From 462adfdc5fb24c8b15c5d48e30a26ddaf11f2789 Mon Sep 17 00:00:00 2001
From: ChristianOertlin <christian.oertlin@scilifelab.se>
Date: Wed, 12 Jun 2024 11:27:51 +0200
Subject: [PATCH] add(mip analysis upload workaround) (#3332) (patch)

# Description

allow multiple data analyses mip upload
---
 cg/meta/workflow/mip_dna.py | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/cg/meta/workflow/mip_dna.py b/cg/meta/workflow/mip_dna.py
index 5d2f245b0c..b96dc6aae5 100644
--- a/cg/meta/workflow/mip_dna.py
+++ b/cg/meta/workflow/mip_dna.py
@@ -1,3 +1,5 @@
+import logging
+
 from cg.constants import DEFAULT_CAPTURE_KIT, Workflow
 from cg.constants.constants import AnalysisType
 from cg.constants.gene_panel import GENOME_BUILD_37
@@ -5,9 +7,11 @@
 from cg.meta.workflow.mip import MipAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.models.mip.mip_analysis import MipAnalysis
-from cg.store.models import CaseSample
+from cg.store.models import CaseSample, Case
 from cg.utils import Process
 
+LOG = logging.getLogger(__name__)
+
 
 class MipDNAAnalysisAPI(MipAnalysisAPI):
     def __init__(self, config: CGConfig, workflow: Workflow = Workflow.MIP_DNA):
@@ -73,3 +77,20 @@ def get_genome_build(self, case_id: str) -> str:
         """Return the reference genome build version of a MIP-DNA analysis."""
         analysis_metadata: MipAnalysis = self.get_latest_metadata(case_id)
         return analysis_metadata.genome_build
+
+    def get_data_analysis_type(self, case_id: str) -> str:
+        """
+        Return the data analysis type of a MIP-DNA analysis.
+        Patch for the typical behaviour of the AnalysisAPI function.
+        It does not raise an error with multiple analysis types.
+        """
+        case: Case = self.get_validated_case(case_id)
+        analysis_types: set[str] = {
+            link.sample.application_version.application.analysis_type for link in case.links
+        }
+        if len(analysis_types) > 1:
+            LOG.warning(
+                f"Multiple analysis types found. Defaulting to {AnalysisType.WHOLE_GENOME_SEQUENCING}."
+            )
+            return AnalysisType.WHOLE_GENOME_SEQUENCING
+        return analysis_types.pop() if analysis_types else None