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] Migrate script fails, no error messages
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! --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 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] 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] Migrate script fails, no error messages
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! --Chris W - 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]
