Add ZEP 8 (URL syntax) draft #48

jbms · 2023-09-10T04:45:55Z

No description provided.

jbms · 2023-09-10T04:46:20Z

@normanrz Please take a look.

jbms · 2023-09-10T05:43:01Z

@MSanKeys963 Looks like there is an issue with the docs build that is unrelated to this PR.

jbms · 2023-09-10T05:44:51Z

@martindurant Would appreciate your perspective on this --- I imagine you might say that we should just use fsspec syntax instead, though.

martindurant · 2023-09-10T13:16:08Z

Well indeed, I could say "why invent another"; although translating between | and :: syntax ought to be straight forward. fsspec also cares about fs parameters that might be embedded in URLs and wildcards for globbing.

normanrz · 2023-09-22T12:22:39Z

While standardizing a URL scheme has benefits on its own, I think the main benefit/motivation for this ZEP is the formalization of Zip stores. Essentially, to comply with this ZEP, implementations need to implement zip stores. Maybe that should be written out more explicitly?

jbms · 2023-09-22T23:24:16Z

While standardizing a URL scheme has benefits on its own, I think the main benefit/motivation for this ZEP is the formalization of Zip stores. Essentially, to comply with this ZEP, implementations need to implement zip stores. Maybe that should be written out more explicitly?

While this ZEP was prompted by our discussion about zip stores, my intention was that we standardize on the syntax for various protocols, but that implementations would choose which ones to support.

I think we could also push implementations to support zip format, but I'm not sure I want to tie that to this URL syntax proposal.

normanrz · 2023-09-26T07:11:21Z

@ap-- I think this might also be interesting for upath to implement.

normanrz · 2023-09-28T18:08:15Z

@bogovicj this might also be relevant for your OME transformations proposal.

sanketverma1704 · 2023-10-25T23:53:16Z

@MSanKeys963 Looks like there is an issue with the docs build that is unrelated to this PR.

@jbms: I have added #51 to fix the RTD build. Can you please update your PR?
(Seems like I'm unable to update your PR)

draft/ZEP0008.md

bogovicj · 2023-11-14T13:52:53Z

Thanks @jbms for putting this together! There are a few situations I came up with for which I'm not sure what the
relative URL should be

What does it look like to use ..: to "go up" multiple levels?
Is this correct / valid?

Is it correct / valid to use .. in the "path part" of relative URL, after a ..:?

Base URL: gs://bucket/0/a/i.zarr|zarr3:foo
Relative URL: ..:../b/i.zarr|zarr3:foo
Resolved URL: gs://bucket/0/b/i.zarr|zarr3:foo

If one needs to add an adapter in a relative way, how does one go about it?
For example:

Base URL: gs://bucket/0/a/i.zarr
Desired Resolved URL: gs://bucket/0/a/i.zarr|zarr3:foo

Which, if any, of these do you think should be used? Are any of these invalid?

.|zarr3:foo (clearest to me)
|zarr3:foo
zarr3:foo

bogovicj · 2023-11-14T15:20:49Z

One more thing:

We've found it useful to be able to reference a particular part of the attributes stored in json
with a URL. For example, for

this zarr3 zarr.json

{
    "zarr_format": 3,
    "node_type": "array",
    "shape": [10000, 1000],
    "dimension_names": ["rows", "columns"],
    "data_type": "float64",
    "chunk_grid": {
        "name": "regular",
        "configuration": {
            "chunk_shape": [1000, 100]
        }
    },
    "chunk_key_encoding": {
        "name": "default",
        "configuration": {
            "separator": "/"
        }
    },
    "codecs": [{
        "name": "gzip",
        "configuration": {
            "level": 1
        }
    }],
    "fill_value": "NaN",
    "attributes": {
        "foo": 42,
        "bar": "apples",
        "baz": [1, 2, 3, 4]
    }
}

/attributes/baz[0] points to 1
/shape points to [10000, 1000]
/chunk_grid/configuration points to { "chunk_shape": [1000, 100] }

Could you envision adding an attributes: or zarr.json:, or similar adapter, that enaables this?

For example: gs://bucket/0.zip|zip:a|zarr3:i|zarr.json:attributes/foo

A specific use case: I often re-use and reference transformations. Since these are described by metadata (not arrays),
and so referencing the specific metadata is helpful.

For example, if this were adopted, something like this would not uncommon in my workflows:

{
    "type" : "sequence",
    "transformations" : [
        { "url" : "..:/localTransformations|zarr.json:/transform[1]" },
        { "url" : "gs://bucket/path/to/templateTransformation.zarr|zarr3:sharedTransforms|zarr.json:/transform[0]" },
    ]
}

jbms · 2023-11-14T23:14:41Z

On Tue, Nov 14, 2023, 05:53 John Bogovic ***@***.***> wrote: Thanks @jbms <https://github.com/jbms> for putting this together! There are a few situations I came up with for which I'm not sure what the relative URL should be What does it look like to use ..: to "go up" multiple levels? Is this correct / valid? Base URL: gs://bucket/0.zip|zip:a|zarr3:i Relative URL: ..:..:1.zip|zip:b|zarr3:ii Resolved URL: gs://bucket/1.zip|zip:b|zarr3:ii

Is it correct / valid to use .. in the "path part" of relative URL, after a ..:? Base URL: gs://bucket/0/a/i.zarr|zarr3:foo Relative URL: ..:../b/i.zarr|zarr3:foo Resolved URL: gs://bucket/0/b/i.zarr|zarr3:foo If one needs to add an adapter in a relative way, how does one go about it? For example: Base URL: gs://bucket/0/a/i.zarr Desired Resolved URL: gs://bucket/0/a/i.zarr|zarr3:foo` Which, if any, of these do you think should be used? Are any of these invalid? - .|zarr3:foo (clearest to me) - |zarr3:foo - zarr3:foo

I was imagining `|zarr3:foo` The existing standard interpretation of a relative url of `.` means to strip everything after the last slash, and we should be consistent with that. Therefore if the base url were specified as `gs://bucket/0/a/i.zarr/` then `.|zarr3:foo` would also be valid, but probably should not be preferred.

…

— Reply to this email directly, view it on GitHub <#48 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAEJ2TUR5G466LQFB4DE63YENZUBAVCNFSM6AAAAAA4R5AJVCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJQGI2DIMZQG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

jbms · 2023-11-15T05:29:35Z

On Tue, Nov 14, 2023, 07:21 John Bogovic ***@***.***> wrote: One more thing: We've found it useful to be able to reference a particular part of the attributes stored in json with a URL. For example, for this zarr3 zarr.json { "zarr_format": 3, "node_type": "array", "shape": [10000, 1000], "dimension_names": ["rows", "columns"], "data_type": "float64", "chunk_grid": { "name": "regular", "configuration": { "chunk_shape": [1000, 100] } }, "chunk_key_encoding": { "name": "default", "configuration": { "separator": "/" } }, "codecs": [{ "name": "gzip", "configuration": { "level": 1 } }], "fill_value": "NaN", "attributes": { "foo": 42, "bar": "apples", "baz": [1, 2, 3, 4] } } - /attributes/baz[0] points to 1 - /shape points to [10000, 1000] - /chunk_grid/configuration points to { "chunk_shape": [1000, 100] } Could you envision adding an attributes: or zarr.json:, or similar adapter, that enaables this?

Yes, having a scheme for accessing an attribute sounds like a good idea. One option would be a specific scheme for zarr attributes, like zarr3a, e.g: "gs://bucket/0.zip|zip:a|zarr3:i|zarr3a:/foo" or "gs://bucket/0.zip|zip:a/i|zarr3a:/foo" Another option would be a json scheme for accessing any json file, e.g.: "gs://bucket/0.zip|zip:a|zarr3:i/zarr.json|json:/attributes/foo" Then there is the question of what syntax to use for specifying the path within the json document. A natural choice would be the existing json pointer syntax (https://datatracker.ietf.org/doc/html/rfc6901), e.g. "/transform/1". The json pointer syntax does use an unusual escaping syntax for handling member names containing "/": for example, if you have an object like: {"foo/bar": 10. "foo~bar": 11} then to access the 10 value you use a json pointer of "/foo~1bar", and to access the 11 value you use a json pointer of "/foo~0bar". In my opinion this escaping mechanism is rather unfortunate since it is easy to forget the meaning of "~0" and "~1", but it isn't an issue if you can avoid using "/" or "~" in member names.

…

For example: gs://bucket/0.zip|zip:a|zarr3:i|zarr.json:attributes/foo A specific use case: I often re-use and reference transformations. Since these are described by metadata (not arrays), and so referencing the specific metadata is helpful. For example, if this were adopted, something like this would not uncommon in my workflows: { "type" : "sequence", "transformations" : [ { "url" : "..:/localTransformations|zarr.json:/transform[1]" }, { "url" : "gs://bucket/path/to/templateTransformation.zarr|zarr3:sharedTransforms|zarr.json:/transform[0]" }, ] } — Reply to this email directly, view it on GitHub <#48 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAEJ2TAPT5G4BH5TRGA2TDYEOD5ZAVCNFSM6AAAAAA4R5AJVCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJQGQ2DCMZYGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

draft/ZEP0008.md

- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

sanketverma1704 · 2025-01-22T19:22:48Z

From today's Zarr community meeting, @jbms has implemented this ZEP in Neuroglancer. Check here: google/neuroglancer#696

draft/ZEP0008.md

This is in line with zarr-developers/zeps#48 and the syntax supported by Neuroglancer. Currently, zip is supported. OCDBT support will be added in a subsequent commit. PiperOrigin-RevId: 755691199 Change-Id: Ia6cb84c12a986a7dd0ba65e41454fbe6d415aed0

joshmoore · 2025-08-07T09:29:46Z

@jbms: I tried pushing a merge of origin to try fixing the build, but was rejected. Could you give it a try?

ianhi

I just did a thorough read of this to understand it and I have left some comments with a few typo fixes.

I also left comments on parts that took me a decent bit of work to understand, or that I don't fully understand in the hope that it's a helpful perspective. I'd rate myself as a competent but not expert reader of a document like this

draft/ZEP0008.md

Co-authored-by: Davis Bennett <[email protected]>

Co-authored-by: Sanket Verma <[email protected]> Co-authored-by: Ian Hunt-Isaak <[email protected]> Co-authored-by: Joe Hamman <[email protected]>

jbms · 2025-09-26T03:54:20Z

I just did a thorough read of this to understand it and I have left some comments with a few typo fixes.

I also left comments on parts that took me a decent bit of work to understand, or that I don't fully understand in the hope that it's a helpful perspective. I'd rate myself as a competent but not expert reader of a document like this

Thanks very much for your review. Based on your comments I made some significant revisions and would appreciate feedback.

Based on my revisions it occurs to me that this may be better as an independent standard, and the zarr spec could just recommend that implementations support it.

ianhi

Thank you for the updates, I found it significantly easier to understand on this close reading. I've left a few more comments on the few remaining areas where I found myself confused.

ianhi · 2025-10-09T15:58:22Z

draft/ZEP0008.md

+- `dataset`: An array, group, or other dataset with a defined format
+  e.g. a zarr array or group.


I still struggled a bit here with the general defintion of "dataset". Is there a convention here that I'm missing. I understand zarr array or group, and when i hear dataset my brain jumps to the xarray dataset.

This definition is referred to multiple times below so any further clarification here would be helpful.

ianhi · 2025-10-09T16:01:16Z

draft/ZEP0008.md

+    A zarr attribute may be defined that specifies the location of some other
+    related array using the relative URL pipeline syntax.
+
+    The referencing array may be located at
+    `s3://bucket/path/to/dataset.zip|zip:path/within/zip/|zarr3:`.  Using only a
+    relative path, it could specify the path of another array within
+    `s3://bucket/path/to/dataset.zip:zip:`, e.g. the relative path
+    `../another/array/` would refer to
+    `s3://bucket/path/to/dataset.zip|zip:path/another/array/`.  To refer to
+    `s3://bucket/path/of/another.zip|zip:other/array/`, the relative URL
+    pipeline `..:../of/another.zip|zip:other/array/|zarr3:` can be used.


The indentation here is conflicting with the backtick formatting. (at least on github)

ianhi · 2025-10-09T16:01:32Z

draft/ZEP0008.md

+    The referencing array may be located at
+    `s3://bucket/path/to/dataset.zip|zip:path/within/zip/|zarr3:`.  Using only a
+    relative path, it could specify the path of another array within
+    `s3://bucket/path/to/dataset.zip:zip:`, e.g. the relative path


Suggested change

`s3://bucket/path/to/dataset.zip:zip:`, e.g. the relative path

`s3://bucket/path/to/dataset.zip|zip:`, e.g. the relative path

I think?

ianhi · 2025-10-09T16:04:41Z

draft/ZEP0008.md

+
+  - `gs://bucket/path/to/data|byte-range:1000-2000`
+
+- `tiff:`, `jpeg:`, `png:`, `bmp:`, `avif:`, `webp:`


For both these and byte-range, I don't know how something like zarr-python is meant to handle this. Surely zarr can't be responsible for reading different image formats?

This feels like it gets to your point:

Based on my revisions it occurs to me that this may be better as an independent standard,

ianhi · 2025-10-09T16:07:12Z

draft/ZEP0008.md

+
+  The following syntaxes are supported:
+
+  - `icechunk:path/to/node/`


I think this is implicitly specifying relative to HEAD on a default branch. Is that the intent? I think we can be more explicit that this points to the latest commit on main which is created by default

ianhi · 2025-10-09T16:07:19Z

draft/ZEP0008.md

+
+- `icechunk:` for [Icechunk](https://icechunk.io/en/latest/)
+
+  The base URL msut refer to a `directory` resource (which is expected


Suggested change

The base URL msut refer to a `directory` resource (which is expected

The base URL must refer to a `directory` resource (which is expected

ianhi · 2025-10-09T16:08:46Z

draft/ZEP0008.md

+  For the purpose of relative URLs, the path component does not include the
+  `@version/` prefix if present.


Suggested change

For the purpose of relative URLs, the path component does not include the

`@version/` prefix if present.

For the purpose of relative URLs, the path component does not include the

`@version/` prefix if present in the base URL.

?

ianhi · 2025-10-09T16:21:09Z

draft/ZEP0008.md

+Note: An `absolute_path` overrides any existing *path* component of the
+inner-most sub-URL of the base , but is still relative to the scheme and other
+components of the inner-most sub-URL of the base URL pipeline that precede its
+path component, if any.  The specific scheme of the sub-URL defines what
+portion, if any, constitutes the path component.


An example of an absolute_path would be very helpful. I don't fully understand how the scheme and other components collapse without hte path.

small typo fix:

Suggested change

Note: An `absolute_path` overrides any existing *path* component of the

inner-most sub-URL of the base , but is still relative to the scheme and other

components of the inner-most sub-URL of the base URL pipeline that precede its

path component, if any. The specific scheme of the sub-URL defines what

portion, if any, constitutes the path component.

Note: An `absolute_path` overrides any existing *path* component of the

inner-most sub-URL of the base, but is still relative to the scheme and other

components of the inner-most sub-URL of the base URL pipeline that precede its

path component, if any. The specific scheme of the sub-URL defines what

portion, if any, constitutes the path component.

ianhi · 2025-10-09T16:22:24Z

draft/ZEP0008.md

+The use of outer-to-inner order for the sub-URLs enables completion of both
+paths and sub-URL schemes as the user types.


I found this very compelling as a reason

ianhi · 2025-10-09T16:23:55Z

draft/ZEP0008.md

+
+  If passed a URL that resolves to a `dataset` resource, returns an error.
+
+- `open_file`: opens a file from a URL


Is this the use case for byte-range and tiff? Would I use zarr.open_file("s3:/some/path/image.tiff") to get a file handle on that tiff that I could then pass to tifffile?

ap-- mentioned this pull request Sep 30, 2023

fsspec URL chaining fsspec/universal_pathlib#28

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Manifest storage transformer zarr-developers/zarr-specs#287

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Zarr extension for stacked / concatenated virtual views zarr-developers/zarr-specs#288

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feature(stores): draft zip file store specification zarr-developers/zarr-specs#311

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Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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Revamp file-based data access google/neuroglancer#696

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 17, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 17, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 17, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 18, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 18, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

jbms added a commit to google/neuroglancer that referenced this pull request Jan 19, 2025

Revamp file-based data access

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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- New datasource URL syntax based on ZEP 8 proposal (zarr-developers/zeps#48) - Support for ZIP archives

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Support ZEP 8 URL Syntax zarr-developers/zarr-python#2943

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Tracking issue for Zarr spec, ZEPs, and extensions support zarrs/zarrs#191

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feat: Implement ZEP 8 URL syntax support for zarr-python zarr-developers/zarr-python#3369

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Add ZEP 8 draft

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Co-authored-by: Davis Bennett <[email protected]>

Apply suggestions from code review

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Co-authored-by: Sanket Verma <[email protected]> Co-authored-by: Ian Hunt-Isaak <[email protected]> Co-authored-by: Joe Hamman <[email protected]>

Add comparison to GDAL and correct typos

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TomNicholas mentioned this pull request Oct 17, 2025

Icechunk support? EarthyScience/Browzarr#379

Closed

		- `dataset`: An array, group, or other dataset with a defined format
		e.g. a zarr array or group.

	`s3://bucket/path/to/dataset.zip:zip:`, e.g. the relative path
	`s3://bucket/path/to/dataset.zip\|zip:`, e.g. the relative path


		- `gs://bucket/path/to/data\|byte-range:1000-2000`

		- `tiff:`, `jpeg:`, `png:`, `bmp:`, `avif:`, `webp:`


		The following syntaxes are supported:

		- `icechunk:path/to/node/`


		- `icechunk:` for [Icechunk](https://icechunk.io/en/latest/)

		The base URL msut refer to a `directory` resource (which is expected

	The base URL msut refer to a `directory` resource (which is expected
	The base URL must refer to a `directory` resource (which is expected

		For the purpose of relative URLs, the path component does not include the
		`@version/` prefix if present.

		The use of outer-to-inner order for the sub-URLs enables completion of both
		paths and sub-URL schemes as the user types.


		If passed a URL that resolves to a `dataset` resource, returns an error.

		- `open_file`: opens a file from a URL

Add ZEP 8 (URL syntax) draft #48

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