{
"$comment": "The normative diagnostic code table (spec 1.0 \u00a715.2, extended by 1.1 \u00a711.2). The single source: the engine embeds it, the validator, conformance corpus and documentation all read it. Codes are stable API: a meaning never changes and a retired code is never reused. Each code names the version whose rules it reports (`since`) and the revision of the table that allocated it (`revision`); `revision` at the top is the table's own, the latest any code names (1.0 \u00a715.2).",
"revision": 2,
"codes": [
{
"code": "E001",
"severity": "error",
"domain": "container",
"summary": "missing or empty `medh5_version`, or the file or an object a check must read cannot be read",
"since": "1.0",
"revision": 1
},
{
"code": "E002",
"severity": "error",
"domain": "container",
"summary": "unsupported major version",
"since": "1.0",
"revision": 1
},
{
"code": "E003",
"severity": "error",
"domain": "container",
"summary": "identifier does not match its syntax: [A-Za-z0-9_.-]{1,128} and not `meta`, or [A-Za-z0-9_.-]{1,255} for a collection's sample key",
"since": "1.0",
"revision": 1
},
{
"code": "E004",
"severity": "error",
"domain": "container",
"summary": "`meta` is absent, is not a dataset holding one string, or is not valid UTF-8 JSON",
"since": "1.0",
"revision": 1
},
{
"code": "E005",
"severity": "error",
"domain": "container",
"summary": "`meta` fails the sample-document JSON Schema",
"since": "1.0",
"revision": 1
},
{
"code": "E006",
"severity": "error",
"domain": "container",
"summary": "missing or unknown `medh5_kind`",
"since": "1.0",
"revision": 1
},
{
"code": "E007",
"severity": "error",
"domain": "container",
"summary": "missing `medh5_profiles`, or an unknown profile",
"since": "1.0",
"revision": 1
},
{
"code": "E008",
"severity": "error",
"domain": "container",
"summary": "a group required by the layout is absent (`grids`, `images`, a collection's `samples`), a group the layout defines is not a group, or a collection holds no sample root",
"since": "1.0",
"revision": 1
},
{
"code": "E009",
"severity": "error",
"domain": "container",
"summary": "declared profile's requirements are not met",
"since": "1.0",
"revision": 1
},
{
"code": "E010",
"severity": "error",
"domain": "container",
"summary": "sample root in a `collection` lacks its own `content_id`",
"since": "1.0",
"revision": 1
},
{
"code": "E011",
"severity": "error",
"domain": "container",
"summary": "a collection's `medh5_version` is lower than a member's",
"since": "1.1",
"revision": 1
},
{
"code": "E101",
"severity": "error",
"domain": "geometry",
"summary": "referenced grid does not exist",
"since": "1.0",
"revision": 1
},
{
"code": "E102",
"severity": "error",
"domain": "geometry",
"summary": "`direction` is not orthonormal to 1e-4",
"since": "1.0",
"revision": 1
},
{
"code": "E103",
"severity": "error",
"domain": "geometry",
"summary": "spatial axes are not contiguous and trailing",
"since": "1.0",
"revision": 1
},
{
"code": "E104",
"severity": "error",
"domain": "geometry",
"summary": "`spacing` is not finite and strictly positive",
"since": "1.0",
"revision": 1
},
{
"code": "E105",
"severity": "error",
"domain": "geometry",
"summary": "a multiscale image's levels are malformed (`levels`, `grid_levels` or `downsample_factors` missing or inconsistent, a level dataset missing), or a level's geometry is inconsistent with level 0",
"since": "1.0",
"revision": 1
},
{
"code": "E106",
"severity": "error",
"domain": "geometry",
"summary": "grid has no `timepoint` in a multi-timepoint sample",
"since": "1.0",
"revision": 1
},
{
"code": "E107",
"severity": "error",
"domain": "geometry",
"summary": "grid `timepoint` names an undeclared timepoint",
"since": "1.0",
"revision": 1
},
{
"code": "E108",
"severity": "error",
"domain": "geometry",
"summary": "`timepoints` is empty, an `id` repeats, or `index` is not dense/increasing",
"since": "1.0",
"revision": 1
},
{
"code": "E109",
"severity": "error",
"domain": "geometry",
"summary": "a grid is not a group, or a grid attribute is missing where required, malformed or the wrong size (including a non-positive or uncountable `shape`, a non-finite `origin` and a non-positive `chunk_hint`), or `units`/`time_units` is outside its vocabulary",
"since": "1.0",
"revision": 1
},
{
"code": "E110",
"severity": "error",
"domain": "geometry",
"summary": "`axis_kinds` is invalid for the declared dimensionality",
"since": "1.0",
"revision": 1
},
{
"code": "E111",
"severity": "error",
"domain": "geometry",
"summary": "`grids` contains no grid",
"since": "1.0",
"revision": 1
},
{
"code": "E201",
"severity": "error",
"domain": "images",
"summary": "`images` contains no image",
"since": "1.0",
"revision": 1
},
{
"code": "E202",
"severity": "error",
"domain": "images",
"summary": "image shape does not equal its grid's `shape`",
"since": "1.0",
"revision": 1
},
{
"code": "E203",
"severity": "error",
"domain": "images",
"summary": "unknown `value_type`",
"since": "1.0",
"revision": 1
},
{
"code": "E204",
"severity": "error",
"domain": "images",
"summary": "`channel_names` length does not match the channel extent",
"since": "1.0",
"revision": 1
},
{
"code": "E205",
"severity": "error",
"domain": "images",
"summary": "required image attribute is missing",
"since": "1.0",
"revision": 1
},
{
"code": "E301",
"severity": "error",
"domain": "labels",
"summary": "a declared profile requires a label set and none is present",
"since": "1.0",
"revision": 1
},
{
"code": "E302",
"severity": "error",
"domain": "labels",
"summary": "duplicate class id or key in the label set",
"since": "1.0",
"revision": 1
},
{
"code": "E303",
"severity": "error",
"domain": "labels",
"summary": "a reserved class id (0 or 65535) was assigned to a class",
"since": "1.0",
"revision": 1
},
{
"code": "E304",
"severity": "error",
"domain": "labels",
"summary": "the class hierarchy contains a cycle",
"since": "1.0",
"revision": 1
},
{
"code": "E305",
"severity": "error",
"domain": "labels",
"summary": "`form: ref` label set lacks `uri`/`sha256`, or is unresolvable",
"since": "1.0",
"revision": 1
},
{
"code": "E306",
"severity": "error",
"domain": "labels",
"summary": "a class entry is missing a required field, has an id out of range or names an unknown parent, or a relation names a class the label set does not hold",
"since": "1.0",
"revision": 1
},
{
"code": "E401",
"severity": "error",
"domain": "annotations",
"summary": "unknown annotation `kind`",
"since": "1.0",
"revision": 1
},
{
"code": "E402",
"severity": "error",
"domain": "annotations",
"summary": "class id is not present in the label set",
"since": "1.0",
"revision": 1
},
{
"code": "E403",
"severity": "error",
"domain": "annotations",
"summary": "`annotated_class_ids` is not a subset of `class_ids`",
"since": "1.0",
"revision": 1
},
{
"code": "E404",
"severity": "error",
"domain": "annotations",
"summary": "encoding invariant violated",
"since": "1.0",
"revision": 1
},
{
"code": "E405",
"severity": "error",
"domain": "annotations",
"summary": "dataset shape is inconsistent with the grid or with the annotation's other datasets, or mesh `faces` index outside its `vertices`",
"since": "1.0",
"revision": 1
},
{
"code": "E406",
"severity": "error",
"domain": "annotations",
"summary": "box `lo` exceeds `hi`, or a box bound is not finite",
"since": "1.0",
"revision": 1
},
{
"code": "E407",
"severity": "error",
"domain": "annotations",
"summary": "`rotations` is not a proper rotation matrix",
"since": "1.0",
"revision": 1
},
{
"code": "E408",
"severity": "error",
"domain": "annotations",
"summary": "offsets decrease or do not delimit their data: an `instances` object's span in `mask_data` is not its packed crop's size or runs past its end, contour or mesh offsets do not end at the number of vertices or faces they index, or polyline offsets do not start at 0 and end at the number of vertices",
"since": "1.0",
"revision": 1
},
{
"code": "E409",
"severity": "error",
"domain": "annotations",
"summary": "`timepoints` references an undeclared timepoint",
"since": "1.0",
"revision": 1
},
{
"code": "E410",
"severity": "error",
"domain": "annotations",
"summary": "a dataset required by the annotation `kind` is absent",
"since": "1.0",
"revision": 1
},
{
"code": "E411",
"severity": "error",
"domain": "annotations",
"summary": "dataset dtype is not permitted for the annotation `kind`, or a stored value is not one it permits (a `probmap` value outside [0, 1], a keypoint `visibility` other than 0, 1 or 2)",
"since": "1.0",
"revision": 1
},
{
"code": "E412",
"severity": "error",
"domain": "annotations",
"summary": "required annotation attribute is missing, or `task`, `closure`, `space` or `scope` holds an unknown value",
"since": "1.0",
"revision": 1
},
{
"code": "E413",
"severity": "error",
"domain": "annotations",
"summary": "a reference does not resolve, or an ignore or validity mask is not a `mask` on the same grid",
"since": "1.0",
"revision": 1
},
{
"code": "E414",
"severity": "error",
"domain": "annotations",
"summary": "`space` is invalid for the annotation's grid or frame",
"since": "1.0",
"revision": 1
},
{
"code": "E501",
"severity": "error",
"domain": "transforms",
"summary": "composite frame chain is broken",
"since": "1.0",
"revision": 1
},
{
"code": "E502",
"severity": "error",
"domain": "transforms",
"summary": "transform `kind` is missing or unknown, or a transform lacks the frames or parameters its kind requires, maps a frame to itself, or names an unknown `vector_space`",
"since": "1.0",
"revision": 1
},
{
"code": "E503",
"severity": "error",
"domain": "transforms",
"summary": "a displacement field or B-spline control points do not fit their grid: `field_grid`/`cp_grid` is missing or not in `from_frame`, a `field` is not `(S, *spatial)` on its grid, or `control_points` are not `(S, *cp_shape)` on the grid's spatial axes with at least `order + 1` points on each",
"since": "1.0",
"revision": 1
},
{
"code": "E504",
"severity": "error",
"domain": "transforms",
"summary": "affine `matrix` is not `(S+1, S+1)` for the S spatial axes of the grids it relates, holds an entry that is not finite, or its last row is not [0 \u2026 0 1]",
"since": "1.0",
"revision": 1
},
{
"code": "E505",
"severity": "error",
"domain": "transforms",
"summary": "`inverse_id` is not mutually consistent",
"since": "1.0",
"revision": 1
},
{
"code": "E506",
"severity": "error",
"domain": "transforms",
"summary": "`units` missing, or not the units of the grids in its frames",
"since": "1.0",
"revision": 1
},
{
"code": "E601",
"severity": "error",
"domain": "curation",
"summary": "`prov` names an activity that does not exist",
"since": "1.0",
"revision": 1
},
{
"code": "E602",
"severity": "error",
"domain": "curation",
"summary": "`quality` names a record that does not exist",
"since": "1.0",
"revision": 1
},
{
"code": "E603",
"severity": "error",
"domain": "curation",
"summary": "unknown agent or activity type",
"since": "1.0",
"revision": 1
},
{
"code": "E604",
"severity": "error",
"domain": "curation",
"summary": "timestamp is not RFC 3339",
"since": "1.0",
"revision": 1
},
{
"code": "E605",
"severity": "error",
"domain": "curation",
"summary": "activity names an agent that does not exist",
"since": "1.0",
"revision": 1
},
{
"code": "E701",
"severity": "error",
"domain": "integrity",
"summary": "object digest does not match its content",
"since": "1.0",
"revision": 1
},
{
"code": "E702",
"severity": "error",
"domain": "integrity",
"summary": "`content_id` does not match the file, or a dataset carries a `digest` that no line of `content_id` covers",
"since": "1.0",
"revision": 1
},
{
"code": "E703",
"severity": "error",
"domain": "integrity",
"summary": "malformed digest string",
"since": "1.0",
"revision": 1
},
{
"code": "E704",
"severity": "error",
"domain": "integrity",
"summary": "an object `content_id` covers is reached at a path that is not its own",
"since": "1.0",
"revision": 1
},
{
"code": "E801",
"severity": "error",
"domain": "clinical",
"summary": "`clinical/meta` is absent, not a scalar UTF-8 string, not JSON, or not canonical JSON",
"since": "1.1",
"revision": 1
},
{
"code": "E802",
"severity": "error",
"domain": "clinical",
"summary": "`clinical/meta` fails the clinical descriptor schema or its clock rules",
"since": "1.1",
"revision": 1
},
{
"code": "E803",
"severity": "error",
"domain": "clinical",
"summary": "clinical content is present but the `clinical` profile is not declared",
"since": "1.1",
"revision": 1
},
{
"code": "E804",
"severity": "error",
"domain": "clinical",
"summary": "a required clinical table or column is absent, or a member is not one the profile defines",
"since": "1.1",
"revision": 1
},
{
"code": "E805",
"severity": "error",
"domain": "clinical",
"summary": "a clinical column has the wrong dtype, rank or row count",
"since": "1.1",
"revision": 1
},
{
"code": "E806",
"severity": "error",
"domain": "clinical",
"summary": "a packed UTF-8 column's offsets are malformed or a cell is not valid UTF-8",
"since": "1.1",
"revision": 1
},
{
"code": "E807",
"severity": "error",
"domain": "clinical",
"summary": "a validity mask is malformed or misplaced, or a null cell holds a value",
"since": "1.1",
"revision": 1
},
{
"code": "E808",
"severity": "error",
"domain": "clinical",
"summary": "a valid floating-point clinical value is NaN or infinite",
"since": "1.1",
"revision": 1
},
{
"code": "E809",
"severity": "error",
"domain": "clinical",
"summary": "a clinical identifier is empty, malformed or not unique",
"since": "1.1",
"revision": 1
},
{
"code": "E810",
"severity": "error",
"domain": "clinical",
"summary": "an enumerated clinical value is outside its vocabulary",
"since": "1.1",
"revision": 1
},
{
"code": "E811",
"severity": "error",
"domain": "clinical",
"summary": "event time bounds are incomplete, inverted or inconsistent with `temporal_type`",
"since": "1.1",
"revision": 1
},
{
"code": "E812",
"severity": "error",
"domain": "clinical",
"summary": "event value, code, comparator, unit or missing-reason fields are inconsistent",
"since": "1.1",
"revision": 1
},
{
"code": "E813",
"severity": "error",
"domain": "clinical",
"summary": "a clinical reference does not resolve within the sample",
"since": "1.1",
"revision": 1
},
{
"code": "E814",
"severity": "error",
"domain": "clinical",
"summary": "a link's text span, instance annotation or imaging timepoint constraint is violated",
"since": "1.1",
"revision": 1
},
{
"code": "E815",
"severity": "error",
"domain": "clinical",
"summary": "a document is not owned by exactly one `document` event, or a `document` event owns more than one",
"since": "1.1",
"revision": 1
},
{
"code": "E816",
"severity": "error",
"domain": "clinical",
"summary": "a revision chain is broken, branching, cyclic or contradicted by availability",
"since": "1.1",
"revision": 1
},
{
"code": "E817",
"severity": "error",
"domain": "clinical",
"summary": "a lesion assessment lacks its timepoint, its instance link or a permitted value",
"since": "1.1",
"revision": 1
},
{
"code": "E818",
"severity": "error",
"domain": "clinical",
"summary": "a dataset under `clinical/` carries no `digest`",
"since": "1.1",
"revision": 1
},
{
"code": "E819",
"severity": "error",
"domain": "clinical",
"summary": "a clinical object carries an attribute the profile does not define",
"since": "1.1",
"revision": 1
},
{
"code": "W901",
"severity": "warning",
"domain": "integrity",
"summary": "no object digests are present",
"since": "1.0",
"revision": 1
},
{
"code": "W902",
"severity": "warning",
"domain": "container",
"summary": "bulk dataset is unchunked or uncompressed",
"since": "1.0",
"revision": 1
},
{
"code": "W903",
"severity": "warning",
"domain": "curation",
"summary": "no `deidentification` record",
"since": "1.0",
"revision": 1
},
{
"code": "W904",
"severity": "warning",
"domain": "annotations",
"summary": "partial coverage without an ignore region",
"since": "1.0",
"revision": 1
},
{
"code": "W905",
"severity": "warning",
"domain": "integrity",
"summary": "`index/` entry is stale for its source annotation",
"since": "1.0",
"revision": 1
},
{
"code": "W906",
"severity": "warning",
"domain": "curation",
"summary": "conflicting split claims for one `set_id`",
"since": "1.0",
"revision": 1
},
{
"code": "W907",
"severity": "warning",
"domain": "images",
"summary": "float storage where int16 + rescale would be lossless",
"since": "1.0",
"revision": 1
},
{
"code": "W908",
"severity": "warning",
"domain": "annotations",
"summary": "`layers` count is far from the greedy-colouring optimum",
"since": "1.0",
"revision": 1
},
{
"code": "W909",
"severity": "warning",
"domain": "annotations",
"summary": "one `instance_id` carries two different class ids",
"since": "1.0",
"revision": 1
},
{
"code": "W910",
"severity": "warning",
"domain": "geometry",
"summary": "grids in different timepoints share a `frame_uid`",
"since": "1.0",
"revision": 1
},
{
"code": "W911",
"severity": "warning",
"domain": "geometry",
"summary": "multi-timepoint sample has no transform relating timepoints",
"since": "1.0",
"revision": 1
},
{
"code": "W912",
"severity": "warning",
"domain": "labels",
"summary": "class id used by an annotation has no ontology binding",
"since": "1.0",
"revision": 1
},
{
"code": "W913",
"severity": "warning",
"domain": "container",
"summary": "a higher minor version: only the supported projection was validated, or an unsupported item was ignored",
"since": "1.1",
"revision": 1
},
{
"code": "W914",
"severity": "warning",
"domain": "clinical",
"summary": "a numeric clinical value carries no unit",
"since": "1.1",
"revision": 1
},
{
"code": "W915",
"severity": "warning",
"domain": "integrity",
"summary": "a dataset inside an object `content_id` covers carries no `digest`",
"since": "1.0",
"revision": 2
},
{
"code": "W916",
"severity": "warning",
"domain": "annotations",
"summary": "under `implicit` closure, a class asserted absent where an `is_a` descendant is asserted present",
"since": "1.0",
"revision": 2
},
{
"code": "W917",
"severity": "warning",
"domain": "geometry",
"summary": "two grids name one `frame_uid` but differ in dimensionality or `coord_system`",
"since": "1.0",
"revision": 2
},
{
"code": "W918",
"severity": "warning",
"domain": "annotations",
"summary": "a voxel annotation declares `closure = \"implicit\"`",
"since": "1.0",
"revision": 2
},
{
"code": "W919",
"severity": "warning",
"domain": "annotations",
"summary": "a contour's `contour_role` disagrees with its depth among its class's polygons in its plane",
"since": "1.0",
"revision": 2
}
]
}