[MRG] switch sbt.zip over to default SBT storage

sourmash/sbt.py

@@ -562,23 +562,23 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False):
         info["index_type"] = self.__class__.__name__  # TODO: check
 
         # choose between ZipStorage and FS (file system/directory) storage.
-        if path.endswith(".sbt.zip"):
+        if not path.endswith(".sbt.json"):
             kind = "Zip"
+            if not path.endswith('.sbt.zip'):
+                path += '.sbt.zip'
             storage = ZipStorage(path)
             backend = "FSStorage"
             name = os.path.basename(path[:-8])
             subdir = '.sbt.{}'.format(name)
             storage_args = FSStorage("", subdir).init_args()
             storage.save(subdir + "/", b"")
             index_filename = os.path.abspath(path)
-        else:
+        else:                             # path.endswith('.sbt.json')
+            assert path.endswith('.sbt.json')
             kind = "FS"
             name = os.path.basename(path)
-            if path.endswith('.sbt.json'):
-                name = name[:-9]
-                index_filename = os.path.abspath(path)
-            else:
-                index_filename = os.path.abspath(path + '.sbt.json')
+            name = name[:-9]
+            index_filename = os.path.abspath(path)
 
             if storage is None:
                 # default storage
@@ -685,22 +685,29 @@ def load(cls, location, *, leaf_loader=None, storage=None, print_version_warning
         sbt_name = None
         tree_data = None
 
-        if storage is None and ZipStorage.can_open(location):
-            storage = ZipStorage(location)
-
-            sbts = storage.list_sbts()
-            if len(sbts) != 1:
-                print("no SBT, or too many SBTs!")
+        if storage is None:
+            if ZipStorage.can_open(location):
+                storage = ZipStorage(location)
             else:
-                tree_data = storage.load(sbts[0])
+                if not location.endswith('.sbt.zip'):
+                    location2 = location + '.sbt.zip'
+                    if ZipStorage.can_open(location2):
+                        storage = ZipStorage(location2)
+
+            if storage:
+                sbts = storage.list_sbts()
+                if len(sbts) != 1:
+                    print("no SBT, or too many SBTs!")
+                else:
+                    tree_data = storage.load(sbts[0])
 
-            tempfile = NamedTemporaryFile()
+                tempfile = NamedTemporaryFile()
 
-            tempfile.write(tree_data)
-            tempfile.flush()
+                tempfile.write(tree_data)
+                tempfile.flush()
 
-            dirname = os.path.dirname(tempfile.name)
-            sbt_name = os.path.basename(tempfile.name)
+                dirname = os.path.dirname(tempfile.name)
+                sbt_name = os.path.basename(tempfile.name)
 
         if sbt_name is None:
             dirname = os.path.dirname(os.path.abspath(location))

tests/test_sbt.py

@@ -318,9 +318,9 @@ def test_sbt_fsstorage():
         print(*old_result, sep='\n')
 
         with FSStorage(location, '.fstree') as storage:
-            tree.save(os.path.join(location, 'tree'), storage=storage)
+            tree.save(os.path.join(location, 'tree.sbt.json'), storage=storage)
 
-        tree = SBT.load(os.path.join(location, 'tree'), leaf_loader=SigLeaf.load)
+        tree = SBT.load(os.path.join(location, 'tree.sbt.json'), leaf_loader=SigLeaf.load)
         print('*' * 60)
         print("{}:".format(to_search.metadata))
         new_result = {str(s) for s in tree.find(search_minhashes,
@@ -352,10 +352,10 @@ def test_sbt_zipstorage(tmpdir):
     print(*old_result, sep='\n')
 
     with ZipStorage(str(tmpdir.join("tree.sbt.zip"))) as storage:
-        tree.save(str(tmpdir.join("tree")), storage=storage)
+        tree.save(str(tmpdir.join("tree.sbt.json")), storage=storage)
 
     with ZipStorage(str(tmpdir.join("tree.sbt.zip"))) as storage:
-        tree = SBT.load(str(tmpdir.join("tree")),
+        tree = SBT.load(str(tmpdir.join("tree.sbt.json")),
                         leaf_loader=SigLeaf.load,
                         storage=storage)
 
@@ -390,12 +390,12 @@ def test_sbt_ipfsstorage():
 
         try:
             with IPFSStorage() as storage:
-                tree.save(os.path.join(location, 'tree'), storage=storage)
+                tree.save(os.path.join(location, 'tree.sbt.json'), storage=storage)
         except ipfshttpclient.exceptions.ConnectionError:
             pytest.xfail("ipfs not installed/functioning probably")
 
         with IPFSStorage() as storage:
-            tree = SBT.load(os.path.join(location, 'tree'),
+            tree = SBT.load(os.path.join(location, 'tree.sbt.json'),
                             leaf_loader=SigLeaf.load,
                             storage=storage)
 
@@ -429,12 +429,12 @@ def test_sbt_redisstorage():
 
         try:
             with RedisStorage() as storage:
-                tree.save(os.path.join(location, 'tree'), storage=storage)
+                tree.save(os.path.join(location, 'tree.sbt.json'), storage=storage)
         except redis.exceptions.ConnectionError:
             pytest.xfail("Couldn't connect to redis server")
 
         with RedisStorage() as storage:
-            tree = SBT.load(os.path.join(location, 'tree'),
+            tree = SBT.load(os.path.join(location, 'tree.sbt.json'),
                             leaf_loader=SigLeaf.load,
                             storage=storage)