SPARQL

This generator allows you to generate a bank of sparql queries from a schema. These queries can then be used for validation.

Note this approach is redundant with more complete RDF shape based strategies – however, it can be convenient to generate individual SPARQL queries as these can be applied on an ad-hoc basis.

Overview

To run:

gen-sparql -d /path/to/sparql-queries/ personinfo.yaml

See also

Data Validation for other validation strategies.

See also

linkml-sparql for an alpha version of a SPARQL based ORM

For example, when running over the personinfo schema, one of the queries “CHECK_permitted_Person.rq” checks to see that only specifically permitted properties are used when the domain is Person.

SELECT ?g ?s ?p WHERE {
 GRAPH ?g {
  ?s rdf:type schema:Person ;
     ?p ?o .
  FILTER ( ?p NOT IN (
   schema:email,
   schema:birthDate,
   personinfo:age_in_years,
   schema:gender,
   personinfo:current_address,
   personinfo:has_employment_history,
   personinfo:has_familial_relationships,
   personinfo:has_medical_history,
   personinfo:aliases,
   schema:identifier,
   schema:name,
   schema:description,
   schema:image,
   rdf:type ))
 }

}

Docs

Command Line

gen-sparql

Generate SPARQL queries for validation

This will generate a directory of queries that cann 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

gen-sparql [OPTIONS] YAMLFILE

Options

-d, --dir <dir>

Directory in which queries will be deposited

-f, --format <format>

Output format

Default

sparql

Options

sparql

--metadata, --no-metadata

Include metadata in output

Default

True

--useuris, --metauris

Include metadata in output

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

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

Arguments

YAMLFILE

Required argument

Code

class linkml.generators.sparqlgen.SparqlGenerator(schema: Union[str, TextIO, SchemaDefinition], format: str = 'sparql', named_graphs: Optional[List[str]] = None, limit: Optional[int] = None, **kwargs)[source]

Generates SPARQL queries that can be used for delayed validation

serialize(directory=None) str[source]

Generate output in the required format

Parameters

kwargs – Generater specific parameters

Returns

Generated output