SPARQL Type Checker

This is a Python package for checking SPARQL queries against ShEx schemas. It provides a command-line tool and function named type_check_sparql to perform the checks.

I hope this tool can check SPARQL queries are badly formatted or collectly formatted. Now this tool checks the format with tripple. So mistakes of checking may be occured especially when the query has long variables or complex format.

Installation

1. First, build the package using setup.py:

   python setup.py sdist bdist_wheel

2. After building, you can install the package locally using:

   pip install .

PyShEx>=0.8.1, rdflib>=7.0.0 would be also installed automatically.

Usage

Once installed, you can use the type_check_sparql command to check SPARQL queries. The command requires the following arguments:

• SELECT * WHERE { ?s ?p ?o }: The SPARQL query you want to check.
• path_to_shex/uniprot_rdf-config.shex: The path to the ShEx schema file.
• False: A boolean flag (in this case, "False").

Example

To execute the command:

type_check_sparql 'SELECT * WHERE { ?s ?p ?o }' path_to_shex/uniprot_rdf-config.shex False

In python:

from sparql_type_check_tools import type_check_sparql

import sys

# Suppress error output for clarity
sys.stderr = open('/dev/null', 'w')

# Example of an invalid SPARQL query
test_query_false = """
PREFIX core: <http://purl.uniprot.org/core/>
PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?uniprot_pdb 
WHERE {
    VALUES ?UniProt__class { core:Protein chembl:UniprotRef }
    ?UniProt a ?UniProt__class ;
        rdfs:seeAlsooooooooo 1 .
    ?uniprot_pdb a core:Structure_Resource .
    ?uniprot_pdb ?x ?y.
}
LIMIT 100
"""

# Example of a valid SPARQL query
test_query_true = """
PREFIX core: <http://purl.uniprot.org/core/>
PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT DISTINCT ?uniprot_orf_name ?uniprot_gene_name
WHERE {
    VALUES ?uniprot_gene_name { "ACE2" }
    VALUES ?UniProt__class { core:Protein chembl:UniprotRef }
    ?UniProt a ?UniProt__class ;
        core:encodedBy / core:orfName ?uniprot_orf_name ;
        core:encodedBy / skos:prefLabel ?uniprot_gene_name .
}
LIMIT 100
"""

# Path to the ShEx schema
path_to_shex = "path_to_your/uniprot_rdf-config.shex"

# Running the false query test
result = type_check_sparql(test_query_false, path_to_shex, False)
print("test_query_false:\n", result)
print("----------" * 10)

# Running the true query test
result = type_check_sparql(test_query_true, path_to_shex, False)
print("test_query_true:\n", result)

Interpreting the Results

The type_check_sparql function returns a dictionary containing information about the correctness of the query:

• correct_query: True if the query is correct, False if there are errors.
• error_variables: A list of variables where errors were detected.
• all_vars: A set of all variables used in the query.

For example:

test_query_false:
 {'correct_query': False, 'error_variables': ['uniprot_pdb', 'UniProt'], 'all_vars': {'y', 'uniprot_pdb', 'UniProt', 'x', 'UniProt__class'}}

test_query_true:
 {'correct_query': True, 'error_variables': [], 'all_vars': {'uniprot_gene_name', 'UniProt', 'uniprot_orf_name', 'UniProt__class'}}