Hi all,
We are trying to go from BASE 2 RC1 to 2.0, and neither updating nor
initializing a new database seems to be working properly. Question is;
is it just us, or a BASE/Java/MySQL versions mismatch? If the latter,
are there any officially recommended/supported versions for BASE 2?
Notes:
- BASE 2 RC1 (compiled or binary) works OK (and can be rolled back, so
I don't suspect the system's broken by all the fiddling).
- It's not a password problem; setting it wrong in either base.config
or to the scripts produces the expected error messages.
Any help would be greatly appreciated!
TIA,
Emil / Linnaeus Centre for Bioinformatics
* System specs
Solaris 10 / SPARC, 6 GB, in a zone
JDK 1.5.0_01
MySQL 4.1.18
Tomcat 5.5
* Problem 1: using binary BASE 2.0
When running the 'updatedb.sh' script, java crashes after building the
initial database:
[0%] Building database........................
[30%] Database built successfully.
java.lang.NullPointerException
at net.sf.basedb.core.Update.getSchemaVersion(Update.java:319)
at
net.sf.basedb.core.Update.adjustExistingItems(Update.java:599)
at net.sf.basedb.install.InitDB.main(InitDB.java:66)
Populating a new database with 'initdb.sh' runs into similar problems:
[0%] Building database.............................
[30%] Database built successfully.
[35%] Initialising database...
java.lang.NullPointerException
at
net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881)
at net.sf.basedb.core.Install.initDatabase(Install.java:605)
at net.sf.basedb.install.InitDB.main(InitDB.java:67)
* Problem 2: compiling BASE 2.0
Base 2.0 does build successfully from source but with LOTS of warnings
using Java 1.5.0_01, but no change from the above situation. Excerpt:
[javac]
/install/source/base-2.0-src/src/core/net/sf/basedb/core/
HibernateUtil.java:1425: warning: [unchecked] unchecked conversion
[javac] found : java.util.Iterator
[javac] required:
java.util.Iterator<org.hibernate.mapping.PersistentClass>
[javac] return cfg.getClassMappings();
[javac] ^
[javac]
/install/source/base-2.0-src/src/core/net/sf/basedb/core/
HibernateUtil.java:1553: warning: [unchecked] unchecked cast
[javac] found : java.util.Iterator
[javac] required: java.util.Iterator<org.hibernate.mapping.Table>
[javac] Iterator<Table> tables =
(Iterator<Table>)cfg.getTableMappings();
[javac]
^
* Problem 3: using BASE 2.0 w/ JDK 1.5.0_08
Suspecting a major java problem, we tried installing a local version of
the latest JDK (1.5.0_08) and repeating the above. Compiling is now OK,
and using binary or source makes no difference. However, when trying
either 'updatedb.sh' or 'initdb.sh', we get the exact same behaviour as
before (NullPointerException).
Note: BASE 2 itself (the tomcat / web service part) works as far as
logging in, but afaik needs to be updated/reinitialized to support the
new features of 2.0.
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