Check if alignment files were removed from server before displaying t…

…heir link (#3383)

* Check if alignment files were removed from server before displaying their link

* Fix code in app.py

* revert app.py

* Fix splice juntion links as well

* fixed code

* Fixed test

* Update CHANGELOG.md

Co-authored-by: Daniel Nilsson <[email protected]>

* Empty-Commit

Co-authored-by: Daniel Nilsson <[email protected]>

CHANGELOG.md

@@ -29,6 +29,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Variants pagination after pressing "Filter variants" or "Clinical filter"
 - Layout of buttons Matchmaker submission panel (case page)
 - Removing cases from Matchmaker (simplified code and fixed functionality)
+- Reintroduce check for missing alignment files purged from server
 
 ## [4.53]
 ### Added

scout/server/blueprints/variant/controllers.py

@@ -1,4 +1,5 @@
 import logging
+import os
 from base64 import b64encode
 from datetime import date
 
@@ -132,8 +133,13 @@ def has_rna_tracks(case_obj):
     # Display junctions track if available for any of the individuals
     for ind in case_obj.get("individuals", []):
         # Track contains 2 files and they should both be present
-        if all([ind.get("splice_junctions_bed"), ind.get("rna_coverage_bigwig")]):
-            return True
+        splicej_bed = ind.get("splice_junctions_bed")
+        rna_cov_bw = ind.get("rna_coverage_bigwig")
+        if None in [splicej_bed, rna_cov_bw]:
+            continue
+        if False in [os.path.exists(splicej_bed), os.path.exists(rna_cov_bw)]:
+            continue
+        return True
     return False
 
 

scout/server/utils.py

@@ -181,7 +181,8 @@ def case_has_alignments(case_obj):
     """
     case_obj["bam_files"] = False  # Availability of alignments for autosomal chromosomes
     for ind in case_obj.get("individuals"):
-        if ind.get("bam_file") and ind.get("bam_file") != "":
+        bam_path = ind.get("bam_file")
+        if bam_path and os.path.exists(bam_path):
             case_obj["bam_files"] = True
             return
 
@@ -194,7 +195,8 @@ def case_has_mt_alignments(case_obj):
     """
     case_obj["mt_bams"] = False  # Availability of alignments for MT chromosome
     for ind in case_obj.get("individuals"):
-        if ind.get("mt_bam") and ind.get("mt_bam") != "":
+        mt_bam_path = ind.get("mt_bam")
+        if mt_bam_path and os.path.exists(mt_bam_path):
             case_obj["mt_bams"] = True
             return
 

tests/server/blueprints/variant/test_variant_controllers.py

@@ -84,16 +84,23 @@ def test_tx_overview(app):
             assert key in tx
 
 
-def test_has_rna_tracks(case_obj):
+def test_has_rna_tracks(case_obj, tmpdir):
     """Test the function that returns True if any individual of a case has RNA tracks available"""
 
-    # GIVEN a case with an individual with RNA tracks:
+    # GIVEN an individual with splice junctions bed file and rna coverage track
+    splicej_bed = tmpdir.join("test.bed")
+    rna_cov_bw = tmpdir.join("test.BigWig")
+    splicej_bed.write("content")
+    rna_cov_bw.write("content")
+
     for ind in case_obj["individuals"]:
         if ind["phenotype"] == 1:  # Lets's assume only the affected individuals has RNA data
             continue
-        ind["splice_junctions_bed"] = "test.bed"
-        ind["rna_coverage_bigwig"] = "test.BigWig"
 
+        ind["splice_junctions_bed"] = str(splicej_bed)
+        ind["rna_coverage_bigwig"] = str(rna_cov_bw)
+
+    # THEN case should result having RNA tracks
     assert has_rna_tracks(case_obj) is True