Patches for scout upload (#3871)

### Fixed

 - Changed call from mip_analysis_api to analysis_api: bugfix for mip-rna
 - Remove in place manipulation for tag list: bugfix for balsamic and mip-dna (cases with multiple samples)

cg/cli/upload/scout.py

@@ -167,7 +167,7 @@ def upload_case_to_scout(context: CGConfig, re_upload: bool, dry_run: bool, case
 @click.pass_obj
 def validate_case_samples_are_rna(context: CGConfig, case_id: str) -> None:
     scout_upload_api: UploadScoutAPI = context.meta_apis["upload_api"].scout_upload_api
-    are_all_samples_rna: bool = scout_upload_api.mip_analysis_api.are_case_samples_rna(case_id)
+    are_all_samples_rna: bool = scout_upload_api.analysis_api.are_case_samples_rna(case_id)
     if not are_all_samples_rna:
         LOG.error(f"{case_id} has non-RNA samples - aborting.")
         raise click.Abort

cg/meta/upload/scout/balsamic_config_builder.py

@@ -5,7 +5,12 @@
 from cg.apps.lims import LimsAPI
 from cg.constants.constants import SampleType
 from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
-from cg.constants.scout import BALSAMIC_CASE_TAGS, BALSAMIC_SAMPLE_TAGS, GenomeBuild, UploadTrack
+from cg.constants.scout import (
+    BALSAMIC_CASE_TAGS,
+    BALSAMIC_SAMPLE_TAGS,
+    GenomeBuild,
+    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

cg/meta/upload/scout/scout_config_builder.py

@@ -1,8 +1,10 @@
 """Functions that handle files in the context of Scout uploading."""
 
 import logging
-from typing import Any
 import re
+from pathlib import Path
+from typing import Any
+
 from housekeeper.store.models import File, Version
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
@@ -12,14 +14,12 @@
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.models.scout.scout_load_config import (
     ScoutIndividual,
+    ScoutLoadConfig,
     ScoutMipIndividual,
     ScoutRarediseaseIndividual,
-    ScoutLoadConfig,
 )
 from cg.store.models import Analysis, Case, CaseSample, Sample
 
-from pathlib import Path
-
 LOG = logging.getLogger(__name__)
 
 
@@ -219,6 +219,7 @@ def include_sample_alignment_file(self, config_sample: ScoutIndividual) -> None:
         config_sample.alignment_path = self.get_sample_file(
             hk_tags=self.sample_tags.alignment_file, sample_id=sample_id
         )
+
         if not config_sample.alignment_path:
             self.include_sample_alignment_bam(config_sample)
 
@@ -231,8 +232,9 @@ def include_sample_alignment_bam(self, config_sample: ScoutIndividual) -> None:
     def get_sample_file(self, hk_tags: set[str], sample_id: str) -> str | None:
         """Return a file that is specific for an individual from Housekeeper."""
         if hk_tags:  # skip if no tag found
-            hk_tags.add(sample_id)
-            return self.get_file_from_hk(hk_tags)
+            tags: set = hk_tags.copy()
+            tags.add(sample_id)
+            return self.get_file_from_hk(hk_tags=tags)
 
     def get_file_from_hk(self, hk_tags: set[str], latest: bool | None = False) -> str | None:
         """Return the Housekeeper file path as a string."""

cg/meta/upload/scout/uploadscoutapi.py

@@ -11,8 +11,12 @@
 from cg.apps.madeline.api import MadelineAPI
 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, HK_DELIVERY_REPORT_TAG
+from cg.constants.constants import FileFormat, GenomeVersion, PrepCategory
+from cg.constants.housekeeper_tags import (
+    HK_DELIVERY_REPORT_TAG,
+    AlignmentFileTag,
+    AnalysisTag,
+)
 from cg.constants.scout import ScoutCustomCaseReportTags
 from cg.exc import CgDataError, HousekeeperBundleVersionMissingError
 from cg.io.controller import WriteFile
@@ -23,7 +27,10 @@
 from cg.meta.upload.scout.rnafusion_config_builder import RnafusionConfigBuilder
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder
 from cg.meta.workflow.analysis import AnalysisAPI
-from cg.meta.workflow.utils.genome_build_helpers import get_genome_build, genome_to_scout_format
+from cg.meta.workflow.utils.genome_build_helpers import (
+    genome_to_scout_format,
+    get_genome_build,
+)
 from cg.models.scout.scout_load_config import ScoutLoadConfig
 from cg.store.models import Analysis, Case, Customer, Sample
 from cg.store.store import Store
@@ -769,7 +776,6 @@ def _get_application_prep_category(
     def get_related_uploaded_dna_cases(self, rna_case_id: str) -> set[str]:
         """Returns all uploaded DNA cases related to the specified RNA case."""
         unique_dna_case_ids: set[str] = self.get_unique_dna_cases_related_to_rna_case(rna_case_id)
-
         uploaded_dna_cases: set[str] = set()
         for dna_case_id in unique_dna_case_ids:
             if self.status_db.get_case_by_internal_id(dna_case_id).is_uploaded: