ENH: treat case of removed files

Summary

The move script could not deal with non-existing entities.

Test Environment

Use a path that does not exist.

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• All automated tests pass
• Reference related Issues
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  • Intent of new code
  • Problems with old code
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Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md
• The test environment setup works and the intended behavior is reproducible in the test environment
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misc/move_files/move_files.py

@@ -62,15 +62,28 @@ def rename(changes, chunksize=10):
             continue
         cont = db.Container()
 
-        for _, (old, new) in chunk.iterrows():
-            cont.append(db.File(path=old))
-
-        cont.retrieve()
-
-        for fi, (_, (old, new)) in zip(cont, chunk.iterrows()):
-            assert fi.path == old
-            fi.path = new
-        cont.update()
+        cmap = {}
+
+        for ii, (old, new) in chunk.iterrows():
+            try:
+                fi = db.File(path=old)
+                fi.retrieve()
+
+                if not fi.is_valid():
+                    continue
+                cont.append(fi)
+                cmap[ii] = len(cont)-1
+            except Exception as e:
+                print(e)
+
+        for ii, (old, new) in chunk.iterrows():
+            if ii not in cmap:
+                continue
+            assert cont[cmap[ii]].path == old
+            cont[cmap[ii]].path = new
+
+        if len(cont) > 0:
+            cont.update(unique=False)
         i += 1