Error during Create Organism

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Error during Create Organism

Ohm, R.A. (Robin)
Hi,

I'm trying to add a new organism, but I get the following error message:
problem saving organism:
org.springframework.dao.DataIntegrityViolationException: Hibernate
operation: could not execute statement; SQL [n/a]; Field
'seq_chunk_prefix' doesn't have a default value; nested exception is
java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value

In the past I've sucessfully created an organism in version 2.0.0. More
recently I upgraded to version 2.0.1 using the instructions in your
announcement email. So the sql database stayed the same. The existing
organism continues to work just fine, but I can't seem to create new
organisms. I tried creating a dummy organism using the data of the
organism that is already working, but I get the same error. So it looks
like there isn't a problem with the data directory.

Your help with this would be greatly appreciated.

Best regards,

Robin

--
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016





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Re: Error during Create Organism

nathandunn
Are you using MySQL?

Nathan

> On Feb 9, 2016, at 8:01 AM, Robin A. Ohm <[hidden email]> wrote:
>
> Hi,
>
> I'm trying to add a new organism, but I get the following error message:
> problem saving organism: org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not execute statement; SQL [n/a]; Field 'seq_chunk_prefix' doesn't have a default value; nested exception is java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value
>
> In the past I've sucessfully created an organism in version 2.0.0. More recently I upgraded to version 2.0.1 using the instructions in your announcement email. So the sql database stayed the same. The existing organism continues to work just fine, but I can't seem to create new organisms. I tried creating a dummy organism using the data of the organism that is already working, but I get the same error. So it looks like there isn't a problem with the data directory.
>
> Your help with this would be greatly appreciated.
>
> Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
> Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error during Create Organism

nathandunn
In reply to this post by Ohm, R.A. (Robin)

I ask about the MySQL as there was an error in the migration script going from 2.0.0 to 2.0.1 that we fixed for MySQL (in eventual 2.0.2).  

I think you could also just run:

alter table sequence drop column ref_seq_file;
alter table sequence drop column splice_acceptor;
alter table sequence drop column splice_donor_site;
alter table sequence drop column translation_table_location;
alter table sequence drop column seq_chunk_prefix;
alter table sequence drop column sequence_directory;

and this should fix it for you, as well..

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 9, 2016, at 8:01 AM, Robin A. Ohm <[hidden email]> wrote:
>
> Hi,
>
> I'm trying to add a new organism, but I get the following error message:
> problem saving organism: org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not execute statement; SQL [n/a]; Field 'seq_chunk_prefix' doesn't have a default value; nested exception is java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value
>
> In the past I've sucessfully created an organism in version 2.0.0. More recently I upgraded to version 2.0.1 using the instructions in your announcement email. So the sql database stayed the same. The existing organism continues to work just fine, but I can't seem to create new organisms. I tried creating a dummy organism using the data of the organism that is already working, but I get the same error. So it looks like there isn't a problem with the data directory.
>
> Your help with this would be greatly appreciated.
>
> Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
> Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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RE: Error during Create Organism

Ohm, R.A. (Robin)
Hi Nathan,

Correct, I'm using MySQL. I never ran a migration script, though. Or was that done automatically?

I ran the commands you gave me. Tried to create an organism. Now I get the following error: Not authorized.
Any suggestions? The file permissions seem in order. I get the same error with the data directory that has worked in the past (in version 2.0.0).

Thanks, Robin


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Tuesday, February 09, 2016 19:40
To: [hidden email]
Subject: Re: [apollo] Error during Create Organism


I ask about the MySQL as there was an error in the migration script going from 2.0.0 to 2.0.1 that we fixed for MySQL (in eventual 2.0.2). 

I think you could also just run:

alter table sequence drop column ref_seq_file;
alter table sequence drop column splice_acceptor;
alter table sequence drop column splice_donor_site;
alter table sequence drop column translation_table_location;
alter table sequence drop column seq_chunk_prefix;
alter table sequence drop column sequence_directory;

and this should fix it for you, as well..

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 9, 2016, at 8:01 AM, Robin A. Ohm <[hidden email]> wrote:
>
> Hi,
>
> I'm trying to add a new organism, but I get the following error message:
> problem saving organism: org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not execute statement; SQL [n/a]; Field 'seq_chunk_prefix' doesn't have a default value; nested exception is java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value
>
> In the past I've sucessfully created an organism in version 2.0.0. More recently I upgraded to version 2.0.1 using the instructions in your announcement email. So the sql database stayed the same. The existing organism continues to work just fine, but I can't seem to create new organisms. I tried creating a dummy organism using the data of the organism that is already working, but I get the same error. So it looks like there isn't a problem with the data directory.
>
> Your help with this would be greatly appreciated.
>
> Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
> Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error during Create Organism

nathandunn

On Feb 9, 2016, at 12:17 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Correct, I'm using MySQL. I never ran a migration script, though. Or was that done automatically?

It was supposed to be done automatically, but it was not being run on MySQL, this is fixed on mainline.  

I ran the commands you gave me. Tried to create an organism. Now I get the following error: Not authorized.
Any suggestions? The file permissions seem in order. I get the same error with the data directory that has worked in the past (in version 2.0.0).

Thanks, Robin

I think that this is another of those things that we’ve subsequently fixed in mainline.  In the interim you could try a few things:

1 - logout and log back in and try again (with your admin user, which is the first on you created anyway)
2 - bounce the server  (and implicitly try 1)
3 - move to our 2.0.2-RC1 or mainline version (semi-tested) version and we can try to fix it there

Nathan


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Tuesday, February 09, 2016 19:40
To: [hidden email]
Subject: Re: [apollo] Error during Create Organism


I ask about the MySQL as there was an error in the migration script going from 2.0.0 to 2.0.1 that we fixed for MySQL (in eventual 2.0.2).  

I think you could also just run:

alter table sequence drop column ref_seq_file;
alter table sequence drop column splice_acceptor;
alter table sequence drop column splice_donor_site;
alter table sequence drop column translation_table_location;
alter table sequence drop column seq_chunk_prefix;
alter table sequence drop column sequence_directory;

and this should fix it for you, as well.. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 9, 2016, at 8:01 AM, Robin A. Ohm <[hidden email]> wrote:
> 
> Hi,
> 
> I'm trying to add a new organism, but I get the following error message:
> problem saving organism: org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not execute statement; SQL [n/a]; Field 'seq_chunk_prefix' doesn't have a default value; nested exception is java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value
> 
> In the past I've sucessfully created an organism in version 2.0.0. More recently I upgraded to version 2.0.1 using the instructions in your announcement email. So the sql database stayed the same. The existing organism continues to work just fine, but I can't seem to create new organisms. I tried creating a dummy organism using the data of the organism that is already working, but I get the same error. So it looks like there isn't a problem with the data directory.
> 
> Your help with this would be greatly appreciated.
> 
> Best regards,
> 
> Robin
> 
> -- 
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
> Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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RE: Error during Create Organism

Ohm, R.A. (Robin)
Thanks Nathan, option number 1 worked perfectly!

Best regards,
Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Tuesday, February 09, 2016 21:29
To: [hidden email]
Subject: Re: [apollo] Error during Create Organism


On Feb 9, 2016, at 12:17 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

Correct, I'm using MySQL. I never ran a migration script, though. Or was that done automatically?

It was supposed to be done automatically, but it was not being run on MySQL, this is fixed on mainline.  

I ran the commands you gave me. Tried to create an organism. Now I get the following error: Not authorized.
Any suggestions? The file permissions seem in order. I get the same error with the data directory that has worked in the past (in version 2.0.0).

Thanks, Robin

I think that this is another of those things that we’ve subsequently fixed in mainline.  In the interim you could try a few things:

1 - logout and log back in and try again (with your admin user, which is the first on you created anyway)
2 - bounce the server  (and implicitly try 1)
3 - move to our 2.0.2-RC1 or mainline version (semi-tested) version and we can try to fix it there

Nathan


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Tuesday, February 09, 2016 19:40
To: [hidden email]
Subject: Re: [apollo] Error during Create Organism


I ask about the MySQL as there was an error in the migration script going from 2.0.0 to 2.0.1 that we fixed for MySQL (in eventual 2.0.2).  

I think you could also just run:

alter table sequence drop column ref_seq_file;
alter table sequence drop column splice_acceptor;
alter table sequence drop column splice_donor_site;
alter table sequence drop column translation_table_location;
alter table sequence drop column seq_chunk_prefix;
alter table sequence drop column sequence_directory;

and this should fix it for you, as well.. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 9, 2016, at 8:01 AM, Robin A. Ohm <[hidden email]> wrote:
> 
> Hi,
> 
> I'm trying to add a new organism, but I get the following error message:
> problem saving organism: org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not execute statement; SQL [n/a]; Field 'seq_chunk_prefix' doesn't have a default value; nested exception is java.sql.SQLException: Field 'seq_chunk_prefix' doesn't have a default value
> 
> In the past I've sucessfully created an organism in version 2.0.0. More recently I upgraded to version 2.0.1 using the instructions in your announcement email. So the sql database stayed the same. The existing organism continues to work just fine, but I can't seem to create new organisms. I tried creating a dummy organism using the data of the organism that is already working, but I get the same error. So it looks like there isn't a problem with the data directory.
> 
> Your help with this would be greatly appreciated.
> 
> Best regards,
> 
> Robin
> 
> -- 
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
> Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.