Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4
Excellent -- that works. Thanks, guys. Is it reasonable to assume that people will want to attach their file if they specify the file name? If so, then it would make sense to make the Data Directory and Data File Type parameters mandatory in the import wizard if someone has specified a file name. But perhaps you want to just retain the option for people to import a minimal, skeletal raw bioassay without any of the above specified (in that case a note in the documentation would be good). The Raw Data Type also needs to be made mandatory as the import will fail without it (that seems to go for all cases, file supplied or not). 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 == -Original Message- From: Nicklas Nordborg [mailto:[EMAIL PROTECTED] Sent: 21 November 2008 19:33 To: BASE ML Subject: Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4 Jari Häkkinen wrote: I have not encountered any problems with attaching files earlier. I decided to play around with partially filled import files. I succeeded in creating a file that fails to attach files even though the importer reports success. BASE 2.8.4 and my 2.9pre test version both fails but the resolution of the problem is only tested on my 2.9pre test machine. Lets go, I am simply using three columns NamePlatformFile A affymetrix A.cel B affymetrix B.cel with the CEL files properly uploaded. A and B raw bioassays are successfully created as Affymetrix data. The file type is set to 'CEL file' but no file was attached. Note, I did not specify type, but when a Data file type column was added NamePlatformFileData file type A affymetrix A.cel CEL file B affymetrix B.cel CEL file things work. Rerunning the import ... voila the raw bioassays where updated with assigned files. I decided to start from scratch with a file like NamePlatformFileData file type C affymetrix A.cel CEL file D affymetrix B.cel CEL file and two raw bioassays were succesfully created with file attached! This is how it is expected to work. You need one column with the file type and one column with the file name. It's because some platform have multiple data files, so the importer needs to know which file that should go where. /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=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ __ 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
Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4
Are the raw data files visible to the plug-in? If you upload the files with ftp they are not automatically assigned to a project. You need to set the parameter defining how the plug-in should find existing items referenced in the file. If this is not the problem, can you try to only map the file and nothing else. Jari Micha Bayer wrote: Hello again, I can't get the raw bioassay batch importer to attach actual file objects to the raw bioassays I am importing. I have - provided a data column with file names in my data batch import file - mapped this column to the File property in the import config - provided a path to the data directory in the import config - put the actual raw data files into that directory The import works without errors but when it is done there are no files attached to my raw bioassays (even after a refresh). Under File in the detail view of the RBAs it just says -none-. Has anyone else seen this behaviour? I don't want the raw data imported into the db, I just want files to be associated with the RBA. 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=100url=/ ___ 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=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4
I have not encountered any problems with attaching files earlier. I decided to play around with partially filled import files. I succeeded in creating a file that fails to attach files even though the importer reports success. BASE 2.8.4 and my 2.9pre test version both fails but the resolution of the problem is only tested on my 2.9pre test machine. Lets go, I am simply using three columns NamePlatformFile A affymetrix A.cel B affymetrix B.cel with the CEL files properly uploaded. A and B raw bioassays are successfully created as Affymetrix data. The file type is set to 'CEL file' but no file was attached. Note, I did not specify type, but when a Data file type column was added NamePlatformFileData file type A affymetrix A.cel CEL file B affymetrix B.cel CEL file things work. Rerunning the import ... voila the raw bioassays where updated with assigned files. I decided to start from scratch with a file like NamePlatformFileData file type C affymetrix A.cel CEL file D affymetrix B.cel CEL file and two raw bioassays were succesfully created with file attached! I hope this helps! I suppose the above should be reported as a ticket. The ticketing work will be left for Monday because the ale next to my keyboard has been flirting with me for a while now. Cheers! Jari Micha Bayer wrote: No, still no joy. Are the raw data files visible to the plug-in? If you upload the files with ftp they are not automatically assigned to a project. I uploaded them with HTTP, and they have definitely been assigned to the project. You need to set the parameter defining how the plug-in should find existing items referenced in the file. I have tried with this parameter set to Name, ID and Name/ID. If this is not the problem, can you try to only map the file and nothing else. I have tried this too, and in conjunction with all three of the above parameters settings for item identification. The import/update seems to go ok and the plugin tells me at the end that it has updated all items but it hasn't actually done so. Is this functionality working for you? 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=100url=/ ___ 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=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject
