Re: [base] regular expression and wildcards
Thanks for quick answers. I would like column mappings to support wildcards or regular expressions. Not a big thing, but I took the liberty to add it as a ticket. Implement it if it is cheap and when you have time. Vegard. -Original Message- From: [EMAIL PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: Thursday, November 01, 2007 6:22 PM To: BASE ML Subject: Re: [base] regular expression and wildcards vegard nygaard wrote: I also have similar problems. Some of my gpr files have different numbers than 635 and 532 as supplied in the GenePix raw data import (cy5/cy3) config shipped with base2. So in the base2 config the column mapping is \F635 Median\ But my column is named F633 Median how will that be using wildcards? I have tried \F635 Median\ not working \F633 Median\ working but not for 635 \F6.. Median\ not working F6.. Median not working F633 Median not working but giving a funny error message: Error: For input string: F633 MEdian on line..., (The E's in the input has been uppercased!) That is because string like '1.23e-2' are not recognised as numbers unless the 'e' is first converted to a capital 'E'. Using wildcard (.) in the header worked well. Then after reading the text in the GUI I am not 100% sure that the column mappings use regular expressions. I hope it does. No. Column mappings do not support wildcards. /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] - 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] regular expression and wildcards
I also have similar problems. Some of my gpr files have different numbers than 635 and 532 as supplied in the GenePix raw data import (cy5/cy3) config shipped with base2. So in the base2 config the column mapping is \F635 Median\ But my column is named F633 Median how will that be using wildcards? I have tried \F635 Median\ not working \F633 Median\ working but not for 635 \F6.. Median\ not working F6.. Median not working F633 Median not working but giving a funny error message: Error: For input string: F633 MEdian on line..., (The E's in the input has been uppercased!) Using wildcard (.) in the header worked well. Then after reading the text in the GUI I am not 100% sure that the column mappings use regular expressions. I hope it does. Vegard. Reha Yildirimman wrote: Hello, I am trying to configure a raw data importer plugin and want to use wildcards for reading raw data files. The dataheader inside those files always contains some changing elements and I would like to use base2 directly on the raw data without preprocessing them beforehand - so far no wildcard syntax worked. Is it possible to use wildcards and if yes what syntax is needed ? Nicklas wrote: You may use regular expressions as Java implements them, which I think is more or less the same as in most other programming languages. The documentation written by Sun should list all options: http://java.sun.com/j2se/1.5.0/docs/api/java/util/regex/Pattern.html /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] - 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] execution of plugin stalled
I have also had this kind of problems once in a while. When restarting base did not help, I did some manual sql in the Job table in mysql. I suspect my hang situation comes from a lot of zombie jobs taking up what seems to be a limited number of slots in a job-queue. I inspect the Job table and delete never finishing jobs. I looked at curStatus and queuePosition. But be careful if you start changing the database yourself like this. Back up the relevant tables first. Vegard Nygaard Software Engineer Department of Tumor Biology (Montebello) Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo Bioinformatics user support (NMC) Phone 0047 22935590 Axel wrote Hi Anthony, I had two main problems with plugins: 1) If a job hangs it is possible to start BASE without the jobManager: startBase.php -m after that one can start the jobManager with the option -R: /usr/Databases/testbase/bin/jobManager.php -R 2) the php-scripts in BASE are run under a linux shell. In my case some scripts had windows-linebreaks and therefore did not run. (Ad that time I developped some things on Windows...) Axel Bob MacCallum wrote: Hi Anthony You need to make sure jobManager.php is running on your system. Sometimes this dies on ours. Not sure which user it should run as, but on ours it's running as base's unix user (the one apache runs as). cheers, Bob. Anthony Pemberton writes: Dear Base users, I am using Base 1.2.15. One of my users is trying to run plugins through the Analyze data menu. Every time she tries to execute the job it just stalls with the Status Enqueued. I have a feeling that as the admin, I need to do something else to get these jobs to run. Would someone tell me what I need top do to get the jobs moving? Regards, Tony P. ** Mr. A. Pemberton Tel:+44 121 414 3388 School of Biosciences, Fax:+44 121 414 5925 The University of Birmingham Email:[EMAIL PROTECTED] Birmingham B15 2TT U.K. ** - 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] - 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] - 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] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
Dominic wrote: Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? No. I installed and tested the AnnotationTypeCvImporter with its own jar file and assumed it was the same. I now changed to use the Tab2MageImporter.jar and the plug-in finished without errors reported to the plug-in window in BASE. Though there were a bunch of error messages in the tomcat log. This is just the start: Executing job: Importing data to raw bioassay: H_PropylParabenC1T1.gpr 13:19:29,197 ERROR jobqueue:435 - Exception while executing job: Job[id=78; name=Importing data to raw bioassay: N_PropylParabenC1T2.gpr] net.sf.basedb.core.BaseException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) at java.lang.Thread.run(Thread.java:595) Caused by: net.sf.basedb.core.ItemModifiedException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.HibernateUtil.commit(HibernateUtil.java:914) at net.sf.basedb.core.DbControl.commit(DbControl.java:393) at net.sf.basedb.plugins.RawDataFlatFileImporter.end(RawDataFlatFileImporter.ja va:521) When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message java.lang.NullPointerException ...at net.sf.basedb.util.overview.ExperimentOverview.addProtocol(ExperimentOvervie w.java:1502) ...at net.sf.basedb.util.overview.ExperimentOverview.addSample(ExperimentOverview. java:1145) ...at net.sf.basedb.util.overview.ExperimentOverview.addExtract(ExperimentOverview .java:1039) ...at net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtract(ExperimentO verview.java:914) ...at net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtracts(Experiment Overview.java:841) ...at net.sf.basedb.util.overview.ExperimentOverview.addHybridization(ExperimentOv erview.java:781) ...at net.sf.basedb.util.overview.ExperimentOverview.addScan(ExperimentOverview.ja va:748) ...at net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssay(ExperimentOver view.java:604) ...at net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssays(ExperimentOve rview.java:580) ...at net.sf.basedb.util.overview.ExperimentOverview.generateOverview(ExperimentOv erview.java:316) ...at net.sf.basedb.util.overview.ExperimentOverview.init(ExperimentOverview.jav a:257) ...at net.sf.basedb.util.overview.ExperimentOverview.getOverview(ExperimentOvervie w.java:188) ...at org.apache.jsp.views.experiments.overview.index_jsp._jspService(index_jsp.ja va:87) ... and more I will now go on and test the tab2mage exporter and see if I get the same as I started with. You will hear from me if I am stuck. Vegard. - 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] How can I associate Illumina data with hybs (and samples)
You can select which scan a raw bioassay belongs to from the Edit rawbioassay page. Thanks Nicklas, this was what I was looking for (but at the wrong place). In order for the importer to be really useful I need to connect the raw data to samples in some way. From reading earlier posts it seems that connecting all the raw bioassays to one single scan is possible, but will there in upcoming base versions be more flexible association possibilities? We have discussed this and came to the conclusion that the current implementation is the most accurate representation of the process. The BASE model assumes that there is a one-to-one relation between a slide and hybridization. An Illumina slide has several (8 or more) arrays on a single slide. This doesn't fit the current model in all aspects. Some compromises has to be made. This is how we decided to do: * The slide is represented a single ArraySlide item in the database * The hybridization event links 8 (or more) labeled extracts to the slide (one for each array) * A single scan event represents the scanning * One raw bioassay for each array is created This will make is possible to accurately record scan and hybridization parameters without having to duplicate (8 times) the same data. The drawback is that the experiment validation will complain about the 8 labeled extracts since it expects only 1 for 1-channel data. It will also complain about all labeled extracts having the same label. But these warnings can be turned off. Another drawback is that all 8 labeled extracts will be treated as parents to all 8 raw bioassays, even though there really is a one-to-one relationship between those. /Nicklas I don't mind those drawbacks as long as the user can connect to one hyb (and one sample indeirectly) from the Edit raw bioassay page. Vegard. - 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] How can I associate Illumina data with hybs (and samples)
Hi I am testing out the Illumina importer and have some questions. Can I connect the created raw bioassays to hybridizations (and indirectly to samples)? On the scan page I looked for a associate raw bioassay , but only found the new raw bioassay. In order for the importer to be really useful I need to connect the raw data to samples in some way. From reading earlier posts it seems that connecting all the raw bioassays to one single scan is possible, but will there in upcoming base versions be more flexible association possibilities? If the Illumina Importer cannot attach raw bioassays to samples I wonder if I can use the Tab2Mage Importer or BatchDataImporter with Illumina data? Best regards. Vegard Nygaard Software Engineer Department of Tumor Biology (Montebello) Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo Bioinformatics user support (NMC) Phone 0047 22935590 - 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]
