バージョン 10 (更新者: wu, 12 年 前)

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* Mulgara 配置

* Load performance

* Sparql query performance

Mulgara 配置

Load Performance

Allie upload

About 89 mins

PDBJ upload

The file includes the characteristics like ABSA_(A2) that can not be dealt with by Mulgara. 2012-01-17 10:10:49,066 WARN [main] itql.TqlSession?? - Couldn't execute command org.mulgara.query.QueryException??: Unable to load file:/opt/services/togordf/data/pdbj/XML/10gs-noatom.rdf.gz into  rmi://localhost/Pdbj#pdbj: Illegal character in path at index 60:  http://pdbj.org/rdf/10GS/pdbx_struct_assembly_prop/1,ABSA_(A^2)

Uniprot upload

2012-07-12 03:20:25,512 WARN [main] itql.TqlSession? - Couldn't execute command org.mulgara.query.QueryException?: Unable to load file:/opt/services/togordf/data/uniprot/uniprotgz/uniprot.rdf.gz into rollback: Unexpected XAException:Cannot send res.rollback:javax.transaction.xa.XAException (error code = -3) --null

at org.mulgara.resolver.DatabaseSession?.execute(DatabaseSession?.java:746) at org.mulgara.resolver.DatabaseSession?.setModel(DatabaseSession?.java:580) at org.mulgara.server.rmi.SessionWrapperRemoteSession?.setModel(SessionWrapperRemoteSession?.java:126) at sun.reflect.NativeMethodAccessorImpl?.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl?.invoke(NativeMethodAccessorImpl?.java:39) at sun.reflect.DelegatingMethodAccessorImpl?.invoke(DelegatingMethodAccessorImpl?.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at sun.rmi.server.UnicastServerRef?.dispatch(UnicastServerRef?.java:305)

DDBJ upload

2012-07-06 23:54:59,770 WARN [main] itql.TqlSession? - Couldn't execute command org.mulgara.query.QueryException?: Unable to load file:/opt/services/togordf/data/ddbj/ddbj_release/ddbjbct3.rdf.gz into  rmi://localhost/ddbj#ddbj: Exception on rollback:java.rmi.RemoteException: rollb ack: Unexpected XAException:Cannot send res.rollback:javax.transaction.xa.XAException (error code = -3) --null

at org.mulgara.resolver.DatabaseSession?.execute(DatabaseSession?.java:746) at org.mulgara.resolver.DatabaseSession?.setModel(DatabaseSession?.java:580)

loadtime Cell Cycle Ontology Allie PDBj UniProt?
1st time 10mins 89mins 537mins
2nd time 9mins mins mins
average 10mins mins mins

Sparql query performance

Cell Cycle query

Query\time(ms) time 1 time 2 time 3 time 4time 5
case1 1299 1293 1290 1297 1297
case2 27 26 18 17 17
case3 2211 2221 2202 2207 2207
case4 10 9 10 9 9
case5 369 332 347 347 347
case6 2353 2319 2358 2314 2314
case7 39 31 34 32 32
case8 59 65 67 54 54
case9 39 33 36 32 32
case10 5 4 5 4 4
case11 14 14 15 14 14
case12 XXXXX
case13 8 9 8 9 9
case14 6 6 6 6 6
case15 XXXXX
case16 XX X X X
case17 XX X X X
case18 XX X X X
case19 34 41 41 39 39

Case 12: "Exception in thread ""main"" org.mulgara.query.QueryException?: Query failed: Unknown ConstraintExpression? type: class org.mulgara.query.ConstraintFalse? known types: [class org.mulgara.resolver.relational.RelationalConstraint?, class org.mulgara.query.ConstraintFilter?, class org.mulgara.resolver.xsd.IntervalConstraint?, class org.mulgara.query.WalkConstraint?, class org.mulgara.query.SingleTransitiveConstraint?, class org.mulgara.query.ConstraintIn?, class org.mulgara.query.ConstraintOptionalJoin?, class org.mulgara.query.ConstraintAssignment?, class org.mulgara.resolver.lucene.LuceneConstraint?, class org.mulgara.query.ConstraintConjunction?, class org.mulgara.query.ConstraintDifference?, class org.mulgara.query.ConstraintImpl?, class org.mulgara.query.ConstraintDisjunction?, class org.mulgara.query.TransitiveConstraint?, class org.mulgara.query.ConstraintIs?]"

Case 16,17 &18: Exception in thread "main" org.mulgara.parser.MulgaraParserException?: Encountered "count" at line

Case 15: Showing 0 results(some unsupported function caused the wrong query result)

Allie query

Query\time(ms) time 1 time 2 time 3 time 4time 5
case1 375 377 373 376 368
case2 123 123 119 120 128
case3 XX X X X
case4 XX X X X
case5 XX X X X

As for case3,4&5: Exception in thread "main" org.mulgara.parser.MulgaraParserException?: Unable to support arbitrarily complex ORDER BY clause

PDBJ query

Uniprot query

DDBJ query