[base] GROUP clause error
We are using BASE 2.2.1 and Mysql Ver 14.7 distrib 4.1.12 Gauthier Jean-Pierre. Bio-informatique. INRA. UMR BIO3P. Domaine de la Motte. BP. 35327. 35653 LE RHEU CEDEX. tel : 33(0)2.23.48.51.68 fax : 33(0)2.23.48.51.50 mail : [EMAIL PROTECTED] - 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] GROUP clause error
Jean-Pierre Gauthier wrote: We are using BASE 2.2.1 and Mysql Ver 14.7 distrib 4.1.12 We have only tested BASE with MySQL 5.0. Can you upgrade and check if it works? I think it may be a problem with the older MySQL version. Unfortunately, we can't support anything before 5.0 and I don't think MySQL supports the older versions either. By the way, I think that 4.1.12 is the real MySQL version. The 14.7 is probably something internal to your operating system which probably comes bundled with MySQL. /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]
Re: [base] genepix 6.0/6.1, multi-image tif-s, spot finding,
Chad Matsalla wrote: Nicklas wrote: Nice work! It seems like you have spent some time on this. I certainly have. JAI isn't exactly intuitive. No, it isn't. Do you have some code and/or images that can be useful for us? I certainly do. I basically check to see if the user provided one and only one image and if so call 'loadMultiImageTiff' with the indices of the desired images: (in SpotImages.mergeColorImages()) : HashMapString,RenderedOp images = loadMultiTiff(red,index_635,index_532); sourceImages[0] = images.get(635); sourceImages[1] = images.get(532); This means nothing to me. Exactly where is this code located? Where can I find the loadMultiTiff() method? Does it still work if you have separate images for the two channels? For the code to be useful I need something I can put in and compile without having to redo things that you probably already have done. A diff would probably work. I'll clean up my code this weekend. Would you like me to send you a diff of some sort? I wrote a Test class based on yours and heavily altered (in parts) SpotImages.java. I certainly have data I can 'lend' you for testing (please email for a url). I'll also ask the Molecular Devices people for a dataset that we can put into the svn for testing.[1] It would be nice to have an image and some raw data with it. It doesn't have to be a complete file. Remove all headers (except those needed for the spot image creation) if you like. We have a locked repository for test data that we aren't allowed to share. I think that adding parameters for which image to use in a multi-image TIFF should be easy to implement. This can be done earliest at the 2.4 release. Great. Another point: The 'zip' that contains spot images isn't a zip. It looks like a zip, but this[2] is what I see when I try to open it in osx. Can you provide a hint as to how to open it? It seems like you are right. All programs I have tried to use also fail to open the zip file. I know that it has worked before so something is probably broken, except that Java seems to not have the same problems. /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]
Re: [base] some base 2 bugs/features (raw data and array design import)
Bob MacCallum wrote: Hi, I just spent the afternoon getting to know the array design and raw data import into BASE2 - starting with genepix format - and have come across a few things. I'm using BASE 2.2.2 (build #3172; schema #30). I have looked through the fixes for 2.2.3 and decided not to upgrade - otherwise I'll just spend my whole life upgrading BASE... ;-) 1. In the view files page, the type menu has a blank entry for 'raw data' although this still seems to work. This might be fixed in 2.2.3 see http://base.thep.lu.se/ticket/559 which looks related. Yes, I think this is the same thing. 2. I think there's some inconsistent handling of trailing spaces in the reporter ID column of a genepix .gpr file. For example I can import reporters, and create an array design from the file pasted below, but I can't then import the raw data! (the following is just 8 lines long - if the long lines get mangled, I'll send a copy by mail on request) ATF 1.0 2743 Type=GenePix Results 1.4 Block ColumnRow Name IDX 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 MeansMedian of Ratios Mean of RatiosRatios SD Rgn Ratio Rgn R²F Pixels B Pixels Sum of MediansSum of Means Log Ratio F635 Median - B635F532 Median - B532F635 Mean - B635 F532 Mean - B532 Flags 1 1 1 demoA demorep1 16905730110 183 181 42 59 62 25 100 98 0 276 270 48 64 65 13 100 100 0 0.585 0.592 0.570 0.576 1.357 0.591 0.782 80 621 336 328 -0.774 124 212 122 206 0 1 2 1 demoB demorep2 19105730120 114 137 175 57 61 37 71 21 0 346 341 80 63 65 35 96 95 0 0.201 0.288 0.192 0.209 2.379 0.398 0.094 120 716 340 358 -2.312 57 283 80 278 0 1 3 1 demoC demorep3 21105740110 145 148 43 63 68 30 92 68 0 208 214 48 69 74 43 98 93 0 0.590 0.586 0.599 0.541 1.987 0.504 0.582 80 566 221 230 -0.761 82 139 85 145 0 1 4 1 demoD demorep4 23005730110 185 187 51 59 63 23 100 96 0 298 294 57 64 67 24 100 98 0 0.538 0.557 0.526 0.538 1.599 0.549 0.730 80 590 360 358 -0.893 126 234 128 230 0 the stacktrace from the raw data import is: net.sf.basedb.core.BaseException: Item not found: Reporter mismatch: The feature has reporter 'demorep2' whereas you have given 'demorep2 ' on line 6: 1 2 1 demoB de... at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:592) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:442) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) at java.lang.Thread.run(Thread.java:619) Caused by: net.sf.basedb.core.ItemNotFoundException: Item not found: Reporter mismatch: The feature has reporter 'demorep2' whereas you have given 'demorep2 ' at net.sf.basedb.core.RawDataBatcher.doInsert(RawDataBatcher.java:390) at net.sf.basedb.core.RawDataBatcher.insert(RawDataBatcher.java:343) at net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(RawDataFlatFileImporter.java:544) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:570) ... 4 more I think BASE1 was more tolerant. Leading and trailing blanks are trimmed from more or less all values before they are inserted in the database and that explains why you get demorep2 instead of demorep2 . I guess we never though of doing the same when checking if a reporter (or something else with a unique value) exists in the database or not. I think there are several other places affected by the same thing. I'll add this as a bug in our trac database. In the meantime you can try using a splitter regexp that also removes white-space. Try something like \s*\t\s* instead of just \t. I have not tested this but it might be enough to make it work. 3. case sensitivity in the reporter ID (external id) column I get Error: Duplicate entry 'demoBLANK' for key 2
