LinkML

Materialize a derived LinkML schema: imports resolved, slots pushed into attributes, and the elements out of scope pruned.

Usage

CLI

ohi get w3c/prov-o
ohi linkml to linkml --full-uris \
  --to prov-o.derived.yaml prov-o.linkml.yaml

Python

import ohi_linkml

with ohi_linkml.load_file("prov-o.linkml.yaml") as schema:
    output = schema.linkml(full_uris=True)

JavaScript

import { readFileSync } from "node:fs";
import { LinkML } from "@neverblink/linkml";

const yaml = readFileSync("prov-o.linkml.yaml", "utf8");
const { view, report } = LinkML.loadFromString(yaml, {});
if (!view) throw new Error(JSON.stringify(report));
const output = view.linkml({ full_uris: true });

Scala

import eu.neverblink.linkml.generator.options.LinkMlGeneratorOptions
import eu.neverblink.linkml.generator.linkml.LinkMlGenerator
import eu.neverblink.linkml.schemaview.{SchemaIssues, SchemaView}

val loaded = SchemaView.loadSchemaViewFromUri("prov-o.linkml.yaml")
given SchemaView = SchemaIssues.orThrow(loaded)
val output = LinkMlGenerator().serialize(
  LinkMlGeneratorOptions(fullUris = true),
)

C

#include <stddef.h>
#include "ohi_linkml.h"

linkml_init_threads();
char *report = NULL, *error = NULL;
long long schema =
    linkml_load_file("prov-o.linkml.yaml", NULL, &report, &error);
char *output = linkml_linkml(schema, "{\"full_uris\": true}", &error);
linkml_free(output);
linkml_free(report);
linkml_free(error);
linkml_close(schema);

Try it in the playground, with PROV-O

Options

formatJsonOutputFormatdefault yaml

CLI --format

The serialization of the output.

• yaml YAML.
• json JSON.

full_urisbooleandefault false

CLI --full-urisScala fullUris

Whether to write URIs in full, instead of compacting them to CURIEs with the schema's prefixes.

pruning_modePruningModedefault skip

CLI --pruning-modeScala pruningMode

The elements of the schema to include in the output.

• tree_root The elements reachable from the tree root class. Without a tree root, the same as schema.
• schema Everything defined in the root schema, and every element reachable from it. This leaves out the unused parts of imported schemas, such as most of linkml:types.
• skip Every element of the root schema and of all its imports.

skip_class_derivationbooleandefault false

CLI --skip-class-derivationScala skipClassDerivation

Whether to copy the classes as they are, instead of deriving them.

tree_rootstring

CLI --tree-rootScala treeRoot

The class to use as the tree root, instead of the class with tree_root: true in the schema. Only for the tree_root pruning mode.