Re: [base] Base2 install errors
Can you try with MySql 5? We have only used that for some time now, so it might be that the latest JDBC driver isn't fully backwards compatible with older MySQL versions. /Nicklas Hi Nicklas, thanks for getting back to me. I am using Mysql 4.1.15-1ubuntu5. I think that translates into version 4.1x in normal mysql version numbers? I also have the option of installing 5.0, but I figured that more things would be compatible with 4.x so I stuck with that. I just did a quick little test, starting mysql with the base2user account mysql -u base2user -p I then switched to the base2 database \u base2 create table test (a INT) ENGINE=MyISAM; insert into test (a) values(25); mysql select * from test; +--+ | a| +--+ | 25 | +--+ 1 row in set (0.00 sec) So I know that the database is working, and that the base2user has access to it, but yeah, I think something is going wrong with the java mysql drivers as you suggest. thanks, Sam On Fri, 2006-04-07 at 07:57 +0200, Nicklas Nordborg wrote: Sam Hunter wrote: Hi, I'm new to Base, and am trying to set it up for testing. I am install on Ubuntu with base-2.0RC1. I downloaded and install the Java SDK, (jdk-1_5_0_06-nb-5_0-linux.bin), and mysql seems to be working fine. When I get to the ./initdb.sh password stage of the install, I get the following output: Which version of MySQL are you using? The problem seems to originate from the MySQL JDBC driver. /Nicklas --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=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 xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=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 xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] how to link labeled extracts to intensity columns or channels
Petr Divina wrote: Hello, how can I link (= associate) a particular labeled extract that was used in a multi-color hybridization to a particular intensity column in the raw bioassays (or particular channel in the experiment) ? It is not possible. /Nicklas I have an 8-channel raw data type properly defined in raw-data-types.xml and the corresponding table created in mysql. I have created a hybridization with 8 labeled extracts (each labeled with distinct dye). Then, I have a scan and a raw bioassay linked to that hybridization. The raw data file that I am importing into that raw bioassay has 8 intensity columns, each corresponding to one channel. How do I associate the intensity columns in that raw bioassay to labeled extracts used in the hybridization? Also, how do I associate the labeled extracts to the channels in the experiment? I would like to see, e.g. labeled extract ID (dye) by the corresponding intensity columns or channels. Thanks for your advice. Petr - 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] Migrate script fails, no error messages
Chris Wiita wrote: Alright, that makes sense. The first time I ran the script the error was different, and in repeating the script, I never noticed it was way off in the first place! I turned logging, dropped both BASE2 DBs and recreated them, and ran initdb.sh. It was successful. Confirmed the databases were present with myphpadmin, and made no login attempts (didn't want to touch the db). I ran the migrate script, and this is the error. It managed to get through the UserTransfers--this is log from the last user transfer, before it moves onto the next part, where it fails. 11:54:39,164 INFO migration:77 - UserTransfer: Assigning role Share With World to user : Yuhei 11:54:39,237 INFO migration:77 - RoleTransfer: getRoleIds: 251658196 11:54:39,259 INFO migration:77 - UserTransfer: Assigning role Power user to use r : Ezra 11:54:39,265 INFO migration:77 - UserTransfer: Assigning role Plugin Administra tor to user : Ezra 11:54:39,280 INFO migration:77 - UserTransfer: Assigning role File Formats Admi nistrator to user : Ezra 11:54:39,287 INFO migration:77 - UserTransfer: Assigning role Hybridizations Vi ewer to user : Ezra 11:54:39,295 INFO migration:77 - UserTransfer: Assigning role Biomaterials View er to user : Ezra 11:54:39,301 INFO migration:77 - UserTransfer: Assigning role Share With World to user : Ezra 11:54:39 0 : 18 100%4 00:00:00 11:54:39 - 11:54:39 Creating home directories 11:54:39 Left DoneItems/sETE 11:54:39 18 : 00% 11:54:39 0 : 18 100% 18 00:00:00 11:54:39 - 11:54:39,915 INFO migration:77 - Migrater: startTransfer: Group 11:54:39 Group 11:54:40,060 INFO migration:68 - Free memory : 360 MByte 11:54:40 Left DoneItems/sETE 11:54:40 1 : 00% 11:54:40,325 INFO migration:68 - Free memory : 382 MByte 11:54:40 0 : 1 100%1 00:00:00 11:54:40 - 11:54:40,329 INFO migration:77 - Migrater: startTransfer: Wizzzard 11:54:40 Wizzzard 11:54:40,463 INFO migration:68 - Free memory : 383 MByte 11:54:40 Left DoneItems/sETE 11:54:40 16 : 00% 11:54:40,481 INFO migration:77 - WizzzardTransfer: setSharedItemData: 15 setSharedItemData : 15 [EMAIL PROTECTED] bin]# Any ideas what may be the cause here? This BASE1 was set up before I started administering this system, but it was pristine as far as I know. I upgraded a few times, and there was never any issue with the database (or issues at all, for that matter). Thanks for any help! I really don't know what is going on. But, it turns out that the migration program is really sensitive about the correctness of the Base1 database. What I suspect is that in your databases there are relations from one item to another that no longer exists. Can you help me verify this? First, check the 'Wizzzard' table for any entry which has gid=15. Then, check the 'UserGroup' table and look for an entry with id=15 and isAccount=0. If what I suspect is true, you will not be able to find that in the UserGroup table. /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]
Re: [base] Nimblegen
Keith Ching wrote: Hi, I am looking into using BASE2 to store ChIP-chip data from the NimbleGen platform. Each whole genome scan has 14 million probes, divided up into 38 arrays of 370k probes each. What is the feasibility of storing this information in BASE2? Say we had 100+ whole genome scans. Would it even be practical? Should I just store the raw datafiles as file attachments? It would be nice to have some compression built into the file attachments as this could save 75% on the disk space as each expt is 3 gigs or so. Wow, that is really a lot of data. I wouldn't store that in the database. It would suck the performance out of the entire application. You could compress the files before you upload them to Base 2. Or, you could let the operating system automatically compress the folder where the file uploads are stored. Note however, if you store the data in files, you will not be able to use any of the existing plugins to analyze the data. If you want to do that you will need to create a plugin that generates a more managable data set from the files. We have created such a plugin for Affymetrix files. See http://lev.thep.lu.se/trac/baseplugins/wiki/thep.lu.se.RMAExpress for more information about it. /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]
[base] BASE 2.0 has been released
Hello all, I am happy to announce that BASE 2.0 is now available for download: http://base.thep.lu.se/wiki/DownloadPage Installation instructions and other documentation are available at the BASE 2 home page: http://base.thep.lu.se/ /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]
Re: [base] Migrate script fails, no error messages
Chris Wiita wrote: That was the problem! Group ID for a user, not a group. I just changed the owner to an actual group, and the migration script appears to have worked now. Thanks a lot! I have bad new for you. While we were trying to fix the original problem, we discovered some other more serious bugs in the migration tool. Most of them are related to the Array LIMS and reporters part. For example: * No reporters were assigned to plates or raw data * Merged plates were incorrectly mapped to parent plates * Plates has swapped row and column coordinates * File formats were lost * And a few more that I can't remember The 2.0 release from yesterday hopefully fixes most of the issues, but we have not had time test or verify this. We are going to do some more tests today and the next week. I have to thank you for pointing out the original problem. Otherwise we wouldn't have found the other bugs. I would also like to ask you if you have any time to spend on helping us test the migration? I am not sure we can weed out all problems with the data we have here. Don't worry if you don't have time, we will try to fix it anyway. Maybe someone else on the list can help? Send a reply to me off the list. Thank you very much. /Nicklas --Chris W Nicklas Nordborg wrote: Chris Wiita wrote: Alright, that makes sense. The first time I ran the script the error was different, and in repeating the script, I never noticed it was way off in the first place! I turned logging, dropped both BASE2 DBs and recreated them, and ran initdb.sh. It was successful. Confirmed the databases were present with myphpadmin, and made no login attempts (didn't want to touch the db). I ran the migrate script, and this is the error. It managed to get through the UserTransfers--this is log from the last user transfer, before it moves onto the next part, where it fails. 11:54:39,164 INFO migration:77 - UserTransfer: Assigning role Share With World to user : Yuhei 11:54:39,237 INFO migration:77 - RoleTransfer: getRoleIds: 251658196 11:54:39,259 INFO migration:77 - UserTransfer: Assigning role Power user to use r : Ezra 11:54:39,265 INFO migration:77 - UserTransfer: Assigning role Plugin Administra tor to user : Ezra 11:54:39,280 INFO migration:77 - UserTransfer: Assigning role File Formats Admi nistrator to user : Ezra 11:54:39,287 INFO migration:77 - UserTransfer: Assigning role Hybridizations Vi ewer to user : Ezra 11:54:39,295 INFO migration:77 - UserTransfer: Assigning role Biomaterials View er to user : Ezra 11:54:39,301 INFO migration:77 - UserTransfer: Assigning role Share With World to user : Ezra 11:54:39 0 : 18 100%4 00:00:00 11:54:39 - 11:54:39 Creating home directories 11:54:39 Left DoneItems/sETE 11:54:39 18 : 00% 11:54:39 0 : 18 100% 18 00:00:00 11:54:39 - 11:54:39,915 INFO migration:77 - Migrater: startTransfer: Group 11:54:39 Group 11:54:40,060 INFO migration:68 - Free memory : 360 MByte 11:54:40 Left DoneItems/sETE 11:54:40 1 : 00% 11:54:40,325 INFO migration:68 - Free memory : 382 MByte 11:54:40 0 : 1 100%1 00:00:00 11:54:40 - 11:54:40,329 INFO migration:77 - Migrater: startTransfer: Wizzzard 11:54:40 Wizzzard 11:54:40,463 INFO migration:68 - Free memory : 383 MByte 11:54:40 Left DoneItems/sETE 11:54:40 16 : 00% 11:54:40,481 INFO migration:77 - WizzzardTransfer: setSharedItemData: 15 setSharedItemData : 15 [EMAIL PROTECTED] bin]# Any ideas what may be the cause here? This BASE1 was set up before I started administering this system, but it was pristine as far as I know. I upgraded a few times, and there was never any issue with the database (or issues at all, for that matter). Thanks for any help! I really don't know what is going on. But, it turns out that the migration program is really sensitive about the correctness of the Base1 database. What I suspect is that in your databases there are relations from one item to another that no longer exists. Can you help me verify this? First, check the 'Wizzzard' table for any entry which has gid=15. Then, check the 'UserGroup' table and look for an entry with id=15 and isAccount=0. If what I suspect is true, you will not be able to find that in the UserGroup table. /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
Re: [base] BASE2 + Solaris crashes recommended JVM
Emil Lundberg wrote: Hi all, We are trying to go from BASE 2 RC1 to 2.0, and neither updating nor initializing a new database seems to be working properly. Question is; is it just us, or a BASE/Java/MySQL versions mismatch? If the latter, are there any officially recommended/supported versions for BASE 2? Notes: - BASE 2 RC1 (compiled or binary) works OK (and can be rolled back, so I don't suspect the system's broken by all the fiddling). - It's not a password problem; setting it wrong in either base.config or to the scripts produces the expected error messages. Any help would be greatly appreciated! TIA, Emil / Linnaeus Centre for Bioinformatics * System specs Solaris 10 / SPARC, 6 GB, in a zone JDK 1.5.0_01 MySQL 4.1.18 Tomcat 5.5 * Problem 1: using binary BASE 2.0 When running the 'updatedb.sh' script, java crashes after building the initial database: [0%]Building database [30%] Database built successfully. java.lang.NullPointerException at net.sf.basedb.core.Update.getSchemaVersion(Update.java:319) at net.sf.basedb.core.Update.adjustExistingItems(Update.java:599) at net.sf.basedb.install.InitDB.main(InitDB.java:66) I have checked the code and it turns out that it is currently not possible to update the RC1 release. The schemaVersion stuff that is triggering the NullPointerException was added after the RC1 release to make it easier to upgrade! If you have important data maybe we can fix this for the 2.0.1 release. Populating a new database with 'initdb.sh' runs into similar problems: [0%]Building database. [30%] Database built successfully. [35%] Initialising database... java.lang.NullPointerException at net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881) at net.sf.basedb.core.Install.initDatabase(Install.java:605) at net.sf.basedb.install.InitDB.main(InitDB.java:67) Are you really using the released 2.0 binary here? The reason that I ask is that we found the same problem in the trunk of our subversion server this morning. But that code was only a couple of days old. We don't get the error with the released 2.0 binary. * Problem 2: compiling BASE 2.0 Base 2.0 does build successfully from source but with LOTS of warnings using Java 1.5.0_01, but no change from the above situation. Excerpt: [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1425: warning: [unchecked] unchecked conversion [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.PersistentClass [javac] return cfg.getClassMappings(); [javac]^ [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1553: warning: [unchecked] unchecked cast [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.Table [javac] IteratorTable tables = (IteratorTable)cfg.getTableMappings(); [javac] ^ This is a problem with the older java compiler which just ignore our diretions not to generate warnings. The problem was fixed in a later version. I don't remember if it was 1.5.0_04 or some other version. * Problem 3: using BASE 2.0 w/ JDK 1.5.0_08 Suspecting a major java problem, we tried installing a local version of the latest JDK (1.5.0_08) and repeating the above. Compiling is now OK, and using binary or source makes no difference. However, when trying either 'updatedb.sh' or 'initdb.sh', we get the exact same behaviour as before (NullPointerException). Note: BASE 2 itself (the tomcat / web service part) works as far as logging in, but afaik needs to be updated/reinitialized to support the new features of 2.0. Yes, you must run the update. /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]
Re: [base] BASE2 + Solaris crashes recommended JVM
I am not able to reproduce the error. Unfortunately there is a glitch in the error handling which causes a second error to hide the original one. If you turn on debugging there might be some more information displayed. You turn on debugging by editing the /www/WEB-INF/classes/log4j.properties file. In the Base 2 CORE loggers section change the line: log4j.logger.net.sf.basedb.core=warn to: log4j.logger.net.sf.basedb.core=debug and run the initdb.sh script again. /Nicklas Emil Lundberg wrote: * System specs Solaris 10 / SPARC, 6 GB, in a zone JDK 1.5.0_01 MySQL 4.1.18 Tomcat 5.5 * Problem 1: using binary BASE 2.0 When running the 'updatedb.sh' script, java crashes after building the initial database: [0%]Building database [30%] Database built successfully. java.lang.NullPointerException at net.sf.basedb.core.Update.getSchemaVersion(Update.java:319) at net.sf.basedb.core.Update.adjustExistingItems(Update.java:599) at net.sf.basedb.install.InitDB.main(InitDB.java:66) I have checked the code and it turns out that it is currently not possible to update the RC1 release. The schemaVersion stuff that is triggering the NullPointerException was added after the RC1 release to make it easier to upgrade! If you have important data maybe we can fix this for the 2.0.1 release. Thanks for the quick reply! So, no pressing need to fix this, we were just taking the shortest route towards testing 2.0 (+ the initialization wasn't working, see below). Populating a new database with 'initdb.sh' runs into similar problems: [0%]Building database. [30%] Database built successfully. [35%] Initialising database... java.lang.NullPointerException at net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881) at net.sf.basedb.core.Install.initDatabase(Install.java:605) at net.sf.basedb.install.InitDB.main(InitDB.java:67) Are you really using the released 2.0 binary here? The reason that I ask is that we found the same problem in the trunk of our subversion server this morning. But that code was only a couple of days old. We don't get the error with the released 2.0 binary. I would assume so, plus we get the same behaviour with the source distribution. We downloaded the Aug 31 release of base-2.0.tar.gz for the binary and base-2.0-src.tar.gz for the self-compiled version, and both yield the same error message, even when using the latest Java (se Problem 3). I'd show you the output from More about this server but it throws an exception too (db version mismatch perhaps): 10:50:16,385 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exception java.lang.NullPointerException at net.sf.basedb.core.Application.getSchemaVersion(Application.java:202) The link used was http://www.thep.lu.se/~jari/base/base-2.0.tar.gz So basically, we're stuck - is there anything else we can do to help you figue out what is going wrong? The only things I can think of are: A) routines called subsequently by net.sf.basedb.install.InitDB are not picking up the new Java installation - if that would even be an issue? B) there's a mySQL version problem (since it's HibernateUtil that's complaining). * Problem 2: compiling BASE 2.0 Base 2.0 does build successfully from source but with LOTS of warnings using Java 1.5.0_01, but no change from the above situation. Excerpt: [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1425: warning: [unchecked] unchecked conversion [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.PersistentClass [javac] return cfg.getClassMappings(); [javac]^ [javac] /install/source/base-2.0-src/src/core/net/sf/basedb/core/ HibernateUtil.java:1553: warning: [unchecked] unchecked cast [javac] found : java.util.Iterator [javac] required: java.util.Iteratororg.hibernate.mapping.Table [javac] IteratorTable tables = (IteratorTable)cfg.getTableMappings(); [javac] ^ This is a problem with the older java compiler which just ignore our diretions not to generate warnings. The problem was fixed in a later version. I don't remember if it was 1.5.0_04 or some other version. OK, good to know. Maybe something for the installation page? We'll stick with 1.5.0_08 then - if we can get the initdb.sh script to work, that is! Regards, /Emil * Problem 3: using BASE 2.0 w/ JDK 1.5.0_08 Suspecting a major java problem, we tried installing a local version of the latest JDK (1.5.0_08) and repeating the above. Compiling is now OK, and using binary or source makes no difference. However, when trying either 'updatedb.sh' or 'initdb.sh', we get the exact same
[base] Base 2.0.1 released
Hello all, BASE 2.0.1 is now available for download at: http://base.thep.lu.se/wiki/DownloadPage Most fixes are related to the migration program and the Base 1 plugin executor. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] BASE2 API: interacting with multiple BASE2 installs
Micha Bayer wrote: Hi, I am working on a web service that talks to a BASE2 install to get data out (for an analysis pipeline) and then store data back into it. We are supporting three separate institutions which eventually will all have separate BASE2 installs, but I would like there to be only one service, for maintenance reasons mostly. That means I need to be able to tell BASE the URL of the actual target install for each separate call to the web service (i.e. the user can specify which of the three installs they want to get data out of). Is there any way of doing this in the API? From what I have gathered so far the URL of the database is stored in the base.config file, and that is where the API gets it from by default, but is there any way I can override this? In the current implementation it is only possible to connect to one database at a time. I hope this will change sometime in the future, but it will not happen in this year and maybe not even in the next year. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] change owner
Robin LIECHTI wrote: Dear Base2 Users, I am a curator (and administrator) of a Base2 installation and I have to load experiment data from several users. So I log in as the administrator, I create the samples, extracts... and load the data. Is there a way of changing the owner of the created samples, extracts, ... ? Not in the current release. We are planning for a Take ownership function in the 2.2 release, but it's kind of the reverse from what you are trying to do. For the 2.2 release we are also planning a Log in as another user feature which a super-user can use. It would allow you to create items for another user. There is no release date for 2.2 yet. /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]
[base] Any interest in running BASE on Oracle?
Hello all, I am just wondering if anybody is interested in running BASE 2 on an Oracle database? The reason that I ask is that I think it is possible to fix the things that is causing the current implementation not to work on Oracle. But we are not spending time on this if there is no interest from the user community. Anybody that is interested in this should also be prepared to help with the implementation and/or testing. If you are interested and willing to help plese answer to the developer mailing list: [EMAIL PROTECTED] /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]
Re: [base] demo server updates and presets Q's
Lepp, Dion wrote: Hi all, I was wondering how often the base2 demo server is updated ie. are the changes shown in the Trac timeline reflected in the server immediately? No, the server has the latest released version. The reason is that there is a risk that updates won't work between arbitrary revisions. In the worst case it could lead to data corruption and that it is impossible to upgrade to the next release. That said, there is no guarnatee that this will not happen with released versions, but we have at least done some testing to make sure it doesn't happen. And if someone finds a problem we will try to fix it. Secondly, I am having trouble understanding the “in current project” preset, and the entire “active project” system for that matter. What I would expect is that when samples, hybs etc. are added, they will automatically be associated with the active project. If “In current project” is then selected in the presets, only those samples, hybs, etc. associated with the active will be displayed. In my hands, setting the active project or the “in current project” preset has no effect. Could someone please shed some light on this? Your description seems correct. What is probably happening is that you still have the Owned by me option selected. If you deselect that option and only leave the In current project option select you should only see items that are part of that project. /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]
Re: [base] updating to Base 2.1 with postgresql
Emmanuel Courcelle wrote: Hello I have setup for a few days a new Base2 installation, running with postgresQL. I know that the update process wan not safe with psql, due a bug in hibernate. However, the updating process ran without problem from 2.0.2 to 2.0.3 This updgrade didn't require any changes to the database. We have as a policy that bugfixes (ie. changes to third digit) shouldn't require changes to the database. So, trying to update to 2.1, here is the output of ./update.sh: -- [EMAIL PROTECTED] bin]$ sh ./updatedb.sh password [0%]Building database. [30%] Database built successfully. The above statement is actually not correct. The database wan't built successfully but Hibernate swallows all exceptions from the database and everything seems to be fine. [70%] The adjustment of the existing items failed: could not execute update query net.sf.basedb.core.BaseException: could not execute update query at net.sf.basedb.core.HibernateUtil.executeUpdate(HibernateUtil.java:1140) at net.sf.basedb.core.Update.adjustExistingItems(Update.java:877) at net.sf.basedb.install.InitDB.main(InitDB.java:66) [snip] Is this the symptom of the hibernate problem, or is there anything else wrong ? Yes, this is caused by the failure to update the database. Is there anything I can do to upgrade anyway (is it required running this script to upgrade to 2.1 ?) Yes, you must update the database before you can run 2.1. I'll try to release a modified hibernate3.jar were the update problem has been fixed. I'll post a note to the mailing list when it's ready for download, or when I have more info. /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]
Re: [base] Workaround for upgrading a Postgres database
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Hello Postgres users, We have now published some information about a workaround to make it possible to upgrade a BASE installation running on a Postgres database. Hi Nicklas Thanks for the workaround. I did the updatedb.sh as you suggested: it ran quite smoothly Then I tried the updateindexes.sh script, and I got the message: The indexes are not really needed but they will increase performance. For example, the Features table may receive lots of data and is one that you want to have indexes on. At first, it may seem unfortunate that this is the table that is causing the problem. But, the index exists, it's just that the update script doesn't find it. This time it is not a bug in Hibernate, but in the BASE code. Well, fix it for the 2.1.1 release. What you can do until then is to remove the index before executing the updateindexes.sh script. You remove it with the following SQL command: ALTER TABLE Features DROP CONSTRAINT Features_uniquecoordinate /Nicklas = Table : Features Unique : uniquecoordinate [column, row, arraydesignblock_id] Exists : false Safe drop : false DROP-SQL : CREATE-SQL : ALTER TABLE Features ADD CONSTRAINT Features_uniquecoordinate UNIQUE (column, row, arraydesignblock_id) Actions: CREATE 13:54:53,569 ERROR core:1723 - Exception org.postgresql.util.PSQLException: ERROR: relation Features_uniquecoordinate already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:340) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:286) at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64) at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1715) at net.sf.basedb.install.InitDB.main(InitDB.java:85) net.sf.basedb.core.BaseException: ERROR: relation Features_uniquecoordinate already exists at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1724) at net.sf.basedb.install.InitDB.main(InitDB.java:85) Caused by: org.postgresql.util.PSQLException: ERROR: relation Features_uniquecoordinate already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:340) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:286) at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64) at net.sf.basedb.core.HibernateUtil.dbIndexes(HibernateUtil.java:1715) ... 1 more Is it serious ? - 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] 2 questions about Plugin configuration
Emmanuel Courcelle wrote: Hi Nicklas Here are the first 44 lines of the file I tried to dos2unix-ify, it did not change anything for Base. Thanks for your help ! I have now tested with your file and it works perfectly. Perhaps it is a browser-related problem. I have tested with Internet Explorer 6 and Firefix 1.5 on Windows and Mozilla 1.7.6 on Linux. What broswer are you using? /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]
Re: [base] logging in BASE2
Micha Bayer wrote: Hi, I am running BASE2.1 under Tomcat 5.5 and I am getting my catalina.out log swamped by BASE log statements. Is there any way I can turn this off? It doesn't sound normal. What kind of log messages do you get? I have tried to change the log levels in the log4j.properties file in www\WEB-INF\classes\, and even deleted this file but it seems to have made no difference. Is the logging configured in the BASE source perhaps? Logging done by BASE is controlled by the log4j.properties file which you already have found. The default settings doesn't log anything except errors and warnings and if these start to appear frequently it is usually something that should be taken care of. Deleting the file is probably not a good idea. It used to cause Hibernate to output lots of INFO-level messages. /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]
[base] create slide wizard numbering
Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) Oops, it shouldn't be. Only the number of slides to create should have a limit. /Nicklas Ps. The next time you send mail to the mailing list, please start a new message instead of replying to an existing one and changing the subject. Your message appears as a reply to the original message and is easily missed by anyone not interested in the original subject. - 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] Plugin configuration (nearly fixed !)
Emmanuel Courcelle wrote: The only significant change you have made is Rgn R? to Rgn R. Does it still work if you change this to Rgn R\E.\Q? Great: I took the autogenerated regex, replaced Rgn ? by Rgn R\E.\Q without changing anything else and it worked. However, I changed also the columns parameters, activating the 'Expression (versus simple) box, and configuring Rgn R2 \Rgn R.\ the import stil does not work. There will still be a problem with the column mappings. Regular expressions can't be used here. It must be an exact string match, so I don't think it is possible to use the column name in this case. You can however use the column number. 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\. Anyway I think I now know what the source of the problem is. When we open the file for parsing we don't specify a character encoding. Then, the encoding used depends on the system the server is running on. On my machine the default encoding is UTF-8. But, the file is not encoded in UTF-8 and the superscripted 2 in Rgn R² is invalid in UTF-8. That is what causes it to be replaced by a ? in the first place. Then, when the file contents is sent to the browser a different encoding is used. This is configurable in the basedir/www/WEB-INF/web.xml file and defaults to ISO-8859-1 (ie. the regular encoding used by the western european languages). This further corrupts the invalid file contents and it is not surprising that the generated regular expression no longer match after this roundtrip. What is a bit surprising is that it worked in my development machine, but that probably has to do with that I had configured my web.xml to use UTF-8. So even if the file wan't parsed correctly in the first place the roundtrip to the browser didn't destroy the regular expressions. As soon as I changed my encoding to ISO-8859-1 I got the same problem as originally reported. Now, if you have managed to follow me this far, the question is what to do about this problem. Clearly we can't parse the files using the system default encoding since it is probably not the correct encoding in most cases. We probably need this to be a configurable option for every file that we parse. This is however a rather big change and as quick-fix I think putting a default encoding option in the base.config file could be a good idea. If no option is specified the default choice will be ISO-8859-1. The quick-fix can be released in 2.1.1 but the more general solution has to wait for 2.2 or maybe even for 2.3. /Nicklas E.C. - 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] 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]
Re: [base] file storage system question
Keith Ching wrote:
it seems you can make a String annotation type and attach it to raw
bioassay and fill it with
a href=javascript:Main.downloadFile('34537569891fa9bf', 142)
img border=0 class=icon title=Download the contents of this file
src=/base2/images/download.gif/a
which will produce a link to the specified raw file.
Wow, that's a bug, HTML tags should be escaped. Besides, it won't work
anyway, since the first parameter to the downloadFile function is a
session ID and is different for every time you login.
/Nicklas
-
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Re: [base] file storage system question
Keith Ching wrote: True, the session id is good only once.. but in subsequent logins, BASE2 will ask to reauthenticate and after success you can still download the file. still, of course.. i would rather have the download link be auto generated upon import of the datafile. is it within the capabilities of a plug-in to take all files in a directory, create a raw bioassay, and generate a link to the source file? It is possible to use the AnyToAny class to create such links. However, they won't be displayed in the web interface in the current implementation. The only exception is for transformations in the analysis section, which is the reason that we introduced the AnyToAny class in the first place. /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]
Re: [base] logging in BASE2
Micha Bayer wrote: Mystery solved. This is nothing to do with BASE -- it's Tomcat's fault. It looks like the Tomcat people have changed tack and they are now including a log4j.xml config file by default with Tomcat (it used to be a log4j.properties file, which is what I was initially looking for). This presumably applies to versions from 5.5 onwards -- I never had this problem with 5.0. I downloaded 5.5.20, which is the latest Tomcat release, just a few weeks ago and there is no log4j.xml in it. I haven't seen it in any of the other (only 2 or 3) 5.5.x releases I have used. Maybe it was included by mistake in some older release. Actually, their documentation (http://tomcat.apache.org/tomcat-5.5-doc/logging.html) states that there are some known issues with using the log4j.xml file and they recommend that people use log4j.properties. So, it is probably a good idea to check that you don't have a log4j.xml file. /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]
Re: [base] question on biosources and messages in base2
Audrey Bihouee wrote: Hi everybody, I just upgrade from base1.2 to base2, and I have a few questions : - What are exactly Biosources ? Does it match with the sample origin in base 1 ? But, I can't see any ontology (tree structure) as in base 1. Have anybody details on it ? It represents the source of biomaterial used to create samples. It's not the same as the sample origin in BASE 1. There is no corresponding construction in BASE 2. The migration tool puts the sample origin info in the description field. - Maybe it's a stupid quesion, but i can't find where can you post a message in the message page ?? You can't post messages. Messages are sent by plugins to indicate success or failure of a job and by a few other background tasks. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] error deleting jobs inside trashcan
Reha Yildirimman wrote: Hello, I have a few import jobs that froze and never finished the imports. After I started a jobs that finished the task I am left with those unfinished jobs still listed inside the execute section of Jobs which I can't delete after moved to the trashcan. The same problems occurs with some files but I guess this is due to a connection to one of those jobs.. A job that is executing can't be deleted. There is no way for the core to know if the job has crashed or if it is still executing. The only way to override this is to change the status for job manually in the database. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Giovanni Coppola wrote: Hi everybody, I have two questions: 1) is there a way to download images or raw data files in batches? No. 2) while I was trying that (to download more than one file at once), in the 'Files and Directories' tree, I accidentally moved Offline some files, and now I don't seem able to download them anymore. Is there a way to restore them in the Primary position? They have been deleted from the server. You have to upload them again. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Imagene data import
Anup Parikh wrote: We have been using base 1.2 for a year now. The batch importer we had created for base 1 is useless for base2. Therefore we are moving to using the UI to import each chip. We are using the ImaGene quantitation software and which seems to be supported in base2. But I cannot figure out now to import raw data. Is there no way to merge files from different channels? The current importers can only import data if everything is in one file. There are two options: 1. Merge the files before uploading them to BASE 2. Create an import plugin that can import Imagene files Anyone who volunteer for this? /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Emmanuel Courcelle wrote: What does mean to move offline ? Is it the same as: Delete THEN Empty trash ? No it is not. A file exists in two places. As an entry in the database and as a file on the disk. The Move offline feature is used when you want to delete the file on disk but keep the entry in the database. The main reason for this may be that your quota is running out and you don't need the file anymore. A file that is offline may be re-uploaded if you need it again. If you delete a file and empty the trashcan both the entry in the database and the file on the disk will be deleted. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already uploaded the user will have an opportunity to upload it. After choosing the zip file/directory the plug-in could start its import and creation of necessary items. The above is fairly straightforward already today and the new code would start at import/creation of necessary items. This will yield very little (or no) changes to the core and the plug-in should probably be started from the experiment listing page. This will of course change the experiment list jsp (a import tab is needed). No change is needed to the jsp. The new plugin will be detected and an Import button will appear. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Micha Bayer wrote: I am just talking to my boss about code ownership issues but I can probably offer up my stuff one way or another, and people can then either cannibalise it and turn it into a plugin, or adopt it (or a modified version) into the core etc etc -- happy with any solution that makes others benefit from my blood sweat and tears shed . :-) Please note that the GPL license BASE is released under requires that work based on it is released as GPL unless you keep it private. In other words if you share your code with others, you are required to release it as GPL as well. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Micha Bayer wrote: Hi Jari, That sounds perfectly reasonable when you put it like this, but I was put off going down that route by a post to the list from Nicklas http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html) where he says that it is best to not use a plugin to do this because of interface issues (whatever they are). That message was referring to how it was done in Base 1, where a lot of information needed to be entered in the web interface. The batch import described earlier in this thread probably doesn't need any advanced user interface since it seems (from the description below) to get all the information it needs from a single zip file. I have just finished writing one. The user uploads a zip file, a new directory is created in the user's raw data directory (with the same name as the zip file) and the files are then unzipped in there. They are then imported one by one as new RawBioAssay objects and at the end a new Experiment is created that has all these hanging off it. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] JEP extra value calculator again...
Emmanuel Courcelle wrote: Hi all. Sorry to bother you again with this point, but I still does not understand everything... I tried to define a new type, called float colored: it is a float, colored with min value as 0, max as 0, mid as 5 I want to add 2 values to my data: -2 * (ch(1) / ch(2)) -3 * (ch(1) / ch(2)) (Probably stupid for the analysis, but I just want to check the functionality) So, I tried the JEP extra value calculator, specifying float coloured as a data type, and 2 * (ch(1) / ch(2)) as the expression. Then, I give a look to the data, and it works: the numbers are preceded with a little coloured square, the colour depends on the value. Great, indeed. So, I tried a second run, this time with 3 * (ch(1) / ch(2)) as expression. It got the following error message: The bioassay set already has extra values of the type: Extra value type[id=2824; name=float colored] You can only calculate one extra value of each type per bioassayset. This sounds very strange to me: If float colored is an Extra Value Type, (this sounds to me as some data type, it's not right ?) why should it be applied ONLY one time ? Because the extra value type itself can be used in further calculations, filters, by plugins, etc. You then refer to it by the External ID of the extra value type. If there are more than one value for each type, it is not possible to know which one to choose. Something else, which is probably a bug. When I go to Administrate/Types/Extra value types, I click on any extra type declared (for instance for editing the type), I get the following: It looks like some internal Tomcat error. Try removing everything from the /usr/local/apache-tomcat-5.5.20/work/Catalina/localhost/base2/ directory. /Nicklas Base version 2.1 (build #2847; schema #20) Web serverApache Tomcat/5.5.20 Database Dialect org.hibernate.dialect.PostgreSQLDialect JDBC Driver org.postgresql.Driver (version 8.1) Java runtime Java(TM) 2 Runtime Environment, Standard Edition (1.5.0_06-b05), Sun Microsystems Inc. http://java.sun.com/ Operating system Linux i386 2.6.16-2-em64t-p4-smp MemoryTotal: 155.3 MB Free: 30.9 MB Max: 986.1 MB Browser Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.8.1) Gecko/20061010 Firefox/2.0 Error message /usr/local/apache-tomcat-5.5.20/work/Catalina/localhost/base2/org/apache/jsp/admin/extravaluetypes/view_005fextravaluetype_jsp.java (Permission denied) Stack trace ...at java.io.FileOutputStream.open(Native Method) ...at java.io.FileOutputStream.(Unknown Source) ...at java.io.FileOutputStream.(Unknown Source) ...at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:140) ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:295) ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:276) ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:264) ...at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:563) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:305) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) ...at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) ...at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) ...at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) ...at org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:688) ...at org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:658) ...at org.apache.jsp.admin.extravaluetypes.index_jsp._jspService(index_jsp.java:278) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at
Re: [base] Offline files
Micha Bayer wrote:
So am I right in thinking that if I change this to the following...
public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter
{
private static final SetGuiContext guiContexts =
Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
then I'll get an import tab created in the Experiment list view which
will let me import the
zip file using my plugin?
If you want the plugin to appear on the list page you should use,
GuiContext.Type.List. The GuiContext.Type.ITEM makes it appear in the
view page for a single experiment.
/Nicklas
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Re: [base] Réplicates in base 2
Emmanuel Courcelle wrote: Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were filtered out). How to make a final bioassay set with 6158 averaged-spots instead of more than 77000 ? There is no merge plugin available for BASE2. You can try using the BASE1 merge plugin which can be found on: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Location of original source files
Charles Girardot wrote: Hi Nicklas, I might have missed something as I am not using BASE2 now and haven't investigated in details. I have a comment on this thread : Very often people come up with some logics in naming their files and, in the context of re-exporting them (eg, submission), they like to see file having original names. They might be various other situation where having the same name is good. I think you should keep original names somewhere like in BASE1, it makes things easier. When you upload files the original filename is kept in the database. There is however no information that links a rawbioassay to the file that was used for importing the data. It has nothing to do with the file names. /Nicklas Am I off track? Cheers Charles On Dec 8, 2006, at 9:00 AM, Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am trying to write a plugin that will download the original source files used to populate the RawBioAssay objects. When you import data into a RawBioAssay, is the name of the original source file saved somewhere in the database? I am at the point where i can select the RawBioAssays that i want to download. It's just I can't find what file was originally used to create it. That information is not saved. /Nicklas -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php? page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] = Charles Girardot European Molecular Biology Laboratory C. Boulin and E. Furlong Groups Tel: +49-6221-387-8426 Email: [EMAIL PROTECTED] Meyerhofstrasse 1 - Postfach 10.2209 69012 Heidelberg, Germany = - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Conversion from string to int after plate import - bug while exporting
david vilanova wrote: Thanks Nicklas for you quick answer regarding the conversion from string to int. I have decided to import the data using the string to int conversion. However I'm trying to export the plate wells back again to a file using the default exporter and get a bug. I'm not sure that in this case the number are back translated into letters. This is not a bug. As I wrote before, BASE uses a numeric coordinate system. It can't know that the importer converted the coordinates from some other coordinate system. Obviously i could afterwards run a perl script on the exported file to get the appropriate conversion. Would it be easier of it was given the possibility to keep letters in the core base or at least give the choice??? No, this is not an option. What you can do if you don't want to use the perl script is to create an export plugin to do the conversion for you. See http://base.thep.lu.se/chrome/site/doc/development/index.html#plugins for more information. /Nicklas Please also find the screenshot of the bug while exporting wells from the plates. Thanks again and congratulation for the software. We are going to use it in a production server even though we will need to cope with some bugs. david - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Réplicates in base 2
Emmanuel Courcelle wrote:
Nicklas Nordborg a écrit :
Emmanuel Courcelle wrote:
Hello
We are trying to create an experiment composed with:
-4 slides
-3 times each reporter on each slide
So, we have up to 12 replicates for each reporter (sometimes less
because some flagged spots were filtered out).
How to make a final bioassay set with 6158 averaged-spots instead of
more than 77000 ?
There is no merge plugin available for BASE2. You can try using the
BASE1 merge plugin which can be found on:
http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload
OK
So I tried the followng:
-download the Merge BioAssay plugin
-Install file inside some directory (/usr/local/base2/plugins)
-Upload mergebioassay.base to my base's home directory
-Create a configuration for Base1PluginExecuter
-Enter /my_home/mergebioassay.base in the field: File
-Enter /usr/local/base2/plugins in the filed: Plugin executables path
-Go to the bioassay Set
-Click the last set (called Filetered Normalized Mediane)
-Run the plugin
Here what I got (copy-and-paster from the screen, because the export
does not show everything):
*
1
javascript:JoustMenu.toggle(0) Median FG
Formula intensity calculator
2
javascript:JoustMenu.toggle(1) Mediane
80640 6229
3
javascript:JoustMenu.toggle(2) Filter: raw('flags') == 0
JEP filter plugin
4
javascript:JoustMenu.toggle(3) Filtered Mediane
77148 6158
5
javascript:JoustMenu.toggle(4) Normalization: Median ratio
Normalization: Median ratio
6
javascript:JoustMenu.toggle(5) Filtered Normalized Mediane
77148 6158
7
javascript:JoustMenu.toggle(6) Something---
Base1PluginExecuter
8
javascript:JoustMenu.toggle(7) Something after
77148 0
9
*Looks buggy, doesn't it ? did I miss something ?
I don't know much about the BASE 1 plugins. What do you think is buggy?
/Nicklas
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Re: [base] downloading files
Keith Ching wrote: I have a List of File objects. what is the best way to zip them all together and download it? I assume that you want to this with a plugin. I think the best way is to create a new File (net.sf.basedb.core.File) object and then use java.util.zip.ZipOutputStream for writing to the new file. Is there a way to get the Httpresponse object from inside a plugin? Not really, since plugins are executed in the background or maybe even on a different server. In the the upcoming 2.2 release we have added the interface net.sf.basedb.core.plugin.ImmediateDownloadExporter that more or less makes it possible for a plugin to send the output to the HTTP response. Look at the source code some of the existing export plugins (for example HelpExporter) to see how to use it. If the files are really large, would it better to write the outputstream to the local filesystem and have the user find and download the archive from inside their home dir? Maybe. I don't think a zip stream needs much memory or uses very much CPU. The main problem is probably slow network connections. If you use the net.sf.basedb.core.plugin.AbstractExportPlugin as a base class it can help you with supporting both immediate download and saving to the file system. is there a nice File.Action.addZip ? No. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] walk thru
Gabe Dagani wrote: Greetings, Has anyone created a simple walkthru for setting up a simple experiment, uploading GPR, GPS, TIFF files into a project and doing some analysis? I am just a beginner and the manual is outdated for base 2.0. The test procedure that we use before a new release should also be usable. It is very minimalistic and doesn't explain anything. It is just stepwise instructions, ie. click there first, then do that, select that option, etc. But it goes through all important things and some less important as well. The instructions can be found at http://base.thep.lu.se/chrome/site/doc/test/roles/index.html Note that the test data that we use is not public data so you will have to get your own data files. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] GPR import plugin error
david vilanova wrote: Hello, I'm trying to import a GPR file and had some problems. I have submitted the bug to the base ticketing system. The problem comes from assigning incorrect wavelengths to the dyes CY5 and CY3 (view opened ticket #467). In the bug descriptions I also submit the correct parameters that need to be changed. The problem has already been fixed and will be release in the 2.2 release later this month. The new configurations will however onlybe installed in new installations. If you are updating an existing installation you should import the new configurations manually. Well, now the the GPR importer is properly working I need to fix another issue. In some cases the log ratio (...) field has some values that are named error. This come from the fact that when the background noise is higher than the intensity of the expressed oligo it is not possible to compute the log ration so genepix will return error as value for this specific field. Well, base is returning an error when trying to import such values. Could that be fixed ?? I want to keep this files so the option of ignoring this lines is not a solution since i want to keep all the lines of the GPR file. The only option in the current implementation is to skip the entire line. Maybe you can replace all error values with an empty string in your files before uploading them to BASE? A better fix would be to have an option of setting invalid values to null, but I think that requires a bigger change in the error handling in the import plugins and we don't have enough time to do it right now. I'll add a new ticket for it. /Nicklas Best, david - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Spot images
david vilanova wrote: Hello, Following the advise given to emanuel for the generation of the spots, I went through the example but could'nt manage to create the spots. Do i have to submit three time the tiff file to create the spots in the editor (it's asking for jpeg files°. Anyway the jpeg files didn't work, i was getting Bad endianness tag (not 0x4949 or 0x4d4d). To create spot images you need the TIFF files. The tiff file worked out by giving only one tiff file to the red channel. However the images generated to not show the correct spot, even after setting the scale and offsets according to the definitions in the gpr file (given by PixelSize and ImageOrigin). The images are black squares and sometimes they are some spots in the same image. This is an indication of incorrect values for one or more of the scale/offset/spot size values. It could also be that the image doesn't match the raw data set. Our test data has a GPR file with the following headers: PixelSize=5 ImageOrigin=0, 0 Thus, the X and Y scale is 5 and the X and Y offset is 0. The spot size is not among the headers, but for this data 32 works fine. Has someone created spots from a gpr file. Could this person detailed: - What type of file he used (tiff or jpeg). Jpeg didn't work for me (Bad endianness tag (not 0x4949 or 0x4d4d)) - What file it did give to red, green and blue channel (if only one channel has been used do you need to fill the others) You can choose to give the file to whichever color you like the best. If you give it to all three colors the spot images will be grey. With two-channel data you should give one of the images to one color and the other to another color. If both channels are stored in the same image file, give the same file to two colors. BASE will pick the first channel for the first color and the second channel for the second color. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Windows
[EMAIL PROTECTED] wrote: Hello, I have use the package Easyphp1.7 (PHP4, PHPMyAdmin) on windows to developp a database, and I would like to know if it is possible to install BASE with it or How to install BASE on Windows? BASE 1 is using PHP and in some parts C/C++. It is not possible to install on Windows. BASE 2 uses Java and probably works well on Windows, however it is nothing that we regularly test or officially support. /Nicklas Thanks, Angélique PhD -- Ce message a été envoyé depuis le webmail IMP (Internet Messaging Program) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Spot images follow-up
david vilanova wrote: Hello, I have tried with: PixelSize=10 ImageOrigin=4440,1000 I have double checked the image within genepix and the coordinates (expressed in µm) are correct (gpr file matches with the tiff file). 1µm correspond to 10pixels in genepix. I think it is the other way around. Each pixel is 10µm in size. See http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr X Offset: 4400 Y Offset: 1000 X and Y scale: 10 Spot size: try 32; this is given in pixels However the spot image is not the expected one. Still getting black squares and sometimes getting spots but a large set of spots instead of only one. Is a zoom applied to the spot that should be seen , otherwise i gets hards to view !?? As stated before the pixel coordinates are calculated as: pixelX = (rawX - offsetX) / scaleX and the same for the Y coordinates. It looks like soemthing is wrong and i don't know where to look ? Could I get your gpr file and tiff image to try and see how it works ?? If you go to http://base.thep.lu.se/browser/trunk/src/test/data you will find everything you need. The file 'spots.tif' is the (two-channel) image and the 'test.rawdata.import.txt' is the corresponding raw data set. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Fwd: Permissions question
david vilanova wrote: Hello, I'm having problem to setup permissions. How can i give permissions to all users to create a new raw bioassay from a scan. Actually I can only do it with account root. I did try to allow the group of users to write access,use,read to raw bioassays in the role. It actually looks like this group users: Raw bioassay CRUW-- But the tag does not appear from the scan page. What tag? Giving a user access to create raw bioassays doesn't give them access to the scans. A user needs USE permission on a scan to be able to use it to create a raw bioassay. Also I have an issue importing plates. The same problem, i don't know to give my group import permissions ?? You have to give permission to the plugin configuration. Go to Administrate - Plugins - Plugin configurations Find the configuration for importing plates. Give USE permission to the group. I'm attaching a shot of the permissions. The attached screen shot is showing the permissions for a role. Roles can't be given permissions to specific items, but are valid for all items of a specific type. Roles and groups are different and shouldn't be mixed up. The preferred way to share items is to create a project and share items to that project. Then it is easy to add members to the project and they will get access to all items in that project. Only share items to individual users and/or groups in special cases where you don't want a user/group to have access to the entire project. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] SPOT IMAGES Problem found
david vilanova wrote: Hi folks, I finally managed to identify the problem. As i said in my previous email i tried a tif image with only a signe channel: [EMAIL PROTECTED] SPOTS]$ ls * -rw-r--r-- 1 david bioinfo 9,1M Jan 23 12:19 532.tif -rw-r--r-- 1 david bioinfo 9,3M Jan 23 12:20 635.tif -rw-r--r-- 1 david bioinfo 20M Jan 23 12:21 All.tif CY5 image [EMAIL PROTECTED] SPOTS]$ identify 635.tif 635.tif TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 9.20849mb Cy3 image [EMAIL PROTECTED] SPOTS]$ identify 532.tif 532.tif TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 9.02034mb [EMAIL PROTECTED] SPOTS]$ identify All.tif All.tif[0] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit 19.8007mb 1.540u 0:09 All.tif[1] TIFF 550x1429 550x1429+0+0 PseudoClass 65536c 16-bit 19.8007mb 1.450u 0:09 All.tif[2] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 19.8007mb 1.380u 0:09 All.tif[3] TIFF 1604x5108 1604x5108+444+100 PseudoClass 65536c 16-bit 19.8007mb 0.700u 0:08 The experiment is a CY5 channel scan. Well the size of the single CY5 tif image is (1604*5108). The same for the CY3 image. The multi-image tif file returns 2 sizes (1604*5108 and 550*1429). With that being said i would say the problem comes from base to handle multi-file generated by genepix. It seems that base is reading the tif file sequentially and therefore get wrong coordinates for the Cy5 channel (base takes 550*1429 whereas the correct coordinates are 1604*5108). I guess this is the problem. Yes, this explains everything. BASE uses the images in the order they are layered in the TIFF file. I don't know why there are two extra layers i your file. Our multi-image files only have two layers, one for each channel. Maybe the two smaller images are some kind of scaled-down preview images? It would explain that some of your spot images contained a lot of small spots and also that some are totally black since the coordinates fall outside the smaller image. I would say that at some point base needs to make the difference from genepix multiple-tiff files and single tif files. When I use the single CY5 image everyting works fine !!! What do you think ? I would recommend that everyone that has a problem with multi-layered image files also try with single-layer image files. It also seems like you save some disk space if you are using single-layer image files. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] can you run a plugin outside of the web interface?
Keith Ching wrote: Hi, i have written a plugin that takes a spreadsheet and creates samples - rawbioassay and links the data file to the rawbioassay. is there a way i can also run the plugin without going through the web interface.. ie. initiate running it from another program? No, unless you write the program yourself. It shouldn't be too difficult. Check the test code for examples, for example the plugin for importing reporters from a file: http://base.thep.lu.se/browser/trunk/src/test/TestReporterFlatFileImporter.java /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Stopping Base after MySQL crash
Marie Mooney wrote: Hi. I don't know much about BASE 1.2 but I think that you must have the MySQL running for stopBase.php to work. And you must also have MySQL running to be able to upgrade from 1.2.14 to 1.2.17. So you have to find a way to start the MySQL server again. /Nicklas I am an extremely (completely) new user to BASE, and I was tasked with migrating from Base 1.2.14 to BASE2. Unfortunately, it seems, I started by installing BASE2, and doing all the other system upgrades necessary for that, which included updating MySQL from 4.1 to 5.0.27. When I did this, I had stopped the 4.1 version, which I had problems restarting. However, to do the migration in BASE, I apparently have to update to 1.2.17 first, then do the migration to BASE2, and to do the first upgrade, I need to stop the old version of BASE 1.2.14 (Does all this sound correct so far?), which won't stop on this error: # stopBase.php PHP Warning: mysql_pconnect(): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (13) in /usr/local/base-1.2.14/include/drivers/mysql.inc.php on line 86 mysql_pconnect() failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (13) Could not connect to database 'base' at host 'localhost' as user 'apache' BASE appears to be running, but connecting to the database failed. My question then is whether there is a way to stop BASE without having access to the old version of MySQL, or is there a way to make BASE 1.2.14 run on the new version of MySQL without stopping it? I tried changing the 'base' db BaseControl table to have startscripts = 0, as mentioned in the forums for after someone else had a problem where MySQL went down before BASE was stopped, but this didn't give me any different results. Any suggestions from anyone would be greatly appreciated. - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problem importing into ReporterLists
Reha Yildirimman wrote: Hello, I am trying to import Reporter into a new reporter list inside a fresh,new base2 installation, getting the following error: Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in 'field list' Can you please submit the entire stacktrace and also a step-by-step description of how to reproduce the error. Also include information about which version of BASE you are using, which database you are using, the Java version, and any other information that you think is important. All of this should be available in the About box or on the error message page. /Nicklas I cannot find the column 'reporterda0_.' inside any mysql table or inside extended-properties.xml/raw-data-types.xml ... When I try to access the - empty - Reporters part I get the following error: could not execute query using scroll Does anybody have a clue ? The file containing the list of reporters is a tab-delimited file with 6 columns, the first with the ID, the other 5 columns with annotations Thanks alot in advance for your help. Cheers, Reha --- Reha Yildirimman Max-Planck-Institute for Molecular Genetics Department Lehrach (Vertebrate Genomics) Ihnestr. 73 14195 Berlin Germany --- - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Imagene data format
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Emmanuel Courcelle wrote: Hello I am trying to configuration the Raw data importer plugin for use with Imagene files. I do not know how to map theproperties Block, MetaGridX, MetaGridY 1/ There is no Block column in the file, but I think this is replaced by the MetaGrid data. 2/ There are no MetaGridX, MetaGridY in the file, but there are a Meta Row and Meta Column fields: may I just assign the Imagene's Meta Row to MetaGridX, and the Imagene's Meta Column to MetaGridY ? This sounds like a good idea. BASE uses either the block coordinate or the meta x and y coordinates. If you have only one coordinate value you should map it to block, if you have two you should map it to the meta coordinates. If you map to both block and meta coordinates only the block coordinate will be used. OK And it does not matter if it is called MetaGridX/Y in base, meaning that the unit isPixel, and Meta Row/Column in the file, meaning the unit is the row number or the column number ? There is no special unit to the meta coordinates in BASE. The only requirement is that they match the coordinates in the array design and they must be the same for all raw data coming from the same array design. I don't think pixels would be a good choice since that would surely differ from one slide to the next. /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]
Re: [base] Bug fix release 2.2.1 is available now
Keith Ching wrote: hmm.. i had restored back to 2.1.2, then upgraded to 2.2.1 and it was working ok until i took ownership of some jobs as root.. then went to the trash can. it gave me this error: Object with id: 2 was not of the specified subclass: net.sf.basedb.core.data.BioMaterialData (Discriminator: 1746955520) and now most of the queries bomb out.. biosources, samples, scans, hybs, etc.. We have now been able to reproduce this on a fresh installation by only creating a single new sample. It appears to be bug in MySQL 5.0.27 and/or the JDBC driver (Connector/J 5.0.4). The problem never appears on MySQL 5.0.15 or 5.0.19 (the only two other version that we have available). MySQL has released 5.0.33 but only as source files and we have not tested if this release solves the problem. The problem also disappears in 5.0.27 if the 'useCursorFetch=true' option is removed from the 'db.url' setting in the base.config file. The drawback of removing this option is that the JDBC driver will load all data from a query into memory before returning it to the client. It will not affect regular interaction in the web interface since it only loads a few items at a time. It may cause problems for export and analysis plugins that handle a lot of data. For example, exporting all reporters or the data in a bioassayset. So, there are two possible solutions: * Don't use MySQL 5.0.27 * Remove the 'useCursorFetch=true' setting Which one is best to use is hard to tell. It probably depends on what the server is running. For a test/demo server I would use the second option, and hope that a new MySQL release will fix the problem. For a production server the second option might also be the best one to try first and then if you get out-of-memory problems try upgrading or downgrading MySQL (if that is possible). /Nicklas the tomcat log looks like this: 16:00:59,475 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exceptionjava.lang.NullPointerExceptionat org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp.appendPermissionLetter(edit_005fplugin_jsp.java:65) at org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp._jspService(edit_005fplugin_jsp.java:1163) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) then 16:03:12,363 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exceptionorg.hibernate.exception.DataException: could not read next row of resultsat org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadSingleRow(Loader.java:268)at org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:231) at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:100) at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:67) at net.sf.basedb.core.ItemResultIterator.hasNext(ItemResultIterator.java:106) ... Caused by: com.mysql.jdbc.exceptions.MySQLDataException: '1340029796353' in column '15' is outside valid range for the datatype INTEGER. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:893) at com.mysql.jdbc.ResultSet.throwRangeException(ResultSet.java:7391) i'll try to reinstall and reproduce the error. Restarting tomcat did not change anything, i think the db is probably corrupted. -keith Jari Häkkinen wrote: Hi all, We are eager to announce the release of BASE 2.2.1. You can download BASE from http://base.thep.lu.se/wiki/DownloadPage This release does not contain the database upgrade that was not working in 2.2. We have also added a check making it impossible to make a backwardsupgrade, i.e., reverting to an earlier version using the update script. This is of course only available from now on so be careful with the older releases. Of course, all the nice things that was added to 2.2 is still there. A list of fixed and added features in 2.2 is found by clicking on this beast: http://base.thep.lu.se/query?status=newstatus=assignedstatus=reopenedstatus=closedmilestone=BASE+2.2order=id Enjoy, The Lund BASE Team - 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] BASE2: Affymetrix.java method calls throw exceptions
Micha Bayer wrote: Hi, I am trying to add Affymetrix support for the batch import plugin I have been working on, and I am having trouble getting things to work with the Affymetrix class. Is there a unit test for this class that I could look at for finding out about proper use of this class? I may just not be doing things right here. I get exceptions from two of the method calls -- setCdfFile(ArrayDesign design, File file) and setCelFile(RawBioAssay rawBioAssay, File file). setCdfFile(ArrayDesign design, File file) throws a NullPointerException which is not related to my own code: Affymetrix.setCdfFile(arrayDesign, cdfFile); I have double checked and both the arrayDesign and cdfFile objects are not null. The stacktrace looks like this: Can you please tell us which BASE version you are using. The stack trace is hard to follow unless I know which version to look at. java.lang.NullPointerException at net.sf.basedb.core.HibernateUtil.createQuery(HibernateUtil.java:1238) at net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1 387) at net.sf.basedb.core.AnyToAny.getByName(AnyToAny.java:129) at net.sf.basedb.core.AnyToAny.getNewOrExisting(AnyToAny.java:169) at net.sf.basedb.core.Affymetrix.setCdfFile(Affymetrix.java:86) at sbrn.base.BatchDataImport.importData(BatchDataImport.java:350) at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest. java:82) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java: 420) at java.lang.Thread.run(Thread.java:595) Further down the line in my code I then try to attach the cel files to my raw bioassays (I have tested this independently from the above problem with a array design that already has a cdf file associated with it): Affymetrix.setCelFile(rawBioAssays[i], dataFiles[i]); ...and this gives me the following exception: net.sf.basedb.core.ConnectionClosedException: The connection has been closed. at net.sf.basedb.core.DbControl.getItem(DbControl.java:696) at net.sf.basedb.core.RawBioAssay.getArrayDesign(RawBioAssay.java:382) at net.sf.basedb.core.Affymetrix.setCelFile(Affymetrix.java:169) at sbrn.base.BatchDataImport.importData(BatchDataImport.java:371) at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest. java:82) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java: 420) at java.lang.Thread.run(Thread.java:595) This is despite the fact that I have a check for a closed connection immediately preceding my method call, so the connection is definitely open before Affymetrix.setCelFile is called. Are you sure that you are checking the same DbControl as you used to get the raw bioassays and files? Ie. the check you must do should correspond to: rawBioAssays[i].getDbControl().isClosed() Otherwise I recommend that you do: rawBioAssays[i] = RawBioAssay.getById(dc, rawBioAssays[i].getId()) where dc is an open DbControl. I don't recommend using the DbControl.reattachItem(). It doesn't reattach linked items and may cause problems if trying to access those. The Affymetrix.setCelFile will access to array design linked to the raw bioassay and this may or may not work depending on what you have done earlier. /Nicklas Any help would be much appreciated. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure
Re: [base] batch importer plugin is available for testing now
Micha Bayer wrote:
Hi Dominic,
Thanks for trying this out.
I tested the batch import today, on an affy experiment and I got the
ff
exception:
=
===NEW BATCH IMPORT =
=
zn =HG-U133A.cdf
experiment: Experiment[id=5; name=Batch Importer Test]
file selected: affyMicher.zip
java.lang.NullPointerException
at
sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
at
sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
-
Is this happeneing because of the file format you mentioned in your
read
me note? The zippped file is in affy format and containes 4 cel file
and
a cdf file. (5 files in total)
This looks like you are running this as user root. For some reason, user
root does not seem to have a home directory but the code needs to find
the user's home directory so that it can unzip the file there.
A user is not required to have a home directory. The home directory may
be null for any user. To solve this the plugin could for example ask for
a directory where the file should be unzipped (use a PathParameterType
object for this). The default value of this directory could then be set
to the user's home directory or maybe even better, the same directory
where the zipped file is located.
/Nicklas
If you
are logged in as root, then
homeDir = user.getHomeDirectory();
returns null and this is where the NullPointerException is thrown. I
guess I can catch that and set an appropriate error message.
Try rerunning this as a non-root user, and if that doesn't work, can you
send me the zip file please so I can try to reproduce the error here.
I'll also put a note in to the documentation to that extent.
Also
--
7:59:52,287 WARN DbControl:1046 - Found unclosed DbControl during
finalize; is
LoggedIn = true; clientId = 0; userId = 1
java.lang.Throwable: Please check the code to make sure that
DbControl.close() i
s always called. Stacktrace of code that created this DbControl:
at net.sf.basedb.core.DbControl.init(DbControl.java:140)
at
net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
0)
at sbrn.base.BatchDataImport.init(BatchDataImport.java:109)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
---
About the above warning, I suggest you close the dbcontrol object in
your code:
i.e. finally
{
if (dc != null)
dc.close();
}
Well spotted -- thanks. I'll get that sorted.
Cheers
Micha
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
SCRI, Invergowrie, Dundee, DD2 5DA.
The Scottish Crop Research Institute is a charitable company limited by
guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
DISCLAIMER:
This email is from the Scottish Crop Research Institute, but the views
expressed by the sender are not necessarily the views of SCRI and its
subsidiaries. This email and any files transmitted with it are confidential
to the intended recipient at the e-mail address to which it has been
addressed. It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this
confidentiality and you must not use, disclose, copy, print or rely on this
e-mail in any way. Please notify [EMAIL PROTECTED] quoting the
name of the sender and delete the email from your system.
Although SCRI has taken reasonable precautions to ensure no viruses are
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responsibility for any viruses, and it is your responsibility to scan the
email
and the attachments (if any).
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Re: [base] batch importer plugin is available for testing now
Jeremy Davis-Turak wrote: On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote: Can someone please give us a hint about how to reproduce this behavior? When I add a new plugin, BASE will complain if I enter an incorrect path. Nicklas, To reproduce this error, I would try creating the definition with the wrong path. Then, when this gives you an error, try again with the correct path. That's when I got an error. I can't reproduce this. If I enter an incorrect path nothing gets added to the database and the second attempt with the correct path is successful. And, if there is an entry already in the database, what is stopping you from using the web interface to edit the plugin definition and enter the correct path? Unfortunately the definition doesn't appear in the web interface after this error, although clearly it made its way into some of the database tables. Have you checked that you don't have any filters that prevents it from being displayed? /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] export function: permission denied
Reha Yildirimman wrote: Hello, everytime I try to export a tab-delimited file or xml file (from e.g. extracts, biosources or any other place) I get the following error: *** # Permission denied: Immediate execution is not allowed for this plugin. *** I gave the user I use read,write rights for all plugins inside the system but that didn't change anything. Does anybody have a clue ? The plugin lacks the immediate execution permission. Go to Administrate - Plugins - Definitions and find the Table exporter plugin. Bring up it's edit dialog and check the Allow immediate execution box. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] export function: permission denied
Ana Conesa wrote: At 19:17 22/03/2007, you wrote: Reha Yildirimman wrote: Hello, everytime I try to export a tab-delimited file or xml file (from e.g. extracts, biosources or any other place) I get the following error: *** # Permission denied: Immediate execution is not allowed for this plugin. *** I gave the user I use read,write rights for all plugins inside the system but that didn't change anything. Does anybody have a clue ? The plugin lacks the immediate execution permission. Go to Administrate - Plugins - Definitions and find the Table exporter plugin. Bring up it's edit dialog and check the Allow immediate execution box. /Nicklas Hi I required this functionality as well. However, when I edit the plug-in there is no Allow immediate execution box to check (although this filed is visible when opening the plug-in) How can we check the option? Strange. It should be the last option in the dialog. I attach a screen shot of how it look on my computer. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] multi-experiment processed data summaries
Bob MacCallum wrote: Developers: are there any plans for BASE2 web gui plugins? Well, yes and no. It is something that we would like to have and we have a ticket for it (http://base.thep.lu.se/ticket/436). At the moment it is not top-priority though so it is difficult to say when (and if) it will be implemented. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] merged data
Julie Naito wrote: Is this the case with BASE version 1.2.16? Sorry, I assumed you were asking about BASE 2. I guess the statement about that the same sample must end up in the same channel is true also for BASE 1. I don't know if that requires different file formats or not in the Imagene case, but it does for Genepix. With Genepix the data headers are different so the dye swapped data can't be imported with the same file format and vice versa. I guess that if you try to import you will find out how to do it. /Nicklas Hello there. Do you need to create two separate result file formats for 2 separate Imagene merged raw data sets if 1 set includes a dye swap? Currently there is no plugin that can import Imagene data so the question is hypothetical (see http://base.thep.lu.se/ticket/450). If the plugin is implemented in a similar way as the existing raw data importer you will probably need two configurations. The important thing is that the same sample ends up in the same channel for both hybridizations. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] NullPointerException when running raw data importer for new ScanArray CSV raw data table
Collett, James R wrote: Dear BASErs, I'm having problems configuring the raw data importer to import data from a ScanArray CSV file into a new raw data table that I created by modifying raw-data-types.xml. Every plugin configuration I try returns a NullPointerException error. Can you give me some clues on how I might fix this? The plugin automatically identifies the correct file type, but it freturns the error whether I have all of the error checking options set to fail or skip. I am able to import GPR raw data files into the RawDataGenePix table using a GenePix configuration without any problems. Error message, plugin job parameters, db schema, and new edits to raw-data-types.xml are below. I thinks there is a bug in the BASE code. It will be fixed in the next release. See http://base.thep.lu.se/ticket/563 The good news is that I think the bug is triggered by an extra space in one of the column mappings for the plugin configuration. Can you please check if there is an extra space after your columns mappings (\Array Row\, etc.)? If there is, remove it and try again. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list [EMAIL PROTECTED] unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] updating extended-properties.xml
Simon McGowan wrote: Hi, We have run into problems after editing the raw-data-types.xml and extended-properties.xml files. After each edit the server was stopped, I ran updatedb.sh and updateindexes.sh and restarted the server. However we can now no longer see any reporters via the gui (they are still accessible in the Reporters table via MySQL) and no new reporters can be imported. Has this kind of problem after modifying these xml files together been seen before? It is hard to tell exactly what happens. There is a known issue about invalid values in the extended-properties.xml and raw-data-types.xml that aren't detected (http://base.thep.lu.se/ticket/480) and later on they will produces errors. To be able to check if your problem is related to this I have to know what changes you made to the configuration files. Another thing to remember is that the updatedb.sh script can only add new columns, it can't modify or delete existing columns. If you have done such changes you must do the corresponding changes manually in MySQL. /Nicklas Many thanks, Simon The stack trace when you go into Experiment Explorer in a pre existing analysis, is: Experiment Options… Unexpected error BaseException on page /views/experiments/explorer/view/view.jsp Version BASE 2.2.1 (build #0; schema #29) Web server Apache Tomcat/5.5.17 Database Dialect org.hibernate.dialect.MySQLInnoDBDialect JDBC Driver com.mysql.jdbc.Driver (version 5.0) Java runtime Java(TM) 2 Runtime Environment, Standard Edition (1.5.0_09-b03), Sun Microsystems Inc. Operating system Linux amd64 2.6.19-1.2895.fc6 Memory Total: 157.0 MB Free: 84.7 MB Max: 444.5 MB Browser Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv:1.8.1.3) Gecko/20070309 Firefox/2.0.0.3 Error message could not load an entity: [net.sf.basedb.core.data.ReporterData#66625] Stack trace ...at HibernateUtil.loadData(HibernateUtil.java:1085) ...at Reporter.getById(Reporter.java:82) ...at net.sf.basedb.clients.web.ExperimentExplorer.getReporter(ExperimentExplorer.java:564) ...at org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService(view_jsp.java:235) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) ...at java.lang.Thread.run(Thread.java:595) Caused by: org.hibernate.exception.SQLGrammarException ...at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67) ...at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) ...at org.hibernate.loader.Loader.loadEntity(Loader.java:1865) ...at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) ...at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) ...at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3038) ...at org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:158) ...at
Re: [base] how can i interact with the spot creator plugin from outside the system
Chad Matsalla wrote: Nicklas Nordborg wrote: Can you tell me how to create the appropriate file objects when the files are here and not connected to the base datbaase? This is not possible. The plugin expects net.sf.basedb.core.File objects not java.io.File object. And you can't work with XxxxData (FileData, SpotImagesData) objects. These are only used internally in BASE. You must use the corresponding objects from the net.sf.basedb.core package (File, SpotImages, etc.) Can you please tell me the best way to do that? I've been looking through the plugin and test code and I'm mystified. I've uploaded the files into the BASE2 directory Root/chad/13298608_532.tif and Root/chad/images/13298608_635.tif. Somehow, I need to build a connection to the BASE2 server running on the host base2server' using the base2 username 'chad' and some password. Then I need to get a reference to those files and pass it to the spot finder. Is there some documentation I can read or can you give me some example code? I tried to mimic the 'ExampleAnalyzer.java' class but I think it's designed to work in the gui. I'm now trying to mimic the migrator because it runs on the commandline. I see that it reads a base.config so I started by copying the base.config from the server named base2server. I think I'm on the wrong track because I need to connect to a running base2 server to ask for the files. Is this the case? You can check the src/test/TestSpotImages.java file. It contains everything that is needed to create the spot images using our test data. It shouldn't be to hard to modify this code to use your files instead. You will of course have to download the source distribution or check it out from the subversion repository. How to do that is described on the download page. Another useful document is: http://base.thep.lu.se/chrome/site/doc/development/build.html You can also check the code for the SpotImageCreator plugin. The ExampleAnalyzer is a plugin and must run on the server. If you are going to run it from the command line it is best to use the same server as your BASE is running on. Otherwise you will need to open up MySQL and the file system so it becomes accessible from the other computer. This is how job agents works (used for running plugins on external computers). How to set this up is rather complex and is documented at http://base.thep.lu.se/chrome/site/doc/admin/jobagent.html /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list [EMAIL PROTECTED] unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] java.lang.NullPointerException while importing raw data
Jean-Pierre Gauthier wrote: Hi BASErs, I am a new Base2 user and I have a java.lang.NullPointerException when trying to import Genepix raw data in: View-Raw Bioassays..-Import My raw data importer seems to work well. I have looked for extra spaces but all looks OK.. Could somebody help me? Row\Row\\ There is an extra \ at the end of this. The correct mapping is \Row\ /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] unknowns
Peter Juvan wrote: Q: How to denote unknown values in a tab-delimited result file (for example M-values of reporters with zero intensity) so that BASE does not interpret them as zeros? Empty places are not OK, they are interpreted as zeros (at least in Base 1.2.17). In BASE 2, empty string are converted to null values (null = unknown). /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,
Nice work! It seems like you have spent some time on this. Do you have some code and/or images that can be useful for us? The image and data we have access to are from Genepix 4.1. 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. /Nicklas Chad Matsalla wrote: Greetings! I've been troubleshooting a problem that exists when trying to use images generated by Genepix 6.0/6.1 as images for spots. Genepix generates a single, multi-image, 16 bit greyscale TIFF. It's composition is as follows: Index Description 1 635 preview (495x1396 pixels) 2 532 preview (495x1396 pixels) 3 635 image (1884x5472 pixels) 4 523 image (1884x5472) The image offsets and scales are found in the .gpr file that Genepix creates. I used those numbers to try to use the single-image tiff for spots but most of the time it failed with an exception that I described in previous posts: java.lang.ClassCastException: [[B at com.sun.media.jai.opimage.BandMergeOpImage.shortLoop(BandMergeOpImage.java:3 41) Once in a while, though, it would succeed but the spots would be tiny in the images. This is because BASE2 is using indices 1 and 2 for the images in a multi-image tiff. In the case of GenePix 6.0/6.1 these are preview images. If you select 'Export Images' in Genepix 6.0/6.1 it does not do what you expect. I would expect that it would run it's own version of tiffsplit and generate two 16-bit greyscale tiffs. It actually creates two RGB images with 8 bits in the appropriate colour channel - red or green. These images cannot be imported into BASE (they provide the same exception as above). The reason why this exception is so mysterious can be balmed on JAI. IN core/net/sf/basedb/core/SpotImages.java the method In private RenderedOp loadTiffImage(File file, int band) executes this: RenderedOp image = JAI.create(tiff, params); For the single-image tiffs described above, this call returns the equivalent of an empty image: (PlanarImage[minX=0 minY=0 width=0 height=0 tileGridXOffset=0 tileGridYOffset=0 tileWidth=0 tileHeight=0 sampleModel=null colorModel=null]) It's my opinion that this should somehow throw an exception either through JAI or have this condition be trapped by BASE because, well, the call CLEARLY failed. Can a developer have this throw an exception? It would make image parsing problems MUCH easier to find. RIGHT! Let's return to the problem of the images. As a user of Genepix, I cannot change it's exporting behavior. However, when I use 'tiffsplit' on the commandline to split the GenePix multi-image tiff and import each image (full-size, not preview) into BASE2 separately everything works. This implies that there is not a fundamental problem with the individual GenePix images (as found in the multi-image tiff). BASE1 had a feature in 'Create Spot Images' that allowed you to specify: 'Index of ch1 TIFF' 'Index of ch2 TIFF' Can you please bring back this feature in BASE2? In the meantime I will modify our local copy to do this without prompting. Thanks for your efforts! Chad Matsalla Plant Biotechnology Institute, National Research Council of Canada Saskatoon, Saskatchewan, Canada - 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] - 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
Re: [base] some base 2 bugs/features (raw data and array design import)
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. I guessed there would be a neat trick like this, but couldn't think of it last night. However I tried \s*\t\s* and ?\s*\t\s*? which also needs Block = \Block\ and Flags = \Flags\ and they both oddly give the same error as before: Error: Item not found: Reporter mismatch: The feature has reporter 'demorep2' whereas you have given 'demorep2 ' on line 6: 1 2 1 demoB de... Ok, I checked your example data again and found that there are quotes around the values and the space is inside the quotes. This makes it more problematic since the splitter regexp also removes the quotes between the values, but not the first and last one one the line. I still think it is possible to create a regexp that can do the work but I am afraid that it will not be very simple. I think we need a trim whitespace option that works similar to the remove quotes option for the importer plugins. This problem is affected how the database handles strings. MySQL is case-insensitive. Postgres on the other hand is case-sensitive and the same problem would never have appeared. The important question is if the demoblank and demoBLANK should be treated as the same reporters or not? In Postgres they are already treated as different and it would be rather hard to change that. The only way is to convert all ID:s to the same case before storing them in the database. In MySQL they are treated as the same and it is equally hard to change that. The problem appears here because the two reporters are in the same file. If there had been two different raw data files, both demoblank and demoBLANK would have mapped to the same reporter. The bug in our code is that when the lines are in the same file we do case-sensitive comparison to check what has already been inserted. I'll add a ticket for that as well. I just wanted to mention that if we solve this problem as described above BASE will behave differently on Postgres and MySQL. On MySQL all reporters will be case-insensitive and demoblank/demoBLANK will be the same reporter. On Postgres they will be two different reporters. Time to balance the negative with some positive... BASE2 is so much nicer to work with than BASE1, keep up the great work guys!! Thanks! /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] Analsis error
See my previous reply to this error. http://sourceforge.net/mailarchive/message.php?msg_name=462CAC84.7020801%40thep.lu.se /Nicklas Jean-Pierre Gauthier wrote: Hi BASEr's I have some trouble to perform my analysis thus I send you what I have done. Could somebody say me what is wrong? We are using BASE 2.2.1 and Mysql Ver 14.7 distrib 4.1.12 thanks Following the Getting started User documentation: Create reporters Raw data importer: from genepix .gpr files like this Block Column Row NameID X Y Dia.F635 Median F635 Mean F635 SD F635 CV B635B635 Median B635 Mean B635 SD B635 CV % B635+1SD% B635+2SDF635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532B532 Median B532 Mean B532 SD B532 CV % B532+1SD% B532+2SDF532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532)Median of Ratios (635/532) Mean of Ratios (635/532)Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532)F PixelsB PixelsCircularity Sum of Medians (635/532)Sum of Means (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635F532 Mean - B532F635 Total IntensityF532 Total IntensitySNR 635 SNR 532 Flags Normalize Autoflag 1 1 1 aphl3sd-xxxi-h6 1a 20802590110 30773005713 23 61 61 76 88 115 100 100 0 616558681449 24 171 171 177 55 31 100 100 0 0.503 0.517 0.509 0.514 1.420.496 0.833 80 656 100 901086413016599429445697240388 469469 33.284 103.473 0 0 0 1 2 1 Ap_SNI1_1_A04_T715a 23802610100 22202216364 16 61 61 68 34 50 100 100 0 22712235334 14 168 168 171 47 27 100 100 0 1.027 1.043 1.026 1.042 1.291 1.055 0.838 80 560 100 42624222 2159210321552067177291 178813 63.176 43.915 0 0 0 10080 lines create ok reporter importer File Block Column Row ID NameDescription 1 1 1 1a aphl3sd-xxxi-h6 (Q76LV1) 90-kDa heat shock protein beta 1 2 1 15a Ap_SNI1_1_A04_T7NONE 10080 lines ok reporter map importer Same file than before ok Uploading files ok reporter import ok reporter map import ok project ok raw bioassays ok experiment + raw bioassays ok the error comes when I try to create a root bioassay set all seems to work well (Base say calculating spot intensities 10 of 12 raw bioassay(s) done). same pb with 1 or 2... raw bioassay. And then error Invalid use of GROUP clause .. (in french). For my last retry I suppress the Log Ratio (635/532) column to avoid *Error* an to have the same lines number in all files... Here is the log. net.sf.basedb.core.BaseException Utilisation invalide de la clause GROUP at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java193) at net.sf.basedb.core.DataCube.countSpotMappings(DataCube.java682) at net.sf.basedb.core.DataCube.onBeforeCommit(DataCube.java171) at net.sf.basedb.core.DbControl.commit(DbControl.java365) at net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java261) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java420) at java.lang.Thread.run(Thread.java595) Caused by java.sql.SQLException Utilisation invalide de la clause GROUP at com.mysql.jdbc.SQLError.createSQLException(SQLError.java946) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java2870) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java1573) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java1665) at com.mysql.jdbc.Connection.execSQL(Connection.java3176) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java1153) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java1266) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java76) at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java184) ... 7 more Job parameters Experimentlsd_experiment FormulaMean FG Bioassay set nameNew bioassayset Raw bioassaysh1ld_cy3, h1ld_cy5, h1sd_cy3, h1sd_cy5, h2ld_cy3, h2ld_cy5, h2sd_cy3, h2sd_cy5, h3ld_cy3, h3ld_cy5, h3sd_cy3, h3sd_cy5 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]
Re: [base] GROUP clause error
Chad Matsalla wrote: Gretings! I see this as well. It's because this query: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY COUNT(*) DESC should say: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY mapCount DESC Hm. For mysql4, anyway. It may be as you say, but I can't verify it since I don't have a MySQL 4 database. Strange that it complains about the GROUP BY clause when the error is in the ORDER BY clause. Anyway, 'ORDER BY mapCount' should work with MySQL 5 as well and it shouldn't be difficult to fix. I have added a ticket for it (http://base.thep.lu.se/ticket/581), but don't expect it to be fixed before the 2.4 release. In the meantime I think upgrading to MySQL 5.0 is the only option. /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] migrator script causes lots of exceptions
If you are using MySQL 5.0.27 this is caused by a bug in that version. Either use an older version of MySQL or remove 'useCursorFetch=true' the db.url setting in your base.config file. The second option may give you out-of-memory problems if you have a large database. In that case, you must either get more memory or use an older MySQL version. For more info see: http://base.thep.lu.se/ticket/568 /Nicklas Bernd Schwendele wrote: Hi, I want to migrate an old BASE installation (1.2) to an newer one (2) on another machine/arch. During the run of migrate_from_1.2.sh there are many exceptions, e.g. 17:50:28,656 ERROR migration:85 - getSampleById net.sf.basedb.core.BaseException: could not load an entity: [net.sf.basedb.core.data.SampleData#2] at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1063) at net.sf.basedb.core.DbControl.loadItem(DbControl.java:681) at net.sf.basedb.core.Sample.getById(Sample.java:88) at net.sf.basedb.clients.migrate.SampleTransfer.getSampleById(SampleTransfer.java:143) at net.sf.basedb.clients.migrate.ExtractTransfer.createItem(ExtractTransfer.java:90) at net.sf.basedb.clients.migrate.ExtractTransfer.createItem(ExtractTransfer.java:44) at net.sf.basedb.clients.migrate.Transfer.run(Transfer.java:346) at net.sf.basedb.clients.migrate.ExtractTransfer.start(ExtractTransfer.java:70) at net.sf.basedb.clients.migrate.Migrater.startTransfer(Migrater.java:218) at net.sf.basedb.clients.migrate.Migrater.run(Migrater.java:125) at net.sf.basedb.clients.migrate.Migrater.main(Migrater.java:478) Caused by: org.hibernate.exception.DataException: could not load an entity: [net.sf.basedb.core.data.SampleData#2] at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadEntity(Loader.java:1865) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3038) at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:395) at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:375) at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:139) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:179) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.get(SessionImpl.java:815) at org.hibernate.impl.SessionImpl.get(SessionImpl.java:808) at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1059) ... 10 more Caused by: com.mysql.jdbc.exceptions.MySQLDataException: '8589934593' in column '15' is outside valid range for the datatype INTEGER. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:893) at com.mysql.jdbc.ResultSet.throwRangeException(ResultSet.java:7391) at com.mysql.jdbc.ResultSet.getNativeInt(ResultSet.java:3967) at com.mysql.jdbc.ResultSet.getNativeInt(ResultSet.java:3892) at com.mysql.jdbc.ResultSet.getInt(ResultSet.java:2555) at com.mysql.jdbc.ResultSet.getInt(ResultSet.java:2570) at com.mchange.v2.c3p0.impl.NewProxyResultSet.getInt(NewProxyResultSet.java:2573) at org.hibernate.type.IntegerType.get(IntegerType.java:28) at org.hibernate.type.NullableType.nullSafeGet(NullableType.java:163) at org.hibernate.type.NullableType.nullSafeGet(NullableType.java:154) at org.hibernate.type.AbstractType.hydrate(AbstractType.java:81) at org.hibernate.type.ComponentType.hydrate(ComponentType.java:560) at org.hibernate.type.ComponentType.nullSafeGet(ComponentType.java:275) at org.hibernate.type.SpecialOneToOneType.hydrate(SpecialOneToOneType.java:58) at org.hibernate.persister.entity.AbstractEntityPersister.hydrate(AbstractEntityPersister.java:2092) at org.hibernate.loader.Loader.loadFromResultSet(Loader.java:1371) at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1299) at org.hibernate.loader.Loader.getRow(Loader.java:1197) at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568) at org.hibernate.loader.Loader.doQuery(Loader.java:689) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) at org.hibernate.loader.Loader.loadEntity(Loader.java:1851) ... 22 more Is there a bug in the migrate-Tool? Regards Bernd - 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.
Re: [base] file format matching problems
Steve Taylor wrote: Hi, I got a confusing message when I was using the Experiments Import. Basically, BASE was expecting a zip file and I was (perhaps stupidly) trying to upload a single file. The BASE WWW interface returned: 'We couldn't find any file format mathing the file /home/Admin/latestbluefuse.txt.' In the error log the problem is clear. = ===NEW BATCH IMPORT = = file is not a zip file java.lang.NullPointerException at sbrn.base.BatchDataImporter.isImportable(BatchDataImporter.java:181) at net.sf.basedb.util.AutoDetectFileFormat.findPlugins(AutoDetectFileFormat.java:145) Could a similar message be shown in the GUI? As it is currently implemented it is not possible. A plugin can only answer yes or no when asked if it can import a file. Unfortunately, it can't give any reason why the file can't be imported. /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] Why aren't you allowed to change the Array Design for a Raw Bioassay?
Chad Matsalla wrote: Greetings, I think the subject is quite clear. I have a Raw Bioassay in which the user forgot to specify the array design at creation time. The user went on to do a bunch of analyses but the experiment validator said the Raw Bioassay had no array design. When you edit the Raw Bioassay you are not allowed to change the Array Design away from '- none -' because there is no popup box there. Is there a reason for this? The reason if that if you have an array design the raw data import will verify that the raw data has the same reporters on the same positions as the array design has. If this is known then certain optimizations can be used in the analysis, ie. we can skip a similar check and don't need to remap positions between different raw bioassays. That is why you can't change the array design. I guess that it would be ok to change to an array design that can be validated against the raw data, but nobody has never mentioned it before and we have not implemented this validation. I have added this as a ticket so it doesn't get lost: http://base.thep.lu.se/ticket/583 So, currently your user has two options. Continue without an array design or create a new raw bioassay which has an array design and redo the analysis. /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] creatItem err while migrate from 1.2 to 2.2.2
Bernd Schwendele wrote: Hi, I have a problem with the mirgrate-script. I do not have any glue what this message means. It seems like the migration of BASE 1 plug-in definitions is broken. If you don't need those you can disable that part of the migration. Change the 'includePlugins' setting in the migrate.properties file to 'no'. The plug-in definitions can be migrated by hand by exporting them from BASE 1 and then importing them to BASE 2. It can be a lot of work if you have many plug-ins, but even if the migration worked, you would still have to copy/recompile the plug-ins on the new server. /Nicklas --- 18:45:40,006 INFO migration:77 - PluginTransfer: createItem: Base1 name=Normalization: Global median ratio; id=1 18:45:40,190 ERROR migration:85 - creatItem err net.sf.basedb.core.ItemNotFoundException: Item not found: PluginConfiguration[id=0] at net.sf.basedb.core.PluginConfiguration.getById(PluginConfiguration.java:101) at net.sf.basedb.plugins.Base1PluginExecuter.configure(Base1PluginExecuter.java:261) at net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:113) at net.sf.basedb.clients.migrate.PluginTransfer.createItem(PluginTransfer.java:129) at net.sf.basedb.clients.migrate.Transfer.runUnBatched(Transfer.java:398) at net.sf.basedb.clients.migrate.PluginTransfer.start(PluginTransfer.java:93) at net.sf.basedb.clients.migrate.Migrater.startTransfer(Migrater.java:218) at net.sf.basedb.clients.migrate.Migrater.run(Migrater.java:92) at net.sf.basedb.clients.migrate.Migrater.main(Migrater.java:478) --- The migration before worked, so this is quite strage. Settings and config-files are the same. The whole output of migrate_from_1.2.sh is attached. Maybe someone can help me :) Regards Bernd - 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] - 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] Problems creating samples and the supervisor role
Serge Eifes wrote: Dear Nicklas Nordborg, I have a similar problem as pointed out in the mail from 2007-03-05 by = Ana Conesa. In one of your replies from 2007-03-06 you give a link to a mail on how to solve this problem but this link only points to some kind of spam mail not related to the subject. Would it be possible to post the content of the correct mail or give the link to it? Thanks in advance! It seems like SourceForge have changed their mail archive system. There are lots of other link that doesn't work any more. And their search function has been broken a long time :( Is this the problem you are talking about? http://sourceforge.net/mailarchive/forum.php?thread_name=45CB29B1.4050109%40thep.lu.seforum_name=basedb-users /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] BASE2: API for storing normalized data
Micha Bayer wrote: Hi, Is there a way of programmatically storing externally normalized microarray data in BASE? I have been looking through the API but can't seem to find an obvious way of doing this. We run a workflow outside BASE (currently in GenePattern) which pulls data out of BASE (using the BASE client API) and then normalizes it using an R script that calls Bioconductor functions. I then need to store that normalized data back into BASE so it can be reused later, rather than having to do the lengthy normalization again. Is there a way of creating BioAssaySet objects directly and importing the external data into it? And do I need to create a root BioAssaySet first? I am kind of out of my depth here.. :-) Yes, it is possible to do this the same way as, for example, the existing Lowess normalization plug-in does it. This is the general outline: 1. Call BioassaySet.newTransformation() to create a new transformation item. Give it a meaningful name and description, e.g. GenePattern normalization using XXX method 2. Call Transformation.newProduct() to create the child bioassayset that stores the normalized data. Give it also a meaningful name and description. 3. Call BioassaySet.getSpotBatcher() to create a SpotBatcher object. Use the insert() method to store the normalized intensities. The above procedure can be used when you already have a (root) bioassayset with your data. If you start out with raw data you must create a root bioassayset. In this case, you should call Experiment.newTransformation() to create the transformation in the first step. In step 3 you may also have to do: BioAssaySet.getPositionBatcher() which is used to assign reporters to the normalized data, and BioAssaySet.getMappingBatcher() if you need to keep links to the raw data. I don't know if this made things clearer for you. There is also some information available at http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html The document is rather old and I can't say if it is correct in all details. You can also check the code for the RMAExpress plug-in athttp://lev.thep.lu.se/trac/baseplugins/wiki/se.lu.thep.affymetrix which also uses an external program (RMAExpress) for normalization of Affymetrix data. /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] affymetrix
Bob MacCallum wrote: Emmanuel Courcelle wrote: Hello Trying to use BASE with affymetrix data. me too! 2/ I can't see any new Reporter in the View/Reporters You need to import the reporter from a reporter annotation file (.csv). See http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6/README for details. could someone point me to these .csv files please? I've downloaded the xxx_libraryfile.zip (containing a .cdf file amongst others) but no .csv file. Do you get this from NetAffx online? Just for information. Base 2.4 will include a plug-in that can create reporters directly from a CDF file. The plug-in can only set the probeset ID since that is the only info that is available in the CDF. To get other annotation information you still need the .csv file(s). There will also be validation to make sure that CEL:s are matched with the proper CDF:s. These two things should make it easier and less error-prone to use Affymetrix data and the RMAExpress and Plier plug-ins. /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] inherited annotations GUI suggestion
Bob MacCallum wrote: A useful GUI addition would be another column on the Raw bioassays list view called 'Has inherited annotations'. The content of that column would be a simple yes/no. Alternatively, it could be called 'Inherited annotations' and could provide more information. Without this I don't see an efficient way to check that I have remembered to inherit annotations for each raw bioassay. Assuming that you have put the raw bioassays in an experiment, and that you have set the selected the annotation types you are interested in as experimental factors, this will show up on the experiment page (Properties tab). Another way is to go to the Overview tab. This will list everything in the experiment in a tree-like structure up to biosources and array designs. It will also check that you have values for all experimental factors and a lot of other things. If something is missing or incorrect there are links that take you directly to a form for fixing it. Read more about this in the user documentation: http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.experiment.overview Obviously this would be suitable for other item types too. It might even be nice to be able to set up default annotation inheritance paths for a Project, but that's probably a bigger task. I think there is need for a better interface for inheriting annotations. or a smart way to make it happen automatically. As it is now the system is a bit cumbersome to use. But I really don't have any ideas how to make things better so any thoughts are welcome. A related aside: So correct me if I'm wrong, but it seems that for most purposes, you only need to inherit annotations from Sample or Biosource to Raw bioassays. Although you can inherit these annotations at each intermediate step (extract, labelled extract, hyb, scan), the last step is the important one (for analysis). Yes, it doesn't make much sense to inherit annotations to anything else than raw bioassays. This is the only place where they are used by BASE. When analyzing only annotations from raw bioassays, bioassay sets and bioassays can be used. /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] small gui feature suggestion
Bob MacCallum wrote: I don't know if this would be dangerous, but how about: shift-click on the (+) symbol (new sample, new extract, new scan etc) will create the new object with the default settings in other words it would be equivalent to clicking on the (+) and then immediately clicking on 'save'. The sensible choice of default protocols and other menu items (project defaults or recently used) seems to be working well for me. Thanks. Shouldn't be too hard to implement, except that are many places to change. I'll add it as a ticket so we don't forget about the idea. Maybe we have time to fix it someday. /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] inherited annotations GUI suggestion
Bob MacCallum wrote: Thanks for that Nicklas, I had only checked out the overview feature briefly once before. It's very powerful (being able to disable certain warnings is nice). And the Properties tab of the experiment page does indeed list the inherited annotations for each experimental factor - it would be pretty easy spot a missing one! Just a general comment... BASE2 is really really nice! Having mainly used Genepix in BASE1, I just installed the Affymetrix plugins for BASE2 and found that it all worked first time. The project feature is excellent. Thanks. Positive feedback is always appreciated. /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] Guest Role tweaks
Bob MacCallum wrote: I just found that my guest user account was unable to get details of bioassayset transformations - for example it would say Plugin - denied - Plugin configuration - denied - and the same under transformation and job. This isn't ideal - a guest user would be very interested to know what transformations had been made. I double checked all the plugin definitions were readable by this user - and they were. I found that the problem could be fixed by giving the Guest Role read permission on Jobs. At the same time I removed all create permissions for this role (files, directories, jobs). Now I believe our guest user is truly read-only. The multi-user account option is invaluable here (it stops the user changing the password). hope that helps someone... Nice to see that someone is really using the permission system. I think there is a minor flaw in the design of jobs. They always get their permissions as if they are standalone items which means that only the user that created a job can view it (unless more permissions are granted to the roles as Bob has done). Jobs that are part of an experiment should really get their permissions from the experiment just as bioassay sets and transformations do. I don't know if it is possible to implement this with a reasonable amount of effort, but I'll check it out. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] BASE 2 Illumina arrays
Nicklas Nordborg wrote: Jeremy Davis-Turak wrote: I have implemented the incorporation of Illumina data into our BASE system, along with a raw data importer. Our version requires that the gene_profile.csv be split up into separate files, which we have done with an R script. This can also be done manually in excel, or feasibly in a BASE script. Nicklas, how do I share the plugin configurations with others? I have created a ticket in our trac system for this issue: http://base.thep.lu.se/ticket/486 Everyone are welcome to comment and it is also possible to attach files to it. Note that you have to be logged in before you can comment or upload files. Use base/base as username/password. I think the best solution would be to have a BASE plugin that can split the file automatically and the import the raw data in one go. If that is possible or not I don't know since I have no knowledge of the file format. We have planned to include the Illumina import plug-in in the next release (2.4). We have not been able to find any good description of the file format or example data files. Does anybody out there have any information to help us implement this? We definitely need one or more example data files that we can use for testing. The files will be put in a protected repository that is only available to the core developers. It would also be nice to have a more formal description, or at least a short overview, of the file format. Since it is only 3 weeks to go before 2.4 is released we need any information as soon as possible (this week!). /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]
Re: [base] svn check out of BASE2 WS enabled
Virginie Garcia wrote: Hi all, I try to download to webservices enabled version of BASE with svn as mentioned on the plugins page (http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients). When I check out the web services branch (svn co http://lev.thep.lu.se/repository/base/branches/webservices BASE-webservices) , I always get the same error : svn: REPORT request failed on '/repository/base/!svn/vcc/default' svn: REPORT of '/repository/base/!svn/vcc/default': 400 Bad Request (http://lev.thep.lu.se) Does anyboby have already tried to get this version ? I just tried it and it works for me. I searched the net for similar problems and most of them seemed to be related to the user beeing behind a proxy that doesn't pass on all types of requests. Check for example this link: http://lists.ipython.scipy.org/pipermail/ipython-dev/2005-September/001737.html A suggested workaround is to change the http:// to https:// /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]
Re: [base] BASE 2 Illumina arrays
Jeremy Davis-Turak wrote: Hi Nicklas, I uploaded some data files to the Ticket. Thanks a lot! That was exactly what we needed. Here is a brief summary of what the data looks like: 1) Annotation data: CSV file. It's too bad that it's a CSV, because some of the fields contain commas! Hmmm... it looks hard to import this with existing importers. I'll have to start with the raw data import and leave this until later. 2) Data: (header is on ~ line 8) a) For each set of chips that are processed at the same time, there is one resulting file. Thus, if you did two rat chips (each of which has 12 arrays on them), you would have 24 arrays contained in one file. b) Depending on the settings of the software at the time of scanning, you can have somewhere from 1-8 data columns per array (I don't know the exact range, but I know that it's variable). c) The first column contains the probe IDs, the rest of them are data. d) Each data column name is a concatenation of 3 things: i) The data type (i.e. 'AVG_Signal' or 'BEAD_STDEV') ii) The chip number (10 digits) iii) A capital letter indicating the position of the array on the chip (i.e. A-F for human, A-H for mouse, or A-L for rat.) EXAMPLE: the first 8 columns in my rat file are: I should be rather easy to create the raw bioassays. Once we have found the column headers, we can extract the chip number and the capital letter and use as name for the raw bioassays. The remaining parts of the headers should be easy to map to raw data properties (since you have already done this in the raw-data-types.xml for us). Do we have to worry about messed up files? For example, if there is AVG_Signal and BEAD_STDEV columns for one data set but only AVG_Signal for another? We could simply stop there and let the users revert to manual work if the needed to connect the imported raw bioassays with scans, array designs and experiments, but I think we can do a little bit more. I just have a few questions. Should all raw bioassays be associated with a single scan (and thus the same hybridization) or do we need to associate the raw bioassys from each chip with separate scan and hybridization? It is difficult to associate the raw bioassays with array designs, since there are no spot coordinates in the file. We could fake this and use block=1, column=1 and row=row number in file. The benefit is that analysis will behave better if all raw bioassays are associated with the same array design. The drawback is that we must also fake the array design in the same way. It should be possible to use the existing ReporterMapImporter for this if we feed it the same raw data file. I am also thinking of the possibility of using the plug-in from the Experiment view page if the experiment is of the 'illumina' data type. Then, the raw bioassays created by the import could be assigned to the experiment by the plug-in, saving yet another manual step. Thanks for making this plugin! Well... it is not implemented yet... The files will be put in a protected repository that is only available to the core developers. Since you uploaded the files to out Trac I assume that you are not worried about other users seeing them. Is it ok to use some of the files in our regular test programs? They will not be included in the binary distribution, only in the source distribution and of course from direct subversion access. /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]
Re: [base] Error: Table 'base2dynamic.D2Spot' doesn't exist
Sergio Contrino wrote: dear base, i was attempting to 'create a new bioassay root' for an experiment with the array affymetrix 250sty, using Plier. i get the error Error: Table 'base2dynamic.D2Spot' doesn't exist This error is a bit strange since the table should automatically be created if it doesn't exist. Maybe there is something going wrong with the creation which isn't reported as a failure. In any case, I need more information to be able to start looking for the problem: * Any related error messages and stack traces that are present in the Tomcat log file or displayed in the browser * Which database you are using (name and version) * Which BASE version you are using /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]
Re: [base] import of affymetrix data - which approach
Reha Yildirimman wrote: I have another approach and if that seems ineffective to you please drop me a line! We also had that approach to begin with. However we were a bit worried about database performance since the Affymtrix chips contains a lot probes. Since most tools needed the CEL and/or CDF files anyway we decided to not put Affymetrix data into the database. My approach is to change the affymetrix data type inside the raw-data-type.xml from a simple file-definition to a database-definition like the other data-types defined inside the xml. You should not change that. I am not sure what will go wrong, but I think there is code that depends on the default setup. We hope to make this more flexible in the future. I added properties for the values: MEAN (float), STDV (float), NPIXELS (float) To be able to import data via a base-plugin from a CEL file each data line has to have an association to a reporter - thus I added a column holding the ProbeSet ID for each CEL file. My problem is that when I associate a CDF file to an array design - which I need for reference purpose - it states under Properties: Features: Yes(0) This will not work unless you also have the CEL file at the raw bioassay. And if you have the CEL file you can't have the data in the database... I would recommend that you use the Affymetrix setup as it is. If you need a different way of calculating the intensity values this should be done by a plug-in. /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]
Re: [base] get reporter ID from 2 columns
Reha Yildirimman wrote: Hello, when configuring a raw-data-importer plug-in one has to state the column where the reportet ID is given. Is it possible to instead state 2 columns which when merged give the reporter ID ? And if yes how can I add another character like - in between those 2 column values? \Col1\-\Col2\ /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]
Re: [base] Error uploading CDF file
jesse paquette wrote: Hi, I'm trying to get BASE up and running, and I've hit a snag attempting to load a CDF file. The HTTP Status 500 page popped up with the following information: org.apache.jasper.JasperException: Unable to compile class for JSP: We know about this problem (http://base.thep.lu.se/ticket/736). It will be fixed in the 2.4.1 release. The problem only happens because the file upload has already failed for some other reason. The error message below is coming from the page that should take care of and display the original error. Unfortunately the original error is lost so there is no way to know what is causing the upload to fail. It could for example be a permission problem, lack of quota, a network timeout, etc. File uploads that are successful are not affected by this bug. /Nicklas An error occurred at line: 54 in the jsp file: /filemanager/upload/show_exception.jsp Unreachable code 51: sc.setSessionSetting(FileUploadProgress, null); 52: sc.setSessionSetting(UnpackProgress, null); 53: throw progress.getException(); 54: % Stacktrace: org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:92) org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:330) org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:423) org.apache.jasper.compiler.Compiler.compile(Compiler.java:308) org.apache.jasper.compiler.Compiler.compile(Compiler.java:286) org.apache.jasper.compiler.Compiler.compile(Compiler.java:273) org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:566) org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:317) org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320) org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266) javax.servlet.http.HttpServlet.service(HttpServlet.java:803) net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) Here's some more useful information: BASE Version: BASE 2.4.0 (build #3693; schema #40) Tomcat Version: Apache Tomcat/6.0.14 JVM Version: 1.5.0-b64 Any idea what's going on? Thanks! Jesse _ Senaste nytt från Hollywood http://starlounge.msn.se/ - 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] BASE 2.4 on Windows
jesse paquette wrote: Thanks Jari, Was the above the only things you needed to do to get BASE to run on MS Windows? Not completely. I submitted a bug ticket via user base. On the Create plugin page, I get a java.lang.ClassFormatError (page admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 in class file se/lu/thep/affymetrix/RMAExpress It is probably a bug in Java. Upgrade to the latest 1.5 or 1.6. For more info see: http://base.thep.lu.se/ticket/747 /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]
Re: [base] Error uploading CDF file
jesse paquette wrote: Ok, I deleted the extra line at the end of the show_exception file. The new error message is: File creation in base.config[userfiles] failed There can be two reasons: 1) The path specified in base.config for the userfiles property doesn't exists 2) The user that Tomcat runs as doesn't have permission to create new files in that directory /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]
Re: [base] Error uploading CDF file
jesse paquette wrote: Ok, I deleted the extra line at the end of the show_exception file. The new error message is: File creation in base.config[userfiles] failed There can be two reasons: 1) The path specified in base.config for the userfiles property doesn't exists 2) The user that Tomcat runs as doesn't have permission to create new files in that directory I'm guessing it's 1) I changed the Tomcat configuration to run as a user with the proper permissions. However, the directory specified by the base.config[userfiles] variable exists. So, I'm rather stuck here. Can you submit the entire stacktrace? If it is not 1 or 2 there might be some information about what the problem is. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Dominic Oyeniran wrote: The workaround works. But thats after I removed each raw bioassay and its associated experiment first and thereafter remove all the other items by emptying the trash. Note I have multiple experiments loaded :affy, genepix and agilent from Biosource to Experiment items. I will try deleting all at one go again and let you know I have only tested with a single raw bioassay, not connected to any experiments or other items. If there are problems deleting a hierarchy of items it is probably unrelated to the Affymetrix issue. There will be a fix for the Affymetrix issue in the 2.4.2 release. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] 2.4.2 = 2.4.3 - any database schema change?
Dave Hau wrote: 2.4.3 release followed closely after 2.4.2 release. I would like to upgrade from 2.4.2 to 2.4.3, but was just wondering if I could keep my database and just copy the entire 2.4.3 www directory to my tomcat server. Preferably I would like to not have to nuke the entire database this time around for the upgrade. Is there a database script in the base package I can do a diff on to see if there's been any schema change? I did a quick search and didn't find any. Our policy is to avoid changes to the database in releases that just differ in the last digit. Ie. 2.4.2 - 2.4.3 has no database change, but 2.3.x - 2.4 has. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Base2 and MeV - fold change
[EMAIL PROTECTED] wrote: : Hi! I'm Pietro, a young bioinformatic from Italy who is trying to make Base2 usable for the researchers here where I work. The problem cames out when I try to make fold change filter on Base2-MeV. As you know MeV allow fold change filter only if you load affymetrix data so when data cames from Base2 I can't reach this filter. I don't know anything about the fold change in MeV. Why does it only work on Affymetrix data? I also tried (with the help of same skilful programmers) to change the code of Base2-MeV cutting the code where there was the IF that checked the type of the data, I had the menù option but MeV didn't apply the filter when I select it. I think the problem is the format of the data that arrive to MeV from Base2. The data that BASE exports to MeV is always the same, no matter where it comes from. For one-channel data the single intensity value is exported. For two-channel data the log-ratio: log2(ch1/ch2) BASE exports this information in TDMS (Tab-delimited Multiple Sample) format. Appendix 15.2 in the MeV documentation (http://www.tm4.org/documentation/MeV_Manual_4_0.pdf) is about this format. /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]
Re: [base] How to use wildcard characters when filtering in BASE2
vegard nygaard wrote:
I am trying to make a sub selection of my data filtering for spots with id
starting with SP. I used the Expression builder and tried:
rep('externalId') == SP*
and
rep('externalId') == SP%
Does the Expression builder support wildcards?
No it doesn't.
In the ticket system I found a reference to a free-text filter
http://base.thep.lu.se/ticket/762
Is that operational?
No. We hope to include it in 2.5.
/Nicklas
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Re: [base] BASE2: problem parsing flag strings to floats
Micha Bayer wrote: Hi, I am trying to import some raw data with flags such as NORMAL and ABNORMAL into raw bioassays. I have mapped this column to the 'Flags' field in the raw data importer config for Genepix format (this is on BASE 2.3.0). For some reason the importer chokes on the values for the flags though and throws a NumberFormatException. It looks to me as though it is trying to parse the String to a float -- see stack trace below. In the raw-data-types.xml config file the Flags field for the Genepix data format is listed as being an integer type. Could that be the problem? Is this a problem with my setup or potentially a bug, and has anyone else seen this behaviour? The 'flags' column is, as you say, a numeric column. It can't hold string values, and of course it will not know how to handle 'NORMAL' and 'ABNORMAL' values since they are not numbers. It is expected behaviour and is not a bug. You can set the importer option 'Invalid numeric value' to either 'null' or 'skip'. The 'null' option will not insert a value for the 'flag' at all and the 'skip' options will skip the entire data line. Another option is that you do a search-and-replace in your file and convert the NORMAL and ABNORMAL to some numeric values. /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]
Re: [base] problems with my trashcan
Chad Matsalla wrote: Nicklas wrote: Are you logged in as the user that is the owner of the experiment? I am logged in as root. Shouldn't root be able to delete anything? Yes, the root user can delete anything, but this is not a permission issue. It's just that the Trashcan can only list items that are owned by the logged in user. /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]
Re: [base] Data cube has already been committed
Chad Matsalla wrote: Greetings All! Is there anything that I can so about this error? I'm completely stuck. I don't really know what a data cube is or how it could have already been committed. A datacube is a representation of the data in the dynamic database that is used to store analysed data. It is a cube because it requires three coordinates to pinpoint data for a spot, the bioassayset, the bioassay and the position. Some parts of the datacube, ie. how positions map to reporters and raw data, can't be modified after the creation of a datacube. I seems like the Base1PluginExecuter is trying to add additional reporter mappings to an already existing data cube and that is why the error happens. We hope to fix this in the next release (2.4.5). /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]
Re: [base] BASE2 login error
Reha Yildirimman wrote: Hello, I have the following setup: BASE2.4.0 tomcat 5.5.17 mysql 5.0.45 64bit linux system The error seems to be related to the Recently view items menu. For some reason the string that holds the information has become corrupt and the code is unfortunately not able to handle this. The best advice I can give right now is to edit the basedir/www/include/menu.jsp to try to avoid the error. It is line 110 in this file that is causing the error. A temporary solution might be to change this to something like: int itemId = tmp.length 2 ? 0 : Values.getInt(tmp[1], 0); I'll try to check in a better fix in subversion tomorrow. /Nicklas Without changing anything, today I get the following error when I try to login: java.lang.ArrayIndexOutOfBoundsException: 1 at org.apache.jsp.include.menu_jsp._jspService(menu_jsp.java:185) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:574) at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:499) at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:966) at org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:614) at net.sf.basedb.clients.web.taglib.Body.doStartTag(Body.java:293) at org.apache.jsp.exception.exception_jsp._jspService(exception_jsp.java:173) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:465) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:363) at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:212) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:134) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) at java.lang.Thread.run(Thread.java:595) I restarted everything, dropped and updated the dbindex wihtout a change. I can access the mysql database and tomcat is working. The BASE2 frontpage is shown, when I put a wrong password I get the appropriate error message and clicking on More about this server opens the pop-window with all the info (version, etc.) - just enterning the correct password results in the above error message Does anybody have encountered this or might have a clue what is going (or not going) on ? Many thanks in advance for your help. Cheers, Reha
Re: [base] How can I associate Illumina data with hybs (and samples)
vegard nygaard wrote: 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)? Yes. When you run the importer you have the option to select a scan that will be associated with the raw bioassays. The scan can be associated with a hybridization which is then associated with labeled extracts, and so on, up to samples. On the scan page I looked for a associate raw bioassay , but only found the new raw bioassay. You can select which scan a raw bioassay belongs to from the Edit rawbioassay page. 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 - 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] BASE2 login error
Nicklas Nordborg wrote: The error seems to be related to the Recently view items menu. For some reason the string that holds the information has become corrupt and the code is unfortunately not able to handle this. The best advice I can give right now is to edit the basedir/www/include/menu.jsp to try to avoid the error. It is line 110 in this file that is causing the error. A temporary solution might be to change this to something like: int itemId = tmp.length 2 ? 0 : Values.getInt(tmp[1], 0); I'll try to check in a better fix in subversion tomorrow. There is now a fix available in the repository. Those who can't wait for 2.4.4 to be released can download the updated file: http://base.thep.lu.se/browser/branches/2.4-stable/www/include/menu.jsp?format=raw Replace the menu.jsp file inside basedir/www/include file with the downloaded file. /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]
