fix(py,ts,mcp): make validation mean the same thing at every version and in both ports - #687
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fix(py,ts,mcp): make validation mean the same thing at every version and in both ports#687vboussot wants to merge 10 commits into
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📝 WalkthroughWalkthroughThe change makes OMERO and axis metadata parsing tolerant of optional fields, adds version-aware structural validation, propagates validation through HCS image loading, and adds Python and TypeScript regression coverage. ChangesMetadata and parsing
Validation
HCS loading
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: 🔵 Low · up to The direct-validation documentation example omits the document version, so users validating newer metadata could receive v0.4 validation behavior; the PR is otherwise mergeable with this bounded documentation follow-up. Suggested reviewers: Poem
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In `@py/ngff_zarr/parse_metadata.py`:
- Around line 84-93: Update the active assignment in OmeroChannel construction
to preserve the value only when isinstance(active, bool) is true; otherwise set
it to None, avoiding bool(active) coercion while leaving the existing color,
label, and window handling unchanged.
In `@py/ngff_zarr/v06/zarr_metadata.py`:
- Around line 930-943: Update the validate=True structural validation call in
the v0.6 metadata reader to pass declared_version to validate_structural,
ensuring version-specific v0.6 rules are applied when validating array
coordinate systems without space axes.
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mcp/ngff_zarr_mcp/tools.pymcp/tests/test_validate_ome_zarr.pypy/ngff_zarr/hcs.pypy/ngff_zarr/parse_metadata.pypy/ngff_zarr/rfc4_validation.pypy/ngff_zarr/structural_validation.pypy/ngff_zarr/v04/zarr_metadata.pypy/ngff_zarr/v05/zarr_metadata.pypy/ngff_zarr/v06/zarr_metadata.pypy/test/test_hcs_validate_reaches_images.pypy/test/test_model_matches_schema.pypy/test/test_rfc4_schema_is_inert.pypy/test/test_rules_against_schemas.pypy/test/test_validate_is_version_independent.pyts/src/types/zarr_metadata.tsts/src/utils/parse_metadata.tsts/src/utils/structural_validation.tsts/test/compute_omero_test.tsts/test/from_ngff_zarr_test.tsts/test/model_matches_schema_test.tsts/test/omero_channel_chunking_test.tsts/test/omero_test.tsts/test/structural_validation_v06_global_transform_test.ts
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The 0.6 axes schema requires only `name` and declares `longName`, and sets no additionalProperties. Both ports required `type`, modelled no `longName`, and handed the raw dict to a constructor, so a document our own schema calls valid died on `Axis.__init__()`. `type` and `longName` are now optional at 0.6, an axis is built from the fields it declares, and a key this version does not model is dropped with a warning naming it. `type` stays required at 0.4 and 0.5, where those schemas require it. An axis with no type carries no ordering constraint, in both ports. The omero channel list is positional, one entry per index of the `c` axis, so dropping a channel that lacks a `color` or a `window` renumbered every channel after it, silently, on the default read path. Both parsers now return one channel per entry with the fields it carries, `color` and `window` are optional, and `Omero.version` and `OmeroChannel.active` are read rather than lost on a round trip. A channel with no color passes the color-format rule: whether the field may be absent is the schema's decision. Ref fideus-labs#667.
The 0.6 reader ran the schema pass alone, so a store whose datasets run coarsest to finest was refused at 0.4 and 0.5 and accepted at 0.6: the meaning of the flag followed the version of the store. The 0.6 reader now runs the structural pass after the schema pass, as the 0.4 and 0.5 readers do. The default validate=False path is unchanged. from_hcs_zarr(validate=True) checked the plate and the well metadata and then read every image with a bare from_ome_zarr, so the images themselves were never checked. The flag now reaches them. _intrinsic_system said it mirrors Metadata.intrinsic_coordinate_system, which it does on a well-formed document and not on a malformed one: it answers with the first listed system wherever that property raises. That tolerance is what lets a malformed document reach the validator instead of crashing ahead of it, so the docstring says so. Ref fideus-labs#667.
validate_ome_zarr ran one schema pass and demoted its failure to a warning, so an invalid document came back valid=True. It also never ran the structural rules, so a store whose datasets go coarsest to finest passed. Both verdicts are errors now and reach the caller through valid. The import fallback was a silent no-op: without the ngff-zarr[validate] extra every store was declared valid on the strength of a check that never ran. It now says the schema pass did not run.
The extra field is documented as carried across version conversion. It is not: to_version starts the converted metadata with an empty extra, which test_clean_roundtrip_read_has_empty_extra already pins. The namespacing rules that read it run inside the parser of the version that captured it, before any conversion. The RFC 4 orientation schema reports nothing. Its root is an open object with every definition parked in $defs and no $ref reaching them, so an axis list of strings, an axes value that is not a list, and an orientation whose type and value are nonsense all pass. Upstream ome/ngff#585 and fideus-labs#586 describe the same two defects. Every rule that fires is the hand-written Python above the call, and test_the_bundled_rfc4_schema_checks_nothing pins that, so those checks are not later removed as redundant with a pass that does not run.
…rinsic axes At v0.6 a multiscale-level coordinateTransformations entry maps between two coordinate systems referenced by name, and spec/0.6/schemas/image.schema requires a name on both its input and its output. Its dimensionality follows those two systems. metadata.axes holds the intrinsic system's axes instead, so a legal document was rejected with scale-length-mismatch. The global arm is skipped when the metadata carries coordinateSystems, which is what the Python port already does by dropping those transforms in _flat_model. Per-dataset transforms do map an array to the intrinsic system, so their arm still runs at every version.
The module docstring claimed the rules state only what a JSON Schema cannot. Three of them overlap a keyword and are kept deliberately: axis-count restates minItems and maxItems and holds the floor at 2 where the 0.6 schema drops it to 1; uniqueItems compares whole axis objects, so it is weaker than axis-names-unique, which refuses two axes sharing a name and differing elsewhere; and no bundled schema constrains the omero channel color format, which 0.6 types as a bare string. test_rules_against_schemas.py measures each claim, so a schema tightened upstream fails there rather than leaving the text false.
validate_structural was called without the version the reader detected. Several rules are gated on it, so a 0.6 array coordinate system and an RFC-3 axis model were both measured against the v0.4 caps and reported as failures the spec does not state. A version ngff-zarr bundles no schema tree for raised a ValueError that the broad handler recorded as a schema failure, so a store at such a version was declared invalid on the strength of a check that never ran. It is reported as a skipped pass, like the missing [validate] extra.
mypy refused two things the CI caught and the local suites do not run: the import fallback rebinds validate_ngff to None, which needs the name annotated as optional, and validate_structural is typed against the v0.4 model while the reader hands back whichever version's model it built. deno fmt splits an import list in the new v0.6 transform test.
bool("false") and bool(1) are True, so coercing the omero channel active
flag made the two ports read the same document differently: the
TypeScript parser keeps the field only when it is a boolean. Python does
the same now.
The v0.6 structural pass ran without the version the reader detected. A
valid v0.6 array coordinate system carries no space axes, so the v0.4
branch of the axis rules refused it.
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Inline comments:
In `@docs/validation/api.md`:
- Around line 47-50: Update the direct-validation example using
validate_structural to pass the document’s version explicitly, and state that
callers must provide version so v0.6 and RFC-3 metadata are validated with the
correct rules instead of the v0.4 defaults.
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The paragraph above says omitting version holds every store to the v0.4 axis caps, and the example that follows omits it. A reader copying it measures v0.6 and RFC-3 metadata against caps their version lifts.
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Closes part of #667. Stacked on #611, which carries the axis model corrections and
axis-names-unique; merge that one first.Six commits, one per defect the issue reports.
The model was stricter than the schema of its own version.
spec/0.6/schemas/axes.schemarequires onlynameand declareslongName, and sets noadditionalProperties.v06.Axisrequiredtype, had nolongName, and received the raw dict unfiltered, so a document the schema calls valid died on a Python constructor.Axis.from_dictnow drops a key the model does not carry and names it in a warning, so a later spec release that adds a property is read rather than refused.OMERO channels were silently dropped.
OmeroWindowrequired all four bounds andOmeroChannelrequiredcolorandwindow, so_parse_omerodiscarded any channel it could not build, on three paths. Sincecompute_omero_from_ngff_imagewrites one channel per index of thecaxis, this library treats the list as positional: dropping one shifts every channel after it onto the wrong plane, with no warning, on the defaultvalidate=Falsepath. The parser now builds one channel per entry, andactiveandversionare carried so a round trip through Python no longer loses them.validate=Truedepended on the store's version. The structural pass ran at 0.4 and 0.5 but not at 0.6, so a 0.6 store whose datasets run coarsest to finest was accepted. It runs at 0.6 now.from_hcs_zarr(validate=True)never reached the images. The flag validated the plate and well metadata, then read every image with a barefrom_ome_zarr(store_path). It is threaded through.The MCP
validate_ome_zarrtool reported an invalid store as valid. A schema failure was demoted to a warning, sovalidstayedTrue, and the structural rules were never run at all. Both verdicts are errors now. The import fallback was a silent no-op that declared every store valid without the[validate]extra; it says the pass did not run.TypeScript measured a v0.6 inter-system transform against the intrinsic axes. At 0.6 a multiscale-level
coordinateTransformationsentry maps between two coordinate systems referenced by name, andimage.schemarequires anameon both itsinputand itsoutput, so its dimensionality follows those two systems rather than the intrinsic axis count. Legal documents were rejected withscale-length-mismatch. The Python port already drops those transforms in_flat_model; TypeScript now matches, with a test per port on the same document.Two docstrings said the opposite of their code. The
extrafield is documented as carried across version conversion;to_versionstarts the converted metadata with an emptyextra, whichtest_clean_roundtrip_read_has_empty_extraalready pins. And the RFC 4 orientation schema reports nothing: its root is an open object with every definition parked in$defsand no$refreaching them, so an axis list of strings, anaxesvalue that is not a list, and an orientation whosetypeandvalueare nonsense all pass. Upstream ome/ngff#585 and #586 describe the same two defects. Every RFC 4 rule that fires is the hand written Python above the call, and a test pins that so those checks are not later removed as redundant with a pass that does not run.Which rules restate a schema keyword. The module docstring claimed the rules state only what a JSON Schema cannot. Three overlap a keyword and are kept deliberately:
axis-countrestatesminItemsandmaxItemsand holds the floor at 2 where the 0.6 schema drops it to 1;uniqueItemscompares whole axis objects, so it is weaker thanaxis-names-unique, which refuses two axes sharing a name and differing elsewhere; and no bundled schema constrains the omero channel color format, which 0.6 types as a bare string.test_rules_against_schemas.pymeasures each claim, so a schema tightened upstream fails there rather than leaving the text false.Not addressed here, and still open in #667:
projectAxis, which is #688.Verified on the branch: Python 1212 passed and 3 skipped, Deno 626 passed, MCP 23 passed, prek clean.
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New Features
Bug Fixes