do not overwrite signature even if duplicate md5sum (#1497)

src/sourmash/sourmash_args.py

@@ -606,7 +606,17 @@ def open(self):
     def add(self, ss):
         super().add(ss)
         md5 = ss.md5sum()
+
+        # don't overwrite even if duplicate md5sum
         outname = os.path.join(self.location, f"{md5}.sig.gz")
+        if os.path.exists(outname):
+            i = 0
+            while 1:
+                outname = os.path.join(self.location, f"{md5}_{i}.sig.gz")
+                if not os.path.exists(outname):
+                    break
+                i += 1
+
         with gzip.open(outname, "wb") as fp:
             sig.save_signatures([ss], fp, compression=1)
 
@@ -663,12 +673,29 @@ def close(self):
     def open(self):
         self.zf = zipfile.ZipFile(self.location, 'w', zipfile.ZIP_STORED)
 
+    def _exists(self, name):
+        try:
+            self.zf.getinfo(name)
+            return True
+        except KeyError:
+            return False
+
     def add(self, ss):
         assert self.zf
         super().add(ss)
 
         md5 = ss.md5sum()
         outname = f"signatures/{md5}.sig.gz"
+
+        # don't overwrite even if duplicate md5sum.
+        if self._exists(outname):
+            i = 0
+            while 1:
+                outname = os.path.join(self.location, f"{md5}_{i}.sig.gz")
+                if not self._exists(outname):
+                    break
+                i += 1
+
         json_str = sourmash.save_signatures([ss], compression=1)
         self.zf.writestr(outname, json_str)
 

tests/test_sourmash_args.py

@@ -135,6 +135,31 @@ def test_save_signatures_to_location_1_zip(runtmp):
     assert len(saved) == 2
 
 
+def test_save_signatures_to_location_1_zip_dup(runtmp):
+    # save to sigfile.zip
+    sig2 = utils.get_test_data('2.fa.sig')
+    ss2 = sourmash.load_one_signature(sig2, ksize=31)
+    sig47 = utils.get_test_data('47.fa.sig')
+    ss47 = sourmash.load_one_signature(sig47, ksize=31)
+
+    outloc = runtmp.output('foo.zip')
+    with sourmash_args.SaveSignaturesToLocation(outloc) as save_sig:
+        print(save_sig)
+        save_sig.add(ss2)
+        save_sig.add(ss47)
+        save_sig.add(ss2)
+        save_sig.add(ss47)
+
+    # can we open as a .zip file?
+    with zipfile.ZipFile(outloc, "r") as zf:
+        assert list(zf.infolist())
+
+    saved = list(sourmash.load_file_as_signatures(outloc))
+    assert ss2 in saved
+    assert ss47 in saved
+    assert len(saved) == 4
+
+
 def test_save_signatures_to_location_1_dirout(runtmp):
     # save to sigout/ (directory)
     sig2 = utils.get_test_data('2.fa.sig')
@@ -154,3 +179,26 @@ def test_save_signatures_to_location_1_dirout(runtmp):
     assert ss2 in saved
     assert ss47 in saved
     assert len(saved) == 2
+
+
+def test_save_signatures_to_location_1_dirout_duplicate(runtmp):
+    # save to sigout/ (directory)
+    sig2 = utils.get_test_data('2.fa.sig')
+    ss2 = sourmash.load_one_signature(sig2, ksize=31)
+    sig47 = utils.get_test_data('47.fa.sig')
+    ss47 = sourmash.load_one_signature(sig47, ksize=31)
+
+    outloc = runtmp.output('sigout/')
+    with sourmash_args.SaveSignaturesToLocation(outloc) as save_sig:
+        print(save_sig)
+        save_sig.add(ss2)
+        save_sig.add(ss47)
+        save_sig.add(ss2)
+        save_sig.add(ss47)
+
+    assert os.path.isdir(outloc)
+
+    saved = list(sourmash.load_file_as_signatures(outloc))
+    assert ss2 in saved
+    assert ss47 in saved
+    assert len(saved) == 4