Re: [base] BASE2: problem parsing flag strings to floats
Micha Bayer wrote: Hi, I am trying to import some raw data with flags such as NORMAL and ABNORMAL into raw bioassays. I have mapped this column to the 'Flags' field in the raw data importer config for Genepix format (this is on BASE 2.3.0). For some reason the importer chokes on the values for the flags though and throws a NumberFormatException. It looks to me as though it is trying to parse the String to a float -- see stack trace below. In the raw-data-types.xml config file the Flags field for the Genepix data format is listed as being an integer type. Could that be the problem? Is this a problem with my setup or potentially a bug, and has anyone else seen this behaviour? The 'flags' column is, as you say, a numeric column. It can't hold string values, and of course it will not know how to handle 'NORMAL' and 'ABNORMAL' values since they are not numbers. It is expected behaviour and is not a bug. You can set the importer option 'Invalid numeric value' to either 'null' or 'skip'. The 'null' option will not insert a value for the 'flag' at all and the 'skip' options will skip the entire data line. Another option is that you do a search-and-replace in your file and convert the NORMAL and ABNORMAL to some numeric values. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] BASE2: problem parsing flag strings to floats
Hi again, Just occurred to me that perhaps I might be barking up the wrong tree here altogether and that the flags should in fact be e.g. 0 and 1 instead of actual Strings like NORMAL? Cheers 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.ac.uk/staff/michabayer == -Original Message- From: [EMAIL PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Micha Bayer Sent: 05 October 2007 10:21 To: BASE ML Subject: [base] BASE2: problem parsing flag strings to floats Hi, I am trying to import some raw data with flags such as NORMAL and ABNORMAL into raw bioassays. I have mapped this column to the 'Flags' field in the raw data importer config for Genepix format (this is on BASE 2.3.0). For some reason the importer chokes on the values for the flags though and throws a NumberFormatException. It looks to me as though it is trying to parse the String to a float -- see stack trace below. In the raw-data-types.xml config file the Flags field for the Genepix data format is listed as being an integer type. Could that be the problem? Is this a problem with my setup or potentially a bug, and has anyone else seen this behaviour? Cheers Micha ===first 2 lines from the data file:= Name Clone IDF595 median F685 median B595 median B685 median Flagged As Block Column Row 3xSLv1(-)3xSLv1 323 461.5 137.5 190 NORMAL 1 3 1 ==stack trace: 09:28:40,961 ERROR jobqueue:434 - Exception while executing job: Job[id=336; name=Run plugin: Raw data importer] net.sf.basedb.core.BaseException: For input string: NORMAL on line 2: 3xSLv1 (-)3xSLv1... at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java : 428) at java.lang.Thread.run(Thread.java:619) Caused by: net.sf.basedb.core.BaseException: For input string: NORMAL on line 2: 3xSLv1(-)3xSLv1... at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFil e Importer.java:581) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImpo r ter.java:432) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest . java:88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java : 420) ... 1 more Caused by: java.lang.NumberFormatException: For input string: NORMAL at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1224 ) at java.lang.Float.valueOf(Float.java:388) at net.sf.basedb.core.Type$1.parseString(Type.java:72) at net.sf.basedb.core.ExtendedProperty.parseString(ExtendedProperty.java:1 7 9) at net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFil e Importer.java:536) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFil e Importer.java:559) ... 4 more == 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.ac.uk/staff/michabayer == _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. 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). --- -- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find
[base] Virtual Machine with BASE installed?
Hi Just wondering if anyone has a Virtual Machine with BASE installed on it? Thanks Mick The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it notify the originator immediately. Unauthorised use, disclosure, copying or alteration of this message is forbidden may be unlawful. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute. This email and associated attachments has been checked locally for viruses but we can accept no responsibility once it has left our systems. Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] problems with my trashcan
Nicklas wrote: Are you logged in as the user that is the owner of the experiment? I am logged in as root. Shouldn't root be able to delete anything? Chad Matsalla - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Data cube has already been committed
Greetings All! Is there anything that I can so about this error? I'm completely stuck. I don't really know what a data cube is or how it could have already been committed. Do I need to delete the experiment or something? I can't help but wonder if it has something to do with my trashcan problems. Is there some sort of database validator that I can run to test if my databases are consistent? They are large - 10G. Chad Matsalla - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
