftest import (
-    mip_case_id,
-    mip_case_ids,
-    mip_dna_context,
-    mip_rna_context,
-)
 from tests.meta.upload.scout.conftest import mip_load_config
 from tests.mocks.hk_mock import MockHousekeeperAPI
 from tests.mocks.madeline import MockMadelineAPI
@@ -248,7 +242,9 @@ def __init__(self, **kwargs):
         self.housekeeper = None
         self.madeline_api = MockMadelineAPI()
         self.analysis = MockAnalysisApi()
-        self.config = ScoutLoadConfig()
+        self.config = ScoutLoadConfig(
+            delivery_report=Path("path", "to", "delivery-report.html").as_posix()
+        )
         self.file_exists = False
         self.lims = MockLims()
         self.missing_mandatory_field = False

tests/conftest.py

@@ -30,6 +30,7 @@
 from cg.constants import FileExtensions, Pipeline, SequencingFileTag
 from cg.constants.constants import CaseActions, FileFormat, Strandedness
 from cg.constants.demultiplexing import BclConverter, DemultiplexingDirsAndFiles
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
 from cg.constants.nanopore_files import NanoporeDirsAndFiles
 from cg.constants.priority import SlurmQos
 from cg.constants.sequencing import SequencingPlatform
@@ -1895,6 +1896,7 @@ def hk_bundle_sample_path(sample_id: str, timestamp: datetime) -> Path:
 def hk_bundle_data(
     case_id: str,
     bed_file: Path,
+    delivery_report_html: Path,
     timestamp_yesterday: datetime,
     sample_id: str,
     father_sample_id: str,
@@ -1910,7 +1912,12 @@ def hk_bundle_data(
                 "path": bed_file.as_posix(),
                 "archive": False,
                 "tags": ["bed", sample_id, father_sample_id, mother_sample_id, "coverage"],
-            }
+            },
+            {
+                "path": delivery_report_html.as_posix(),
+                "archive": False,
+                "tags": [HK_DELIVERY_REPORT_TAG],
+            },
         ],
     }