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https://issues.apache.org/jira/browse/JENA-230?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13245446#comment-13245446
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Andy Seaborne commented on JENA-230:
------------------------------------
Bill,
Thanks for the detail. Fix put into TDB.
The fix is to use a ThreadLocal variable to hold the transaction support part
of the state of a dataset.
This will work for Fuseki -- it's effectively a connection pool.
The TDB documentation states that "Dataset" should be used per thread. Fuseki
uses a slightly lower level route in.
The fix applied addresses the problem for Fuseki - whether it's the best fix
for the whole system is something to think about but any other solution must
support Fuseki's mode of use so any future change will be purely internal to
support other usages (if a change is made at all - the current, ne appraoch may
be the best anyway).
> Running queries during graph PUT leads to PUT failing
> -----------------------------------------------------
>
> Key: JENA-230
> URL: https://issues.apache.org/jira/browse/JENA-230
> Project: Apache Jena
> Issue Type: Bug
> Components: Fuseki
> Affects Versions: Fuseki 0.2.1
> Environment: Macosx.
> Reporter: Bill Roberts
>
> 1. create empty dir for TDB and start fuseki with that directory as the
> tdb:location
> 2. PUT a small file to the graph protocol endpoint
> curl -v -H "Content-Type: text/turtle" --upload-file small.ttl
> http://localhost:3030/crashtest/data?graph=http://test1
> 3. Run a count of all triples (this step not necessary to reproduce, but just
> a baseline check to compare against later stages).
> select (count(*) as ?c) where {?s ?p ?o}
> Answer in my case is 25 (as expected)
> 4. PUT a big file
> curl -v -H "Content-Type: text/turtle" --upload-file big.ttl
> http://localhost:3030/crashtest/data?graph=http://test2
> (big enough that it takes at least several seconds to load, so you have time
> to run some other stuff. My example was about 200,000 triples)
> 5. Before it finishes, run the count query another 2 or more times.
> It comes back with 25 each time. So far so good.
> 6. After the big file load is finished (check for 201 Created in log), run
> the count again.
> This is where the problem is evident: the count still shows 25, when it
> should show 200,000 or so.
> (Probably not significant, but my small test file has a few blank nodes in
> it. The big file does not).
> ls -l of the TDB dir shows lots of data still in nodes.dat-jrnl. The log
> includes the line:
> "WARN TDB :: Transaction not active: 5"
> (full copy of the log below)
> Going through the same procedure without running the COUNTs mentioned in
> stage 5, then everything goes smoothly.
> I'd be interested to hear if anyone else can reproduce this - and of course
> to hear what you think might be wrong!
> Many thanks
> Bill
> Details:
> OS: Macosx 10.6.8
> fuseki-server --version
> ------------------------------
> Jena: VERSION: 2.7.0-incubating
> Jena: BUILD_DATE: 2011-12-14T14:54:09+0000
> ARQ: VERSION: 2.9.0-incubating
> ARQ: BUILD_DATE: 2011-12-14T15:04:27+0000
> TDB: VERSION: 0.9.0-incubating
> TDB: BUILD_DATE: 2012-02-29T19:39:52+0000
> Fuseki: VERSION: 0.2.2-incubating-SNAPSHOT
> Fuseki: BUILD_DATE: 20120330-0505
> java -version
> ------------------
> java version "1.6.0_29"
> Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-10M3527)
> Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02-402, mixed mode)
> Config file:
> ---------------
> @prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> [] rdf:type fuseki:Server ;
> # Services available. Only explicitly listed services are configured.
> # If there is a service description not linked from this list, it is
> ignored.
> fuseki:services (
> <#service1>
> ) .
> [] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
> tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset .
> tdb:GraphTDB rdfs:subClassOf ja:Model .
> <#service1> rdf:type fuseki:Service ;
> fuseki:name "crashtest" ; # http://host:port/blah
> fuseki:serviceQuery "query" ; # SPARQL query service
> fuseki:serviceUpdate "update" ; # SPARQL update service
> fuseki:serviceReadWriteGraphStore "data" ; # SPARQL Graph store
> protocol (read and write)
> fuseki:dataset <#dataset-blah> ;
> .
> <#dataset-blah> rdf:type tdb:DatasetTDB ;
> tdb:location "/Users/bill/tdb/crashtest" ;
> # Query timeout on this dataset (1s, 1000 milliseconds)
> ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "10000" ] ;
> tdb:unionDefaultGraph true ;
> fuseki log:
> --------------
> 20:23:51 INFO Config :: Configuration file: test.ttl
> 20:23:51 INFO Config :: Service:
> <file:///Users/bill/code/fuseki-0.2.2/test.ttl#service1>
> 20:23:51 INFO Config :: name = crashtest
> 20:23:51 INFO Config :: query = /crashtest/query
> 20:23:51 INFO Config :: update = /crashtest/update
> 20:23:51 INFO Config :: graphStore(RW) = /crashtest/data
> 20:23:52 INFO Server :: Dataset path = /crashtest
> 20:23:52 INFO Server :: Fuseki 0.2.2-incubating-SNAPSHOT
> 20120330-0505
> 20:23:52 INFO Server :: Jetty 7.x.y-SNAPSHOT
> 20:23:52 INFO Server :: Started 2012/04/01 20:23:52 BST on
> port 3030
> 20:24:15 INFO Fuseki :: [1] PUT
> http://localhost:3030/crashtest/data?graph=http://test1
> 20:24:16 INFO Fuseki :: [1] 201 Created
> 20:24:43 INFO Fuseki :: [2] GET
> http://localhost:3030/crashtest/query?query=select+%28count%28*%29+as+%3Fc%29+where+%7B%3Fs+%3Fp+%3Fo%7D+&output=text&stylesheet=%2Fxml-to-html.xsl
> 20:24:43 INFO Fuseki :: [2] Query = select (count(*) as ?c)
> where {?s ?p ?o}
> 20:24:43 INFO Fuseki :: [2] OK/select
> 20:24:43 INFO Fuseki :: [2] 200 OK
> 20:29:12 INFO Fuseki :: [3] PUT
> http://localhost:3030/crashtest/data?graph=http://test2
> 20:29:14 INFO Fuseki :: [4] GET
> http://localhost:3030/crashtest/query?query=select+%28count%28*%29+as+%3Fc%29+where+%7B%3Fs+%3Fp+%3Fo%7D+&output=text&stylesheet=%2Fxml-to-html.xsl
> 20:29:14 INFO Fuseki :: [4] Query = select (count(*) as ?c)
> where {?s ?p ?o}
> 20:29:14 INFO Fuseki :: [4] OK/select
> 20:29:14 INFO Fuseki :: [4] 200 OK
> 20:29:18 INFO Fuseki :: [5] GET
> http://localhost:3030/crashtest/query?query=select+%28count%28*%29+as+%3Fc%29+where+%7B%3Fs+%3Fp+%3Fo%7D+&output=text&stylesheet=%2Fxml-to-html.xsl
> 20:29:18 INFO Fuseki :: [5] Query = select (count(*) as ?c)
> where {?s ?p ?o}
> 20:29:18 INFO Fuseki :: [5] OK/select
> 20:29:18 INFO Fuseki :: [5] 200 OK
> 20:29:28 WARN TDB :: Transaction not active: 5
> 20:29:28 INFO Fuseki :: [3] 201 Created
> 20:29:28 INFO Fuseki :: [6] GET
> http://localhost:3030/crashtest/query?query=select+%28count%28*%29+as+%3Fc%29+where+%7B%3Fs+%3Fp+%3Fo%7D+&output=text&stylesheet=%2Fxml-to-html.xsl
> 20:29:28 INFO Fuseki :: [6] Query = select (count(*) as ?c)
> where {?s ?p ?o}
> 20:29:28 INFO Fuseki :: [6] OK/select
> 20:29:28 INFO Fuseki :: [6] 200 OK
> ls -l crashtest
> ------------------
> drwxr-xr-x 31 bill bill 1054 1 Apr 20:24 ./
> drwxr-xr-x 15 bill bill 510 1 Apr 20:23 ../
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 GOSP.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 GOSP.idn
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 GPOS.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 GPOS.idn
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 GSPO.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 GSPO.idn
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 OSP.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 OSP.idn
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 OSPG.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 OSPG.idn
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 POS.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 POS.idn
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 POSG.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 POSG.idn
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 SPO.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 SPO.idn
> -rw-r--r-- 1 bill bill 16777216 1 Apr 20:29 SPOG.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 SPOG.idn
> -rw-r--r-- 1 bill bill 0 1 Apr 20:24 journal.jrnl
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:24 node2id.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:24 node2id.idn
> -rw-r--r-- 1 bill bill 2485 1 Apr 20:24 nodes.dat
> -rw-r--r-- 1 bill bill 5596812 1 Apr 20:29 nodes.dat-jrnl
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 prefix2id.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 prefix2id.idn
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 prefixIdx.dat
> -rw-r--r-- 1 bill bill 8388608 1 Apr 20:23 prefixIdx.idn
> -rw-r--r-- 1 bill bill 0 1 Apr 20:23 prefixes.dat
> -rw-r--r-- 1 bill bill 0 1 Apr 20:24 prefixes.dat-jrnl
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