In the future please send questions about BASE to the mailing list:
basedb-users@lists.sourceforge.net
It seems like the missing query was accidentally removed between BASE 2.12.1
and BASE 2.13. The query is needed in the update between 2.11 and 2.12.
The simplest workaround is to manually add the missing query to
mysql-queries.xml
(or postgres-queries.xml for users that are running PostgreSQL). Those files
should be
located in the www/WEB-INF/classes directory. Open the file that matches the
database
and add the following entry to it:
<query id="SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS" type="HQL">
<sql>
UPDATE BioAssaySetData bas
SET bas.intensityTransform = :transform
WHERE bas.intensityTransform IS NULL
</sql>
<description>
An update query that sets the intensityTransform on all
bioassay sets that doesn't have a value.
</description>
</query>
Then, run the ./updatedb.sh script again.
/Nicklas
Chad Matsalla wrote:
>
> Greetings Nicklas,
>
> I'm trying to install base-2.14.0.
>
> When I run the updatedb.sh script, I get this.[1]
>
> This query doesn't exist in the stuff I downloaded:
> c...@lemon:/home/tomcat/base-2.14.0$ find . -exec grep --with-filename
> SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS {} \;
> c...@lemon:/home/tomcat/base-2.14.0$
>
> The last BASE I ran was 2.9.2, as indicated by the text of the exception
> in the web browser:
> net.sf.basedb.core.BaseException: Schema version mismatch: database
> schema version=65; expected=76; Please update the database with the
> 'updatedb.sh' script before starting BASE.
>
> What do I do?
>
> Thank you for your time,
>
> Chad Matsalla
>
>
>
>
>
>
> [1]
> [0%] --System information-----------------------------
> BASE : 2.14.0
> Database :
> jdbc:mysql://db.bioinfo.pbi/base2_9_2?useCursorFetch=true&defaultFetchSize=1000&useServerPrepStmps=true
>
> Dialect : org.hibernate.dialect.MySQLInnoDBDialect
> JDBC : com.mysql.jdbc.Driver; version 5.1
> Java : Java(TM) SE Runtime Environment; 1.6.0_13-b03; Sun
> Microsystems Inc.
> OS : Linux; i386; 2.6.29-1-amd64
> -------------------------------------------------
> [0%] Building database.............
> [30%] Database built successfully.
> [70%] The adjustment of the existing items failed: Node '<query
> id="SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS">' was not found in file
> '/common-queries.xml' or in file '/mysql-queries.xml'
>
>
> net.sf.basedb.core.BaseException: Node '<query
> id="SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS">' was not found in file
> '/common-queries.xml' or in file '/mysql-queries.xml'
> at
> net.sf.basedb.core.PredefinedQuery.getQueryString(PredefinedQuery.java:158)
> at
> net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1685)
>
> at
> net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1671)
>
> at
> net.sf.basedb.core.Update.adjustExistingItems(Update.java:3128)
> at net.sf.basedb.install.InitDB.main(InitDB.java:73)
>
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