Re: [base] GROUP clause error
Chad Matsalla wrote: Gretings! I see this as well. It's because this query: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY COUNT(*) DESC should say: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY mapCount DESC Hm. For mysql4, anyway. It may be as you say, but I can't verify it since I don't have a MySQL 4 database. Strange that it complains about the GROUP BY clause when the error is in the ORDER BY clause. Anyway, 'ORDER BY mapCount' should work with MySQL 5 as well and it shouldn't be difficult to fix. I have added a ticket for it (http://base.thep.lu.se/ticket/581), but don't expect it to be fixed before the 2.4 release. In the meantime I think upgrading to MySQL 5.0 is the only option. /Nicklas - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Base Lowess normalization program
Dear All: I am using Base Lowess program to normalize my Microarray data. But seems it works with my small dataset input (e.g. 44k-probe records). But it doesn't work with my big data input file (e.g. 244K-probe array). So does Lowess have data file size limitation? If so, how can I fix it? By the way, I only have the executable? Is there any way I could get source code? Thank you very much, George - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Lowess, plug-ins
Dear Jari and other experienced users: We once installed your Lowess normalization plugin model several years ago. It worked fine. Recently we are dealing with larger dataset such as 244K agilent array which has about 244,000 records in each array. Then the program failed because of segmentation (core dump). We are wondering if your lowess plug-in model had updated to deal with the issue. If you could provide a information link on downloading and installing this model, we would greatly appreciate. Thank you very much; George -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: Monday, January 16, 2006 10:13 AM To: basedb-users@lists.sourceforge.net Subject: Re: [base] MAGE-ML for ArrayExpress update, plug-ins Yes ... but probably after release. We have already assigned enough for us all to do, but this wil be added asap after Feb 23. There are more R related stuff to be implemented during the spring. Jari charles girardot wrote: Hi Jari, Could you make sure that the R dispatcher (AROMA BASE, by Henrik Bengtsson from Lund) continues to work in BASE 2.0 Thanks Charles On 16 janv. 06, at 13:40, Jari Häkkinen wrote: Hi Angela, BASE plug-ins ... we are slowly working on getting the web page up again. Meanwhile we urge those of you who have plug-ins to send them to us through http://lev.thep.lu.se/trac/baseplugins Jari Angela Burr wrote: Hi, Our group has been using BASE for over a year and we have been eagerly awaiting the completion of MAGE-ML creation corrections (so that MAGE-ML files created by BASE are acceptable for ArrayExpress submission). We have data in BASE that we need to submit to ArrayExpress. Would you please give an update on the progress and possibly a timeline for when these changes will be incorporated into BASE 1.2.x? We really appreciate all the work on this project, adding this function in BASE will be very helpful. Also, when will more plug-ins be added to the new BASE plug-in development site? Our group is interested in adding more analysis plug-ins to our BASE installation and I'm sure that many BASE plugins have already been written. We would prefer not replicate the work if others have already written similar plug-ins. Thank you for the updates in advance. Angela Burr Center for Genomics and Bioinformatics Indiana University, Bloomington --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37alloc_id865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK!
Re: [base] migrator script causes lots of exceptions
If you are using MySQL 5.0.27 this is caused by a bug in that version. Either use an older version of MySQL or remove 'useCursorFetch=true' the db.url setting in your base.config file. The second option may give you out-of-memory problems if you have a large database. In that case, you must either get more memory or use an older MySQL version. For more info see: http://base.thep.lu.se/ticket/568 /Nicklas Bernd Schwendele wrote: Hi, I want to migrate an old BASE installation (1.2) to an newer one (2) on another machine/arch. During the run of migrate_from_1.2.sh there are many exceptions, e.g. 17:50:28,656 ERROR migration:85 - getSampleById net.sf.basedb.core.BaseException: could not load an entity: [net.sf.basedb.core.data.SampleData#2] at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1063) at net.sf.basedb.core.DbControl.loadItem(DbControl.java:681) at net.sf.basedb.core.Sample.getById(Sample.java:88) at net.sf.basedb.clients.migrate.SampleTransfer.getSampleById(SampleTransfer.java:143) at net.sf.basedb.clients.migrate.ExtractTransfer.createItem(ExtractTransfer.java:90) at net.sf.basedb.clients.migrate.ExtractTransfer.createItem(ExtractTransfer.java:44) at net.sf.basedb.clients.migrate.Transfer.run(Transfer.java:346) at net.sf.basedb.clients.migrate.ExtractTransfer.start(ExtractTransfer.java:70) at net.sf.basedb.clients.migrate.Migrater.startTransfer(Migrater.java:218) at net.sf.basedb.clients.migrate.Migrater.run(Migrater.java:125) at net.sf.basedb.clients.migrate.Migrater.main(Migrater.java:478) Caused by: org.hibernate.exception.DataException: could not load an entity: [net.sf.basedb.core.data.SampleData#2] at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadEntity(Loader.java:1865) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3038) at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:395) at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:375) at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:139) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:179) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.get(SessionImpl.java:815) at org.hibernate.impl.SessionImpl.get(SessionImpl.java:808) at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1059) ... 10 more Caused by: com.mysql.jdbc.exceptions.MySQLDataException: '8589934593' in column '15' is outside valid range for the datatype INTEGER. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:893) at com.mysql.jdbc.ResultSet.throwRangeException(ResultSet.java:7391) at com.mysql.jdbc.ResultSet.getNativeInt(ResultSet.java:3967) at com.mysql.jdbc.ResultSet.getNativeInt(ResultSet.java:3892) at com.mysql.jdbc.ResultSet.getInt(ResultSet.java:2555) at com.mysql.jdbc.ResultSet.getInt(ResultSet.java:2570) at com.mchange.v2.c3p0.impl.NewProxyResultSet.getInt(NewProxyResultSet.java:2573) at org.hibernate.type.IntegerType.get(IntegerType.java:28) at org.hibernate.type.NullableType.nullSafeGet(NullableType.java:163) at org.hibernate.type.NullableType.nullSafeGet(NullableType.java:154) at org.hibernate.type.AbstractType.hydrate(AbstractType.java:81) at org.hibernate.type.ComponentType.hydrate(ComponentType.java:560) at org.hibernate.type.ComponentType.nullSafeGet(ComponentType.java:275) at org.hibernate.type.SpecialOneToOneType.hydrate(SpecialOneToOneType.java:58) at org.hibernate.persister.entity.AbstractEntityPersister.hydrate(AbstractEntityPersister.java:2092) at org.hibernate.loader.Loader.loadFromResultSet(Loader.java:1371) at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1299) at org.hibernate.loader.Loader.getRow(Loader.java:1197) at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568) at org.hibernate.loader.Loader.doQuery(Loader.java:689) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) at org.hibernate.loader.Loader.loadEntity(Loader.java:1851) ... 22 more Is there a bug in the migrate-Tool? Regards Bernd - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now.
Re: [base] file format matching problems
Steve Taylor wrote: Hi, I got a confusing message when I was using the Experiments Import. Basically, BASE was expecting a zip file and I was (perhaps stupidly) trying to upload a single file. The BASE WWW interface returned: 'We couldn't find any file format mathing the file /home/Admin/latestbluefuse.txt.' In the error log the problem is clear. = ===NEW BATCH IMPORT = = file is not a zip file java.lang.NullPointerException at sbrn.base.BatchDataImporter.isImportable(BatchDataImporter.java:181) at net.sf.basedb.util.AutoDetectFileFormat.findPlugins(AutoDetectFileFormat.java:145) Could a similar message be shown in the GUI? As it is currently implemented it is not possible. A plugin can only answer yes or no when asked if it can import a file. Unfortunately, it can't give any reason why the file can't be imported. /Nicklas - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
