linkml generate

Summary

See the individual generator pages, or run linkml generate {format} --help for additional usage information

linkml generate

Generate formats from a LinkML schema

linkml generate [OPTIONS] COMMAND [ARGS]...

Options

-V, --version

Show the version and exit.

Commands

cli

Generate typescript interfaces and types

cli

CLI for LinkML to DBML generator.

csv

Generate CSV/TSV file from LinkML model

doc

Generate documentation folder from a…

erdiagram

Generate a mermaid ER diagram from a schema.

excel

Generate Excel representation of a LinkML…

gen-pandera

golang

Generate Golang types

golr-views

Generate GOLR representation of a LinkML…

graphql

Generate graphql representation of a…

graphviz

Generate graphviz representations of the…

java

Generate java classes to represent a…

json-schema

Generate JSON Schema representation of a…

jsonld

Generate JSONLD file from LinkML schema.

jsonld-context

Generate jsonld @context definition from…

linkml

markdown

Generate markdown documentation of a…

namespaces

Generate a namespace manager for all of…

owl

Generate an OWL representation of a LinkML…

plantuml

Generate a UML representation of a LinkML…

prefix-map

Generate jsonld @context definition from…

project

Generate an entire project LinkML schema

proto

Generate proto representation of LinkML model

pydantic

Generate pydantic classes to represent a…

python

Generate python classes to represent a…

rdf

Generate an RDF representation of a LinkML…

shacl

Generate SHACL turtle from a LinkML model

shex

Generate a ShEx Schema for a LinkML model

sparql

Generate SPARQL queries for validation

sqla

Generate SQL DDL representation

sqltables

Generate SQL DDL representation.

sssom

Generate SSSOM TSV to represent a LinkML…

summary

Generate TSV summary files for viewing in…

terminusdb

Generate graphql representation of a…

yaml

Validate input and produce fully resolved…

yuml

Generate a yUML representation of a LinkML…

Complete

You’ll probably need to use the side navigation bar…

Note

The command isn’t actually linkml generate (full) it’s just a quirk of the package we use for documenting the cli

linkml generate (full)

Generate formats from a LinkML schema

linkml generate (full) [OPTIONS] COMMAND [ARGS]...

Options

-V, --version

Show the version and exit.

cli

Generate typescript interfaces and types

See https://github.com/linkml/linkml-runtime.js

linkml generate (full) cli [OPTIONS] YAMLFILE

Options

--output <output>

--include-induced-slots

Generate slots induced through inheritance

-u, --gen-type-utils

Generate Type checking utils

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'text'

Options:

text

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

cli

CLI for LinkML to DBML generator.

linkml generate (full) cli [OPTIONS]

Options

-s, --schema <schema>

Required Path to the LinkML schema YAML file

-o, --output <output>

Path to save the generated DBML file. If not specified, DBML will be printed to stdout.

csv

Generate CSV/TSV file from LinkML model

linkml generate (full) csv [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-r, --root <root>

Class(es) to transform

-f, --format <format>

Output format

Default:

'csv'

Options:

csv | tsv

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

doc

Generate documentation folder from a LinkML YAML schema

Currently a default set of templates for markdown is provided (see the folder linkml/generators/docgen/)

If you specify another format (e.g. html) then you need to provide a template_directory argument, with a template for each type of entity inside.

Examples can optionally be integrated into the documentation; to enable this, pass in the –example-directory argument. The example directory should contain one file per example, following the naming convention <ClassName>-<ExampleName>.<extension>.

For example, to include examples on the page for Person, include examples

Person-001.yaml, Person-002.yaml, etc.

Currently examples must be in yaml

linkml generate (full) doc [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--truncate-descriptions <truncate_descriptions>

Whether to truncate long (potentially spanning multiple lines) descriptions of classes, slots, etc., in the docs. Set to true for truncated descriptions, and false to display full descriptions.

Default:

True

--subfolder-type-separation, --no-subfolder-type-separation

Separate type (class, slot, etc.) outputs in different subfolders for navigation purposes

--include <include>

Include LinkML Schema outside of imports mechanism. Helpful in including deprecated classes and slots in a separate YAML, and including it when necessary but not by default (e.g. in documentation or for backwards compatibility)

--example-directory <example_directory>

Folder in which example files are found. These are used to make inline examples

--render-imports, --no-render-imports

Render also the documentation of elements from imported schemas

Default:

False

--hierarchical-class-view, --no-hierarchical-class-view

Render class table on index page in a hierarchically indented view

--use-class-uris, --no-use-class-uris

Use IDs from class_uri instead of names

--use-slot-uris, --no-use-slot-uris

Use IDs from slot_uri instead of names

--template-directory <template_directory>

Path to the directory with custom jinja2 templates

--genmeta, --no-genmeta

Generating metamodel. Only use this for generating meta.py

Default:

False

--sort-by <sort_by>

Metaslot to use to sort elements by e.g. rank, name, title

Default:

'name'

--include-top-level-diagram, --no-include-top-level-diagram

Include ER diagram of the entire schema on index page.

Default:

False

--diagram-type <diagram_type>

Type of UML diagram to be rendered on class documentation pages.

Options:

mermaid_class_diagram | plantuml_class_diagram | er_diagram

--dialect <dialect>

Dialect or ‘flavor’ of Markdown used.

--index-name <index_name>

Name of the index document.

Default:

'index'

-d, --directory <directory>

Required Path to the directory where you want the Markdown files to be written to

-f, --format <format>

Output format

Default:

'markdown'

Options:

markdown | rst | html | latex

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

erdiagram

Generate a mermaid ER diagram from a schema.

By default, all entities traversable from the tree_root are included. If no tree_root is present, then all entities are included.

To create an ER diagram for selected classes, use the –classes option.

linkml generate (full) erdiagram [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--include-upstream

Include upstream classes

-c, --classes <classes>

List of classes to serialize

--max-hops <max_hops>

Maximum number of hops

-f, --format <format>

Options:

markdown | mermaid

--follow-references, --no-follow-references

If True, follow references even if not inlined

--exclude-abstract-classes, --no-exclude-abstract-classes

If True, do not include abstract classes in the diagram

--exclude-attributes, --no-exclude-attributes

If True, do not include attributes in entities

--structural, --no-structural

If True, then only the tree_root and entities reachable from the root are drawn

-f, --format <format>

Output format

Default:

'markdown'

Options:

markdown | mermaid

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

excel

Generate Excel representation of a LinkML model

linkml generate (full) excel [OPTIONS] YAMLFILE

Options

--split-workbook-by-class

Split model into separate Excel workbooks/files, one for each class

--include-mixins

Include mixin classes in the generated Excel workbook/workbooks

-o, --output <output>

Name of Excel spreadsheet to be created, or name of directory to create split workbooks in

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'xlsx'

Options:

xlsx

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

gen-pandera

linkml generate (full) gen-pandera [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--template-file <template_file>

Optional jinja2 template to use for class generation

--template-path <template_path>

Optional jinja2 template directory within module

--package <package>

Package name where relevant for generated class files

Arguments

YAMLFILE

Required argument

golang

Generate Golang types

This very simple generator produces a Golang package named after the given schema with structs that implement the classes in that schema.

linkml generate (full) golang [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'text'

Options:

text

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

golr-views

Generate GOLR representation of a LinkML model

linkml generate (full) golr-views [OPTIONS] YAMLFILE

Options

-d, --dir <dir>

Output directory

Default:

'golr-views'

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'golr'

Options:

golr

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

graphql

Generate graphql representation of a LinkML model

linkml generate (full) graphql [OPTIONS] YAMLFILE

Options

--strict-naming

Treat warnings about invalid names or schema elements as errors.

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'graphql'

Options:

graphql

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

graphviz

Generate graphviz representations of the LinkML model

linkml generate (full) graphviz [OPTIONS] YAMLFILE

Options

-d, --directory <directory>

Output directory - if supplied, a graph per class will be generated

-o, --out <out>

Target file – if supplied, one large graph will be generated

-c, --classname <classname>

Class(es) to transform

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'png'

Options:

png | bmp | canon | cgimage | cmap | cmapx | cmapx_np | dot | dot_json | eps | exr | fig | gd | gd2 | gif | gtk | gv | ico | imap | imap_np | ismap | jp2 | jpe | jpeg | jpg | json | json0 | pct | pdf | pic | pict | plain | plain-ext | png | pov | ps | ps2 | psd | sgi | svg | svgz | tga | tif | tiff | tk | vml | vmlz | vrml | wbmp | webp | x11 | xdot | xdot1.2 | xdot1.4 | xdot_json | xlib

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

java

Generate java classes to represent a LinkML model

linkml generate (full) java [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--generate-records, --no-generate-records

Optional Java 17 record implementation

--template-file <template_file>

Optional jinja2 template to use for class generation

--package <package>

Package name where relevant for generated class files

--output-directory <output_directory>

Output directory for individually generated class files

Default:

'output'

-f, --format <format>

Output format

Default:

'java'

Options:

java

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

json-schema

Generate JSON Schema representation of a LinkML model

linkml generate (full) json-schema [OPTIONS] YAMLFILE

Options

-i, --inline

Generate references to types rather than inlining them. Note that declaring a slot as inlined: true will always inline the class

-t, --top-class <top_class>

Top level class; slots of this class will become top level properties in the json-schema

--not-closed, --closed

Set additionalProperties=False if closed otherwise true if not closed at the global level

Default:

True

--include-range-class-descendants, --no-range-class-descendants

When handling range constraints, include all descendants of the range class instead of just the range class

--indent <indent>

If this is a positive number the resulting JSON will be pretty-printed with that indent level. Set to 0 to disable pretty-printing and return the most compact JSON representation

Default:

4

--title-from <title_from>

Specify from which slot are JSON Schema ‘title’ annotations generated.

Options:

name | title

-d, --include <include>

Include LinkML Schema outside of imports mechanism. Helpful in including deprecated classes and slots in a separate YAML, and including it when necessary but not by default (e.g. in documentation or for backwards compatibility)

--materialize-patterns, --no-materialize-patterns

If set, patterns will be materialized in the generated JSON Schema.

Default:

True

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'json'

Options:

json

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

jsonld

Generate JSONLD file from LinkML schema.

Status: incomplete

linkml generate (full) jsonld [OPTIONS] YAMLFILE

Options

--context <context>

JSONLD context file (default: https://w3id.org/linkml/meta.context.jsonld and <model>.prefixes.context.jsonld)

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'jsonld'

Options:

jsonld | json

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

jsonld-context

Generate jsonld @context definition from LinkML model

linkml generate (full) jsonld-context [OPTIONS] YAMLFILE

Options

--base <base>

Base URI for model

--prefixes, --no-prefixes

Emit context for prefixes (default=–prefixes)

Default:

True

--model, --no-model

Emit context for model elements (default=–model)

Default:

True

--flatprefixes, --no-flatprefixes

Emit non-JSON-LD compliant prefixes as an object (deprecated: use gen-prefix-map instead).

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'context'

Options:

context | json

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

linkml

linkml generate (full) linkml [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-o, --output <output>

Name of JSON or YAML file to be created

--materialize-patterns, --no-materialize-patterns

Materialize structured patterns as patterns

Default:

True

--materialize-attributes, --no-materialize-attributes

Materialize induced slots as attributes

Default:

True

--materialize, --no-materialize

Materialize both, induced slots as attributes and structured patterns as patterns

Default:

True

-f, --format <format>

Output format

Default:

'json'

Options:

json | yaml

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

markdown

Generate markdown documentation of a LinkML model.

Warning

gen-markdown is deprecated. Please use gen-doc instead.

linkml generate (full) markdown [OPTIONS] YAMLFILE

Options

-d, --dir <dir>

Required Output directory

-c, --classes <classes>

Class(es) to emit

-M, --map-fields <map_fields>

Map metamodel fields, e.g. slot=field

-i, --img

Download YUML images to ‘image’ directory

-I, --index-file <index_file>

Name of markdown file that holds index

--noimages

Do not (re-)generate images

--noyuml

Do not add yUML figures to pages

--notypesdir

Do not create a separate types directory

--warnonexist

Warn if output file already exists

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'md'

Options:

md

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

namespaces

Generate a namespace manager for all of the prefixes represented in a LinkML model

linkml generate (full) namespaces [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'py'

Options:

py

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

owl

Generate an OWL representation of a LinkML model

Generate OWL using default parameters:

gen-owl my_schema.yaml

Note that in previous versions of this generator, the default was to use type objects and to include metaclasses. To restore this behavior:

gen-owl –metaclasses –type-objects my_schema.yaml

For more info, see: https://linkml.io/linkml/generators/owl

linkml generate (full) owl [OPTIONS] YAMLFILE

Options

-o, --output <output>

Output file name

--metadata-profile <metadata_profile>

What kind of metadata profile to use for annotations on generated OWL objects

Default:

'linkml'

Options:

linkml | rdfs | ols

--type-objects, --no-type-objects

If true, will model linkml types as objects, not literals

Default:

False

--metaclasses, --no-metaclasses

If true, include linkml metamodel classes as metaclasses. Note this introduces punning in OWL-DL

Default:

False

--add-root-classes, --no-add-root-classes

If true, include linkml metamodel classes as superclasses.

Default:

False

--add-ols-annotations, --no-add-ols-annotations

If true, auto-include annotations from https://www.ebi.ac.uk/ols/docs/installation-guide

Default:

True

--ontology-uri-suffix <ontology_uri_suffix>

Suffix to append to schema id to generate OWL Ontology IRI

Default:

'.owl.ttl'

--assert-equivalent-classes, --no-assert-equivalent-classes

If true, add owl:equivalentClass between a class and a class_uri

Default:

False

--mixins-as-expressions, --no-mixins-as-expressions

If true, then mixins are represented as existential expressions

Default:

False

--use-native-uris, --no-use-native-uris

Use model URIs rather than class/slot URIs

Default:

True

--default-permissible-value-type <default_permissible_value_type>

Default OWL type for permissible values

Default:

'http://www.w3.org/2002/07/owl#Class'

--enum-iri-separator <enum_iri_separator>

IRI separator for enums.

Default:

'#'

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'owl'

Options:

owl | ttl | json-ld | xml | n3 | turtle | ttl | ntriples | nt | nt11 | nquads | trix | trig | hext | patch

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

plantuml

Generate a UML representation of a LinkML model

linkml generate (full) plantuml [OPTIONS] YAMLFILE

Options

-c, --classes <classes>

Class(es) to emit

-d, --directory <directory>

Output directory - if supplied, PlantUML rendering will be saved in file

-k, --kroki-server <kroki_server>

URL of the Kroki server to use for diagram drawing

--dry-run

Print out Kroki URL calls instead of sending the real requests

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'puml'

Options:

puml | plantuml | png | pdf | jpg | json | svg

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

prefix-map

Generate jsonld @context definition from LinkML model

linkml generate (full) prefix-map [OPTIONS] YAMLFILE

Options

--base <base>

Base URI for model

-o, --output <output>

Output file path

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'json'

Options:

json | tsv

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

project

Generate an entire project LinkML schema

Generate all downstream artefacts using default configuration:

Exclusion lists: all except ShEx:

Inclusion lists: only jsonschema and python:

Configuration, on command line:

Configuration, via yaml file:

config.yaml:

linkml generate (full) project [OPTIONS] YAMLFILE

Options

-d, --dir <dir>

directory in which to place generated files. E.g. linkml_model, biolink_model

-A, --generator-arguments <generator_arguments>

yaml configuration for generators

-C, --config-file <config_file>

path to yaml configuration

-X, --exclude <exclude>

list of artefacts to be excluded

-I, --include <include>

list of artefacts to be included. If not set, defaults to all

--mergeimports, --no-mergeimports

Merge imports into source file

Default:

True

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-V, --version

Show the version and exit.

Arguments

YAMLFILE

Required argument

proto

Generate proto representation of LinkML model

linkml generate (full) proto [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'proto'

Options:

proto

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

pydantic

Generate pydantic classes to represent a LinkML model

linkml generate (full) pydantic [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--meta <meta>

How to include linkml schema metadata in generated pydantic classes. See docs for MetadataMode for full description of choices. Default (auto) is to include all metadata that can’t be otherwise represented

Options:

full | except_children | auto | None

--black

Format generated models with black (must be present in the environment)

--extra-fields <extra_fields>

How to handle extra fields in BaseModel.

Options:

allow | ignore | forbid

--array-representations <array_representations>

List of array representations to accept for array slots. Default is list of lists.

Options:

list | numpydantic

--template-dir <template_dir>

Optional jinja2 template directory to use for class generation.

Pass a directory containing templates with the same name as any of the default PydanticTemplateModel templates to override them. The given directory will be searched for matching templates, and use the default templates as a fallback if an override is not found

Available templates to override:

- attribute.py.jinja

- base_model.py.jinja

- class.py.jinja

- conditional_import.py.jinja

- enum.py.jinja

- imports.py.jinja

- module.py.jinja

- validator.py.jinja

-f, --format <format>

Output format

Default:

'pydantic'

Options:

pydantic

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

python

Generate python classes to represent a LinkML model

linkml generate (full) python [OPTIONS] YAMLFILE

Options

--head, --no-head

Emit metadata heading

Default:

True

--genmeta, --no-genmeta

Generating metamodel. Only use this for generating meta.py

Default:

False

--classvars, --no-classvars

Generate CLASSVAR info

Default:

True

--slots, --no-slots

Generate Slot information

Default:

True

--validate, --no-validate

Validate generated code by compiling it

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'py'

Options:

py

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

rdf

Generate an RDF representation of a LinkML model

linkml generate (full) rdf [OPTIONS] YAMLFILE

Options

-o, --output <output>

Output file name

--context <context>

JSONLD context file (default: https://w3id.org/linkml/meta.context.jsonld)

Default:

'https://w3id.org/linkml/meta.context.jsonld'

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'ttl'

Options:

ttl | hext | json-ld | n3 | nquads | nt | nt11 | ntriples | patch | trig | trix | ttl | turtle | xml

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

shacl

Generate SHACL turtle from a LinkML model

linkml generate (full) shacl [OPTIONS] YAMLFILE

Options

--closed, --non-closed

Use ‘–closed’ to generate closed SHACL shapes. Use ‘–non-closed’ to generate open SHACL shapes.

Default:

True

-s, --suffix <suffix>

Use –suffix to append given string to SHACL class name (e. g. –suffix Shape: Person becomes PersonShape).

--include-annotations, --exclude-annotations

Use –include-annotations to include annotations of slots, types, and classes in the generated SHACL shapes.

Default:

False

--exclude-imports, --include-imports

Use –exclude-imports to exclude imported elements from the generated SHACL shapes. This is useful when extending a substantial ontology to avoid large output files.

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'ttl'

Options:

ttl

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

shex

Generate a ShEx Schema for a LinkML model

linkml generate (full) shex [OPTIONS] YAMLFILE

Options

-o, --output <output>

Output file name

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'shex'

Options:

shex | json | rdf

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

sparql

Generate SPARQL queries for validation

This will generate a directory of queries that can be used for QC over a triplestore that is conformant to the same LinkML schema.

Each query in the directory will be of the form

CHECK_<ConstraintType>_<SchemaElement>.rq

Example:

gen-sparql -d ./sparql/ personinfo.yaml

linkml generate (full) sparql [OPTIONS] YAMLFILE

Options

-d, --dir <dir>

Directory in which queries will be deposited

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'sparql'

Options:

sparql

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

sqla

Generate SQL DDL representation

linkml generate (full) sqla [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

--use-foreign-keys, --no-use-foreign-keys

Emit FK declarations

Default:

True

--pydantic, --no-pydantic

If True, generate Pydantic classes (imperative mode only)

Default:

False

--generate-classes, --no-generate-classes

If True, generate Python datamodel (imperative mode only)

Default:

False

--declarative, --no-declarative

Generate SQL Alchemy declarative vs imperative

Default:

True

-f, --format <format>

Output format

Default:

'sqla'

Options:

sqla

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

sqltables

Generate SQL DDL representation.

linkml generate (full) sqltables [OPTIONS] YAMLFILE

Options

--dialect <dialect>

SQL-Alchemy dialect, e.g. sqlite, mysql+odbc

Default:

'sqlite'

--sqla-file <sqla_file>

Path to sqlalchemy generated python

--relmodel-output <relmodel_output>

Path to intermediate LinkML YAML of transformed relational model

--python-import <python_import>

Python import header for generated sql-alchemy code

--use-foreign-keys, --no-use-foreign-keys

Emit FK declarations

Default:

True

--default_length_oracle <default_length_oracle>

Default length of varchar based arguments for oracle dialects

Default:

4096

--autogenerate_index <autogenerate_index>

Enable the creation of indexes on all columns generated

Default:

False

--generate_abstract_class_ddl <generate_abstract_class_ddl>

A manual override to omit the abstract classes, set to true as a default for testing sake

Default:

True

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'sql'

Options:

sql

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

sssom

Generate SSSOM TSV to represent a LinkML model

linkml generate (full) sssom [OPTIONS] YAMLFILE

Options

-o, --output <output>

Output file name

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'tsv'

Options:

tsv

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

summary

Generate TSV summary files for viewing in Excel and the like

linkml generate (full) summary [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'tsv'

Options:

tsv

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

terminusdb

Generate graphql representation of a LinkML model

linkml generate (full) terminusdb [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'json'

Options:

json

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

yaml

Validate input and produce fully resolved yaml equivalent

linkml generate (full) yaml [OPTIONS] YAMLFILE

Options

--raw, --no-raw

Use the raw loader and do not inject additional information

Default:

False

-V, --validateonly, -g, --generate

Just validate / generate output (default: generate)

Default:

False

-V, --version

Show the version and exit.

-f, --format <format>

Output format

Default:

'yaml'

Options:

yaml

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument

yuml

Generate a yUML representation of a LinkML model

Warning

gen-yuml is deprecated. Please use gen-doc, gen-plantuml or gen-mermaid-class-diagram.

linkml generate (full) yuml [OPTIONS] YAMLFILE

Options

-c, --classes <classes>

Class(es) to emit

-d, --directory <directory>

Output directory - if supplied, YUML rendering will be saved in file

--diagram-name <diagram_name>

Name of the diagram in the output directory (without suffix!)

-f, --format <format>

Output format

Default:

'yuml'

Options:

yuml | png | pdf | jpg | json | svg

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument