From 08490420a2381fb892ed1cc3fa2c8840c4d9c05a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 8 Feb 2026 18:08:13 +0100
Subject: [PATCH] Fix whitespace in test script and add merge consistency tests

This commit fixes minor whitespace issues in the test script and adds new tests to ensure merge attribute consistency between in-memory and on-disk paths.

- Removed trailing spaces in log messages
- Added tests for merge consistency between in-memory and on-disk paths
- These tests catch a bug where shared classifier in on-disk dereplication path caused incorrect merged attributes
---
 obitests/obitools/obiuniq/test.sh | 75 ++++++++++++++++++++++++++-----
 1 file changed, 64 insertions(+), 11 deletions(-)

diff --git a/obitests/obitools/obiuniq/test.sh b/obitests/obitools/obiuniq/test.sh
index 0f9c9aa..4ddb11e 100755
--- a/obitests/obitools/obiuniq/test.sh
+++ b/obitests/obitools/obiuniq/test.sh
@@ -39,7 +39,7 @@ cleanup() {
     rm -rf "$TMPDIR"  # Suppress the temporary directory
 
     if [ $failed -gt 0 ]; then
-       log "$TEST_NAME tests failed" 
+       log "$TEST_NAME tests failed"
         log
         log
        exit 1
@@ -55,10 +55,10 @@ log() {
     echo -e "[$TEST_NAME @ $(date)] $*" 1>&2
 }
 
-log "Testing $TEST_NAME..." 
-log "Test directory is $TEST_DIR" 
-log "obitools directory is $OBITOOLS_DIR" 
-log "Temporary directory is $TMPDIR" 
+log "Testing $TEST_NAME..."
+log "Test directory is $TEST_DIR"
+log "obitools directory is $OBITOOLS_DIR"
+log "Temporary directory is $TMPDIR"
 log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
 
 ######################################################################
@@ -89,12 +89,12 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
 
 
 ((ntest++))
-if $CMD -h > "${TMPDIR}/help.txt" 2>&1 
+if $CMD -h > "${TMPDIR}/help.txt" 2>&1
 then
-    log "$MCMD: printing help OK" 
+    log "$MCMD: printing help OK"
     ((success++))
 else
-    log "$MCMD: printing help failed" 
+    log "$MCMD: printing help failed"
     ((failed++))
 fi
 
@@ -102,7 +102,7 @@ fi
 if obiuniq "${TEST_DIR}/touniq.fasta" \
     > "${TMPDIR}/touniq_u.fasta"
 then
-    log "OBIUniq simple: running OK" 
+    log "OBIUniq simple: running OK"
     ((success++))
 else
     log "OBIUniq simple: running failed"
@@ -134,7 +134,7 @@ fi
 if obiuniq -c a "${TEST_DIR}/touniq.fasta" \
     > "${TMPDIR}/touniq_u_a.fasta"
 then
-    log "OBIUniq one category: running OK" 
+    log "OBIUniq one category: running OK"
     ((success++))
 else
     log "OBIUniq one category: running failed"
@@ -167,7 +167,7 @@ fi
 if obiuniq -c a -c b "${TEST_DIR}/touniq.fasta" \
     > "${TMPDIR}/touniq_u_a_b.fasta"
 then
-    log "OBIUniq two categories: running OK" 
+    log "OBIUniq two categories: running OK"
     ((success++))
 else
     log "OBIUniq two categories: running failed"
@@ -195,6 +195,59 @@ else
     ((failed++))
 fi
 
+##
+## Test merge attributes consistency between in-memory and on-disk paths
+## This test catches the bug where the shared classifier in the on-disk
+## dereplication path caused incorrect merged attributes.
+##
+
+((ntest++))
+if obiuniq -m a -m b --in-memory \
+    "${TEST_DIR}/touniq.fasta" \
+    > "${TMPDIR}/touniq_u_merge_mem.fasta" 2>/dev/null
+then
+    log "OBIUniq merge in-memory: running OK"
+    ((success++))
+else
+    log "OBIUniq merge in-memory: running failed"
+    ((failed++))
+fi
+
+((ntest++))
+if obiuniq -m a -m b --chunk-count 4 \
+    "${TEST_DIR}/touniq.fasta" \
+    > "${TMPDIR}/touniq_u_merge_disk.fasta" 2>/dev/null
+then
+    log "OBIUniq merge on-disk: running OK"
+    ((success++))
+else
+    log "OBIUniq merge on-disk: running failed"
+    ((failed++))
+fi
+
+# Extract sorted annotations (JSON attributes) from both outputs
+# to compare merge results independently of sequence ordering
+grep '^>' "${TMPDIR}/touniq_u_merge_mem.fasta" \
+| sed 's/^>seq[0-9]* //' \
+| sort \
+> "${TMPDIR}/touniq_u_merge_mem.json"
+
+grep '^>' "${TMPDIR}/touniq_u_merge_disk.fasta" \
+| sed 's/^>seq[0-9]* //' \
+| sort \
+> "${TMPDIR}/touniq_u_merge_disk.json"
+
+((ntest++))
+if diff "${TMPDIR}/touniq_u_merge_mem.json" \
+        "${TMPDIR}/touniq_u_merge_disk.json" > /dev/null
+then
+    log "OBIUniq merge on-disk vs in-memory: result OK"
+    ((success++))
+else
+    log "OBIUniq merge on-disk vs in-memory: result failed"
+    ((failed++))
+fi
+
 #########################################
 #
 # At the end of the tests