Re: [base] Workaround for upgrading a Postgres database
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Hello Postgres users, We have now published some information about a workaround to make it possible to upgrade a BASE installation running on a Postgres database. Hi Nicklas Thanks for the workaround. I did the updatedb.sh as you suggested: it ran quite smoothly Then I tried the updateindexes.sh script, and I got the message: The indexes are not really needed but they will increase performance. For example, the Features table may receive lots of data and is one that you want to have indexes on. At first, it may seem unfortunate that this is the table that is causing the problem. But, the index exists, it's just that the update script doesn't find it. This time it is not a bug in Hibernate, but in the BASE code. Well, fix it for the 2.1.1 release. What you can do until then is to remove the index before executing the updateindexes.sh script. You remove it with the following SQL command: ALTER TABLE Features DROP CONSTRAINT Features_uniquecoordinate /Nicklas = Table : Features Unique : uniquecoordinate [column, row, arraydesignblock_id] Exists : false Safe drop : false DROP-SQL : CREATE-SQL : ALTER TABLE Features ADD CONSTRAINT Features_uniquecoordinate UNIQUE (column, row, arraydesignblock_id) Actions: CREATE 13:54:53,569 ERROR core:1723 - Exception org.postgresql.util.PSQLException: ERROR: relation Features_uniquecoordinate already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:340) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:286) at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64) at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1715) at net.sf.basedb.install.InitDB.main(InitDB.java:85) net.sf.basedb.core.BaseException: ERROR: relation Features_uniquecoordinate already exists at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1724) at net.sf.basedb.install.InitDB.main(InitDB.java:85) Caused by: org.postgresql.util.PSQLException: ERROR: relation Features_uniquecoordinate already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:340) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:286) at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64) at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1715) ... 1 more Is it serious ? - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] 2 questions about Plugin configuration
Nicklas Nordborg wrote: Emmanuel Courcelle wrote: Hello Now using Base 2.1... I am trying to configure the Raw Data importer plugin, to upload and parse genepix-type files. 1/ Pb configuring this plugin -- I click Plugin/Configuration/New -configuration name: bla bla -Raw DataType: Genepix -Next -Test with file/Select some uploaded file/Parse the file Then I get an error: Start of data couldn't be found. Please try again with different settings. In the window with the data file, I search the line marked Block Column Raw a.s.o., (it is the nb 30 for me), I have a box marked 'Unknown': I choose in the list Data header, I click and this fills up the field Data header regexp I then click again on Parse the File, this produces THE SAME error: I tried with some other (simpler) regular expressions, same behaviour: am I doing anything wrong ? I don't think so. It seems strange that it can't find the data the second time you click on Parse the file button. I really don't know why that is happening. Most of our test data files are Genepix files and we have not had any problems with them. I am thinking that maybe something gets trunkated or there is a problem with different types of linebreaks. Can you send me a few lines from a file with this problem? If should be enough with one line of data. If your headers have sensitive information please remove them as well. I noticed a similar problem as Emmanuel. I choose a data header line and tried to parse the file. It did not work so I only used the first part of the regexp created by the wizzard. This solved the problem for me and the wizzard could parse the file. I'll try to see if I can reproduce this problem and report back later. Cheers, Jari - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] logging in BASE2
Hi, I am running BASE2.1 under Tomcat 5.5 and I am getting my catalina.out log swamped by BASE log statements. Is there any way I can turn this off? I have tried to change the log levels in the log4j.properties file in www\WEB-INF\classes\, and even deleted this file but it seems to have made no difference. Is the logging configured in the BASE source perhaps? Thanks Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] create slide wizard numbering
Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) thanks, Keith Ching - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] 2 questions about Plugin configuration
Emmanuel Courcelle wrote: Hi Nicklas Here are the first 44 lines of the file I tried to dos2unix-ify, it did not change anything for Base. Thanks for your help ! I have now tested with your file and it works perfectly. Perhaps it is a browser-related problem. I have tested with Internet Explorer 6 and Firefix 1.5 on Windows and Mozilla 1.7.6 on Linux. What broswer are you using? /Nicklas - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] logging in BASE2
Micha Bayer wrote: Hi, I am running BASE2.1 under Tomcat 5.5 and I am getting my catalina.out log swamped by BASE log statements. Is there any way I can turn this off? It doesn't sound normal. What kind of log messages do you get? I have tried to change the log levels in the log4j.properties file in www\WEB-INF\classes\, and even deleted this file but it seems to have made no difference. Is the logging configured in the BASE source perhaps? Logging done by BASE is controlled by the log4j.properties file which you already have found. The default settings doesn't log anything except errors and warnings and if these start to appear frequently it is usually something that should be taken care of. Deleting the file is probably not a good idea. It used to cause Hibernate to output lots of INFO-level messages. /Nicklas - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] create slide wizard numbering
Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) Oops, it shouldn't be. Only the number of slides to create should have a limit. /Nicklas Ps. The next time you send mail to the mailing list, please start a new message instead of replying to an existing one and changing the subject. Your message appears as a reply to the original message and is easily missed by anyone not interested in the original subject. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
