use mip-rna rna upload for tomte

Author: rannick

cg/apps/scout/scoutapi.py

@@ -278,6 +278,54 @@ def upload_rna_coverage_bigwig(
                 "Something went wrong when uploading rna coverage bigwig file"
             ) from error
 
+
+    def upload_rna_fraser(
+        self, file_path: str, case_id: str, customer_sample_id: str
+    ) -> None:
+        """Load a rna fraser file into a case in the database."""
+
+        upload_command: list[str] = [
+            "update",
+            "individual",
+            "--case-id",
+            case_id,
+            "--ind",
+            customer_sample_id,
+            "--fraser",
+            file_path,
+        ]
+        try:
+            LOG.info(f"Uploading rna fraser file {file_path} to case {case_id}")
+            self.process.run_command(upload_command)
+        except CalledProcessError as error:
+            raise ScoutUploadError(
+                "Something went wrong when uploading rna fraser file"
+            ) from error
+
+    def upload_rna_outrider(
+        self, file_path: str, case_id: str, customer_sample_id: str
+    ) -> None:
+        """Load a rna outrider file into a case in the database."""
+
+        upload_command: list[str] = [
+            "update",
+            "individual",
+            "--case-id",
+            case_id,
+            "--ind",
+            customer_sample_id,
+            "--outrider",
+            file_path,
+        ]
+        try:
+            LOG.info(f"Uploading rna outrider file {file_path} to case {case_id}")
+            self.process.run_command(upload_command)
+        except CalledProcessError as error:
+            raise ScoutUploadError(
+                "Something went wrong when uploading rna outrider file"
+            ) from error
+
+
     def upload_rna_alignment_file(
         self, case_id: str, customer_sample_id: str, file_path: str
     ) -> None:

cg/cli/upload/base.py

@@ -23,6 +23,7 @@
     create_scout_load_config,
     upload_case_to_scout,
     upload_multiqc_to_scout,
+    upload_omics_to_scout,
     upload_rna_alignment_file_to_scout,
     upload_rna_fusion_report_to_scout,
     upload_rna_junctions_to_scout,
@@ -144,6 +145,7 @@ def upload_all_completed_analyses(context: click.Context, workflow: Workflow = N
 upload.add_command(upload_coverage)
 upload.add_command(upload_delivery_report_to_scout)
 upload.add_command(upload_genotypes)
+upload.add_command(upload_omics_to_scout)
 upload.add_command(upload_multiqc_to_scout)
 upload.add_command(upload_observations_to_loqusdb)
 upload.add_command(upload_rna_alignment_file_to_scout)

cg/cli/upload/scout.py

@@ -21,6 +21,7 @@
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
+from cg.meta.workflow.tomte import TomteAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.models.scout.scout_load_config import ScoutLoadConfig
 from cg.store.models import Case
@@ -173,16 +174,18 @@ def validate_case_samples_are_rna(context: CGConfig, case_id: str) -> None:
 @click.option("-r", "--research", is_flag=True, help="Upload research report instead of clinical")
 @click.argument("case_id")
 @click.pass_context
-def upload_rna_to_scout(context, case_id: str, dry_run: bool, research: bool) -> None:
+def upload_rna_to_scout(context, case_id: str, dry_run: bool, research: bool, analysis: str) -> None:
     """Upload an RNA case's gene fusion report and junction splice files for all samples connect via subject ID."""
     LOG.info("----------------- UPLOAD RNA TO SCOUT -----------------------")
 
     context.invoke(validate_case_samples_are_rna, 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_fusion_report_to_scout, case_id=case_id, dry_run=dry_run, research=research
-    )
+    if analysis != Workflow.TOMTE:
+        context.invoke(
+            upload_rna_fusion_report_to_scout, case_id=case_id, dry_run=dry_run, research=research
+        )
+    context.invoke(upload_omics_to_scout, case_id=case_id, dry_run=dry_run)
     context.invoke(upload_rna_junctions_to_scout, case_id=case_id, dry_run=dry_run)
 
 
@@ -228,6 +231,20 @@ def upload_rna_junctions_to_scout(context: CGConfig, case_id: str, dry_run: bool
     scout_upload_api.upload_rna_junctions_to_scout(dry_run=dry_run, case_id=case_id)
 
 
+@click.command(name="rna-omics-to-scout")
+@DRY_RUN
+@click.argument("case_id")
+@click.pass_obj
+def upload_omics_to_scout(context: CGConfig, case_id: str, dry_run: bool) -> None:
+    """Upload RNA omics files to Scout."""
+    LOG.info("----------------- UPLOAD RNA OMICS TO SCOUT -----------------------")
+
+    scout_upload_api: UploadScoutAPI = context.meta_apis["upload_api"].scout_upload_api
+
+    scout_upload_api.upload_omics_to_scout(dry_run=dry_run, case_id=case_id)
+
+
+
 @click.command(name="multiqc-to-scout")
 @DRY_RUN
 @click.argument("case_id")
@@ -267,6 +284,7 @@ def get_upload_api(case: Case, cg_config: CGConfig) -> UploadAPI:
         Workflow.MIP_RNA: MipRNAAnalysisAPI,
         Workflow.MIP_DNA: MipDNAAnalysisAPI,
         Workflow.RNAFUSION: RnafusionAnalysisAPI,
+        Workflow.TOMTE: TomteAnalysisAPI,
     }
 
     return UploadAPI(

cg/constants/housekeeper_tags.py

@@ -64,14 +64,21 @@ class AnalysisTag(StrEnum):
 
     ARRIBA: str = "arriba"
     ARRIBA_VISUALIZATION: str = "arriba-visualisation"
+    BED: str = "bed"
+    BIGWIG: str = "bigwig"
+    CLINICAL: str = "clinical"
+    COVERAGE: str = "coverage"
+    FRASER: str = "fraser"
     FUSION: str = "fusion"
     FUSIONCATCHER: str = "fusioncatcher"
     FUSIONCATCHER_SUMMARY: str = "fusioncatcher-summary"
     FUSIONINSPECTOR: str = "fusioninspector"
     FUSIONINSPECTOR_HTML: str = "fusioninspector-html"
     FUSIONREPORT: str = "fusionreport"
     GENE_COUNTS: str = "gene-counts"
+    JUNCTION: str = "junction"
     MULTIQC_HTML: str = "multiqc-html"
+    OUTRIDER: str = "outrider"
     RESEARCH: str = "research"
     RNA: str = "rna"
     STARFUSION: str = "star-fusion"

cg/meta/upload/mip/mip_rna.py

@@ -7,7 +7,7 @@
 
 from cg.cli.upload.clinical_delivery import upload_clinical_delivery
 from cg.cli.upload.scout import upload_rna_to_scout
-from cg.constants import DataDelivery
+from cg.constants import DataDelivery, Workflow
 from cg.meta.upload.upload_api import UploadAPI
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
 from cg.models.cg_config import CGConfig
@@ -34,7 +34,7 @@ def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
         # Scout specific upload
         if DataDelivery.SCOUT in case.data_delivery:
             try:
-                ctx.invoke(upload_rna_to_scout, case_id=case.internal_id)
+                ctx.invoke(upload_rna_to_scout, case_id=case.internal_id, analysis=Workflow.MIP_RNA)
             except CalledProcessError as error:
                 LOG.error(error)
                 return

cg/meta/upload/nf_analysis.py

@@ -7,6 +7,7 @@
 
 from cg.cli.generate.report.base import generate_delivery_report
 from cg.cli.upload.clinical_delivery import upload_clinical_delivery
+from cg.cli.upload.scout import upload_rna_to_scout
 from cg.cli.upload.scout import upload_to_scout
 from cg.constants import (
     REPORT_SUPPORTED_DATA_DELIVERY,
@@ -46,7 +47,10 @@ def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
 
         # Scout specific upload
         if DataDelivery.SCOUT in case.data_delivery:
-            ctx.invoke(upload_to_scout, case_id=case.internal_id, re_upload=restart)
+            if case.data_analysis == Workflow.TOMTE:
+                ctx.invoke(upload_rna_to_scout, case_id=case.internal_id, re_upload=restart, analysis=case.data_analysis)
+            else:
+                ctx.invoke(upload_to_scout, case_id=case.internal_id, re_upload=restart)
         LOG.info(
             f"Upload of case {case.internal_id} was successful. Setting uploaded at to {dt.datetime.now()}"
         )

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
-from cg.constants.housekeeper_tags import AlignmentFileTag
+from cg.constants.housekeeper_tags import AlignmentFileTag, AnalysisTag
 from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.exc import CgDataError, HousekeeperBundleVersionMissingError
 from cg.io.controller import WriteFile
@@ -132,18 +132,18 @@ def get_multiqc_html_report(
     def get_fusion_report(self, case_id: str, research: bool) -> File | None:
         """Return a fusion report for a case in housekeeper."""
 
-        tags = {"fusion"}
+        tags = {AnalysisTag.FUSION}
         if research:
-            tags.add("research")
+            tags.add(AnalysisTag.RESEARCH)
         else:
-            tags.add("clinical")
+            tags.add(AnalysisTag.CLINICAL)
 
         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."""
 
-        tags: set[str] = {"junction", "bed", sample_id}
+        tags: set[str] = {AnalysisTag.JUNCTION, AnalysisTag.BED, sample_id}
         splice_junctions_bed: File | None = None
         try:
             splice_junctions_bed = self.housekeeper.get_file_from_latest_version(
@@ -156,11 +156,22 @@ def get_splice_junctions_bed(self, case_id: str, sample_id: str) -> File | None:
 
     def get_rna_coverage_bigwig(self, case_id: str, sample_id: str) -> File | None:
         """Return an RNA coverage bigwig file for a case in Housekeeper."""
+        tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.BIGWIG, sample_id}
+        return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
+
+
+    def get_rna_omics_fraser(self, case_id: str, sample_id: str) -> File | None:
+        """Return an fraser file for a case in Housekeeper."""
+        tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.FRASER, sample_id}
+        return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
-        tags: set[str] = {"coverage", "bigwig", sample_id}
 
+    def get_rna_omics_outrider(self, case_id: str, sample_id: str) -> File | None:
+        """Return an outrider file for a case in Housekeeper."""
+        tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.OUTRIDER, sample_id}
         return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
+
     def get_unique_dna_cases_related_to_rna_case(self, case_id: str) -> set[str]:
         """Return a set of unique DNA cases related to an RNA case."""
         case: Case = self.status_db.get_case_by_internal_id(case_id)
@@ -326,6 +337,82 @@ def upload_rna_coverage_bigwig_to_scout(self, case_id: str, dry_run: bool) -> No
             LOG.info(upload_statement)
         LOG.info("Upload RNA coverage bigwig file finished!")
 
+
+    def upload_rna_fraser_to_scout(self, dry_run: bool, case_id: str) -> None:
+        """Upload omics fraser file for a case to Scout."""
+        status_db: Store = self.status_db
+        rna_case = status_db.get_case_by_internal_id(case_id)
+        rna_dna_collections: list[RNADNACollection] = self.create_rna_dna_collections(rna_case)
+        for rna_dna_collection in rna_dna_collections:
+            rna_sample_internal_id: str = rna_dna_collection.rna_sample_internal_id
+            dna_sample_name: str = rna_dna_collection.dna_sample_name
+            rna_fraser: File | None = self.get_rna_omics_fraser(
+                case_id=case_id, sample_id=rna_sample_internal_id
+            )
+
+            if not rna_fraser:
+                raise FileNotFoundError(
+                    f"No RNA fraser file was found in housekeeper for {rna_sample_internal_id}."
+                )
+
+            LOG.debug(f"RNA fraser file {rna_fraser.path} found.")
+            for dna_case_id in rna_dna_collection.dna_case_ids:
+                LOG.info(
+                    f"Uploading RNA fraser file for sample {dna_sample_name} "
+                    f"in case {dna_case_id} in Scout."
+                )
+
+                if dry_run:
+                    continue
+
+                self.scout_api.upload_rna_fraser(
+                    file_path=rna_fraser.full_path,
+                    case_id=dna_case_id,
+                    customer_sample_id=dna_sample_name,
+                )
+
+        for upload_statement in self.get_rna_fraser_upload_summary(rna_dna_collections):
+            LOG.info(upload_statement)
+        LOG.info("Upload RNA fraser file finished!")
+
+
+    def upload_rna_outrider_to_scout(self, dry_run: bool, case_id: str) -> None:
+        """Upload omics outrider file for a case to Scout."""
+        status_db: Store = self.status_db
+        rna_case = status_db.get_case_by_internal_id(case_id)
+        rna_dna_collections: list[RNADNACollection] = self.create_rna_dna_collections(rna_case)
+        for rna_dna_collection in rna_dna_collections:
+            rna_sample_internal_id: str = rna_dna_collection.rna_sample_internal_id
+            dna_sample_name: str = rna_dna_collection.dna_sample_name
+            rna_outrider: File | None = self.get_rna_omics_outrider(
+                case_id=case_id, sample_id=rna_sample_internal_id
+            )
+            if not rna_outrider:
+                raise FileNotFoundError(
+                    f"No RNA outrider file was found in housekeeper for {rna_sample_internal_id}."
+                )
+
+            LOG.debug(f"RNA outrider file {rna_outrider.path} found.")
+            for dna_case_id in rna_dna_collection.dna_case_ids:
+                LOG.info(
+                    f"Uploading RNA outrider file for sample {dna_sample_name} "
+                    f"in case {dna_case_id} in Scout."
+                )
+
+                if dry_run:
+                    continue
+
+                self.scout_api.upload_rna_outrider(
+                    file_path=rna_outrider.full_path,
+                    case_id=dna_case_id,
+                    customer_sample_id=dna_sample_name,
+                )
+        for upload_statement in self.get_rna_outrider_upload_summary(rna_dna_collections):
+            LOG.info(upload_statement)
+        LOG.info("Upload RNA outrider file finished!")
+
+
+
     def upload_splice_junctions_bed_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload splice_junctions_bed file for a case to Scout."""
 
@@ -400,11 +487,42 @@ def get_rna_bigwig_coverage_upload_summary(
             )
         return upload_summary
 
+    @staticmethod
+    def get_rna_fraser_upload_summary(
+        rna_dna_collections: list[RNADNACollection],
+    ) -> list[str]:
+        upload_summary: list[str] = []
+        for rna_dna_collection in rna_dna_collections:
+            upload_summary.extend(
+                f"Uploaded fraser coverage file for sample {rna_dna_collection.dna_sample_name} in case {dna_case}."
+                for dna_case in rna_dna_collection.dna_case_ids
+            )
+        return upload_summary
+
+    @staticmethod
+    def get_rna_outrider_upload_summary(
+        rna_dna_collections: list[RNADNACollection],
+    ) -> list[str]:
+        upload_summary: list[str] = []
+        for rna_dna_collection in rna_dna_collections:
+            upload_summary.extend(
+                f"Uploaded outrider coverage file for sample {rna_dna_collection.dna_sample_name} in case {dna_case}."
+                for dna_case in rna_dna_collection.dna_case_ids
+            )
+        return upload_summary
+
     def upload_rna_junctions_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload RNA junctions splice files to Scout."""
         self.upload_splice_junctions_bed_to_scout(dry_run=dry_run, case_id=case_id)
         self.upload_rna_coverage_bigwig_to_scout(case_id=case_id, dry_run=dry_run)
 
+
+    def upload_omics_to_scout(self, dry_run: bool, case_id: str) -> None:
+        """Upload RNA omics files to Scout."""
+        self.upload_rna_fraser_to_scout(dry_run=dry_run, case_id=case_id)
+        self.upload_rna_outrider_to_scout(case_id=case_id, dry_run=dry_run)
+
+
     def get_config_builder(self, analysis, hk_version) -> ScoutConfigBuilder:
         config_builders = {
             Workflow.BALSAMIC: BalsamicConfigBuilder(