[base] Plugin configuration (still some pb)

[Emmanuel Courcelle]

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 ? 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\ Remove quotes true X \X\ Y \Y\ -- Emmanuel COURCELLE [EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE ------

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