Hi,
I'm attempting to run a backup of a fuseki database. I've done this
successfully many times on other systems, which I have configured
identically (AFAIK; it is all done by hand, so an inconsistency is
possible).
Based on the logs, fuseki appears to run through all the motions, but
the file that's written is a 20-byte .gz file (i.e., an empty file that
got gzip'd). Logs and info below.
I was running 3.6.0 standalone. I tried upgrading to 3.7.0 standalone,
which didn't fix it.
Am i doing something wrong, or is this a bug?
In the spirit of full disclosure...I think it's probably fine, but It's
possible that there is some corruption in the database.
In general queries work fine. We have one triple with a null value
that we can't figure out how to delete with sparql. Our two experts are
unavailable today and the rest of us are sparql-incompetent. I don't
need help with that, we will figure it out when one of them returns
and/or by reading some more docs.
This led me to the ham-fisted idea of backing up, deleting the offending
line, and restoring. I agree with any suggestion that it's a stupid
solution to this problem - but I still want to be able to back up this
database, it's inconvenient to recreate it.
database has about 20 million triples.
Java:
log/archonnex/fuseki@acxcore-awstest0% java -version
openjdk version "1.8.0_171"
OpenJDK Runtime Environment (build 1.8.0_171-b10)
OpenJDK 64-Bit Server VM (build 25.171-b10, mixed mode)
fuseki command line:
fuseki 16548 1.1 0.6 12341352 209636 ? Sl 13:26
00:00:04 /etc/alternatives/java_sdk_1.8.0/bin/java -Xmx8G
-Dlog4j.configuration=file:/etc/archonnex/fuseki/log4j.properties
-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps
-XX:+PrintGCTimeStamps -XX:+UseGCLogFileRotation
-XX:NumberOfGCLogFiles=10 -XX:GCLogFileSize=100m
-XX:+PrintTenuringDistribution
-Xloggc:/var/log/archonnex/fuseki/gc-%t.log -jar
/usr/local/apache-jena-fuseki-3.7.0/fuseki-server.jar
--config=/etc/archonnex/fuseki/fcrepo.ttl
ttl config:
# cat fcrepo.ttl
@prefix : <http://base/#> .
@prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
:service_tdb_all a fuseki:Service ;
rdfs:label "TDB fcrepo" ;
fuseki:dataset :tdb_dataset_readwrite ;
fuseki:name "fcrepo" ;
fuseki:serviceQuery "query" , "sparql" ;
fuseki:serviceReadGraphStore "get" ;
fuseki:serviceReadWriteGraphStore
"data" ;
fuseki:serviceUpdate "update" ;
fuseki:serviceUpload "upload" .
:tdb_dataset_readwrite
a tdb:DatasetTDB ;
tdb:location "/var/archonnex/fuseki/data/fcrepo" .
log file:
[2018-05-15 14:18:35] Admin INFO [1] POST
http://127.0.0.1:3030/$/backup/fcrepo
[2018-05-15 14:18:35] Admin INFO [1] Backup dataset /fcrepo
[2018-05-15 14:18:35] Server INFO Task : 1 : backup
[2018-05-15 14:18:35] Server INFO [Task 1] starts : backup
[2018-05-15 14:18:35] Backup INFO [1] >>>> Start backup /fcrepo ->
/var/archonnex/fuseki/backups/fcrepo_2018-05-15_14-18-35
[2018-05-15 14:18:35] TDB DEBUG Txn[2]/R: begin$
[2018-05-15 14:18:35] info DEBUG Triple table: SPO :: SPO,POS,OSP
[2018-05-15 14:18:35] info DEBUG Quad table: GSPO ::
GSPO,GPOS,GOSP,POSG,OSPG,SPOG
[2018-05-15 14:18:35] info DEBUG Prefixes: GPU :: GPU
[2018-05-15 14:18:35] LockMRSW DEBUG Lock : pool-2-thread-1
[2018-05-15 14:18:35] TDB DEBUG Txn[2]/R: start
[2018-05-15 14:18:35] LockMRSW DEBUG pool-2-thread-1 >> enterCS:
Thread R/W: 0/0 :: Model R/W: 0/0 (thread: pool-2-thread-1)
[2018-05-15 14:18:35] LockMRSW DEBUG pool-2-thread-1 << enterCS:
Thread R/W: 1/0 :: Model R/W: 1/0 (thread: pool-2-thread-1)
[2018-05-15 14:18:35] Admin INFO [1] 200 OK (8 ms)
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] BlockAccessMapped DEBUG Segment: 0
[2018-05-15 14:18:35] TDB DEBUG Txn[2]/R: finish
[2018-05-15 14:18:35] LockMRSW DEBUG pool-2-thread-1 >> leaveCS:
Thread R/W: 1/0 :: Model R/W: 1/0 (thread: pool-2-thread-1)
[2018-05-15 14:18:35] LockMRSW DEBUG pool-2-thread-1 << leaveCS:
Thread R/W: 0/0 :: Model R/W: 0/0 (thread: pool-2-thread-1)
[2018-05-15 14:18:35] Backup INFO [1] <<<< Finish backup /fcrepo ->
/var/archonnex/fuseki/backups/fcrepo_2018-05-15_14-18-35
[2018-05-15 14:18:35] Server INFO [Task 1] finishes : backup
log/archonnex/fuseki@acxcore-awstest0% ls -l
/var/archonnex/fuseki/backups/fcrepo_2018-05-15_14-18-35*
-rw-rw-r--. 1 fuseki fuseki 20 May 15 14:18
/var/archonnex/fuseki/backups/fcrepo_2018-05-15_14-18-35.nq.gz
--
Dan Pritts
ICPSR Computing & Network Services
University of Michigan
<https://www.postbox-inc.com>
