removedInput schema / properties / against
Removed value: -{
- "description": "Compare with this second file instead (e.g. an OME-TIFF export of `file`): metadata differences, geometry, channels, physical sizes and per-plane hashes.",
- "type": "string"
-}
addedInput schema / properties / headers_only
Added value: +{
+ "default": false,
+ "description": "Check headers and structure only (offsets, declared sizes and counts, missing parts): no decompression, decoding or checksums over the data.",
+ "type": "boolean"
+}
removedInput schema / properties / ignore
Removed value: -{
- "default": [],
- "description": "against: JSON pointers (into openreadout_info output) to leave out of the metadata diff; `*` matches one segment.",
- "items": {
- "type": "string"
- },
- "type": "array"
-}
removedInput schema / properties / image
Removed value: -{
- "description": "against: only this image index (in both files).",
- "minimum": 0,
- "type": "integer"
-}
removedInput schema / properties / include_text
Removed value: -{
- "default": false,
- "description": "report: keep free text from the file (sample, image and channel names, comments); the path and personal data are still replaced. Default false: only with the user's consent.",
- "type": "boolean"
-}
removedInput schema / properties / no_pixels
Removed value: -{
- "default": false,
- "description": "against: metadata and geometry only, no pixels.",
- "type": "boolean"
-}
removedInput schema / properties / output
Removed value: -{
- "description": "report: also write the bundle to this new local file. Default: only return it.",
- "type": "string"
-}
removedInput schema / properties / report
Removed value: -{
- "default": false,
- "description": "Build a privacy-reviewed diagnostic bundle for the maintainers instead (for a file that is refused, fails, or is not validated).",
- "type": "boolean"
-}
removedInput schema / properties / select
Removed value: -{
- "default": [],
- "description": "against: plane selection strings such as `c=0`, `z=2-5`, `t=0,3`. A second file holding only the selected planes (an export with the same selection) is matched to them in order.",
- "items": {
- "type": "string"
- },
- "type": "array"
-}
removedInput schema / properties / tolerance
Removed value: -{
- "description": "against: largest absolute sample difference that still counts as equal. Default: bit-identical planes (same xxh3-128).",
- "type": "number"
-}
changedOutput schema / $defs / Acquisition / description
Previous value: -"`acquisition` in `info`, `info --view structure`, `check` and `check --planes`: present only for\nfiles that are not finished. See `book/src/guides/lab-shares.md`."New value: +"`acquisition` in `info`, `info --view structure`, `check` and `planes`: present only for\nfiles that are not finished. See `book/src/guides/lab-shares.md`."
removedOutput schema / $defs / CheckReport
Removed value: -{
- "description": "Output of `check`.",
- "properties": {
- "acquisition": {
- "anyOf": [
- {
- "$ref": "#/$defs/Acquisition"
- },
- {
- "type": "null"
- }
- ],
- "description": "Present when the file is not finished: still being written (`in_progress`: findings\nabout the unfinished tail are warnings and `ok` covers the complete part) or stopped\nbefore the end (`interrupted`). See `book/src/guides/lab-shares.md`."
- },
- "assurance": {
- "anyOf": [
- {
- "$ref": "#/$defs/Assurance"
- },
- {
- "type": "null"
- }
- ],
- "description": "Whether the file lies inside what its reader has been validated on (the same block as\n`info` → `assurance`). `ok` says the file is intact; `assurance` says whether its values\ncan be trusted. Filled by the `check` command when the header can be read."
- },
- "checks_performed": {
- "description": "What was verified, in plain words, so the caller knows what \"ok\" covers.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "findings": {
- "description": "Everything found, in the order checked.",
- "items": {
- "$ref": "#/$defs/Finding"
- },
- "type": "array"
- },
- "format": {
- "description": "Format id of the input file.",
- "type": "string"
- },
- "ok": {
- "description": "True when no finding has severity `error`.",
- "type": "boolean"
- },
- "path": {
- "description": "The input file.",
- "type": "string"
- }
- },
- "required": [
- "path",
- "format",
- "ok",
- "checks_performed",
- "findings"
- ],
- "type": "object"
-}
removedOutput schema / $defs / CompareOutput
Removed value: -{
- "description": "Output of `check --against`.",
- "properties": {
- "identical": {
- "description": "Nothing compared differs: metadata (unless skipped), geometry, channel names,\nphysical sizes and planes (within the tolerance). The exit code is 0 when true, 1\nwhen false.",
- "type": "boolean"
- },
- "images": {
- "description": "Geometry, channel-name and physical-size comparison per image index.",
- "items": {
- "$ref": "#/$defs/ImageComparison"
- },
- "type": "array"
- },
- "metadata": {
- "$ref": "#/$defs/MetadataComparison",
- "description": "The normalized-metadata diff."
- },
- "notes": {
- "description": "Caveats (e.g. formats that store different metadata for the same acquisition).",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "ours": {
- "$ref": "#/$defs/CompareSide",
- "description": "The first file."
- },
- "planes": {
- "$ref": "#/$defs/PlaneComparison",
- "description": "The plane-by-plane comparison."
- },
- "theirs": {
- "$ref": "#/$defs/CompareSide",
- "description": "The second file."
- }
- },
- "required": [
- "identical",
- "ours",
- "theirs",
- "metadata",
- "images",
- "planes",
- "notes"
- ],
- "type": "object"
-}
removedOutput schema / $defs / CompareSide
Removed value: -{
- "description": "One file of the pair.",
- "properties": {
- "format": {
- "description": "Its format id.",
- "type": "string"
- },
- "images": {
- "description": "Number of images.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "path": {
- "description": "The file as given.",
- "type": "string"
- },
- "tables": {
- "description": "Number of tables.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "traces": {
- "description": "Number of traces.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "path",
- "format",
- "images",
- "tables",
- "traces"
- ],
- "type": "object"
-}
removedOutput schema / $defs / DetectionSummary
Removed value: -{
- "description": "The reader that claimed the input.",
- "properties": {
- "confidence": {
- "description": "`definite`, `likely` or `extension_only`.",
- "type": "string"
- },
- "format": {
- "description": "Format id.",
- "type": "string"
- },
- "note": {
- "description": "Why the match is less than definite.",
- "type": [
- "string",
- "null"
- ]
- },
- "reader_confidence": {
- "description": "The reader's confidence level (`high`, `medium`, `low`).",
- "type": "string"
- }
- },
- "required": [
- "format",
- "confidence",
- "reader_confidence"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Difference
Removed value: -{
- "description": "A value that differs, at an RFC 6901 JSON pointer into `info --json` `data`.",
- "properties": {
- "ours": {
- "description": "Value in the first file; absent when the first file lacks the field."
- },
- "pointer": {
- "description": "RFC 6901 JSON pointer to the value, e.g. `/images/0/physical_size/x`.",
- "type": "string"
- },
- "theirs": {
- "description": "Value in the second file; absent when the second file lacks the field."
- }
- },
- "required": [
- "pointer"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Generator
Removed value: -{
- "description": "Program name and version.",
- "properties": {
- "name": {
- "description": "`openreadout`.",
- "type": "string"
- },
- "version": {
- "description": "Its version.",
- "type": "string"
- }
- },
- "required": [
- "name",
- "version"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Geometry
Removed value: -{
- "description": "Geometry of one image.",
- "properties": {
- "pixel_type": {
- "$ref": "#/$defs/PixelType",
- "description": "Sample type."
- },
- "samples_per_pixel": {
- "description": "1 for grayscale, 3 for interleaved RGB.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "size_c": {
- "description": "Number of channels.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "size_t": {
- "description": "Number of time points.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "size_x": {
- "description": "Width in pixels.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "size_y": {
- "description": "Height in pixels.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "size_z": {
- "description": "Number of Z planes.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "size_x",
- "size_y",
- "size_z",
- "size_c",
- "size_t",
- "pixel_type",
- "samples_per_pixel"
- ],
- "type": "object"
-}
removedOutput schema / $defs / HexSample
Removed value: -{
- "description": "A hex excerpt.",
- "properties": {
- "at": {
- "description": "`head` or the structure entry (`kind name`).",
- "type": "string"
- },
- "hex": {
- "description": "Space-separated bytes; masked text bytes are `__`.",
- "type": "string"
- },
- "offset": {
- "description": "Byte offset.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "at",
- "offset",
- "hex"
- ],
- "type": "object"
-}
removedOutput schema / $defs / ImageComparison
Removed value: -{
- "description": "One image index present in either file.",
- "properties": {
- "channel_names_equal": {
- "description": "Channel names agree.",
- "type": "boolean"
- },
- "geometry_equal": {
- "description": "Both files have the image and their geometries agree (with `selected`, after the\nselection).",
- "type": "boolean"
- },
- "image": {
- "description": "Image index.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "ours": {
- "anyOf": [
- {
- "$ref": "#/$defs/Geometry"
- },
- {
- "type": "null"
- }
- ],
- "description": "Absent when the first file has no image with this index."
- },
- "ours_channels": {
- "description": "Channel names of the first file (listed only when they differ).",
- "items": {
- "type": [
- "string",
- "null"
- ]
- },
- "type": "array"
- },
- "ours_physical_size": {
- "anyOf": [
- {
- "$ref": "#/$defs/PhysicalSize"
- },
- {
- "type": "null"
- }
- ],
- "description": "Physical pixel size in the first file (listed only when the sizes differ)."
- },
- "physical_size_equal": {
- "description": "Physical sizes agree to a relative 1e-6 (both absent counts as equal).",
- "type": "boolean"
- },
- "selected": {
- "description": "The second file holds only the selected planes of this image (an export made with the\nsame selection): planes, channels and the metadata diff were matched in selection\norder, and `ours` is the geometry after the selection.",
- "type": "boolean"
- },
- "theirs": {
- "anyOf": [
- {
- "$ref": "#/$defs/Geometry"
- },
- {
- "type": "null"
- }
- ],
- "description": "Absent when the second file has no image with this index."
- },
- "theirs_channels": {
- "description": "Channel names of the second file (listed only when they differ).",
- "items": {
- "type": [
- "string",
- "null"
- ]
- },
- "type": "array"
- },
- "theirs_physical_size": {
- "anyOf": [
- {
- "$ref": "#/$defs/PhysicalSize"
- },
- {
- "type": "null"
- }
- ],
- "description": "Physical pixel size in the second file (listed only when the sizes differ)."
- }
- },
- "required": [
- "image",
- "geometry_equal",
- "channel_names_equal",
- "ours_channels",
- "theirs_channels",
- "physical_size_equal"
- ],
- "type": "object"
-}
removedOutput schema / $defs / InputSummary
Removed value: -{
- "description": "The input without its name.",
- "properties": {
- "extension": {
- "description": "Lower-case extension without the dot (`nd2`, `raw`, `d`), when there is one.",
- "type": [
- "string",
- "null"
- ]
- },
- "kind": {
- "description": "`file` or `directory`.",
- "type": "string"
- },
- "member_extensions": {
- "additionalProperties": {
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "description": "Member counts per extension.",
- "type": "object"
- },
- "members": {
- "description": "A directory's members: relative paths with names that are not plain tokens replaced.",
- "items": {
- "$ref": "#/$defs/Member"
- },
- "type": "array"
- },
- "members_omitted": {
- "description": "Members not listed (more than 2000).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "sha256": {
- "description": "SHA-256 of the whole file (files up to 1 GiB).",
- "type": [
- "string",
- "null"
- ]
- },
- "sha256_first_64mib": {
- "description": "SHA-256 of the first 64 MiB (larger files).",
- "type": [
- "string",
- "null"
- ]
- },
- "signature_hex": {
- "description": "The first 16 bytes in hex; printable runs that are not a plain token are masked (`__`).",
- "type": [
- "string",
- "null"
- ]
- },
- "signature_text": {
- "description": "The same bytes as text where they are a plain token (`ZISRAWFILE`, `ABF2`).",
- "type": [
- "string",
- "null"
- ]
- },
- "size_bytes": {
- "description": "Bytes (a directory: the sum over its members).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "text_like": {
- "description": "The file looks like text (a delimited export, XML, JSON).",
- "type": "boolean"
- }
- },
- "required": [
- "kind",
- "size_bytes"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Integrity
Removed value: -{
- "description": "Integrity findings.",
- "properties": {
- "checks_performed": {
- "description": "What was verified.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "findings": {
- "description": "Findings: severity, code, message (scrubbed), offset.",
- "items": true,
- "type": "array"
- },
- "mode": {
- "description": "`headers` (`check --headers-only`) or `full`.",
- "type": "string"
- },
- "ok": {
- "description": "No finding of severity error.",
- "type": "boolean"
- }
- },
- "required": [
- "mode",
- "ok",
- "checks_performed",
- "findings"
- ],
- "type": "object"
-}
removedOutput schema / $defs / KindCount
Removed value: -{
- "description": "Count and bytes of one entry kind.",
- "properties": {
- "bytes": {
- "description": "Their total size, where sizes are known.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "count": {
- "description": "How many.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "kind": {
- "description": "Entry kind.",
- "type": "string"
- }
- },
- "required": [
- "kind",
- "count",
- "bytes"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Member
Removed value: -{
- "description": "One member of a directory data set.",
- "properties": {
- "path": {
- "description": "Path relative to the data set, `/`-separated.",
- "type": "string"
- },
- "size": {
- "description": "Bytes.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "path",
- "size"
- ],
- "type": "object"
-}
removedOutput schema / $defs / MetadataComparison
Removed value: -{
- "description": "The normalized-metadata diff.",
- "properties": {
- "compared": {
- "description": "False with `--no-metadata`.",
- "type": "boolean"
- },
- "difference_count": {
- "description": "Total number of differences (the list holds at most 1000).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "differences": {
- "description": "The differences, at most 1000.",
- "items": {
- "$ref": "#/$defs/Difference"
- },
- "type": "array"
- },
- "equal": {
- "description": "True when no difference was found.",
- "type": "boolean"
- },
- "ignored": {
- "description": "Pointers left out (defaults plus `--ignore`); `extra` objects are also left out unless\n`include_extra`.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "include_extra": {
- "description": "Whether `extra` objects were compared.",
- "type": "boolean"
- }
- },
- "required": [
- "compared",
- "equal",
- "ignored",
- "include_extra",
- "difference_count",
- "differences"
- ],
- "type": "object"
-}
removedOutput schema / $defs / PhysicalSize
Removed value: -{
- "description": "Physical pixel size in micrometres (the OME default unit). Every present value is > 0.",
- "properties": {
- "unit": {
- "description": "Always `µm` in this schema version.",
- "type": "string"
- },
- "x": {
- "description": "Pixel width in µm (the distance between neighbouring columns).",
- "format": "double",
- "type": [
- "number",
- "null"
- ]
- },
- "y": {
- "description": "Pixel height in µm (the distance between neighbouring rows).",
- "format": "double",
- "type": [
- "number",
- "null"
- ]
- },
- "z": {
- "description": "Spacing between Z planes (focal slices) in µm.",
- "format": "double",
- "type": [
- "number",
- "null"
- ]
- }
- },
- "required": [
- "unit"
- ],
- "type": "object"
-}
removedOutput schema / $defs / PixelType
Removed value: -{
- "description": "Sample type of one channel value. Names follow OME-XML `PixelType` values.",
- "oneOf": [
- {
- "const": "int8",
- "description": "Signed 8-bit integer.",
- "type": "string"
- },
- {
- "const": "int16",
- "description": "Signed 16-bit integer.",
- "type": "string"
- },
- {
- "const": "int32",
- "description": "Signed 32-bit integer.",
- "type": "string"
- },
- {
- "const": "uint8",
- "description": "Unsigned 8-bit integer.",
- "type": "string"
- },
- {
- "const": "uint16",
- "description": "Unsigned 16-bit integer (the usual microscope camera output).",
- "type": "string"
- },
- {
- "const": "uint32",
- "description": "Unsigned 32-bit integer.",
- "type": "string"
- },
- {
- "const": "float",
- "description": "32-bit IEEE 754 floating point.",
- "type": "string"
- },
- {
- "const": "double",
- "description": "64-bit IEEE 754 floating point.",
- "type": "string"
- },
- {
- "const": "int64",
- "description": "Signed 64-bit integer.",
- "type": "string"
- },
- {
- "const": "uint64",
- "description": "Unsigned 64-bit integer.",
- "type": "string"
- },
- {
- "const": "complex",
- "description": "Complex number of two 32-bit floats (real, then imaginary): OME `complex`.",
- "type": "string"
- },
- {
- "const": "double-complex",
- "description": "Complex number of two 64-bit floats (real, then imaginary): OME `double-complex`.",
- "type": "string"
- }
- ]
-}
removedOutput schema / $defs / PlaneComparison
Removed value: -{
- "description": "Plane-by-plane comparison.",
- "properties": {
- "compared": {
- "description": "False with `--no-pixels`.",
- "type": "boolean"
- },
- "identical": {
- "description": "Planes with identical xxh3-128.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "mismatched": {
- "description": "Planes that differ beyond the tolerance (or at all, without one).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "mismatches": {
- "description": "At most 1000 entries, in plane order.",
- "items": {
- "$ref": "#/$defs/PlaneMismatch"
- },
- "type": "array"
- },
- "planes": {
- "description": "Planes read from both files.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "skipped_images": {
- "description": "Image indices not compared plane by plane (missing on one side or geometry differs).",
- "items": {
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "type": "array"
- },
- "tolerance": {
- "description": "The `--tolerance` used, if any.",
- "format": "double",
- "type": [
- "number",
- "null"
- ]
- },
- "within_tolerance": {
- "description": "Planes that differ but within the tolerance.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "compared",
- "planes",
- "identical",
- "within_tolerance",
- "mismatched",
- "skipped_images",
- "mismatches"
- ],
- "type": "object"
-}
removedOutput schema / $defs / PlaneMismatch
Removed value: -{
- "description": "A plane that differs.",
- "properties": {
- "c": {
- "description": "Channel index.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "differing_samples": {
- "description": "Samples that differ (absent when the planes' shapes differ).",
- "format": "uint64",
- "minimum": 0,
- "type": [
- "integer",
- "null"
- ]
- },
- "image": {
- "description": "Image index.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "max_abs_diff": {
- "description": "Largest absolute difference between corresponding samples.",
- "format": "double",
- "type": [
- "number",
- "null"
- ]
- },
- "note": {
- "description": "Why the samples could not be compared (e.g. the plane shapes differ).",
- "type": [
- "string",
- "null"
- ]
- },
- "ours_xxh3": {
- "description": "xxh3-128 of the plane in the first file.",
- "type": "string"
- },
- "t": {
- "description": "Time index.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- },
- "theirs_xxh3": {
- "description": "xxh3-128 of the plane in the second file.",
- "type": "string"
- },
- "within_tolerance": {
- "description": "With a tolerance: whether `max_abs_diff` is within it (then the plane counts as equal).",
- "type": "boolean"
- },
- "z": {
- "description": "Z index.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "image",
- "c",
- "z",
- "t",
- "ours_xxh3",
- "theirs_xxh3",
- "within_tolerance"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Privacy
Removed value: -{
- "description": "The privacy statement of a bundle.",
- "properties": {
- "excluded": {
- "description": "What it leaves out.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "included": {
- "description": "What the bundle contains, in plain words.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "mode": {
- "description": "`structure_only` (default) or `with_text` (`--include-text`).",
- "type": "string"
- },
- "personal_data": {
- "description": "Personal-data flags (kind and rule, never the value) found in the metadata.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "redacted_strings": {
- "description": "Distinct strings from the file replaced by `<redacted-N>` or `<text:LEN>` placeholders.",
- "format": "uint32",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "mode",
- "included",
- "excluded",
- "redacted_strings"
- ],
- "type": "object"
-}
removedOutput schema / $defs / Report
Removed value: -{
- "description": "The diagnostic bundle.",
- "properties": {
- "assurance": {
- "anyOf": [
- {
- "$ref": "#/$defs/Assurance"
- },
- {
- "type": "null"
- }
- ],
- "description": "The assurance block (`info` → `assurance`), text scrubbed."
- },
- "candidates": {
- "description": "Readers registered for the input's extension (what the user probably expected).",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "detection": {
- "anyOf": [
- {
- "$ref": "#/$defs/DetectionSummary"
- },
- {
- "type": "null"
- }
- ],
- "description": "The reader that claimed the input, when one did."
- },
- "generator": {
- "$ref": "#/$defs/Generator",
- "description": "The program that wrote it."
- },
- "input": {
- "$ref": "#/$defs/InputSummary",
- "description": "The input, without its name or path."
- },
- "integrity": {
- "anyOf": [
- {
- "$ref": "#/$defs/Integrity"
- },
- {
- "type": "null"
- }
- ],
- "description": "Integrity findings (`check`)."
- },
- "metadata": {
- "description": "The normalized metadata (`info`) with numbers kept and free text replaced."
- },
- "privacy": {
- "$ref": "#/$defs/Privacy",
- "description": "What the bundle contains and leaves out; read before sharing."
- },
- "report_version": {
- "description": "Bundle layout version ([`REPORT_VERSION`]).",
- "type": "string"
- },
- "samples": {
- "description": "Hex excerpts (only with `hex_bytes`).",
- "items": {
- "$ref": "#/$defs/HexSample"
- },
- "type": "array"
- },
- "stages": {
- "description": "The decode path: each stage in order with its result.",
- "items": {
- "$ref": "#/$defs/Stage"
- },
- "type": "array"
- },
- "structure": {
- "anyOf": [
- {
- "$ref": "#/$defs/StructureMap"
- },
- {
- "type": "null"
- }
- ],
- "description": "The container's structure (`info --view structure`)."
- },
- "vendor_keys": {
- "anyOf": [
- {
- "$ref": "#/$defs/VendorKeys"
- },
- {
- "type": "null"
- }
- ],
- "description": "Key skeleton of the vendor metadata tree (`info --view full` → `vendor`): paths and value\ntypes."
- }
- },
- "required": [
- "report_version",
- "generator",
- "privacy",
- "input",
- "stages"
- ],
- "type": "object"
-}
removedOutput schema / $defs / ReportOutput
Removed value: -{
- "description": "What `openreadout check FILE --report` prints under `--json`.",
- "properties": {
- "bytes": {
- "description": "Size of the written bundle.",
- "format": "uint64",
- "minimum": 0,
- "type": [
- "integer",
- "null"
- ]
- },
- "issue_url": {
- "description": "Where to file it (never contacted by the program).",
- "type": "string"
- },
- "output": {
- "description": "Where the bundle was written; `None` with `--dry-run` (or from MCP without `output`).",
- "type": [
- "string",
- "null"
- ]
- },
- "report": {
- "$ref": "#/$defs/Report",
- "description": "The bundle, exactly as written."
- }
- },
- "required": [
- "issue_url",
- "report"
- ],
- "type": "object"
-}
changedOutput schema / $defs / Scope / oneOf
Previous value: -[
- {
- "const": "metadata",
- "description": "The normalized metadata (`info`, all its views): sizes, channels, instrument, times.",
- "type": "string"
- },
- {
- "const": "pixels",
- "description": "Image planes (`check --planes`, `stats`, `export` of images, `preview`).",
- "type": "string"
- },
- {
- "const": "spectra",
- "description": "Mass spectra and scan headers (`spectra`, `analyze chromatogram`, mzML export).",
- "type": "string"
- },
- {
- "const": "traces",
- "description": "Sampled signals (`trace`, electrophysiology, chromatograms, NMR and IR/Raman spectra).",
- "type": "string"
- },
- {
- "const": "tables",
- "description": "Tables (FCS events, plate reads, qPCR results, event and peak tables).",
- "type": "string"
- }
-]New value: +[
+ {
+ "const": "metadata",
+ "description": "The normalized metadata (`info`, all its views): sizes, channels, instrument, times.",
+ "type": "string"
+ },
+ {
+ "const": "pixels",
+ "description": "Image planes (`planes`, `stats`, `export` of images, `preview`).",
+ "type": "string"
+ },
+ {
+ "const": "spectra",
+ "description": "Mass spectra and scan headers (`scans`, `spectrum`, `analyze chromatogram`, mzML export).",
+ "type": "string"
+ },
+ {
+ "const": "traces",
+ "description": "Sampled signals (`trace`, electrophysiology, chromatograms, NMR and IR/Raman spectra).",
+ "type": "string"
+ },
+ {
+ "const": "tables",
+ "description": "Tables (FCS events, plate reads, qPCR results, event and peak tables).",
+ "type": "string"
+ }
+]
removedOutput schema / $defs / Stage
Removed value: -{
- "description": "One stage of the decode path.",
- "properties": {
- "detail": {
- "description": "What the stage found, in a few words (`12 entries`, `plane 512x512 uint16`).",
- "type": [
- "string",
- "null"
- ]
- },
- "elapsed_ms": {
- "description": "Milliseconds the stage took.",
- "format": "uint64",
- "minimum": 0,
- "type": [
- "integer",
- "null"
- ]
- },
- "error": {
- "anyOf": [
- {
- "$ref": "#/$defs/StageError"
- },
- {
- "type": "null"
- }
- ],
- "description": "The error, when the stage failed."
- },
- "stage": {
- "description": "`detect`, `open`, `info`, `assurance`, `ls`, `check`, `vendor`, `first_read`.",
- "type": "string"
- },
- "status": {
- "description": "`ok`, `error`, `skipped` or `panic` (a bug: the reader crashed in this stage).",
- "type": "string"
- }
- },
- "required": [
- "stage",
- "status"
- ],
- "type": "object"
-}
removedOutput schema / $defs / StageError
Removed value: -{
- "description": "An error as the CLI would report it, text scrubbed.",
- "properties": {
- "code": {
- "description": "Stable code (`corrupt_file`, `unsupported_feature`, ...).",
- "type": "string"
- },
- "exit_code": {
- "description": "Process exit code the CLI would return.",
- "format": "int32",
- "type": "integer"
- },
- "hint": {
- "description": "The hint.",
- "type": [
- "string",
- "null"
- ]
- },
- "message": {
- "description": "The message.",
- "type": "string"
- },
- "offset": {
- "description": "Byte offset of the problem, when the reader knows it.",
- "format": "uint64",
- "minimum": 0,
- "type": [
- "integer",
- "null"
- ]
- }
- },
- "required": [
- "code",
- "exit_code",
- "message"
- ],
- "type": "object"
-}
removedOutput schema / $defs / StructureMap
Removed value: -{
- "description": "The container's structure.",
- "properties": {
- "by_kind": {
- "description": "Count and bytes per entry kind.",
- "items": {
- "$ref": "#/$defs/KindCount"
- },
- "type": "array"
- },
- "entries": {
- "description": "The first 400 entries in file order.",
- "items": true,
- "type": "array"
- },
- "entries_total": {
- "description": "Entries `info --view structure` lists.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "entries_total",
- "by_kind",
- "entries"
- ],
- "type": "object"
-}
removedOutput schema / $defs / VendorKeys
Removed value: -{
- "description": "Key skeleton of the vendor tree.",
- "properties": {
- "omitted": {
- "description": "Paths not listed (beyond 3000).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "paths": {
- "description": "`path`, value `type` (`string`, `number`, `bool`, `null`, `object`, `array`), `count`.",
- "items": {
- "$ref": "#/$defs/VendorPath"
- },
- "type": "array"
- },
- "total_paths": {
- "description": "Distinct key paths (array indices folded to `[]`).",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- }
- },
- "required": [
- "total_paths",
- "paths"
- ],
- "type": "object"
-}
removedOutput schema / $defs / VendorPath
Removed value: -{
- "description": "One vendor key path.",
- "properties": {
- "count": {
- "description": "Occurrences.",
- "format": "uint64",
- "minimum": 0,
- "type": "integer"
- },
- "path": {
- "description": "Dotted key path, arrays as `[]`.",
- "type": "string"
- },
- "type": {
- "description": "JSON type of the values (several joined by `|`).",
- "type": "string"
- }
- },
- "required": [
- "path",
- "type",
- "count"
- ],
- "type": "object"
-}
removedOutput schema / anyOf
Removed value: -[
- {
- "$ref": "#/$defs/CheckReport",
- "description": "The integrity check."
- },
- {
- "$ref": "#/$defs/CompareOutput",
- "description": "against: the comparison."
- },
- {
- "$ref": "#/$defs/ReportOutput",
- "description": "report: the diagnostic bundle."
- }
-]
addedOutput schema / properties
Added value: +{
+ "acquisition": {
+ "anyOf": [
+ {
+ "$ref": "#/$defs/Acquisition"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Present when the file is not finished: still being written (`in_progress`: findings\nabout the unfinished tail are warnings and `ok` covers the complete part) or stopped\nbefore the end (`interrupted`). See `book/src/guides/lab-shares.md`."
+ },
+ "assurance": {
+ "anyOf": [
+ {
+ "$ref": "#/$defs/Assurance"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Whether the file lies inside what its reader has been validated on (the same block as\n`info` → `assurance`). `ok` says the file is intact; `assurance` says whether its values\ncan be trusted. Filled by the `check` command when the header can be read."
+ },
+ "checks_performed": {
+ "description": "What was verified, in plain words, so the caller knows what \"ok\" covers.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "findings": {
+ "description": "Everything found, in the order checked.",
+ "items": {
+ "$ref": "#/$defs/Finding"
+ },
+ "type": "array"
+ },
+ "format": {
+ "description": "Format id of the input file.",
+ "type": "string"
+ },
+ "ok": {
+ "description": "True when no finding has severity `error`.",
+ "type": "boolean"
+ },
+ "path": {
+ "description": "The input file.",
+ "type": "string"
+ }
+}
addedOutput schema / required
Added value: +[
+ "path",
+ "format",
+ "ok",
+ "checks_performed",
+ "findings"
+]
