Bug raredisease delivery report tags

cg/apps/housekeeper/hk.py

@@ -185,6 +185,21 @@ def get_latest_file(
         files: Query = self._store.get_files(bundle_name=bundle, tag_names=tags, version_id=version)
         return files.order_by(File.id.desc()).first()
 
+    def get_file_by_exact_tags(
+        self, bundle: str, tags: list, version: int | None = None
+    ) -> File | None:
+        """Return a file that matches exact tags and optionally filtered by bundle and version."""
+        if not tags:
+            LOG.debug("No tags provided, skipping")
+            return None
+        files: list[File] = self.files(bundle=bundle, version=version, tags=tags).all()
+        for file in files:
+            file_tags = {tag.name for tag in file.tags}
+            LOG.debug(f"Using tags {file_tags}")
+            if file_tags == set(tags):
+                LOG.debug(f"Found file {file}")
+                return file
+
     def check_bundle_files(
         self,
         bundle_name: str,

cg/constants/housekeeper_tags.py

@@ -57,6 +57,7 @@ class HermesFileTag(StrEnum):
 
     CLINICAL_DELIVERY: str = "clinical-delivery"
     LONG_TERM_STORAGE: str = "long-term-storage"
+    SCOUT: str = "scout"
 
 
 class AnalysisTag(StrEnum):
@@ -81,8 +82,12 @@ class AnalysisTag(StrEnum):
     OUTRIDER: str = "outrider"
     RESEARCH: str = "research"
     RNA: str = "rna"
+    SMN_CALLING: str = "smn-calling"
     STARFUSION: str = "star-fusion"
     VCF_FUSION: str = "vcf-fusion"
+    VCF_SNV_CLINICAL: str = "vcf-snv-clinical"
+    VCF_STR: str = "vcf-str"
+    VCF_SV_CLINICAL: str = "vcf-sv-clinical"
 
 
 class HkMipAnalysisTag:

cg/constants/scout.py

@@ -39,6 +39,8 @@ class ScoutUploadKey(StrEnum):
     SV_VCF = auto()
     VCF_STR = auto()
     VCF_FUSION = auto()
+    VCF_SNV = auto()
+    VCF_SV = auto()
 
 
 RAREDISEASE_CASE_TAGS = dict(

cg/meta/delivery_report/raredisease.py

@@ -1,6 +1,7 @@
 """Raredisease Delivery Report API."""
 
 from cg.clients.chanjo2.models import CoverageMetrics
+from cg.constants.housekeeper_tags import HermesFileTag, AnalysisTag
 from cg.constants.report import (
     REQUIRED_APPLICATION_FIELDS,
     REQUIRED_CASE_FIELDS,
@@ -64,18 +65,46 @@ def is_report_accredited(
     def get_scout_variants_files(self, case_id: str) -> ScoutVariantsFiles:
         """Return Raredisease files that will be uploaded to Scout."""
         return ScoutVariantsFiles(
-            snv_vcf=self.get_scout_uploaded_file_from_hk(
-                case_id=case_id, scout_key=ScoutUploadKey.SNV_VCF
-            ),
-            sv_vcf=self.get_scout_uploaded_file_from_hk(
-                case_id=case_id, scout_key=ScoutUploadKey.SV_VCF
-            ),
-            vcf_str=self.get_scout_uploaded_file_from_hk(
-                case_id=case_id, scout_key=ScoutUploadKey.VCF_STR
-            ),
-            smn_tsv=self.get_scout_uploaded_file_from_hk(
-                case_id=case_id, scout_key=ScoutUploadKey.SMN_TSV
-            ),
+            snv_vcf=self.housekeeper_api.get_file_by_exact_tags(
+                bundle=case_id,
+                tags=[
+                    AnalysisTag.VCF_SNV_CLINICAL,
+                    case_id,
+                    HermesFileTag.CLINICAL_DELIVERY,
+                    HermesFileTag.LONG_TERM_STORAGE,
+                    HermesFileTag.SCOUT,
+                ],
+            ).full_path,
+            sv_vcf=self.housekeeper_api.get_file_by_exact_tags(
+                bundle=case_id,
+                tags=[
+                    AnalysisTag.VCF_SV_CLINICAL,
+                    case_id,
+                    HermesFileTag.CLINICAL_DELIVERY,
+                    HermesFileTag.LONG_TERM_STORAGE,
+                    HermesFileTag.SCOUT,
+                ],
+            ).full_path,
+            vcf_str=self.housekeeper_api.get_file_by_exact_tags(
+                bundle=case_id,
+                tags=[
+                    AnalysisTag.VCF_STR,
+                    case_id,
+                    HermesFileTag.CLINICAL_DELIVERY,
+                    HermesFileTag.LONG_TERM_STORAGE,
+                    HermesFileTag.SCOUT,
+                ],
+            ).full_path,
+            smn_tsv=self.housekeeper_api.get_file_by_exact_tags(
+                bundle=case_id,
+                tags=[
+                    AnalysisTag.SMN_CALLING,
+                    case_id,
+                    HermesFileTag.CLINICAL_DELIVERY,
+                    HermesFileTag.LONG_TERM_STORAGE,
+                    HermesFileTag.SCOUT,
+                ],
+            ).full_path,
         )
 
     @staticmethod