`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 | svg_inline | 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