fix for genome-grist alpha test

src/sourmash/commands.py

@@ -631,6 +631,10 @@ def gather(args):
                query.minhash.scaled, int(args.scaled))
         query.minhash = query.minhash.downsample(scaled=args.scaled)
 
+    # flatten if needed @CTB do we need this here?
+    if query.minhash.track_abundance:
+        query.minhash = query.minhash.flatten()
+
     # empty?
     if not len(query.minhash):
         error('no query hashes!? exiting.')

src/sourmash/index.py

@@ -280,6 +280,9 @@ def location(self):
     def signatures(self):
         return iter(self._signatures)
 
+    def __bool__(self):
+        return bool(self._signatures)
+
     def __len__(self):
         return len(self._signatures)
 
@@ -329,6 +332,9 @@ def __init__(self, zf, selection_dict=None,
         self.selection_dict = selection_dict
         self.traverse_yield_all = traverse_yield_all
 
+    def __bool__(self):
+        return bool(self.zf)
+
     def __len__(self):
         return len(list(self.signatures()))
 
@@ -464,7 +470,8 @@ def gather(self, query, *args, **kwargs):
             result = IndexSearchResult(cont, match, location)
 
         # calculate intersection of this "best match" with query, for removal.
-        match_mh = match.minhash.downsample(scaled=scaled)
+        # @CTB note flatten
+        match_mh = match.minhash.downsample(scaled=scaled).flatten()
         intersect_mh = query_mh.intersection(match_mh)
 
         # Prepare counter for finding the next match by decrementing

src/sourmash/lca/lca_db.py

@@ -212,6 +212,10 @@ def load(cls, db_name):
             xopen = gzip.open
 
         with xopen(db_name, 'rt') as fp:
+            if fp.read(1) != '{':
+                raise ValueError(f"'{db_name}' is not an LCA database file.")
+            fp.seek(0)
+
             load_d = {}
             try:
                 load_d = json.load(fp)

src/sourmash/sourmash_args.py

@@ -306,7 +306,7 @@ def _load_database(filename, traverse_yield_all, *, cache_size=None):
             debug_literal(f"_load_databases: FAIL on fn {desc}.")
             debug_literal(traceback.format_exc())
 
-        if db:
+        if db is not None:
             loaded = True
             break