Update Array to respect FSStore's key_separator #718

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Merged
joshmoore merged 5 commits into from
Apr 16, 2021
Merged

Update Array to respect FSStore's key_separator #718

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168bd97
BUG: respect key_separator for FSStore
grlee77 Apr 15, 2021
323b20a
TST: add test case for nested FSStore
grlee77 Apr 15, 2021
c249a58
TST: switch from zarr.open to open_group
grlee77 Apr 15, 2021
bea6b10
TST: avoid FSStore test method duplication
grlee77 Apr 15, 2021
14db70e
skip FSStore tests unless fsspec is available
grlee77 Apr 16, 2021
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6 changes: 5 additions & 1 deletion zarr/core.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
return self._encode_chunk(chunk)

def _chunk_key(self, chunk_coords):
return self._key_prefix + '.'.join(map(str, chunk_coords))
if hasattr(self._store, 'key_separator'):

@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.

@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?

@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.

@d-v-bd-v-bApr 29, 2021•
edited
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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054

separator = self._store.key_separator
else:
separator = '.'
return self._key_prefix + separator.join(map(str, chunk_coords))

def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
# decompress
Expand Down
45 changes: 39 additions & 6 deletions zarr/tests/test_hierarchy.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

@staticmethod
def create_store():
path = tempfile.mkdtemp()
atexit.register(atexit_rmtree, path)
store = FSStore(path)
return store, None

def test_round_trip_nd(self):
data = np.arange(1000).reshape(10, 10, 10)
name = 'raw'

store, _ = self.create_store()
f = open_group(store, mode='w')
f.create_dataset(name, data=data, chunks=(5, 5, 5),
compressor=None)
h = open_group(store, mode='r')
np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

@staticmethod
def create_store():
path = tempfile.mkdtemp()
atexit.register(atexit_rmtree, path)
store = FSStore(path, key_separator='/', auto_mkdir=True)
return store, None


class TestGroupWithZipStore(TestGroup):

@staticmethod
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Update Array to respect FSStore's key_separator #718

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 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update Array to respect FSStore's key_separator #718

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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to your account

 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
Show file tree
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5 commits


Select commit
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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update Array to respect FSStore's key_separator #718

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
Show file tree
Hide file tree
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Commits

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5 commits


Select commit
Hold shift + click to select a range
168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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ContributorAuthor
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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Update Array to respect FSStore's key_separator #718

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 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update Array to respect FSStore's key_separator #718

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 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update Array to respect FSStore's key_separator #718

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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to your account

 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
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5 commits


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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

Copy link


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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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ContributorAuthor
Choose a reason for hiding this comment

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

edited

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
Expand Down

45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Update Array to respect FSStore's key_separator #718

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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 Merged

joshmoore
merged 5 commits into

from

Apr 16, 2021
 Merged


Update Array to respect FSStore's key_separator #718
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5 commits


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168bd97

BUG: respect key_separator for FSStore


grlee77 Apr 15, 2021
323b20a

TST: add test case for nested FSStore


grlee77 Apr 15, 2021
c249a58

TST: switch from zarr.open to open_group


grlee77 Apr 15, 2021
bea6b10

TST: avoid FSStore test method duplication


grlee77 Apr 15, 2021
14db70e

skip FSStore tests unless fsspec is available


grlee77 Apr 16, 2021

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6 changes: 5 additions & 1 deletion
zarr/core.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -1950,7 +1950,11 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 return self._encode_chunk(chunk)

 def _chunk_key(self, chunk_coords):
 return self._key_prefix + '.'.join(map(str, chunk_coords))
 if hasattr(self._store, 'key_separator'):
@joshmoorejoshmooreApr 15, 2021

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A heads up that #716 deprecates key_separator in favor store._dimension_separator. Looking at this usage, I imagine wrapping stores like LRUCacheStore and ConsolidatedMetadataStore are going to need to set `_dimension_separator as well.
@grlee77grlee77Apr 16, 2021

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Okay, thanks for letting me know. Should we hold off on this PR until #716 is in and then revisit?
@joshmoorejoshmooreApr 16, 2021

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Nah, let's get this out as a point release. Just a warning that this "API" will change. It's all kismet.
@d-v-bd-v-bApr 29, 2021•

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The behavior of _chunk_key should not be changed here. Instead, the behavior of FSStore.getitems should be changed to properly remap the keys. See https://github.com/zarr-developers/zarr-python/pull/709/files#diff-565e487a2f60258b6baa2e4db8ef175cc16b8a949651834bd43d0a9f21e07358R1054
 separator = self._store.key_separator
 else:
 separator = '.'
 return self._key_prefix + separator.join(map(str, chunk_coords))

 def _decode_chunk(self, cdata, start=None, nitems=None, expected_shape=None):
 # decompress
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45 changes: 39 additions & 6 deletions
zarr/tests/test_hierarchy.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -21,13 +21,13 @@
from zarr.core import Array
from zarr.creation import open_array
from zarr.hierarchy import Group, group, open_group
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, LMDBStore,
LRUStoreCache, MemoryStore, NestedDirectoryStore,
SQLiteStore, ZipStore, array_meta_key, atexit_rmglob,
atexit_rmtree, group_meta_key, init_array,
 init_group)
from zarr.storage import (ABSStore, DBMStore, DirectoryStore, FSStore,
LMDBStore, LRUStoreCache, MemoryStore,
NestedDirectoryStore, SQLiteStore, ZipStore,
array_meta_key, atexit_rmglob, atexit_rmtree,
group_meta_key, init_array, init_group)
from zarr.util import InfoReporter
from zarr.tests.util import skip_test_env_var
from zarr.tests.util import skip_test_env_var, have_fsspec


# noinspection PyStatementEffect
Expand DownExpand Up@@ -971,6 +971,39 @@ def create_store():
 return store, None


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithFSStore(TestGroup):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path)
 return store, None

 def test_round_trip_nd(self):
 data = np.arange(1000).reshape(10, 10, 10)
 name = 'raw'

 store, _ = self.create_store()
 f = open_group(store, mode='w')
 f.create_dataset(name, data=data, chunks=(5, 5, 5),
 compressor=None)
 h = open_group(store, mode='r')
 np.testing.assert_array_equal(h[name][:], data)


@pytest.mark.skipif(have_fsspec is False, reason="needs fsspec")
class TestGroupWithNestedFSStore(TestGroupWithFSStore):

 @staticmethod
 def create_store():
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = FSStore(path, key_separator='/', auto_mkdir=True)
 return store, None


class TestGroupWithZipStore(TestGroup):

 @staticmethod
Expand Down