Re: [base] Illumina design not playing its role
Nicklas Nordborg wrote: The array design concept was intended to provide a way of checking if the right raw data files are linked with right samples/extracts in the experiment, and that the right data is analyzed in experiment. It seems that it might not be the case for Illumina. Do you think there is a way to improve this and provide control over what gets imported with what design? One problem is that the raw data files contains no information whatsoever about which array design that was used. Do you have any ideas yourself? Given a BGX file and two raw data files (one matching and one none-matching) how do you tell them apart? I know our lab people is able to trace this somehow, I'll forward the question. The only thing I can think of is to report an error if the number of skipped data lines goes above a certain threshold. Any idea about what a good value for that threshold might be? 10? 100? Wouldn't a percentage make sense here? If more than say 5% of the Features in a raw data file does not match the design = bgx file, than there is probably an error? This will allow for some changes in the bgx file that then wouldn't require the definition of a new array design. Another possibility is to add a check in the experiment overview that compare the number of features on the array design with the number of raw data spots in the raw bioassay. If the difference is too big a warning could be generated. Would also be a nice solution. best, Kjell -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] BASE 1.2.10 to 1.2.17
Hi Steve, It might look like you've updated to the latest CVS instead of the official latest release 1.2.17 ? The error message is related to the code related to MAGE-ML export to be released as part of 1.2.18. The error message should be harmless, but shouldn't be there if you've upgraded to the official 1.2.17 release... Cheers, Kjell Steve Taylor wrote: Hi, We have recently upgraded to BASE 1.2.17 (from BASE 1.2.10) in preparation for moving to BASE2. From the web interface, for all experiments under 'Experiments' under the 'Info' tab I get the error message: Error: No Property described for legacy column experimentType Please contact administratorError: No Property described for legacy column experimentDesign Please contact administrator We didn't see such a message in BASE1.2.10. Does it mean the upgrade didn't work completely and if not can we fix it? Many Thanks, Steve -- Computational Biology Research Group Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University - 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] - 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] BASE1 cvs compilation errors
Dear Zong-Pei, I'll post an answer on the base-devel list. Cheers, Kjell [EMAIL PROTECTED] wrote: Dear All, Our attempt to install the latest CVS of BASE1 (1.2.17 something which is downloaded today) on an Opteron box has been unsuccessful. Here're some background information: $ uname -a Linux xx 2.6.16-1.2069_FC4smp #1 SMP Tue Mar 28 12:48:20 EST 2006 x86_64 x86_64 x86_64 GNU/Linux $ gcc --version gcc (GCC) 4.0.2 20051125 (Red Hat 4.0.2-8) $ java -version java version 1.4.2 gij (GNU libgcj) version 4.0.2 20051125 (Red Hat 4.0.2-8) $javac -v Eclipse Java Compiler v_579_R31x, 3.1.1 release The warning and error messages are enclosed below. Your comments and suggestions are much appreciated. ... make[3]: Entering directory `/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/jobRunner' if gcc -DHAVE_CONFIG_H -I. -I. -I../..-DJOBRUNNER_USER_UID=6000 -DBASE_USER_UID=6000 -Wall -O3 -MT jobRunner-jobRunner.o -MD -MP -MF .deps/jobRunner-jobRunner.Tpo -c -o jobRunner-jobRunner.o `test -f 'jobRunner.c' || echo './'`jobRunner.c; \ then mv -f .deps/jobRunner-jobRunner.Tpo .deps/jobRunner-jobRunner.Po; else rm -f .deps/jobRunner-jobRunner.Tpo; exit 1; fi gcc -Wall -O3-o jobRunner jobRunner-jobRunner.o make[3]: Leaving directory `/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/jobRunner' Making all in mageml make[3]: Entering directory `/usr/local/source_code/Linux/BASE/base-1.2.17b-cvs/src/mageml' javac -d . -classpath .:./../../include/java/MAGEstk-current.jar:./../../include/java/baseDNR.jar:./../../include/java/iText.jar:./../../include/java/xercesImpl.jar: ./ArrayDesign_package_BASE.java ./ArrayManufacture_BASE.java ./Array_BASE.java ./Array_package_BASE.java ./AuditAndSecurity_package_BASE.java ./BASEutils.java ./BioAssayData_package_BASE.java ./BioAssay_package_BASE.java ./BioDataCube_BASE.java ./BioMaterial_package_BASE.java ./BioSample_BASE.java ./BioSequence_BASE.java ./BioSequence_package_BASE.java ./BioSource_BASE.java ./Channel_BASE.java ./Compound_BASE.java ./DOMValidator.java ./Database_BASE.java ./DerivedBioAssay_BASE.java ./Description_package_BASE.java ./DesignElement_package_BASE.java ./ExperimentDesign_BASE.java ./Experiment_BASE.java ./Experiment_package_BASE.java ./FeatureDimension_BASE.java ./FeatureExtraction_BASE.java ./FeatureReporterMap_BASE.java ./Feature_BASE.java ./Hardware_BASE.java ./Hybridization_BASE.java ./ImageAcquisition_BASE.java . /Image_BASE.java ./LabeledExtract_BASE.java ./MeasuredBioAssayData_BASE.java ./MeasuredBioAssay_BASE.java ./MyErrorHandler.java ./Person_BASE.java ./PhysicalArrayDesign_BASE.java ./PhysicalBioAssay_BASE.java ./Protocol_BASE.java ./Protocol_package_BASE.java ./QuantitationTypeDimension_BASE.java ./QuantitationType_package_BASE.java ./Reporter_BASE.java ./SaxHandler.java ./Software_BASE.java ./Zone_BASE.java ./exportMAGEML.java \ jar cf base_to_mageml.jar *.class -- 1. WARNING in ./ArrayDesign_package_BASE.java (at line 8) public class ArrayDesign_package_BASE extends ArrayDesign_package The serializable class ArrayDesign_package_BASE does not declare a static final serialVersionUID field of type long -- -- 2. WARNING in ./ArrayManufacture_BASE.java (at line 2) import java.util.Date; ^^ The import java.util.Date is never used -- -- 3. WARNING in ./ArrayManufacture_BASE.java (at line 3) import java.text.DateFormat; The import java.text.DateFormat is never used -- -- 4. WARNING in ./ArrayManufacture_BASE.java (at line 14) public class ArrayManufacture_BASE extends ArrayManufacture ^ The serializable class ArrayManufacture_BASE does not declare a static final serialVersionUID field of type long -- -- 5. WARNING in ./Array_BASE.java (at line 2) import java.text.DateFormat; The import java.text.DateFormat is never used -- -- 6. WARNING in ./Array_BASE.java (at line 9) import org.biomage.AuditAndSecurity.Person; ^^^ The import org.biomage.AuditAndSecurity.Person is never used -- -- 7. WARNING in ./Array_BASE.java (at line 10) import org.biomage.AuditAndSecurity.Audit; ^^ The import org.biomage.AuditAndSecurity.Audit is never used -- -- 8. WARNING in ./Array_BASE.java (at line 16) public class Array_BASE extends Array ^^ The serializable class Array_BASE does not declare a static final serialVersionUID field of type long -- -- 9. WARNING in ./Array_package_BASE.java (at line 8) public class Array_package_BASE extends Array_package ^^ The serializable
Re: [base] Java Exception on MAGE-ML export
Hi Audrey, The BASE MAGE-ML export coding is no ongoing for full steam, so soon the code below givinmg you trouble should be obsolete. But I'll try to giv you a couple of hints to help you by. Audrey Bihouee wrote: Hi, Sine I changed my server, I get a java error when I try to export my data in MAGE-ML. This is my message : dirname= /var/BASE_production/data/mageml/0/1/experiment1 stage= all dtdpath= /usr/local/BASE_production/misc/MAGE-ML.dtd Failed to load current driver. java.sql.SQLException: Invalid authorization specification message from server: Access denied for user 'base'@'localhost.localdomain' (using password: YES) q= java.lang.NullPointerException at BASEutils.getStatement(BASEutils.java:141) at Experiment_BASE.fromBASE(Experiment_BASE.java:40) at Experiment_package_BASE.getExperiment(Experiment_package_BASE.java:47) at exportMAGEML.retrive(exportMAGEML.java:125) at exportMAGEML.main(exportMAGEML.java:76) created mageobjects writeMAGEML repair java.lang.NullPointerException at BASEutils.quickfix1(BASEutils.java:1076) at BASEutils.repairMAGEML(BASEutils.java:1035) at exportMAGEML.main(exportMAGEML.java:78) validate error: Attribute identifier is required and must be specified for element type MAGE-ML. org.xml.sax.SAXParseException: Attribute identifier is required and must be specified for element type MAGE-ML. at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:151) at BASEutils.validate(BASEutils.java:1137) at exportMAGEML.main(exportMAGEML.java:79) My version of Mysql is : 4.1.12 and I have mysql-connector-java-3.0.15-ga-bin.jar in BASEpath/include/java The first error (failed to load driver) seem to be causing the rest. See below. When I try to update my mysql-connector to 3.1.12-bin.jar I get this message : dirname= /var/BASE_production/data/mageml/0/1/experiment1 stage= all dtdpath= /usr/local/BASE_production/misc/MAGE-ML.dtd Failed to load current driver. java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver This is because your new driver jar is not explicitly in the classpath of the jvm (set in a script before starting the java code). A quick hack for now would be to rename your new driver to the same name as the old driver jar (and keep a copy of the old one around of course). Good look! Kjell ;^) --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] reporter_columns.inc.php BUG ?
Hi Charles, charles girardot wrote: Hi Kjell, OK will commit. Two little things: 1. Where is the place I should make the change in CVS: under include, there is a local and local_distr directory that both contain reporter_columns.inc.php local_distr is present in the source tree, and gets copied to local in the installation tree. If you install on top of the source, you will see them beside eachother. local_distr is the one we need to update. 2. Kjell, what the version of the pgsql you use? We have problem to load reporter map, all crashes when we do this. Reporter lines are inserted but nothing in the feature table (and other). version 7.3.9, but we are running an old version of base in production (1.2.10) that haven't gotten the Feature table in place yet. But I haven't run into any problems loading a reporter map on the development machine either, a fresh install of 1.2.17. Is the installation an upgraded one? Maybe there was a problem in the migrate script when the Feature table was introduced or similar ? K. Thanks Charles On 11 févr. 06, at 20:14, Kjell Petersen wrote: Hi Charles, all, Yes, I had to do the exact same change a couple of weeks ago! And I also wondered why I hadn't bumped into the error before when inserting rows. I may have been some code that was updated and now tried to insert using the insert statement itself, instead of defaults stated in the SQL definition of the table. I think it's an edit that can be safely committed to the CVS. Cheers, Kjell charles girardot wrote: Hi, We use BASE with MySQL but we are planning to move to pgsql at some point. So we installed BASE (latest) with pqsql (version 8.1.0). We just tried to load a reporter map and BASE was reporting errors due to invalid SQL about the omim and locuslink columns. It is clearly something that works with MySQL and I can't imagine this to be buggy in PgSQL since this should have been reported already. We traced the error and found that, in the SQL (both mysql and pgsql), these 2 columns are defined as integer while the reporter_columns.inc.php defines them as XCOL_STRING. We changed XCOL_STRING to XCOL_INT and it worked fine. In fact, I wonder why it works with MySQL and , maybe with older version of PgSQL... I haven't made the change in CVS yet as I am a bit surprised by the fact it worked so far and because it seems that it was not a problem until here. Could PgSQL users comment on this? Do you changed this ( XCOL_STRING to XCOL_INT) on your installations? Cheers Charles --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel? cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel? cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=kkid3432bid#0486dat1642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] reporter_columns.inc.php BUG ?
Hi Charles, all, Yes, I had to do the exact same change a couple of weeks ago! And I also wondered why I hadn't bumped into the error before when inserting rows. I may have been some code that was updated and now tried to insert using the insert statement itself, instead of defaults stated in the SQL definition of the table. I think it's an edit that can be safely committed to the CVS. Cheers, Kjell charles girardot wrote: Hi, We use BASE with MySQL but we are planning to move to pgsql at some point. So we installed BASE (latest) with pqsql (version 8.1.0). We just tried to load a reporter map and BASE was reporting errors due to invalid SQL about the omim and locuslink columns. It is clearly something that works with MySQL and I can't imagine this to be buggy in PgSQL since this should have been reported already. We traced the error and found that, in the SQL (both mysql and pgsql), these 2 columns are defined as integer while the reporter_columns.inc.php defines them as XCOL_STRING. We changed XCOL_STRING to XCOL_INT and it worked fine. In fact, I wonder why it works with MySQL and , maybe with older version of PgSQL... I haven't made the change in CVS yet as I am a bit surprised by the fact it worked so far and because it seems that it was not a problem until here. Could PgSQL users comment on this? Do you changed this ( XCOL_STRING to XCOL_INT) on your installations? Cheers Charles --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
