Java

Overview

The Java Generator produces java class files from a linkml model, with optional support for user-supplied jinja2 templates to generate classes with alternate annotations or additional documentation.

Docs

Command Line

gen-java

Generate java classes to represent a LinkML model

gen-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

Code

class linkml.generators.javagen.JavaGenerator(schema: str | ~typing.TextIO | ~linkml_runtime.linkml_model.meta.SchemaDefinition | Generator | ~pathlib.Path, schemaview: ~linkml_runtime.utils.schemaview.SchemaView = None, format: str | None = None, metadata: bool = True, useuris: bool | None = None, log_level: int | None = 30, mergeimports: bool | None = True, source_file_date: str | None = None, source_file_size: int | None = None, logger: ~logging.Logger | None = None, verbose: bool | None = None, output: str | None = None, namespaces: ~linkml_runtime.utils.namespaces.Namespaces | None = None, directory_output: bool = False, base_dir: str = None, metamodel_name_map: dict[str, str] = None, importmap: str | ~collections.abc.Mapping[str, str] | None = None, emit_prefixes: set[str] = <factory>, metamodel: ~linkml.utils.schemaloader.SchemaLoader = None, stacktrace: bool = False, include: str | ~pathlib.Path | ~linkml_runtime.linkml_model.meta.SchemaDefinition | None = None, template_file: str | None = None, package: str = 'example', generate_records: bool = False, gen_classvars: bool = True, gen_slots: bool = True, genmeta: bool = False, emit_metadata: bool = True)

Generates java code from a LinkML schema.

Two styles are supported:

• java classes, using lombok annotations

• java records

serialize(directory: str, **kwargs) → None

Generate output in the required format

Parameters:

kwargs – Generator specific parameters

Returns:

Generated output

Additional Notes

The Java generator’s default template uses Project Lombok’s @Data annotation, which provides getters, setters, equals and hashcode functionality.

Biolink Example

Begin by downloading the Biolink Model YAML and adding a virtual environment and installing linkml.

curl -OJ https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml
python3 -m venv venv
source venv/bin/activate
pip install linkml

Now generate the classes using the gen-java command

gen-java --package org.biolink.model --output-directory org/biolink/model biolink-model.yaml

Finally, fetch the Lombok jar, build the java classes and package into a jar file

curl -OJ https://repo1.maven.org/maven2/org/projectlombok/lombok/1.18.20/lombok-1.18.20.jar
javac org/biolink/model/*.java -cp lombok-1.18.20.jar
jar -cf biolink-model.jar org

Alternate Template Example

Here is an alternate template using Hibernate JPA annotations, named example_template.java.jinja2

package {{ doc.package }};

import java.util.List;
import lombok.*;
import javax.persistence.*;
import org.hibernate.search.engine.backend.types.*;
import org.hibernate.envers.Audited;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.*;


@Audited
@Indexed
@Entity
@Data @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
public class {{ cls.name }} {% if cls.is_a -%} extends {{ cls.is_a }} {%- endif %} {
{% for f in cls.fields %}
  private {{f.range}} {{ f.name }};
{%- endfor %}

}

The alternate template for the generator can be specified with the –template_file option

gen-java --package org.biolink.model --output-directory org/biolink/model \
         --template_file example_template.java.jinja2 biolink-model.yaml