24. mzPeak file index JSON¶
Describe the JSON format of the file index
Type: object
24.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
files |
array of 24.3.1 file |
Yes | The files described in the index |
metadata |
object |
Yes |
24.2 Property Details¶
files - array of 24.3.1 file (required)
The files described in the index
metadata - object (required)
24.3 Definitions¶
24.3.1 file¶
A single file in the mzPeak archive of a certain type
Type: object
24.3.1.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
name |
string |
Yes | The name of the file, relative to the root of the archive |
entity_type |
string |
Yes | The things being described in one facet or another by this file |
data_kind |
string |
Yes | The facet of the thing being described in this file |
column_mapping |
array of 24.3.2 column_mapping |
A list of Parquet column to controlled vocabulary term mappings | |
parameters |
array of param |
A list of parameters describing the file stored in the mzPeak archive itself | |
checksum |
string |
Yes | The 128 character SHA-512 hex digest of the entire file, excluding any ZIP-related headers or padding, rendered without byte separators and all alphabetic characters lowercase. |
24.3.1.2 Property Details¶
name - string (required)
The name of the file, relative to the root of the archive
entity_type - string (required)
The things being described in one facet or another by this file
Examples: "spectrum", "chromatogram", "other", "proprietary", "wavelength_spectrum"
data_kind - string (required)
The facet of the thing being described in this file
Examples: "data_arrays", "metadata", "peaks", "scans", "precursors", "selected_ions", "products", "other", "proprietary"
column_mapping - array of 24.3.2 column_mapping (optional)
A list of Parquet column to controlled vocabulary term mappings
parameters - array of param (optional)
A list of parameters describing the file stored in the mzPeak archive itself
checksum - string (required)
The 128 character SHA-512 hex digest of the entire file, excluding any ZIP-related headers or padding, rendered without byte separators and all alphabetic characters lowercase.
Examples: "b3350bbd8ff55e3aca1f3e3b0e20da79b8ffcf7a8a0de1dad09b51fc7ad6c01dcd6179e76d7dd06a1a6d7162edd3e2d0be790b2b9bb35b7bd4113952b7fe665d", "44655c4a48320cb90ad366690857543e4882059730f6cc364d6500ff02c1b43b918364bbcae25d99c99c7b4366b0d184a7e2f50fea8632a0d44e90ccff03f46d", "314da0d112ed0cb150b140af703951f5c8ca4a08725c0bcc7bd5b58e9031f707767c3035debb3284e4e53fc1a4fff7592be132bc55394e284132bf223be507c4"
24.3.2 column_mapping¶
A mapping from a Parquet column to a controlled vocabulary term
Type: object
24.3.2.1 Properties¶
| Property | Type | Required | Description |
|---|---|---|---|
name |
string |
Yes | The human-readable term name |
path |
string |
Yes | The path in a Parquet schema for the mapped column delimited at nesting levels by '.', omitting [list, item |
accession |
string or null |
The CURIE for the controlled vocabulary term, or null if no controlled vocabulary term is available. Null may be used to indicate that a column has a human readable name but does not map to a controlled vocabulary term | |
unit |
string or null |
||
term_marker |
boolean |
Whether this column is marks the presence/absence of a specific value-less controlled vocabulary term or subtree. When the column is a string, the value MUST be a CURIE for a child of this mapping's accession. When the column is boolean true when the term is present in the row, false or null otherwise. If this is absent or false, the value of the column should be used verbatim. |
24.3.2.2 Property Details¶
name - string (required)
The human-readable term name
Examples: "ms level", "filter string", "selected ion m/z", "collision energy", "scan window lower limit"
path - string (required)
The path in a Parquet schema for the mapped column delimited at nesting levels by '.', omitting [list, item|element] tokens
Examples: "ms_level", "isolation_window.target_mz", "activation.collision_energy", "scan_windows.scan_window_lower_limit"
accession - string or null (optional)
The CURIE for the controlled vocabulary term, or null if no controlled vocabulary term is available. Null may be used to indicate that a column has a human readable name but does not map to a controlled vocabulary term
unit - string or null (optional)
term_marker - boolean (optional)
Whether this column is marks the presence/absence of a specific value-less controlled vocabulary term or subtree. When the column is a string, the value MUST be a CURIE for a child of this mapping's accession. When the column is boolean true when the term is present in the row, false or null otherwise. If this is absent or false, the value of the column should be used verbatim.