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How to delete all triples/clear the triplestore using SPARQL commands?
DELETE { ?s ?p ?o } WHERE { ?s ?p ?o }
leads to
Virtuoso 37000 Error SP031: SPARQL compiler: No plain default graph specified
as outlined in:
see https://github.com/openlink/virtuoso-opensource/issues/417
What is the proper method to delete all triples e.g. via API?
I tried
CLEAR ALL
and got
Virtuoso 42000 Error SR186:SECURITY: No permission to execute procedure DB.DBA.SPARUL_CLEAR with user ID 107, group ID 107
SPARQL query:
define sql:big-data-const 0
#output-format:text/html
define sql:signal-void-variables 1
CLEAR ALL
then
DELETE WHERE {
GRAPH <urn:virtuoso:default> { ?s ?p ?o }
}
and got
Virtuoso 42000 Error SR186:SECURITY: No permission to execute procedure DB.DBA.SPARQL_DELETE_DICT_CONTENT with user ID 107, group ID 107
SPARQL query:
define sql:big-data-const 0
#output-format:text/html
define sql:signal-void-variables 1
DELETE WHERE {
GRAPH <urn:virtuoso:default> { ?s ?p ?o }
}
docker exec virtuoso-omnigraph-test env | grep SPARQL
SPARQL_UPDATE=true
After:
GRANT SPARQL_UPDATE TO \"SPARQL"
i get
Virtuoso RDF02 Error SR619: SPARUL DELETE access denied: database user 107 (SPARQL) has no write permission on graph urn:virtuoso:default\n\nSPARQL query:\ndefine sql:big-data-const 0\n#\nDELETE WHERE {\n GRAPH <urn:virtuoso:default> { ?s ?p ...
see https://community.openlinksw.com/t/sparul-insert-access-denied-even-after-granting-update-permission/3448/7
The error does not go away even with:
"GRANT SPARQL_UPDATE TO \"SPARQL\";",
# workaround of 2023-01 as per https://community.openlinksw.com/t/sparul-insert-access-denied-even-after-granting-update-permission/3448/7
"DB.DBA.RDF_DEFAULT_USER_PERMS_SET ('nobody', 7);"
as implemented in
"""
Created on 2025-06-03
OpenLink Virtuoso SPARQL support
@author: wf
"""
from dataclasses import dataclass
from omnigraph.server_config import ServerLifecycleState, ServerStatus
from omnigraph.sparql_server import ServerConfig, ServerEnv, SparqlServer,\
ShellResult
@dataclass
class VirtuosoConfig(ServerConfig):
"""
Virtuoso configuration
"""
def __post_init__(self):
"""
configure the configuration
"""
super().__post_init__()
# Clean URLs without credentials
self.status_url = f"{self.base_url}/sparql"
self.sparql_url = f"{self.base_url}/sparql"
self.update_url = f"{self.base_url}/sparql"
self.upload_url = f"{self.base_url}/sparql-graph-crud"
self.web_url = f"{self.base_url}/sparql"
def get_docker_run_command(self, data_dir) -> str:
"""
Generate docker run command with bind mount for data directory.
Args:
data_dir: Host directory path to bind mount to container
Returns:
Complete docker run command string
"""
# Docker command setup
env = "-e SPARQL_UPDATE=true"
if self.auth_password:
env += f" -e DBA_PASSWORD={self.auth_password}"
# run as root - no user flag
docker_run_command = (
f"docker run {env} -d --name {self.container_name} "
f"-p {self.port}:8890 "
f"-v {data_dir}:/database "
f"{self.image}"
)
return docker_run_command
class Virtuoso(SparqlServer):
"""
Dockerized OpenLink Virtuoso SPARQL server
"""
def __init__(self, config: ServerConfig, env: ServerEnv):
"""
Initialize the Virtuoso manager.
Args:
config: Server configuration
env: Server environment (includes log, shell, debug, verbose)
"""
super().__init__(config=config, env=env)
def post_create(self):
"""
Setup permissions after container creation.
"""
super().post_create()
self.setup_permissions()
def run_isql_cmd(self, cmd: str) -> ShellResult:
"""
Run SQL command via isql.
"""
args = f"isql 1111 dba {self.config.auth_password or 'dba'} \"EXEC='{cmd}'\""
shell_result = self.run_docker_cmd("exec", args=args)
return shell_result
def setup_permissions(self) -> bool:
"""
Grant necessary permissions to SPARQL user.
"""
# Grant general SPARQL update capability
success=True
grants = [
"GRANT SPARQL_UPDATE TO \"SPARQL\";",
# workaround of 2023-01 as per https://community.openlinksw.com/t/sparul-insert-access-denied-even-after-granting-update-permission/3448/7
"DB.DBA.RDF_DEFAULT_USER_PERMS_SET ('nobody', 7);"
]
for sql in grants:
shell_result = self.run_isql_cmd(sql)
success=success and shell_result.success
return success
def status(self) -> ServerStatus:
"""
Get server status information.
Returns:
ServerStatus object with status information
"""
server_status = super().status()
logs = server_status.logs
if logs and "Server online at" in logs and "HTTP/WebDAV server online at" in logs:
server_status.at = ServerLifecycleState.READY
return server_status
def get_clear_query(self)->str:
"""
the clear query to be used
overrides the default query
"""
clear_query="""DELETE WHERE {
GRAPH <urn:virtuoso:default> { ?s ?p ?o }
}"""
return clear_query
def get_web_url(self) -> str:
web_url = self.config.web_url
if self.config.auth_user and self.config.auth_password:
proto, rest = web_url.split("://", 1)
auth=f"{self.config.auth_user}:{self.config.auth_password}@"
web_url=f"{proto}://{auth}{rest}"
return web_url
@HughWilliams thank you for tha pointer. I whould have been more precise in my question - i changed the header including "using SPARQL commands". Having to bother with the nittry gritty technical details of the underlying software is IMHO only a valid workaround but not a long term viable solution.
Just trying to provide a solution for you.
With this SPARQL query you can list all graphs:
SELECT DISTINCT ?graph WHERE { GRAPH ?graph { ?s ?p ?o } }
Then with that list you can clear individual graphs:
CLEAR <graph-name-from-the-resultset-of-the-previous-query>
