Stateful tests for array/group manipulation (#2189)

* Stateful tests for array/group manipulation

Port over some stateful tests from [Arraylake](https://docs.earthmover.io/).

Co-authored-by: Sebastián Galkin <[email protected]>

* add TODOs

---------

Co-authored-by: Sebastián Galkin <[email protected]>

Author: dcherian

tests/test_store/test_stateful_hierarchy.py

@@ -0,0 +1,223 @@
+import hypothesis.extra.numpy as npst
+import hypothesis.strategies as st
+import pytest
+from hypothesis import assume, note
+from hypothesis.stateful import (
+    RuleBasedStateMachine,
+    Settings,
+    initialize,
+    invariant,
+    precondition,
+    rule,
+    run_state_machine_as_test,
+)
+
+import zarr
+from zarr import Array
+from zarr.abc.store import Store
+from zarr.core.sync import SyncMixin
+from zarr.storage import MemoryStore, ZipStore
+from zarr.testing.strategies import node_names, np_array_and_chunks, numpy_arrays
+
+
+def split_prefix_name(path):
+    split = path.rsplit("/", maxsplit=1)
+    if len(split) > 1:
+        prefix, name = split
+    else:
+        prefix = ""
+        (name,) = split
+    return prefix, name
+
+
+class ZarrHierarchyStateMachine(SyncMixin, RuleBasedStateMachine):
+    """
+    This state machine models operations that modify a zarr store's
+    hierarchy. That is, user actions that modify arrays/groups as well
+    as list operations. It is intended to be used by external stores, and
+    compares their results to a MemoryStore that is assumed to be perfect.
+    """
+
+    def __init__(self, store) -> None:
+        super().__init__()
+
+        self.store = store
+
+        self.model = MemoryStore(mode="w")
+        zarr.group(store=self.model)
+
+        # Track state of the hierarchy, these should contain fully qualified paths
+        self.all_groups = set()
+        self.all_arrays = set()
+
+    @initialize()
+    def init_store(self):
+        # This lets us reuse the fixture provided store.
+        self._sync(self.store.clear())
+        zarr.group(store=self.store)
+
+    def can_add(self, path):
+        return path not in self.all_groups and path not in self.all_arrays
+
+    # -------------------- store operations -----------------------
+    @rule(name=node_names, data=st.data())
+    def add_group(self, name, data):
+        if self.all_groups:
+            parent = data.draw(st.sampled_from(sorted(self.all_groups)), label="Group parent")
+        else:
+            parent = ""
+        path = f"{parent}/{name}".lstrip("/")
+        assume(self.can_add(path))
+        note(f"Adding group: path='{path}'")
+        self.all_groups.add(path)
+        zarr.group(store=self.store, path=path)
+        zarr.group(store=self.model, path=path)
+
+    @rule(
+        data=st.data(),
+        name=node_names,
+        array_and_chunks=np_array_and_chunks(arrays=numpy_arrays(zarr_formats=st.just(3))),
+    )
+    def add_array(self, data, name, array_and_chunks):
+        array, chunks = array_and_chunks
+        fill_value = data.draw(npst.from_dtype(array.dtype))
+        if self.all_groups:
+            parent = data.draw(st.sampled_from(sorted(self.all_groups)), label="Array parent")
+        else:
+            parent = ""
+        # TODO: support creating deeper paths
+        # TODO: support overwriting potentially by just skipping `self.can_add`
+        path = f"{parent}/{name}".lstrip("/")
+        assume(self.can_add(path))
+        note(f"Adding array:  path='{path}'  shape={array.shape}  chunks={chunks}")
+        for store in [self.store, self.model]:
+            zarr.array(array, chunks=chunks, path=path, store=store, fill_value=fill_value)
+        self.all_arrays.add(path)
+
+    # @precondition(lambda self: bool(self.all_groups))
+    # @precondition(lambda self: bool(self.all_arrays))
+    # @rule(data=st.data())
+    # def move_array(self, data):
+    #     array_path = data.draw(st.sampled_from(self.all_arrays), label="Array move source")
+    #     to_group = data.draw(st.sampled_from(self.all_groups), label="Array move destination")
+
+    #     # fixme renaiming to self?
+    #     array_name = os.path.basename(array_path)
+    #     assume(self.model.can_add(to_group, array_name))
+    #     new_path = f"{to_group}/{array_name}".lstrip("/")
+    #     note(f"moving array '{array_path}' -> '{new_path}'")
+    #     self.model.rename(array_path, new_path)
+    #     self.repo.store.rename(array_path, new_path)
+
+    # @precondition(lambda self: len(self.all_groups) >= 2)
+    # @rule(data=st.data())
+    # def move_group(self, data):
+    #     from_group = data.draw(st.sampled_from(self.all_groups), label="Group move source")
+    #     to_group = data.draw(st.sampled_from(self.all_groups), label="Group move destination")
+    #     assume(not to_group.startswith(from_group))
+
+    #     from_group_name = os.path.basename(from_group)
+    #     assume(self.model.can_add(to_group, from_group_name))
+    #     # fixme renaiming to self?
+    #     new_path = f"{to_group}/{from_group_name}".lstrip("/")
+    #     note(f"moving group '{from_group}' -> '{new_path}'")
+    #     self.model.rename(from_group, new_path)
+    #     self.repo.store.rename(from_group, new_path)
+
+    @precondition(lambda self: len(self.all_arrays) >= 1)
+    @rule(data=st.data())
+    def delete_array_using_del(self, data):
+        array_path = data.draw(
+            st.sampled_from(sorted(self.all_arrays)), label="Array deletion target"
+        )
+        prefix, array_name = split_prefix_name(array_path)
+        note(f"Deleting array '{array_path}' ({prefix=!r}, {array_name=!r}) using del")
+        for store in [self.model, self.store]:
+            group = zarr.open_group(path=prefix, store=store)
+            group[array_name]  # check that it exists
+            del group[array_name]
+        self.all_arrays.remove(array_path)
+
+    @precondition(lambda self: len(self.all_groups) >= 2)  # fixme don't delete root
+    @rule(data=st.data())
+    def delete_group_using_del(self, data):
+        group_path = data.draw(
+            st.sampled_from(sorted(self.all_groups)), label="Group deletion target"
+        )
+        prefix, group_name = split_prefix_name(group_path)
+        note(f"Deleting group '{group_path=!r}', {prefix=!r}, {group_name=!r} using delete")
+        members = zarr.open_group(store=self.model, path=group_path).members(max_depth=None)
+        for _, obj in members:
+            if isinstance(obj, Array):
+                self.all_arrays.remove(obj.path)
+            else:
+                self.all_groups.remove(obj.path)
+        for store in [self.store, self.model]:
+            group = zarr.open_group(store=store, path=prefix)
+            group[group_name]  # check that it exists
+            del group[group_name]
+        if group_path != "/":
+            # The root group is always present
+            self.all_groups.remove(group_path)
+
+    # # --------------- assertions -----------------
+    # def check_group_arrays(self, group):
+    #     # note(f"Checking arrays of '{group}'")
+    #     g1 = self.model.get_group(group)
+    #     g2 = zarr.open_group(path=group, mode="r", store=self.repo.store)
+    #     model_arrays = sorted(g1.arrays(), key=itemgetter(0))
+    #     our_arrays = sorted(g2.arrays(), key=itemgetter(0))
+    #     for (n1, a1), (n2, a2) in zip_longest(model_arrays, our_arrays):
+    #         assert n1 == n2
+    #         assert_array_equal(a1, a2)
+
+    # def check_subgroups(self, group_path):
+    #     g1 = self.model.get_group(group_path)
+    #     g2 = zarr.open_group(path=group_path, mode="r", store=self.repo.store)
+    #     g1_children = [name for (name, _) in g1.groups()]
+    #     g2_children = [name for (name, _) in g2.groups()]
+    #     # note(f"Checking {len(g1_children)} subgroups of group '{group_path}'")
+    #     assert g1_children == g2_children
+
+    # def check_list_prefix_from_group(self, group):
+    #     prefix = f"meta/root/{group}"
+    #     model_list = sorted(self.model.list_prefix(prefix))
+    #     al_list = sorted(self.repo.store.list_prefix(prefix))
+    #     # note(f"Checking {len(model_list)} keys under '{prefix}'")
+    #     assert model_list == al_list
+
+    #     prefix = f"data/root/{group}"
+    #     model_list = sorted(self.model.list_prefix(prefix))
+    #     al_list = sorted(self.repo.store.list_prefix(prefix))
+    #     # note(f"Checking {len(model_list)} keys under '{prefix}'")
+    #     assert model_list == al_list
+
+    # @precondition(lambda self: self.model.is_persistent_session())
+    # @rule(data=st.data())
+    # def check_group_path(self, data):
+    #     t0 = time.time()
+    #     group = data.draw(st.sampled_from(self.all_groups))
+    #     self.check_list_prefix_from_group(group)
+    #     self.check_subgroups(group)
+    #     self.check_group_arrays(group)
+    #     t1 = time.time()
+    #     note(f"Checks took {t1 - t0} sec.")
+
+    @invariant()
+    def check_list_prefix_from_root(self):
+        model_list = self._sync_iter(self.model.list_prefix(""))
+        store_list = self._sync_iter(self.store.list_prefix(""))
+        note(f"Checking {len(model_list)} keys")
+        assert sorted(model_list) == sorted(store_list)
+
+
+def test_zarr_hierarchy(sync_store: Store):
+    def mk_test_instance_sync() -> ZarrHierarchyStateMachine:
+        return ZarrHierarchyStateMachine(sync_store)
+
+    if isinstance(sync_store, ZipStore):
+        pytest.skip(reason="ZipStore does not support delete")
+    if isinstance(sync_store, MemoryStore):
+        run_state_machine_as_test(
+            mk_test_instance_sync, settings=Settings(report_multiple_bugs=False)
+        )