API for command line tools¶

pynxtools supports a number of command line applications. This page provides documentation for their current API.

Data conversion¶

Note that simply calling dataconverter defaults to dataconverter convert.

dataconverter¶

Usage:

dataconverter [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
`--help`	boolean	Show this message and exit.	`False`

Subcommands

convert: This command allows you to use the converter functionality of the dataconverter.
generate-template: Generates and prints a template to use for your nxdl.
get-readers: Prints a list of all installed readers.

dataconverter convert¶

This command allows you to use the converter functionality of the dataconverter.

Usage:

dataconverter convert [OPTIONS] [FILES]...

Options:

Name	Type	Description	Default
`--input-file`	text	Deprecated: Please use the positional file arguments instead. The path to the input data file to read. Repeat for more than one file. default=[] This option is required if no '--params-file' is supplied.	`[]`
`--reader`	choice (`example` \| `json_map` \| `json_yml` \| `multi`)	The reader to use. Examples are json_map or readers from a pynxtools plugin. default='json_map' This option is required if no '--params-file' is supplied.	`json_map`
`--nxdl`	text	The name of the NeXus application definition file to use without the extension nxdl.xml. This option is required if no '--params-file' is supplied.	None
`--output`	text	The path to the output NeXus file to be generated. default='output.nxs'	`output.nxs`
`--params-file`	filename	Allows to pass a .yaml file with all the parameters the converter supports.	None
`--append`	boolean	Appends instance data to the given file if the file already exists.Will prevent an overwriting of existent data and adding of new NXentry instances.If True, will skip the validation whatever irrespective if --skip-verify is passed.	`False`
`--ignore-undocumented`	boolean	Ignore all undocumented concepts during validation.	`False`
`--fail`	boolean	Fail conversion and don't create an output file if the validation fails.	`False`
`--skip-verify`	boolean	Skips the verification routine during conversion.When --append is used the verification is always skippedirrespective if --skip-verify is used or not.	`False`
`--mapping`	text	Takes a .mapping.json file and converts data from given input files. Deprecated. Will be removed in a future release. The --config flag can be used instead.	`Sentinel.UNSET`
`-c`, `--config`	file	A json config file for the reader	None
`--help`	boolean	Show this message and exit.	`False`

dataconverter generate-template¶

Generates and prints a template to use for your nxdl.

Usage:

dataconverter generate-template [OPTIONS]

Options:

Name	Type	Description	Default
`--nxdl`	text	The name of the NeXus application definition file to use without extension. For example: NXmpes	_required
`--required`	boolean	Use this flag to only get the required template.	`False`
`--pythonic`	boolean	Prints a valid Python dictionary instead of JSON	`False`
`--output`	path	Writes the output into the filepath provided.	`Sentinel.UNSET`
`--help`	boolean	Show this message and exit.	`False`

dataconverter get-readers¶

Prints a list of all installed readers.

Usage:

dataconverter get-readers [OPTIONS]

Options:

Name	Type	Description	Default
`--help`	boolean	Show this message and exit.	`False`

NeXus file validation¶

validate_nexus¶

Validates a NeXus HDF5 file.

FILE: The path to the NeXus file to validate.

Usage:

validate_nexus [OPTIONS] FILE

Options:

Name	Type	Description	Default
`--ignore-undocumented`	boolean	Ignore all undocumented concepts during validation.	`False`
`--help`	boolean	Show this message and exit.	`False`

NeXus annotator¶

read_nexus¶

Functionality to extract documentation and concept definition information about the individual parts of a NeXus/HDF5 file.

Usage:

read_nexus [OPTIONS]

Options:

Name	Type	Description	Default
`-f`, `--nexus-file`	text	NeXus file with extension .nxs.	None
`-d`, `--documentation`	text	Definition path in nexus output (.nxs) file. Returns debug log relevant with that definition path. Example input: /entry/data/delays	None
`-c`, `--concept`	text	Concept path from application definition file (.nxdl.xml). Finds out all the available concept definition (IS-A relation) for a given concept path. Example input: /NXarpes/ENTRY/INSTRUMENT/analyser	None
`--help`	boolean	Show this message and exit.	`False`

NOTE: Only one option from (-d and -c) is acceptable.

ELN generation¶

generate_eln¶

Helper tool for generating ELN files in YAML format.

Usage:

generate_eln [OPTIONS]

Options:

Name	Type	Description	Default
`--nxdl`	text	Name of NeXus definition without extension (.nxdl.xml).	`Sentinel.UNSET`
`--skip-top-levels`	integer	To skip the level of parent hierarchy level. For example, by default the part Entry[ENTRY] from /Entry[ENTRY]/Instrument[INSTRUMENT]/... will be skipped.	`0`
`--output-file`	text	Name of file that is needed to generated output file.	None
`--eln-type`	choice (`reader` \| `schema`)	Choose a type of ELN output (reader or schema).	`eln`
`--optionality`	choice (`required` \| `recommended` \| `optional`)	Level of requiredness to generate. If any of ('required', 'recommended', 'optional', only those concepts matching this requiredness level are created.	`required`
`--filter-file`	text	JSON configuration file to filter NeXus concepts (based on the presence of the '@eln' keyword). This is a positive filter, i.e., all concepts in the filter file will be included in the ELN.	None
`--help`	boolean	Show this message and exit.	`False`