chado support

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

chado support

Michael Paulini
Hia,


I was playing around with your docker images (and our jbrowse tracks)
and tried the "export to chado" option. Which happily creates a new
organism and inserts the annotations into the postgres chado database,
but any subsequence "export to chado" end up with SQL errors about
conflicting keys.

as example:

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value
violates unique constraint "feature_c1"
   Detail: Key (organism_id, uniquename, type_id)=(2,
6861ebf0-0083-4183-bda0-f0db99062b0e, 2364) already exists.
     at
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

which seems like the chado adaptor can only insert and not update?


I had a bit a look around for documentation, but all I could find was
for the old 1.x webapollo, which required that you load the annotation
into chado first before webapollo could export it,

Is that still the case? I perhaps naively thought that dbCreate =
"update" means that it should be able to update things.

And as a side remark: the volvox example data is not included in the
image, but described in the documentation.


best regards,


Michael





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.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: chado support

Deepak Unni
Hi Michael,

In Apollo 2, the ability to export to Chado makes the assumption that the Chado database is empty. You are correct in your guess that chado export is capable of doing inserts and not updates. 
This is not due to a limitation on the way the database is configured, but rather the way the Chado export itself works. Which would explain why you are seeing errors about duplicate keys.

Adding the ability to perform updates to an existing Chado database has been a feature request and it has been in our things-to-do. But as always there are several other things that are part of the Apollo development roadmap and thus we haven't gotten around to it yet.

Hope this helps :)

Cheers,

Deepak


On Fri, Jul 21, 2017 at 7:29 AM, Michael Paulini <[hidden email]> wrote:
Hia,


I was playing around with your docker images (and our jbrowse tracks) and tried the "export to chado" option. Which happily creates a new organism and inserts the annotations into the postgres chado database, but any subsequence "export to chado" end up with SQL errors about conflicting keys.

as example:

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "feature_c1"
  Detail: Key (organism_id, uniquename, type_id)=(2, 6861ebf0-0083-4183-bda0-f0db99062b0e, 2364) already exists.
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

which seems like the chado adaptor can only insert and not update?


I had a bit a look around for documentation, but all I could find was for the old 1.x webapollo, which required that you load the annotation into chado first before webapollo could export it,

Is that still the case? I perhaps naively thought that dbCreate = "update" means that it should be able to update things.

And as a side remark: the volvox example data is not included in the image, but described in the documentation.


best regards,


Michael





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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: chado support

nathandunn


Michael,

If it helps, Deepak also added a script in the scripts directory called “load_chado_schema.sh” that will dump and clean your database for re-export. 

Nathan

On Jul 21, 2017, at 7:40 AM, Deepak Unni <[hidden email]> wrote:

Hi Michael,

In Apollo 2, the ability to export to Chado makes the assumption that the Chado database is empty. You are correct in your guess that chado export is capable of doing inserts and not updates. 
This is not due to a limitation on the way the database is configured, but rather the way the Chado export itself works. Which would explain why you are seeing errors about duplicate keys.

Adding the ability to perform updates to an existing Chado database has been a feature request and it has been in our things-to-do. But as always there are several other things that are part of the Apollo development roadmap and thus we haven't gotten around to it yet.

Hope this helps :)

Cheers,

Deepak


On Fri, Jul 21, 2017 at 7:29 AM, Michael Paulini <[hidden email]> wrote:
Hia,


I was playing around with your docker images (and our jbrowse tracks) and tried the "export to chado" option. Which happily creates a new organism and inserts the annotations into the postgres chado database, but any subsequence "export to chado" end up with SQL errors about conflicting keys.

as example:

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "feature_c1"
  Detail: Key (organism_id, uniquename, type_id)=(2, 6861ebf0-0083-4183-bda0-f0db99062b0e, 2364) already exists.
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

which seems like the chado adaptor can only insert and not update?


I had a bit a look around for documentation, but all I could find was for the old 1.x webapollo, which required that you load the annotation into chado first before webapollo could export it,

Is that still the case? I perhaps naively thought that dbCreate = "update" means that it should be able to update things.

And as a side remark: the volvox example data is not included in the image, but described in the documentation.


best regards,


Michael





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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



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.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: chado support

Michael Paulini
thanks, that is quite useful.

in the past, I just did drop the database and load the sql dump back in, but fly in my way was always that I had to stop tomcat to drop the database (as postgres wouldn't let me drop the database if there are open connections to it).

M

On 21/07/17 16:25, Nathan Dunn wrote:


Michael,

If it helps, Deepak also added a script in the scripts directory called “load_chado_schema.sh” that will dump and clean your database for re-export. 

Nathan

On Jul 21, 2017, at 7:40 AM, Deepak Unni <[hidden email]> wrote:

Hi Michael,

In Apollo 2, the ability to export to Chado makes the assumption that the Chado database is empty. You are correct in your guess that chado export is capable of doing inserts and not updates. 
This is not due to a limitation on the way the database is configured, but rather the way the Chado export itself works. Which would explain why you are seeing errors about duplicate keys.

Adding the ability to perform updates to an existing Chado database has been a feature request and it has been in our things-to-do. But as always there are several other things that are part of the Apollo development roadmap and thus we haven't gotten around to it yet.

Hope this helps :)

Cheers,

Deepak


On Fri, Jul 21, 2017 at 7:29 AM, Michael Paulini <[hidden email]> wrote:
Hia,


I was playing around with your docker images (and our jbrowse tracks) and tried the "export to chado" option. Which happily creates a new organism and inserts the annotations into the postgres chado database, but any subsequence "export to chado" end up with SQL errors about conflicting keys.

as example:

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "feature_c1"
  Detail: Key (organism_id, uniquename, type_id)=(2, 6861ebf0-0083-4183-bda0-f0db99062b0e, 2364) already exists.
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

which seems like the chado adaptor can only insert and not update?


I had a bit a look around for documentation, but all I could find was for the old 1.x webapollo, which required that you load the annotation into chado first before webapollo could export it,

Is that still the case? I perhaps naively thought that dbCreate = "update" means that it should be able to update things.

And as a side remark: the volvox example data is not included in the image, but described in the documentation.


best regards,


Michael





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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



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.

Loading...