Fix raredisease custom images (#3877)

### Fixed

- Custom images where also added while empty, causing an error in the scout upload. Now only adding custom images if images are present

Author: rannick

cg/meta/upload/scout/raredisease_config_builder.py

@@ -61,28 +61,33 @@ def build_load_config(self) -> RarediseaseLoadConfig:
         self.include_case_files(load_config)
         self.get_sample_information(load_config)
         self.include_pedigree_picture(load_config)
-        load_config.custom_images = self.load_custom_image_sample()
+        self.load_custom_image_sample(load_config)
         load_config.human_genome_build = GenomeBuild.hg19
         return load_config
 
-    def load_custom_image_sample(self) -> CustomImages:
+    def load_custom_image_sample(self, load_config: RarediseaseLoadConfig) -> None:
         """Build custom images config."""
         LOG.info("Adding custom images")
+
         eklipse_images: list = []
-        for db_sample in self.analysis_obj.case.links:
-            sample_id: str = db_sample.sample.internal_id
-            eklipse_image = Eklipse(
-                title=sample_id,
-                path=self.get_file_from_hk(hk_tags=self.sample_tags.eklipse_path),
-                description="eKLIPse MT images",
-                width="800",
-                height="800",
+        for sample in self.analysis_obj.case.samples:
+            sample_id: str = sample.internal_id
+            eklipse_image_path = self.get_file_from_hk(
+                hk_tags=set(self.sample_tags.eklipse_path).union({sample_id})
             )
-            eklipse_images.append(eklipse_image)
-
-        case_images = CaseImages(eKLIPse=eklipse_images)
-        config_custom_images = CustomImages(case_images=case_images)
-        return config_custom_images
+            if eklipse_image_path:
+                eklipse_image = Eklipse(
+                    title=sample_id,
+                    path=eklipse_image_path,
+                    description="eKLIPse MT images",
+                    width="800",
+                    height="800",
+                )
+                eklipse_images.append(eklipse_image)
+        if eklipse_images:
+            case_images = CaseImages(eKLIPse=eklipse_images)
+            config_custom_images = CustomImages(case_images=case_images)
+            load_config.custom_images = config_custom_images
 
     def include_case_files(self, load_config: RarediseaseLoadConfig) -> None:
         """Include case level files for mip case."""

cg/models/cg_config.py

@@ -30,10 +30,8 @@
 from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
     DeliveryServiceFactory,
 )
-from cg.services.deliver_files.rsync.service import (
-    DeliveryRsyncService,
-)
 from cg.services.deliver_files.rsync.models import RsyncDeliveryConfig
+from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
     FastqConcatenationService,
 )
@@ -47,13 +45,21 @@
 from cg.services.run_devices.pacbio.housekeeper_service.pacbio_houskeeper_service import (
     PacBioHousekeeperService,
 )
-from cg.services.run_devices.pacbio.metrics_parser.metrics_parser import PacBioMetricsParser
-from cg.services.run_devices.pacbio.post_processing_service import PacBioPostProcessingService
+from cg.services.run_devices.pacbio.metrics_parser.metrics_parser import (
+    PacBioMetricsParser,
+)
+from cg.services.run_devices.pacbio.post_processing_service import (
+    PacBioPostProcessingService,
+)
 from cg.services.run_devices.pacbio.run_data_generator.pacbio_run_data_generator import (
     PacBioRunDataGenerator,
 )
-from cg.services.run_devices.pacbio.run_file_manager.run_file_manager import PacBioRunFileManager
-from cg.services.run_devices.pacbio.run_validator.pacbio_run_validator import PacBioRunValidator
+from cg.services.run_devices.pacbio.run_file_manager.run_file_manager import (
+    PacBioRunFileManager,
+)
+from cg.services.run_devices.pacbio.run_validator.pacbio_run_validator import (
+    PacBioRunValidator,
+)
 from cg.services.run_devices.run_names.pacbio import PacbioRunNamesService
 from cg.services.sequencing_qc_service.sequencing_qc_service import SequencingQCService
 from cg.services.slurm_service.slurm_cli_service import SlurmCLIService
@@ -248,18 +254,18 @@ class TomteConfig(CommonAppConfig):
 
 
 class RnafusionConfig(CommonAppConfig):
-    root: str
-    references: str
     binary_path: str
-    workflow_path: str
-    conda_env: str
     compute_env: str
-    profile: str
     conda_binary: str | None = None
+    conda_env: str
     launch_directory: str
+    profile: str
+    references: str
     revision: str
+    root: str
     slurm: SlurmConfig
     tower_workflow: str
+    workflow_path: str
 
 
 class TaxprofilerConfig(CommonAppConfig):