[MRG] catch TypeError in search w/abund vs flat at the command line (#…

…1928)

* catch TypeError in search w/abund vs flat

* added a test

src/sourmash/commands.py

@@ -492,12 +492,16 @@ def search(args):
 
     # do the actual search
     if query.minhash.track_abundance:
-        results = search_databases_with_abund_query(query, databases,
-                                   threshold=args.threshold,
-                                   do_containment=args.containment,
-                                   do_max_containment=args.max_containment,
-                                   best_only=args.best_only,
-                                   unload_data=True)
+        try:
+            results = search_databases_with_abund_query(query, databases,
+                                       threshold=args.threshold,
+                                       do_containment=args.containment,
+                                       do_max_containment=args.max_containment,
+                                       best_only=args.best_only,
+                                       unload_data=True)
+        except TypeError as exc:
+            error(f"ERROR: {str(exc)}")
+            sys.exit(-1)
     else:
         results = search_databases_with_flat_query(query, databases,
                                    threshold=args.threshold,

tests/test_sourmash.py

@@ -826,6 +826,17 @@ def test_search_ignore_abundance(runtmp):
     assert out1 != out2
 
 
+def test_search_abund_subj_flat(runtmp):
+    # test Index.search_abund requires an abund subj
+    sig47 = utils.get_test_data('track_abund/47.fa.sig')
+    sig63 = utils.get_test_data('63.fa.sig')
+
+    with pytest.raises(SourmashCommandFailed) as exc:
+        runtmp.sourmash('search', sig47, sig63)
+
+    assert "'search_abund' requires subject signatures with abundance information" in str(exc.value)
+
+
 def test_search_abund_csv(runtmp):
     # test search with abundance signatures, look at CSV output
     testdata1 = utils.get_test_data('short.fa')