[apollo] Error during Create Organism

Discussion:

Robin A. Ohm

2016-02-09 16:01:40 UTC

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

Lbl

2016-02-09 16:46:05 UTC

Permalink

Are you using MySQL?

Nathan

Hi,
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/

Nathan Dunn

2016-02-09 18:40:12 UTC

Permalink

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

Ohm, R.A. (Robin)

2016-02-09 20:17:55 UTC

Permalink

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: apollo-***@lists.lbl.gov [apollo-***@lists.lbl.gov] on behalf of Nathan Dunn [***@lbl.gov]
Sent: Tuesday, February 09, 2016 19:40
To: ***@lists.lbl.gov
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

Nathan Dunn

2016-02-09 20:29:42 UTC

Permalink

Post by Ohm, R.A. (Robin)
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.

Post by Ohm, R.A. (Robin)
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 weâve 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

Post by Ohm, R.A. (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
Sent: Tuesday, February 09, 2016 19:40
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).
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

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

Ohm, R.A. (Robin)

2016-02-09 22:53:07 UTC

Permalink

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: apollo-***@lists.lbl.gov [apollo-***@lists.lbl.gov] on behalf of Nathan Dunn [***@lbl.gov]
Sent: Tuesday, February 09, 2016 21:29
To: ***@lists.lbl.gov
Subject: Re: [apollo] Error during Create Organism

On Feb 9, 2016, at 12:17 PM, Ohm, R.A. (Robin) <***@uu.nl<mailto:***@uu.nl>> 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 weve 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: apollo-***@lists.lbl.gov<mailto:apollo-***@lists.lbl.gov> [apollo-***@lists.lbl.gov<mailto:apollo-***@lists.lbl.gov>] on behalf of Nathan Dunn [***@lbl.gov<mailto:***@lbl.gov>]
Sent: Tuesday, February 09, 2016 19:40
To: ***@lists.lbl.gov<mailto:***@lists.lbl.gov>
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

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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