add rna_delivery_report from tomte in related dna cases (#3782) | minor

### Added

- Upload of the tomte rna case to the related dna under report section: "rna_delivery_report"/"RNA Delivery Report"

Author: rannick

cg/apps/scout/scoutapi.py

@@ -350,6 +350,15 @@ def upload_rna_genome_build(
         except CalledProcessError as error:
             raise ScoutUploadError("Something went wrong when updating rna genome build") from error
 
+    def upload_rna_delivery_report(self, case_id: str, report_path: str) -> None:
+        """Load a RNA report into a case in the database."""
+
+        self.upload_report(
+            case_id=case_id,
+            report_path=report_path,
+            report_type=ScoutCustomCaseReportTags.RNA_DELIVERY,
+        )
+
     def load_variant_outlier(self, case_id: str) -> None:
         """Load a rna fraser file into a case in the database."""
 

cg/cli/upload/scout.py

@@ -203,6 +203,7 @@ def upload_tomte_to_scout(
     LOG.info("----------------- UPLOAD RNA TO SCOUT -----------------------")
 
     context.invoke(validate_case_samples_are_rna, case_id=case_id)
+    context.invoke(upload_rna_delivery_report_to_scout, case_id=case_id)
     context.invoke(upload_rna_alignment_file_to_scout, case_id=case_id, dry_run=dry_run)
     context.invoke(upload_multiqc_to_scout, case_id=case_id, dry_run=dry_run)
     context.invoke(upload_rna_omics_to_scout, case_id=case_id, dry_run=dry_run)
@@ -238,6 +239,19 @@ def upload_rna_fusion_report_to_scout(
     )
 
 
+@click.command(name="rna-delivery-report-to-scout")
+@DRY_RUN
+@click.argument("case_id")
+@click.pass_obj
+def upload_rna_delivery_report_to_scout(context: CGConfig, dry_run: bool, case_id: str) -> None:
+    """Upload rna delivery report file for a case to Scout."""
+
+    LOG.info("----------------- UPLOAD RNA DELIVERY REPORT TO SCOUT -----------------------")
+
+    scout_upload_api: UploadScoutAPI = context.meta_apis["upload_api"].scout_upload_api
+    scout_upload_api.upload_rna_delivery_report_to_scout(dry_run=dry_run, case_id=case_id)
+
+
 @click.command(name="rna-junctions-to-scout")
 @DRY_RUN
 @click.argument("case_id")

cg/constants/scout.py

@@ -23,6 +23,7 @@ class UploadTrack(StrEnum):
 
 class ScoutCustomCaseReportTags(StrEnum):
     DELIVERY: str = "delivery_report"
+    RNA_DELIVERY: str = "rna_delivery_report"
     CNV: str = "cnv_report"
     COV_QC: str = "coverage_qc_report"
     MULTIQC: str = "multiqc"

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, Workflow
 from cg.constants.constants import FileFormat, PrepCategory, GenomeVersion
-from cg.constants.housekeeper_tags import AlignmentFileTag, AnalysisTag
+from cg.constants.housekeeper_tags import AlignmentFileTag, AnalysisTag, HK_DELIVERY_REPORT_TAG
 from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.exc import CgDataError, HousekeeperBundleVersionMissingError
 from cg.io.controller import WriteFile
@@ -159,6 +159,13 @@ def get_fusion_report(self, case_id: str, research: bool) -> File | None:
 
         return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
+    def get_rna_delivery_report(self, case_id: str) -> File | None:
+        """Return a RNA report for a case in housekeeper."""
+
+        tags = {HK_DELIVERY_REPORT_TAG}
+
+        return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
+
     def get_splice_junctions_bed(self, case_id: str, sample_id: str) -> File | None:
         """Return a splice junctions bed file for a case in Housekeeper."""
 
@@ -256,7 +263,7 @@ def upload_fusion_report_to_scout(
 
         related_dna_cases: set[str] = self.get_related_uploaded_dna_cases(case_id)
         if not related_dna_cases:
-            raise CgDataError("No connected DNA case has been uploaded.")
+            raise CgDataError("No connected DNA case found.")
 
         for dna_case_id in related_dna_cases:
             LOG.info(f"Uploading {report_type} fusion report to Scout for case {dna_case_id}.")
@@ -272,6 +279,37 @@ def upload_fusion_report_to_scout(
 
         LOG.info(f"Upload {report_type} fusion report finished!")
 
+    def upload_rna_delivery_report_to_scout(self, dry_run: bool, case_id: str) -> None:
+        """Upload rna delivery report file for a case to Scout."""
+
+        rna_delivery_report: File | None = self.get_rna_delivery_report(case_id)
+        if not rna_delivery_report:
+            raise FileNotFoundError(
+                f"Rna delivery report was not found in Housekeeper for {case_id}."
+            )
+
+        LOG.info(f"Rna delivery report {rna_delivery_report.path} found")
+
+        related_dna_cases: set[str] = self.get_related_uploaded_dna_cases(case_id)
+        if not related_dna_cases:
+            raise CgDataError("No connected DNA case has been uploaded.")
+
+        for dna_case_id in related_dna_cases:
+            LOG.debug(f"Uploading rna delivery report to Scout for case {dna_case_id}.")
+
+            if dry_run:
+                LOG.debug(
+                    f"Dry run - Would have uploaded rna delivery report to Scout for case {dna_case_id}."
+                )
+                continue
+            self.scout_api.upload_rna_delivery_report(
+                case_id=dna_case_id,
+                report_path=rna_delivery_report.full_path,
+            )
+            LOG.debug(f"Uploaded rna delivery report for {dna_case_id}.")
+
+        LOG.info(f"Upload rna delivery report finished for case {case_id}!")
+
     def upload_rna_report_to_dna_case_in_scout(
         self,
         dry_run: bool,

cg/meta/upload/tomte/tomte.py

@@ -5,9 +5,14 @@
 
 import click
 
-
+from cg.cli.generate.delivery_report.base import generate_delivery_report
 from cg.cli.upload.scout import upload_tomte_to_scout
-from cg.constants import DataDelivery, Workflow
+from cg.constants import (
+    REPORT_SUPPORTED_DATA_DELIVERY,
+    REPORT_SUPPORTED_WORKFLOW,
+    DataDelivery,
+    Workflow,
+)
 from cg.meta.upload.nf_analysis import NfAnalysisUploadAPI
 from cg.models.cg_config import CGConfig
 from cg.store.models import Analysis, Case
@@ -16,7 +21,7 @@
 
 
 class TomteUploadAPI(NfAnalysisUploadAPI):
-    """MIP-RNA upload API."""
+    """Tomte upload API."""
 
     def __init__(self, config: CGConfig):
         super().__init__(config=config, workflow=Workflow.TOMTE)
@@ -26,6 +31,13 @@ def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
         analysis: Analysis = case.analyses[0]
         self.update_upload_started_at(analysis=analysis)
 
+        # Delivery report generation
+        if (
+            case.data_analysis in REPORT_SUPPORTED_WORKFLOW
+            and case.data_delivery in REPORT_SUPPORTED_DATA_DELIVERY
+        ):
+            ctx.invoke(generate_delivery_report, case_id=case.internal_id)
+
         self.upload_files_to_customer_inbox(case=case)
 
         # Scout specific upload

tests/meta/upload/scout/conftest.py

@@ -403,6 +403,73 @@ def mip_rna_analysis_hk_bundle_data(
     }
 
 
+@pytest.fixture(scope="function")
+def tomte_analysis_hk_bundle_data(
+    rna_case_id: str,
+    timestamp: datetime,
+    tomte_analysis_dir: Path,
+    rna_sample_son_id: str,
+    rna_sample_daughter_id: str,
+    rna_sample_mother_id: str,
+    rna_sample_father_id: str,
+) -> dict:
+    """Return MIP RNA bundle data for Housekeeper."""
+
+    files: list[dict] = [
+        {
+            "path": Path(tomte_analysis_dir, f"{rna_case_id}.cram").as_posix(),
+            "archive": False,
+            "tags": ["cram", rna_case_id],
+        },
+        {
+            "path": Path(tomte_analysis_dir, f"{rna_case_id}_report.selected.pdf").as_posix(),
+            "archive": False,
+            "tags": ["fusion", "pdf", "clinical", rna_case_id],
+        },
+        {
+            "path": Path(tomte_analysis_dir, f"{rna_case_id}_report.pdf").as_posix(),
+            "archive": False,
+            "tags": ["fusion", "pdf", "research", rna_case_id],
+        },
+        {
+            "path": Path(tomte_analysis_dir, f"{rna_case_id}_report.pdf").as_posix(),
+            "archive": False,
+            "tags": ["delivery-report", "rna", rna_case_id],
+        },
+    ]
+    for sample_id in [
+        rna_sample_son_id,
+        rna_sample_daughter_id,
+        rna_sample_mother_id,
+        rna_sample_father_id,
+    ]:
+        files.extend(
+            [
+                {
+                    "path": Path(
+                        tomte_analysis_dir, f"{sample_id}_lanes_1_star_sorted_sj.bigWig"
+                    ).as_posix(),
+                    "archive": False,
+                    "tags": ["coverage", "bigwig", "scout", sample_id],
+                },
+                {
+                    "path": Path(
+                        tomte_analysis_dir, f"{sample_id}_lanes_1234_star_sorted_sj.bed.gz.tbi"
+                    ).as_posix(),
+                    "archive": False,
+                    "tags": ["bed", "scout", "junction", sample_id],
+                },
+            ]
+        )
+
+    return {
+        "name": rna_case_id,
+        "created": timestamp,
+        "expires": timestamp,
+        "files": files,
+    }
+
+
 @pytest.fixture(scope="function")
 def balsamic_analysis_hk_bundle_data(
     case_id: str,
@@ -515,6 +582,15 @@ def mip_rna_analysis_hk_api(
     return housekeeper_api
 
 
+@pytest.fixture
+def tomte_analysis_hk_api(
+    housekeeper_api: MockHousekeeperAPI, tomte_analysis_hk_bundle_data: dict, helpers
+) -> MockHousekeeperAPI:
+    """Return a Housekeeper API populated with MIP RNA analysis files."""
+    helpers.ensure_hk_version(housekeeper_api, tomte_analysis_hk_bundle_data)
+    return housekeeper_api
+
+
 @pytest.fixture
 def balsamic_analysis_hk_api(
     housekeeper_api: MockHousekeeperAPI, balsamic_analysis_hk_bundle_data: dict, helpers
@@ -706,6 +782,29 @@ def upload_mip_analysis_scout_api(
     )
 
 
+@pytest.fixture
+def upload_tomte_analysis_scout_api(
+    cg_context: CGConfig,
+    scout_api: MockScoutAPI,
+    madeline_api: MockMadelineAPI,
+    lims_samples: list[dict],
+    tomte_analysis_hk_api: MockHousekeeperAPI,
+    store: Store,
+) -> Generator[UploadScoutAPI, None, None]:
+    """Return MIP upload Scout API."""
+    analysis_mock = MockMipAnalysis(config=cg_context, workflow=Workflow.TOMTE)
+    lims_api = MockLimsAPI(samples=lims_samples)
+
+    yield UploadScoutAPI(
+        hk_api=tomte_analysis_hk_api,
+        scout_api=scout_api,
+        madeline_api=madeline_api,
+        analysis_api=analysis_mock,
+        lims_api=lims_api,
+        status_db=store,
+    )
+
+
 @pytest.fixture
 def upload_balsamic_analysis_scout_api(
     cg_context: CGConfig,