[base] Plugin configuration (still some pb)
file we have been testing on the "Rgn R" column should be column number 32 and the mapping to use \32\. hum... rather 33, I think (it was 33 in Base 1.2). Does the column numbers start at 0 or at 1 ? If they start at 1 it is 33 Sorry to bother you, but I still have a problem (not sure it is related to this point, however): when I try to import the file I sent to you, I get an error. Error: Item not found: Reporter[externalId=SMa1894] on line 31: 1 1 1 SMa1894 24... I do not understand the error: he says he cannot find the reporter, but he displays SMa1894 which is the reporter ID. Did I do anything stupid ? -- Here is the stack trace generated: net.sf.basedb.core.BaseException: Item not found: Reporter[externalId=SMa1894] on line 31: 1 1 1 SMa1894 24... at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:571) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:421) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:82) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) at java.lang.Thread.run(Thread.java:595) Caused by: net.sf.basedb.core.ItemNotFoundException: Item not found: Reporter[externalId=SMa1894] at net.sf.basedb.core.RawDataBatcher.doInsert(RawDataBatcher.java:367) at net.sf.basedb.core.RawDataBatcher.insert(RawDataBatcher.java:343) at net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFileImporter.java:535) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:549) ... 4 more and here are the plugin parameters: Job parameters Default error handling fail featureMismatchError File /home/manu/raw data/genepix/H058446.txt Missing a required value Reporter not found Invalid numeric value Numeric value out of range Raw bioassay T0-T2 058446 - manu.s1.r1 String too long Plugin configuration parameters Parameter version 15 (15) Block \Block\ Column \Column\ Data footer Data header \QBlock Column Row Name ID X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % B635+1SD % B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % B532+1SD % B532+2SD F532 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R\E.\Q F Pixels B Pixels Sum of Medians Sum of Means Log Ratio F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags\E Data splitter \t Header (.+)=(.*) Ignore Max data columns 0 MetaGridX MetaGridY Min data columns 0 CV Background pixels \B Pixels\ Channel 1 background mean \B532 Mean\ Channel 1 background median \B532 Median\ Channel 1 background standard deviation \B532 SD\ Channel 1 foreground mean \F532 Mean\ Channel 1 foreground median \F532 Median\ Channel 1 foreground standard deviation \F532 SD\ Percent saturated pixels \F532 % Sat.\ Percent pixels within 1 standard deviation \% B532+1SD\ Percent pixels within 2 standard deviations \% B532+2SD\ Channel 2 background mean \B635 Mean\ Channel 2 background median \B635 Median\ Channel 2 background standard deviation \B635 SD\ Channel 2 foreground mean \F635 Mean\ Channel 2 foreground median \F635 Median\ Channel 2 foreground standard deviation \F635 SD\ Percent saturated pixels \F635 % Sat.\ Percent pixels within 1 standard deviation \% B635+1SD\ Percent pixels within 2 standard deviations \% B635+2SD\ Spot diameter \Dia.\ Foreground pixels \F Pixels\ Flags \Flags\ M value Standard deviation of ratios \Ratios SD\ Rgn R2 \33\ Rgn ratio \Rgn Ratio\ Raw data type genepix Reporter ID \ID\ Row \Row\
Re: [base] Plugin configuration (still some pb)
Emmanuel Courcelle wrote: file we have been testing on the Rgn R² column should be column number 32 and the mapping to use \32\. hum... rather 33, I think (it was 33 in Base 1.2). Does the column numbers start at 0 or at 1 ? As I wrote in the previous mail: The columns are numbered from 0 so the file we have been testing on the Rgn R² column should be column number 32 and the mapping to use \32\. I counted twice, but of course you should check that it is correct. If they start at 1 it is 33 Sorry to bother you, but I still have a problem (not sure it is related to this point, however): when I try to import the file I sent to you, I get an error. Error: Item not found: Reporter[externalId=SMa1894] on line 31: 1 1 1 SMa1894 24... I do not understand the error: he says he cannot find the reporter, but he displays SMa1894 which is the reporter ID. Did I do anything stupid ? You have to import reporters before you can import raw data. The error message means that there is no reporter with external ID=SMa1894 in the database. This is a change since BASE 1 where the raw data import could add missing reporters. This is no longed possible since it tended to fill the reporters table with bogus reporter information. What you have instead is that you can ignore missing reporters, putting a null value instead. It is useful if you just want to quickly check the intensity values. Select the null option of the Reporter not found setting. /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]
