Received the following stack trace after running a .bxs script using basexclient from the command line:
Version: BaseX 7.6 Java: Sun Microsystems Inc., 1.6.0_27 OS: Linux, amd64 Stack Trace: java.lang.NegativeArraySizeException org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:390) org.basex.data.Data.insert(Data.java:931) org.basex.data.Data.insert(Data.java:820) org.basex.data.atomic.Insert.apply(Insert.java:31) org.basex.data.atomic.AtomicUpdateList.applyStructuralUpdates(AtomicUpdateList.java:297) org.basex.data.atomic.AtomicUpdateList.execute(AtomicUpdateList.java:285) org.basex.query.up.DatabaseUpdates.apply(DatabaseUpdates.java:183) org.basex.query.up.ContextModifier.apply(ContextModifier.java:90) org.basex.query.up.Updates.apply(Updates.java:120) org.basex.query.QueryContext.update(QueryContext.java:270) org.basex.query.QueryContext.value(QueryContext.java:255) org.basex.query.QueryContext.iter(QueryContext.java:240) org.basex.query.QueryProcessor.iter(QueryProcessor.java:76) org.basex.core.cmd.AQuery.query(AQuery.java:84) org.basex.core.cmd.XQuery.run(XQuery.java:22) org.basex.core.Command.run(Command.java:342) org.basex.core.Command.exec(Command.java:321) org.basex.core.Command.execute(Command.java:78) org.basex.server.ClientListener.run(ClientListener.java:145)
What the script does is very complex (large xquery functions, db:node-pre() indexing and lookups, etc) so if you need it to isolate this issue we can discuss directly.
However I get a similar stack trace when I attempt to OPTIMIZE ALL:
open deepbills
Database 'deepbills' was opened in 114.99 ms.
optimize all
Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 7.6 Java: Sun Microsystems Inc., 1.6.0_27 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 65 org.basex.util.Compress.pull(Compress.java:156) org.basex.util.Compress.unpack(Compress.java:112) org.basex.data.DiskData.txt(DiskData.java:268) org.basex.data.DiskData.text(DiskData.java:235) org.basex.io.serial.Serializer.node(Serializer.java:343) org.basex.io.serial.Serializer.serialize(Serializer.java:99) org.basex.core.cmd.OptimizeAll$DBParser.parse(OptimizeAll.java:199) org.basex.build.Builder.parse(Builder.java:73) org.basex.build.DiskBuilder.build(DiskBuilder.java:90) org.basex.core.cmd.OptimizeAll.optimizeAll(OptimizeAll.java:124) org.basex.core.cmd.OptimizeAll.run(OptimizeAll.java:44) org.basex.core.Command.run(Command.java:342) org.basex.core.Command.exec(Command.java:321) org.basex.core.Command.execute(Command.java:78) org.basex.server.ClientListener.run(ClientListener.java:145)
info database
Database Properties Name: deepbills Size: 901 MB Nodes: 25598080 Documents: 15528 Binaries: 0 Timestamp: 2013-04-08-15-02-07
Resource Properties Timestamp: 2013-04-08-15-02-07 Encoding: UTF-8 Whitespace Chopping: ON
Indexes Up-to-date: false Text Index: OFF Attribute Index: OFF Full-Text Index: OFF UPDINDEX: OFF MAXCATS: 100 MAXLEN: 96
If I restore from a backup (taken after this issue appeared), I still can't "optimize all", but the stack trace appears truncated:
restore deepbills
'deepbills-2013-04-08-15-54-32.zip' was restored in 40918.34 ms.
optimize all
No database opened.
open deepbills
Database 'deepbills' was opened in 136.22 ms.
optimize all
Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 7.6 Java: Sun Microsystems Inc., 1.6.0_27 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException
If I restore a backup that is just a little bit older (a little over an hour), it seems fine:
restore deepbills-2013-04-08-14-22-22
'deepbills-2013-04-08-14-22-22.zip' was restored in 38982.91 ms.
optimize all
Database 'deepbills' was optimized in 129658.46 ms.
So I have two similar databases, one 363MB zip, one 372MB zip, one of which is fine and the other which seems to encounter this problem. Could I be looking at database corruption here? If so, how to fix?