Re: [base] error during batch import of raw bioassays -- BASE 2.8.4
Micha Bayer wrote: > Howdy again, > > I am trying out the new batch importers, and so far I have been > impressed. But now I am stuck on the raw bioassays and I can't get the > import to complete there. I have got it configured and the job starts > running but then fails with this error: > > Invalid use of null. The 'rawDataType must be specified for > platform: Generic' value cannot be set to null. on line 2: Pa expI (12h) > 1.s... > > Any clues? > > My data has a column called "Platform" containing the value "Generic" > for all rows and another column called "Raw data type" which contains > the value "Agilent" for all rows. Have I got this wrong? The raw data types are looked up by the value of the 'id' attribute for the tags in the raw-data-types.xml. In most cases this value is the same as the 'name' attribute but has lower-case letters. For Agilent you should use 'agilent' instead. /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] error during batch import of raw bioassays -- BASE 2.8.4
Howdy again, I am trying out the new batch importers, and so far I have been impressed. But now I am stuck on the raw bioassays and I can't get the import to complete there. I have got it configured and the job starts running but then fails with this error: Invalid use of null. The 'rawDataType must be specified for platform: Generic' value cannot be set to null. on line 2: Pa expI (12h) 1.s... Any clues? My data has a column called "Platform" containing the value "Generic" for all rows and another column called "Raw data type" which contains the value "Agilent" for all rows. Have I got this wrong? 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.ac.uk/staff/michabayer == __ 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 present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). __ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Problem on Tomcat shutdown
Moore, Jay wrote: > Hi, > > I have the latest base2 installed, Mac OS X 10.5, java 1.6.0, Tomcat > > I can start and stop Tomcat, but I get the following message on shutdown > in logs/catalina.out: > > SEVERE: IOException while saving persisted sessions: > java.io.FileNotFoundException: > /Library/Tomcat/work/Catalina/localhost/base2/SESSIONS.ser (No such file > or directory) > > I think the result will be that the base2 sessions do not survive a > Tomcat restart. The other directories in ...localhost (axis2, docs, > examples etc) all persist through the shutdown. BASE is not using Tomcat session, so it is not expected that sessions should survive a restart. I have seen that message as well, but have not investigated it further, since BASE doesn't really care if that file is created or not. > I have tried creating the ...localhost/base2 directory, and on Tomcat > startup it gets populated with a file called axis22550core.aar but on > shutdown, the directory gets deleted each time. > > The nearest I could find in Google was this thread: > http://www.mail-archive.com/[EMAIL PROTECTED]/msg38924.html > > It seems that in this case it was a bug in axis. Does anyone else see > this problem? Everything under the Tomcat/work directory is temporary files that Tomcat needs for working properly. I guess it is normal for things to appear/disappear. /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] Problem on Tomcat shutdown
Hi, I have the latest base2 installed, Mac OS X 10.5, java 1.6.0, Tomcat I can start and stop Tomcat, but I get the following message on shutdown in logs/catalina.out: SEVERE: IOException while saving persisted sessions: java.io.FileNotFoundException: /Library/Tomcat/work/Catalina/localhost/base2/SESSIONS.ser (No such file or directory) I think the result will be that the base2 sessions do not survive a Tomcat restart. The other directories in ...localhost (axis2, docs, examples etc) all persist through the shutdown. I have tried creating the ...localhost/base2 directory, and on Tomcat startup it gets populated with a file called axis22550core.aar but on shutdown, the directory gets deleted each time. The nearest I could find in Google was this thread: http://www.mail-archive.com/[EMAIL PROTECTED]/msg38924.html It seems that in this case it was a bug in axis. Does anyone else see this problem? Best wishes Jay - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] batchimport example spreadsheet seems corrupted
Micha Bayer wrote: > Hi, > > I have been trying to look at the example file for the batch import but > it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the > file does load but then Calc instantly hangs. The file is created with OpenOffice 2.4 and works. I downloaded it and could successfully open the file. > Has anyone else had the same problem? More to the point, has anyone got > a version that works, or better still, an Excel version of it? Generating an excel version from my OpenOffice creates a non-fully working sheet. You can browse the Google docs version linked from http://base.thep.lu.se/wiki/DocBookSupport There is no real need to use the sample directly simply create a file using your data following the sample. Jari - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] batchimport example spreadsheet seems corrupted
You mean this one ? http://base.thep.lu.se/attachment/wiki/DocBookSupport/batchimport_sample.ods?format=raw It works for me (OpenOffice 2.3). Here you have an Excel file that was exported from the original OpenOffice Calc: http://base.cbu.uib.no/tutorials/files/batch_import_all.xls All the best, Pawel Micha Bayer wrote: > Hi, > > I have been trying to look at the example file for the batch import but > it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the > file does load but then Calc instantly hangs. > > Has anyone else had the same problem? More to the point, has anyone got > a version that works, or better still, an Excel version of it? > > 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.ac.uk/staff/michabayer > == > > > > __ > 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 > present in this email, neither the Institute nor the sender accepts any > responsibility for any viruses, and it is your responsibility to scan > the email and the attachments (if any). > __ > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > 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 the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] raw bioassay listing workaround request
I know it's not possible, but I'd like to be able to do these two things: 1. list raw bioassays with their "Generic raw data" or "CEL file" filenames 2. list raw bioassays with their inherited annotations (and, I guess, the same for all item types) And ideally, of course, 1 & 2 together. Does anyone know a workaround? many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] batchimport example spreadsheet seems corrupted
Hi, I have been trying to look at the example file for the batch import but it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the file does load but then Calc instantly hangs. Has anyone else had the same problem? More to the point, has anyone got a version that works, or better still, an Excel version of it? 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.ac.uk/staff/michabayer == __ 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 present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). __ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
