[MRG] Remove TarStorage and replace usage with ZipStorage

doc/storage.md

@@ -14,15 +14,15 @@ Saves internal SBT data in a hidden directory near the SBT JSON description.
         We used to create a tar file of JSON + hidden directory,
         which requires extracting and using more disk space.
 
-### TarStorage
+### ZipStorage
 
 Similar to FSStorage,
-but saves the internal SBT data in a `tar` file.
+but saves the internal SBT data in a `zip` file.
 - Pros
-  * easy to distribute (two files)
+  * easy to distribute (one file)
 - Cons
   * still need to distribute and download everything
-    (you need the full tar file available locally to be able to use the SBT).
+    (you need the full zip file available locally to be able to use the SBT).
 
 ### IPFSStorage
 

sourmash/sbt.py

@@ -55,13 +55,12 @@ def search_transcript(node, seq, threshold):
 from cachetools import Cache
 
 from .exceptions import IndexNotSupported
-from .sbt_storage import FSStorage, TarStorage, IPFSStorage, RedisStorage, ZipStorage
+from .sbt_storage import FSStorage, IPFSStorage, RedisStorage, ZipStorage
 from .logging import error, notify, debug
 from .index import Index
 from .nodegraph import Nodegraph, extract_nodegraph_info, calc_expected_collisions
 
 STORAGES = {
-    'TarStorage': TarStorage,
     'FSStorage': FSStorage,
     'IPFSStorage': IPFSStorage,
     'RedisStorage': RedisStorage,
@@ -1310,8 +1309,8 @@ def convert_cmd(name, backend):
         backend = IPFSStorage
     elif backend.lower() in ('redis', 'redisstorage'):
         backend = RedisStorage
-    elif backend.lower() in ('tar', 'tarstorage'):
-        backend = TarStorage
+    elif backend.lower() in ('zip', 'zipstorage'):
+        backend = ZipStorage
     elif backend.lower() in ('fs', 'fsstorage'):
         backend = FSStorage
         if options:

sourmash/sbt_storage.py

@@ -82,47 +82,6 @@ def load(self, path):
         return path.read_bytes()
 
 
-class TarStorage(Storage):
-
-    def __init__(self, path=None):
-        # TODO: leave it open, or close/open every time?
-
-        if path is None:
-            # TODO: Open a temporary file?
-            pass                          # CTB: should raise an exception, no?
-
-        self.path = os.path.abspath(path)
-
-        dirname = os.path.dirname(self.path)
-        if not os.path.exists(dirname):
-            os.makedirs(dirname)
-
-        if os.path.exists(self.path):
-            self.tarfile = tarfile.open(path, 'r')
-        else:
-            self.tarfile = tarfile.open(path, 'w:gz')
-
-    def save(self, path, content):
-        info = tarfile.TarInfo(path)
-        info.size = len(content)
-
-        # TODO: check tarfile mode, if read-only reopen as writable
-        self.tarfile.addfile(info, BytesIO(content))
-
-        return path
-
-    def load(self, path):
-        content = self.tarfile.getmember(path)
-        f = self.tarfile.extractfile(content)
-        return f.read()
-
-    def init_args(self):
-        return {'path': self.path}
-
-    def __exit__(self, type, value, traceback):
-        self.tarfile.close()
-
-
 class ZipStorage(Storage):
 
     def __init__(self, path):

tests/test_sbt.py

@@ -10,7 +10,7 @@
 from sourmash.sbt import SBT, GraphFactory, Leaf, Node
 from sourmash.sbtmh import (SigLeaf, search_minhashes,
                             search_minhashes_containment)
-from sourmash.sbt_storage import (FSStorage, TarStorage, RedisStorage,
+from sourmash.sbt_storage import (FSStorage, RedisStorage,
                                   IPFSStorage, ZipStorage)
 
 from . import sourmash_tst_utils as utils
@@ -333,41 +333,6 @@ def test_sbt_fsstorage():
         assert os.path.exists(os.path.join(location, '.fstree'))
 
 
-def test_sbt_tarstorage():
-    factory = GraphFactory(31, 1e5, 4)
-    with utils.TempDirectory() as location:
-        tree = SBT(factory)
-
-        for f in utils.SIG_FILES:
-            sig = load_one_signature(utils.get_test_data(f))
-
-            leaf = SigLeaf(os.path.basename(f), sig)
-            tree.add_node(leaf)
-            to_search = leaf
-
-        print('*' * 60)
-        print("{}:".format(to_search.metadata))
-        old_result = {str(s) for s in tree.find(search_minhashes,
-                                                to_search.data, 0.1)}
-        print(*old_result, sep='\n')
-
-        with TarStorage(os.path.join(location, 'tree.tar.gz')) as storage:
-            tree.save(os.path.join(location, 'tree'), storage=storage)
-
-        with TarStorage(os.path.join(location, 'tree.tar.gz')) as storage:
-            tree = SBT.load(os.path.join(location, 'tree'),
-                            leaf_loader=SigLeaf.load,
-                            storage=storage)
-
-            print('*' * 60)
-            print("{}:".format(to_search.metadata))
-            new_result = {str(s) for s in tree.find(search_minhashes,
-                                                    to_search.data, 0.1)}
-            print(*new_result, sep='\n')
-
-            assert old_result == new_result
-
-
 def test_sbt_zipstorage(tmpdir):
     # create tree, save to a zip, then load and search.
     factory = GraphFactory(31, 1e5, 4)

tests/test_sourmash.py

@@ -3893,8 +3893,8 @@ def test_storage_convert():
                    for (n1, n2) in zip(sorted(original), sorted(ipfs)))
 
         args = ['storage', 'convert',
-                '-b', """'TarStorage("{}")'""".format(
-                    os.path.join(location, 'v2.sbt.tar.gz')),
+                '-b', """'ZipStorage("{}")'""".format(
+                    os.path.join(location, 'v2.sbt.zip')),
                 testsbt]
         status, out, err = utils.runscript('sourmash', args,
                                            in_directory=location)