From 0478077123aba38625d68059843bf8cd4c9c769d Mon Sep 17 00:00:00 2001
From: Eva C <29628428+fevac@users.noreply.github.com>
Date: Tue, 28 Nov 2023 12:19:41 +0100
Subject: [PATCH] Skip lims data retrieval if downsampled for rnafusion report
 (#2705)

### Changed

- Skip lims sample metadata collection for rnafusion report generation if down sampled
---
 cg/meta/report/rnafusion.py             | 12 +++++++--
 tests/meta/report/test_rnafusion_api.py | 34 +++++++++++++++++++++++--
 2 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/cg/meta/report/rnafusion.py b/cg/meta/report/rnafusion.py
index 6a5772c1c0..ef0cfafeda 100644
--- a/cg/meta/report/rnafusion.py
+++ b/cg/meta/report/rnafusion.py
@@ -38,11 +38,19 @@ def get_sample_metadata(
     ) -> RnafusionSampleMetadataModel:
         """Return sample metadata to include in the report."""
         sample_metrics: RnafusionQCMetrics = analysis_metadata.sample_metrics[sample.internal_id]
+
+        # Skip LIMS data collection if down sampled
+        input_amount = None
+        rin = None
+        if not sample.downsampled_to:
+            input_amount = self.lims_api.get_latest_rna_input_amount(sample_id=sample.internal_id)
+            rin = self.lims_api.get_sample_rin(sample_id=sample.internal_id)
+
         return RnafusionSampleMetadataModel(
             bias_5_3=sample_metrics.bias_5_3,
             duplicates=sample_metrics.pct_duplication,
             gc_content=sample_metrics.after_filtering_gc_content,
-            input_amount=self.lims_api.get_latest_rna_input_amount(sample_id=sample.internal_id),
+            input_amount=input_amount,
             insert_size=None,
             insert_size_peak=None,
             mapped_reads=sample_metrics.reads_aligned
@@ -58,7 +66,7 @@ def get_sample_metadata(
             q20_rate=sample_metrics.after_filtering_q20_rate,
             q30_rate=sample_metrics.after_filtering_q30_rate,
             ribosomal_bases=sample_metrics.pct_ribosomal_bases,
-            rin=self.lims_api.get_sample_rin(sample_id=sample.internal_id),
+            rin=rin,
             uniquely_mapped_reads=sample_metrics.uniquely_mapped_percent,
         )
 
diff --git a/tests/meta/report/test_rnafusion_api.py b/tests/meta/report/test_rnafusion_api.py
index fa046ce844..fa50b111db 100644
--- a/tests/meta/report/test_rnafusion_api.py
+++ b/tests/meta/report/test_rnafusion_api.py
@@ -1,6 +1,5 @@
 """Test module for the Rnafusion delivery report API."""
-
-
+from cg.constants import NA_FIELD
 from cg.meta.report.rnafusion import RnafusionReportAPI
 from cg.models.report.metadata import RnafusionSampleMetadataModel
 from cg.models.rnafusion.rnafusion import RnafusionAnalysis
@@ -34,3 +33,34 @@ def test_get_sample_metadata(
 
     # THEN the sample metadata should be correctly retrieved and match the expected validated metrics
     assert sample_metadata.model_dump() == rnafusion_validated_metrics
+
+
+def test_get_down_sample_metadata(
+    report_api_rnafusion: RnafusionReportAPI,
+    sample_id: str,
+    rnafusion_case_id: str,
+    rnafusion_validated_metrics: dict[str, str],
+    mock_analysis_finish,
+):
+    """Test Rnafusion sample metadata extraction."""
+
+    # GIVEN a Rnafusion case and associated sample that has been down sampled
+    case: Case = report_api_rnafusion.status_db.get_case_by_internal_id(
+        internal_id=rnafusion_case_id
+    )
+    sample: Sample = report_api_rnafusion.status_db.get_sample_by_internal_id(internal_id=sample_id)
+    sample.downsampled_to = 10000
+
+    # GIVEN an analysis metadata object
+    latest_metadata: RnafusionAnalysis = report_api_rnafusion.analysis_api.get_latest_metadata(
+        case_id=rnafusion_case_id
+    )
+
+    # WHEN getting the sample metadata
+    sample_metadata: RnafusionSampleMetadataModel = report_api_rnafusion.get_sample_metadata(
+        case=case, sample=sample, analysis_metadata=latest_metadata
+    )
+
+    # THEN the rin and input_amount should be N/A
+    assert sample_metadata.rin == NA_FIELD
+    assert sample_metadata.input_amount == NA_FIELD