Hi Pantelis,
If you want fine control over processing of results then Daniel's answer
is the way to go, PLSQL allows you to do basically anything with your
results.
However it's not necessary in this instance I think. We can probably do
what you want with a subquery. Since you only want to process a select
number of records (subject to some memory constraint that you'll find
out by trial-and-error) then we can do this with a subquery in SPARQL.
Additionally, select statements have (or used to have) a hard limit of
10,000 results that might complicate the process.
------------------------------
SPARQL DEFINE sql:log-enable 3
WITH GRAPH <TargetGraph>
DELETE {
?S ?P ?O .
} WHERE {
{ SELECT ?S ?P ?O
{ ?S ?P ?O .
FILTER ( ?P = <TargetPredicate> )
} LIMIT 10 }
}
------------------------------
This will delete 10 matching records at a time from the target graph,
filtering on the target predicate.
Upscale as required and rerun as many times as required.
If you want to do it more elegantly, put it in a PLSQL function similar
to Daniel's below and just loop it together with a select query and stop
the function when the select query finds zero count of matching
predicates.
------------------------------
SELECT PCount FROM (
SPARQL
SELECT COUNT(*) as ?PCount FROM <TargetGraph>
{
?S ?P ?O .
FILTER ( ?P = <TargetPredicate> )
} ) AS PCount...
------------------------------
Make that a SELECT INTO and store the result, loop with the delete until
the result is zero.
If you want to track progress, write the count at each iteration to the
debug log (http://docs.openlinksw.com/virtuoso/fn_dbg_printf/) and
restart Virtuoso in debug&foreground mode to display the debug
statements.
That will eventually clean up your table.
Regards,
Quentin.
Guiding Hand Solutions
On 2016-08-17 22:54, Pantelis Natsiavas wrote:
> Thank you for your advice Daniel.
>
> Actually I want to delete only the statements containing the specific
> predicate. I don't want to delete all the triples containing the subject of
> the predicate. As I have already said, I don't feel comfortable with the
> DELETE queries.
> Is my query wrong? Could you suggest the correct query?
>
> Kind regards,
> Pantelis Natsiavas
>
> 2016-08-17 17:19 GMT+03:00 Davis, Daniel (NIH/NLM) [C] <daniel.da...@nih.gov>:
>
> So, this has nothing to do with the large vector size, but just to be sure
> the SPARQL is correct - do you wish to delete the subjects (and all their
> triples) where the subject has the predicate, or just the predicate itself?
>
> As far as avoiding the maximum vector size, I think your best approach is to
> limit the number of matches and repeat the query until there are no results,
> maybe with a count query in-between. I have had to do similar sorts of
> work-arounds to avoid the maximum # of results and maximum size of string
> issues. For instance, my first attempts to export large NTriples files after
> processing failed due to these issues. You may be able to adapt the code
> below, but I think that a repeated deleted query limited to a # of triples
> will be best in your case.
>
> Anyway, the code:
>
> CREATE PROCEDURE meshrdf_export(in graph_uri varchar, in file_name varchar) {
>
> DECLARE banner any;
>
> DECLARE env, ses any;
>
> DECLARE ses_len, max_ses_len any;
>
> SET isolation = 'uncommitted';
>
> max_ses_len := 10000000;
>
> --
>
> -- Truncate file and write a comment line indicating the graph and datetime
> of export.
>
> --
>
> --no_c_escapes-
>
> banner := sprintf('# <%s> exported at %sn', graph_uri, datestring(now()));
>
> string_to_file (file_name, banner, -2);
>
> env := vector (0, 0, 0);
>
> ses := string_output ();
>
> FOR (SELECT * FROM (SPARQL
>
> define input:storage ""
>
> SELECT ?s ?p ?o WHERE {
>
> GRAPH `iri(?:graph_uri)` {
>
> ?s ?p ?o
>
> }
>
> } ORDER BY ?s ?p ?o) AS sub OPTION (loop)) DO {
>
> http_nt_triple (env, "s", "p", "o", ses);
>
> ses_len := length (ses);
>
> IF (ses_len > max_ses_len) {
>
> string_to_file (file_name, ses, -1);
>
> ses := string_output ();
>
> }
>
> }
>
> IF (length (ses)) {
>
> string_to_file (file_name, ses, -1);
>
> }
>
> }
>
> Dan Davis, Systems/Applications Architect (Contractor),
>
> Office of Computer and Communications Systems,
>
> National Library of Medicine, NIH
>
> FROM: Pantelis Natsiavas [mailto:natsia...@gmail.com]
> SENT: Wednesday, August 17, 2016 4:36 AM
> TO: virtuoso-users <virtuoso-users@lists.sourceforge.net>
> SUBJECT: [Virtuoso-users] Deleting large number of triples
>
> Hi everybody.
>
> I am trying to delete a large number of triples of a very big graph. The
> graph contains 217.609.545 triples and I want to delete all the triples
> having a specific predicate (64.884.016 triples).
>
> I am trying to do it through the isql-v command line interface, using the
> command:
>
> SPARQL DEFINE sql:log-enable 3
>
> WITH <graph>
>
> DELETE { ?s <predicate> ?o }
>
> WHERE{ ?s <predicate> ?o }
>
> After some time (I don't know exactly how much) I got the error
>
> *** Error 42000: [Virtuoso Driver][Virtuoso Server]FRVEC: array in for
> vectored over max vector length 2000000 > 1000000
> at line 1 of Top-Level:
>
> I checked the virtuoso.log and I see nothing related to the specific error.
>
> I changed the parameters in virtuoso.ini:
>
> MaxQueryMem = 8G ; from 2G
> VectorSize = 1000 ; not changed
> MaxVectorSize = 2000000 ; from 1000000
> AdjustVectorSize = 1 ; from 0
>
> I am not very confident about these changes in virtuoso settings, but
> checking the http://docs.openlinksw.com/virtuoso/dbadm.html [1] these changes
> seemed the right thing to do.
>
> I restarted the VM and retried the whole process. After one hour, the memory
> consumed by Virtuoso got around 100% and got an error:
>
> *** Error 08S01: [Virtuoso Driver]CL065: Lost connection to server
>
> Please note that from previous similar errors, I already have the following
> virtuoso.ini settings:
>
> NumberOfBuffers = 1360000
> MaxDirtyBuffers = 1000000
> ThreadCleanupInterval = 1
> ResourcesCleanupInterval = 1
>
> My questions:
>
> 1. Is there any way to improve my query in order to facilitate its
> processing? It is the first time I am doing a DELETE query and I am not
> comfortable with it.
>
> 2. Is there any way to "split" the query so that it doesn't need to handle
> all these triples at once?
>
> 3. Alternatively, is there any configuration change that might improve memory
> handling in order to handle such big queries?
>
> Kind regards,
>
> Pantelis Natsiavas
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