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Error

Zacher, Stacy

Hello:

 

Our developer is getting an error when trying to get intermine up and running on a server that we just rebuilt.   Originally these databases were built years ago and whoever built intermine chose the postgres superuser to own all the databases.  If possible, we would like to appoint a different database owner instead of postgres.

Is that possible or will intermine not cooperate?   Is it a matter of just altering the database and selecting a new owner or would other permissions in postgres need to be changed as well.


Here is the error the developer is getting: 

 

/data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98: org.postgresql.util.PSQLException: ERROR: permission denied for relation intermine_metadata

 

Any assistance would be appreciate.


Thanks!

 

Stacy Zacher

Database Administrator | Information Services

Medical College of Wisconsin

[hidden email]

414-955-5654

 


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Re: Error

Julie Sullivan-2
Hi Stacy

Yes! You can change the owner of the database in postgres, then update
the credentials in your ratmine.properties file. You'll have to redeploy
your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto
our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

> Hello:
>
> Our developer is getting an error when trying to get intermine up and
> running on a server that we just rebuilt.   Originally these databases
> were built years ago and whoever built intermine chose the postgres
> superuser to own all the databases. If possible, we would like to
> appoint a different database owner instead of postgres.
>
> Is that possible or will intermine not cooperate?   Is it a matter of
> just altering the database and selecting a new owner or would other
> permissions in postgres need to be changed as well.
>
>
> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for relation
> intermine_metadata
>
> Any assistance would be appreciate.
>
>
> Thanks!
>
> *Stacy Zacher*
>
> Database Administrator | Information Services
>
> *Medical College of Wisconsin*
>
> [hidden email] <mailto:[hidden email]>
>
> 414-955-5654
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Error

Zacher, Stacy
Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

> Hello:
>
> Our developer is getting an error when trying to get intermine up and
> running on a server that we just rebuilt.   Originally these databases
> were built years ago and whoever built intermine chose the postgres
> superuser to own all the databases. If possible, we would like to
> appoint a different database owner instead of postgres.
>
> Is that possible or will intermine not cooperate?   Is it a matter of
> just altering the database and selecting a new owner or would other
> permissions in postgres need to be changed as well.
>
>
> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for
> relation intermine_metadata
>
> Any assistance would be appreciate.
>
>
> Thanks!
>
> *Stacy Zacher*
>
> Database Administrator | Information Services
>
> *Medical College of Wisconsin*
>
> [hidden email] <mailto:[hidden email]>
>
> 414-955-5654
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>
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Re: Error

Zacher, Stacy
In reply to this post by Julie Sullivan-2
Hi again:

We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.
He indicated:

"I am getting the error when trying to run acceptance tests or when trying to deploy the web app.

For the webapp, from the webapp directory
$ ant default remove-webapp deploy-webapp

From tests, from the integrate directory
$ ant acceptance-tests
"

> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for
> relation intermine_metadata
>

Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.

If you have any ideas, please let me know. Thanks again for your assistance.

Stacy

-----Original Message-----
From: Zacher, Stacy
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; [hidden email]
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

> Hello:
>
> Our developer is getting an error when trying to get intermine up and
> running on a server that we just rebuilt.   Originally these databases
> were built years ago and whoever built intermine chose the postgres
> superuser to own all the databases. If possible, we would like to
> appoint a different database owner instead of postgres.
>
> Is that possible or will intermine not cooperate?   Is it a matter of
> just altering the database and selecting a new owner or would other
> permissions in postgres need to be changed as well.
>
>
> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for
> relation intermine_metadata
>
> Any assistance would be appreciate.
>
>
> Thanks!
>
> *Stacy Zacher*
>
> Database Administrator | Information Services
>
> *Medical College of Wisconsin*
>
> [hidden email] <mailto:[hidden email]>
>
> 414-955-5654
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>
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Re: Error

joe carlson

What do you see with the psql commands:

\dt+ gene

and

\dp+ gene

The output of first command will tell you who owns the table, the second
tells you the access privileges. The owner is still probably set to
postgres and - if the access privileges column is blank - the select
access probably has not been granted.

If so, you need to

ALTER TABLE gene OWNER TO <new owner>;

(and so on for ALL tables. There's a way to do this by updating system
tables. But that is riskier. It's safer to type \dt to print the tables,
capture that in a file and use that to generate a file of SQL commands.)

After doing this, make sure you can select from the table. Connect with
psql using the webapp's credentials and type:

select count(*) from gene;

The webapp also needs to create temporary tables when it is running. Be
sure that you can do this with the commands:

create table foo (id int);

If that is successful:

drop table foo;

Joe
On 01/26/2018 11:45 AM, Zacher, Stacy wrote:

> Hi again:
>
> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.
> He indicated:
>
> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.
>
> For the webapp, from the webapp directory
> $ ant default remove-webapp deploy-webapp
>
>  From tests, from the integrate directory
> $ ant acceptance-tests
> "
>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.
>
> If you have any ideas, please let me know. Thanks again for your assistance.
>
> Stacy
>
> -----Original Message-----
> From: Zacher, Stacy
> Sent: Friday, January 26, 2018 12:50 PM
> To: 'Julie Sullivan'; [hidden email]
> Subject: RE: [InterMine Dev] Error
>
> Thank you very much Julie! I will try this.
>
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Friday, January 26, 2018 2:43 AM
> To: Zacher, Stacy; [hidden email]
> Subject: Re: [InterMine Dev] Error
>
> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
> ________________________________
>
> Hi Stacy
>
> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.
>
> intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/
>
> If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org
>
> Cheers
> Julie
>
> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>> Hello:
>>
>> Our developer is getting an error when trying to get intermine up and
>> running on a server that we just rebuilt.   Originally these databases
>> were built years ago and whoever built intermine chose the postgres
>> superuser to own all the databases. If possible, we would like to
>> appoint a different database owner instead of postgres.
>>
>> Is that possible or will intermine not cooperate?   Is it a matter of
>> just altering the database and selecting a new owner or would other
>> permissions in postgres need to be changed as well.
>>
>>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
>> Any assistance would be appreciate.
>>
>>
>> Thanks!
>>
>> *Stacy Zacher*
>>
>> Database Administrator | Information Services
>>
>> *Medical College of Wisconsin*
>>
>> [hidden email] <mailto:[hidden email]>
>>
>> 414-955-5654
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error

Sam Hokin-3
Joe's the psql king, but I'll chime in that I'm particularly fond of:

REASSIGN OWNED BY old_role [, ...] TO new_role

for bulk ownership changes. I use this when I load a database as, say, sam, and want to change everything to being owned by
intermine in one swell foop.

On 01/26/2018 02:39 PM, Joe Carlson wrote:

>
> What do you see with the psql commands:
>
> \dt+ gene
>
> and
>
> \dp+ gene
>
> The output of first command will tell you who owns the table, the second tells you the access privileges. The owner is still
> probably set to postgres and - if the access privileges column is blank - the select access probably has not been granted.
>
> If so, you need to
>
> ALTER TABLE gene OWNER TO <new owner>;
>
> (and so on for ALL tables. There's a way to do this by updating system tables. But that is riskier. It's safer to type \dt to print
> the tables, capture that in a file and use that to generate a file of SQL commands.)
>
> After doing this, make sure you can select from the table. Connect with psql using the webapp's credentials and type:
>
> select count(*) from gene;
>
> The webapp also needs to create temporary tables when it is running. Be sure that you can do this with the commands:
>
> create table foo (id int);
>
> If that is successful:
>
> drop table foo;
>
> Joe
> On 01/26/2018 11:45 AM, Zacher, Stacy wrote:
>> Hi again:
>>
>> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that
>> is where we are getting errrors.
>> He indicated:
>>
>> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.
>>
>> For the webapp, from the webapp directory
>> $ ant default remove-webapp deploy-webapp
>>
>>  From tests, from the integrate directory
>> $ ant acceptance-tests
>> "
>>
>>> Here is the error the developer is getting:
>>>
>>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>>> org.postgresql.util.PSQLException: ERROR: permission denied for
>>> relation intermine_metadata
>>>
>> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.
>>
>> If you have any ideas, please let me know. Thanks again for your assistance.
>>
>> Stacy
>>
>> -----Original Message-----
>> From: Zacher, Stacy
>> Sent: Friday, January 26, 2018 12:50 PM
>> To: 'Julie Sullivan'; [hidden email]
>> Subject: RE: [InterMine Dev] Error
>>
>> Thank you very much Julie! I will try this.
>>
>>
>>
>> -----Original Message-----
>> From: Julie Sullivan [mailto:[hidden email]]
>> Sent: Friday, January 26, 2018 2:43 AM
>> To: Zacher, Stacy; [hidden email]
>> Subject: Re: [InterMine Dev] Error
>>
>> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
>> ________________________________
>>
>> Hi Stacy
>>
>> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll
>> have to redeploy your webapp to apply these changes however.
>>
>> intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/
>>
>> If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org
>>
>> Cheers
>> Julie
>>
>> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>>> Hello:
>>>
>>> Our developer is getting an error when trying to get intermine up and
>>> running on a server that we just rebuilt.   Originally these databases
>>> were built years ago and whoever built intermine chose the postgres
>>> superuser to own all the databases. If possible, we would like to
>>> appoint a different database owner instead of postgres.
>>>
>>> Is that possible or will intermine not cooperate?   Is it a matter of
>>> just altering the database and selecting a new owner or would other
>>> permissions in postgres need to be changed as well.
>>>
>>>
>>> Here is the error the developer is getting:
>>>
>>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>>> org.postgresql.util.PSQLException: ERROR: permission denied for
>>> relation intermine_metadata
>>>
>>> Any assistance would be appreciate.
>>>
>>>
>>> Thanks!
>>>
>>> *Stacy Zacher*
>>>
>>> Database Administrator | Information Services
>>>
>>> *Medical College of Wisconsin*
>>>
>>> [hidden email] <mailto:[hidden email]>
>>>
>>> 414-955-5654
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
>>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
>>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
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Re: Error

joe carlson
Dang! that's a good one. I did not know of that trick.

(but isn't the expression 'one fell swoop'?)

joe

On 01/26/2018 01:49 PM, Sam Hokin wrote:

> Joe's the psql king, but I'll chime in that I'm particularly fond of:
>
> REASSIGN OWNED BY old_role [, ...] TO new_role
>
> for bulk ownership changes. I use this when I load a database as, say,
> sam, and want to change everything to being owned by intermine in one
> swell foop.
>
> On 01/26/2018 02:39 PM, Joe Carlson wrote:
>>
>> What do you see with the psql commands:
>>
>> \dt+ gene
>>
>> and
>>
>> \dp+ gene
>>
>> The output of first command will tell you who owns the table, the
>> second tells you the access privileges. The owner is still probably
>> set to postgres and - if the access privileges column is blank - the
>> select access probably has not been granted.
>>
>> If so, you need to
>>
>> ALTER TABLE gene OWNER TO <new owner>;
>>
>> (and so on for ALL tables. There's a way to do this by updating
>> system tables. But that is riskier. It's safer to type \dt to print
>> the tables, capture that in a file and use that to generate a file of
>> SQL commands.)
>>
>> After doing this, make sure you can select from the table. Connect
>> with psql using the webapp's credentials and type:
>>
>> select count(*) from gene;
>>
>> The webapp also needs to create temporary tables when it is running.
>> Be sure that you can do this with the commands:
>>
>> create table foo (id int);
>>
>> If that is successful:
>>
>> drop table foo;
>>
>> Joe
>> On 01/26/2018 11:45 AM, Zacher, Stacy wrote:
>>> Hi again:
>>>
>>> We did change the owner to a new user, updated the
>>> ratmine.properties file but when the developer tries to redeploy the
>>> app, that is where we are getting errrors.
>>> He indicated:
>>>
>>> "I am getting the error when trying to run acceptance tests or when
>>> trying to deploy the web app.
>>>
>>> For the webapp, from the webapp directory
>>> $ ant default remove-webapp deploy-webapp
>>>
>>>  From tests, from the integrate directory
>>> $ ant acceptance-tests
>>> "
>>>
>>>> Here is the error the developer is getting:
>>>>
>>>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>>>> org.postgresql.util.PSQLException: ERROR: permission denied for
>>>> relation intermine_metadata
>>>>
>>> Since the developer is on loan to us, I'm trying to troubleshoot
>>> this for him along with the systems administrator.
>>>
>>> If you have any ideas, please let me know. Thanks again for your
>>> assistance.
>>>
>>> Stacy
>>>
>>> -----Original Message-----
>>> From: Zacher, Stacy
>>> Sent: Friday, January 26, 2018 12:50 PM
>>> To: 'Julie Sullivan'; [hidden email]
>>> Subject: RE: [InterMine Dev] Error
>>>
>>> Thank you very much Julie! I will try this.
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Julie Sullivan [mailto:[hidden email]]
>>> Sent: Friday, January 26, 2018 2:43 AM
>>> To: Zacher, Stacy; [hidden email]
>>> Subject: Re: [InterMine Dev] Error
>>>
>>> ATTENTION: This email originated from a sender outside of MCW. Use
>>> caution when clicking on links or opening attachments.
>>> ________________________________
>>>
>>> Hi Stacy
>>>
>>> Yes! You can change the owner of the database in postgres, then
>>> update the credentials in your ratmine.properties file. You'll have
>>> to redeploy your webapp to apply these changes however.
>>>
>>> intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/
>>>
>>>
>>> If you have more troubles, I am happy to skype! You can also pop
>>> onto our discord server: chat.intermine.org
>>>
>>> Cheers
>>> Julie
>>>
>>> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>>>> Hello:
>>>>
>>>> Our developer is getting an error when trying to get intermine up and
>>>> running on a server that we just rebuilt.   Originally these databases
>>>> were built years ago and whoever built intermine chose the postgres
>>>> superuser to own all the databases. If possible, we would like to
>>>> appoint a different database owner instead of postgres.
>>>>
>>>> Is that possible or will intermine not cooperate?   Is it a matter of
>>>> just altering the database and selecting a new owner or would other
>>>> permissions in postgres need to be changed as well.
>>>>
>>>>
>>>> Here is the error the developer is getting:
>>>>
>>>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>>>> org.postgresql.util.PSQLException: ERROR: permission denied for
>>>> relation intermine_metadata
>>>>
>>>> Any assistance would be appreciate.
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> *Stacy Zacher*
>>>>
>>>> Database Administrator | Information Services
>>>>
>>>> *Medical College of Wisconsin*
>>>>
>>>> [hidden email] <mailto:[hidden email]>
>>>>
>>>> 414-955-5654
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
>>>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
>>>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>>>
>>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
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Re: Error

Zacher, Stacy
In reply to this post by joe carlson
Thank you for all the assistance everyone.  I will check into this and let you know what I find.
Best regards,
Stacy

-----Original Message-----
From: Joe Carlson [mailto:[hidden email]]
Sent: Friday, January 26, 2018 3:39 PM
To: Zacher, Stacy; Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

What do you see with the psql commands:

\dt+ gene

and

\dp+ gene

The output of first command will tell you who owns the table, the second tells you the access privileges. The owner is still probably set to postgres and - if the access privileges column is blank - the select access probably has not been granted.

If so, you need to

ALTER TABLE gene OWNER TO <new owner>;

(and so on for ALL tables. There's a way to do this by updating system tables. But that is riskier. It's safer to type \dt to print the tables, capture that in a file and use that to generate a file of SQL commands.)

After doing this, make sure you can select from the table. Connect with psql using the webapp's credentials and type:

select count(*) from gene;

The webapp also needs to create temporary tables when it is running. Be sure that you can do this with the commands:

create table foo (id int);

If that is successful:

drop table foo;

Joe
On 01/26/2018 11:45 AM, Zacher, Stacy wrote:

> Hi again:
>
> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.
> He indicated:
>
> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.
>
> For the webapp, from the webapp directory $ ant default remove-webapp
> deploy-webapp
>
>  From tests, from the integrate directory $ ant acceptance-tests "
>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.
>
> If you have any ideas, please let me know. Thanks again for your assistance.
>
> Stacy
>
> -----Original Message-----
> From: Zacher, Stacy
> Sent: Friday, January 26, 2018 12:50 PM
> To: 'Julie Sullivan'; [hidden email]
> Subject: RE: [InterMine Dev] Error
>
> Thank you very much Julie! I will try this.
>
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Friday, January 26, 2018 2:43 AM
> To: Zacher, Stacy; [hidden email]
> Subject: Re: [InterMine Dev] Error
>
> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
> ________________________________
>
> Hi Stacy
>
> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.
>
> intermine.readthedocs.io/en/latest/webapp/properties/intermine-propert
> ies/
>
> If you have more troubles, I am happy to skype! You can also pop onto
> our discord server: chat.intermine.org
>
> Cheers
> Julie
>
> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>> Hello:
>>
>> Our developer is getting an error when trying to get intermine up and
>> running on a server that we just rebuilt.   Originally these databases
>> were built years ago and whoever built intermine chose the postgres
>> superuser to own all the databases. If possible, we would like to
>> appoint a different database owner instead of postgres.
>>
>> Is that possible or will intermine not cooperate?   Is it a matter of
>> just altering the database and selecting a new owner or would other
>> permissions in postgres need to be changed as well.
>>
>>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
>> Any assistance would be appreciate.
>>
>>
>> Thanks!
>>
>> *Stacy Zacher*
>>
>> Database Administrator | Information Services
>>
>> *Medical College of Wisconsin*
>>
>> [hidden email] <mailto:[hidden email]>
>>
>> 414-955-5654
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.
>> o
>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYP
>> Q
>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5Yd
>> AwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwICaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=_g3UPSfxPccS7ZTTQFXwII1khmH8rd2ozf
> WG_vru-y8&s=-reAJcqbNawCYMPxZNFxIw2ISgEVToOlZIVDTfxhMS8&e=

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Re: Error

Zacher, Stacy
In reply to this post by joe carlson
Hi:

I just posted before I re-read your message.  Is there a simple query that will tell me ALL the objects that are owned by the previous owner?
I see tables and sequences for example that are owned by the previous owner and I will need to change them all for the 6 intermine databases we have.
Something similar to Oracle's

Select owner, object_name, object_type from dba_objects where owner = 'ratmine_previousowner';

Thanks again
Stacy


-----Original Message-----
From: Joe Carlson [mailto:[hidden email]]
Sent: Friday, January 26, 2018 3:39 PM
To: Zacher, Stacy; Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

What do you see with the psql commands:

\dt+ gene

and

\dp+ gene

The output of first command will tell you who owns the table, the second tells you the access privileges. The owner is still probably set to postgres and - if the access privileges column is blank - the select access probably has not been granted.

If so, you need to

ALTER TABLE gene OWNER TO <new owner>;

(and so on for ALL tables. There's a way to do this by updating system tables. But that is riskier. It's safer to type \dt to print the tables, capture that in a file and use that to generate a file of SQL commands.)

After doing this, make sure you can select from the table. Connect with psql using the webapp's credentials and type:

select count(*) from gene;

The webapp also needs to create temporary tables when it is running. Be sure that you can do this with the commands:

create table foo (id int);

If that is successful:

drop table foo;

Joe
On 01/26/2018 11:45 AM, Zacher, Stacy wrote:

> Hi again:
>
> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.
> He indicated:
>
> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.
>
> For the webapp, from the webapp directory $ ant default remove-webapp
> deploy-webapp
>
>  From tests, from the integrate directory $ ant acceptance-tests "
>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.
>
> If you have any ideas, please let me know. Thanks again for your assistance.
>
> Stacy
>
> -----Original Message-----
> From: Zacher, Stacy
> Sent: Friday, January 26, 2018 12:50 PM
> To: 'Julie Sullivan'; [hidden email]
> Subject: RE: [InterMine Dev] Error
>
> Thank you very much Julie! I will try this.
>
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Friday, January 26, 2018 2:43 AM
> To: Zacher, Stacy; [hidden email]
> Subject: Re: [InterMine Dev] Error
>
> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
> ________________________________
>
> Hi Stacy
>
> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.
>
> intermine.readthedocs.io/en/latest/webapp/properties/intermine-propert
> ies/
>
> If you have more troubles, I am happy to skype! You can also pop onto
> our discord server: chat.intermine.org
>
> Cheers
> Julie
>
> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>> Hello:
>>
>> Our developer is getting an error when trying to get intermine up and
>> running on a server that we just rebuilt.   Originally these databases
>> were built years ago and whoever built intermine chose the postgres
>> superuser to own all the databases. If possible, we would like to
>> appoint a different database owner instead of postgres.
>>
>> Is that possible or will intermine not cooperate?   Is it a matter of
>> just altering the database and selecting a new owner or would other
>> permissions in postgres need to be changed as well.
>>
>>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
>> Any assistance would be appreciate.
>>
>>
>> Thanks!
>>
>> *Stacy Zacher*
>>
>> Database Administrator | Information Services
>>
>> *Medical College of Wisconsin*
>>
>> [hidden email] <mailto:[hidden email]>
>>
>> 414-955-5654
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.
>> o
>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYP
>> Q
>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5Yd
>> AwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwICaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=_g3UPSfxPccS7ZTTQFXwII1khmH8rd2ozf
> WG_vru-y8&s=-reAJcqbNawCYMPxZNFxIw2ISgEVToOlZIVDTfxhMS8&e=

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Re: Error

Steven Neuhauser
Hi Stacy,

Try this

select * from pg_tables where tableowner =

-Steve

-----Original Message-----
From: dev [mailto:[hidden email]] On Behalf Of Zacher, Stacy
Sent: Friday, February 02, 2018 3:45 PM
To: Joe Carlson; Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

Hi:

I just posted before I re-read your message.  Is there a simple query that will tell me ALL the objects that are owned by the previous owner?
I see tables and sequences for example that are owned by the previous owner and I will need to change them all for the 6 intermine databases we have.
Something similar to Oracle's

Select owner, object_name, object_type from dba_objects where owner = 'ratmine_previousowner';

Thanks again
Stacy


-----Original Message-----
From: Joe Carlson [mailto:[hidden email]]
Sent: Friday, January 26, 2018 3:39 PM
To: Zacher, Stacy; Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

What do you see with the psql commands:

\dt+ gene

and

\dp+ gene

The output of first command will tell you who owns the table, the second tells you the access privileges. The owner is still probably set to postgres and - if the access privileges column is blank - the select access probably has not been granted.

If so, you need to

ALTER TABLE gene OWNER TO <new owner>;

(and so on for ALL tables. There's a way to do this by updating system tables. But that is riskier. It's safer to type \dt to print the tables, capture that in a file and use that to generate a file of SQL commands.)

After doing this, make sure you can select from the table. Connect with psql using the webapp's credentials and type:

select count(*) from gene;

The webapp also needs to create temporary tables when it is running. Be sure that you can do this with the commands:

create table foo (id int);

If that is successful:

drop table foo;

Joe
On 01/26/2018 11:45 AM, Zacher, Stacy wrote:

> Hi again:
>
> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.
> He indicated:
>
> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.
>
> For the webapp, from the webapp directory $ ant default remove-webapp
> deploy-webapp
>
>  From tests, from the integrate directory $ ant acceptance-tests "
>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.
>
> If you have any ideas, please let me know. Thanks again for your assistance.
>
> Stacy
>
> -----Original Message-----
> From: Zacher, Stacy
> Sent: Friday, January 26, 2018 12:50 PM
> To: 'Julie Sullivan'; [hidden email]
> Subject: RE: [InterMine Dev] Error
>
> Thank you very much Julie! I will try this.
>
>
>
> -----Original Message-----
> From: Julie Sullivan [mailto:[hidden email]]
> Sent: Friday, January 26, 2018 2:43 AM
> To: Zacher, Stacy; [hidden email]
> Subject: Re: [InterMine Dev] Error
>
> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
> ________________________________
>
> Hi Stacy
>
> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.
>
> intermine.readthedocs.io/en/latest/webapp/properties/intermine-propert
> ies/
>
> If you have more troubles, I am happy to skype! You can also pop onto
> our discord server: chat.intermine.org
>
> Cheers
> Julie
>
> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
>> Hello:
>>
>> Our developer is getting an error when trying to get intermine up and
>> running on a server that we just rebuilt.   Originally these databases
>> were built years ago and whoever built intermine chose the postgres
>> superuser to own all the databases. If possible, we would like to
>> appoint a different database owner instead of postgres.
>>
>> Is that possible or will intermine not cooperate?   Is it a matter of
>> just altering the database and selecting a new owner or would other
>> permissions in postgres need to be changed as well.
>>
>>
>> Here is the error the developer is getting:
>>
>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
>> org.postgresql.util.PSQLException: ERROR: permission denied for
>> relation intermine_metadata
>>
>> Any assistance would be appreciate.
>>
>>
>> Thanks!
>>
>> *Stacy Zacher*
>>
>> Database Administrator | Information Services
>>
>> *Medical College of Wisconsin*
>>
>> [hidden email] <mailto:[hidden email]>
>>
>> 414-955-5654
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.
>> o
>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYP
>> Q
>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5Yd
>> AwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwICaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=_g3UPSfxPccS7ZTTQFXwII1khmH8rd2ozf
> WG_vru-y8&s=-reAJcqbNawCYMPxZNFxIw2ISgEVToOlZIVDTfxhMS8&e=

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Re: Error

Zacher, Stacy
Thanks Steve, that works.  I found a site with commands where I'm able to change the objects to the new owner.

I ran the following

Set the password so it didn't ask me for it 900+ times:
e.g.  
$ export PGPASSWORD=postgresdbpasswordhere (not the real password of course)
echo $PGPASSWORD  
$ postgresdbpasswordhere

Then I ran these statements at the command line for the objects I found owned by the old owner:  

$ for tbl in `psql -qAt -c "select tablename from pg_tables where schemaname = 'public';" ratmine` ; do  psql -c "alter table \"$tbl\" owner to ratmine_user" ratmine ; done
$ for tbl in `psql -qAt -c "select sequence_name from information_schema.sequences where sequence_schema = 'public';" ratmine` ; do  psql -c "alter table \"$tbl\" owner to ratmine_user" ratmine ; done
$ for tbl in `psql -qAt -c "select table_name from information_schema.views where table_schema = 'public';" ratmine` ; do  psql -c "alter table \"$tbl\" owner to ratmine_user" ratmine ; done

Etc.

Thanks so much for your help Steve and everyone and have a great weekend.
Stacy

-----Original Message-----
From: Steven Neuhauser [mailto:[hidden email]]
Sent: Friday, February 02, 2018 3:12 PM
To: Zacher, Stacy; Joe Carlson; Julie Sullivan; [hidden email]
Subject: RE: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy,



Try this



select * from pg_tables where tableowner =



-Steve



-----Original Message-----

From: dev [mailto:[hidden email]] On Behalf Of Zacher, Stacy

Sent: Friday, February 02, 2018 3:45 PM

To: Joe Carlson; Julie Sullivan; [hidden email]

Subject: Re: [InterMine Dev] Error



Hi:



I just posted before I re-read your message.  Is there a simple query that will tell me ALL the objects that are owned by the previous owner?

I see tables and sequences for example that are owned by the previous owner and I will need to change them all for the 6 intermine databases we have.

Something similar to Oracle's



Select owner, object_name, object_type from dba_objects where owner = 'ratmine_previousowner';



Thanks again

Stacy





-----Original Message-----

From: Joe Carlson [mailto:[hidden email]]

Sent: Friday, January 26, 2018 3:39 PM

To: Zacher, Stacy; Julie Sullivan; [hidden email]

Subject: Re: [InterMine Dev] Error



ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.

________________________________



What do you see with the psql commands:



\dt+ gene



and



\dp+ gene



The output of first command will tell you who owns the table, the second tells you the access privileges. The owner is still probably set to postgres and - if the access privileges column is blank - the select access probably has not been granted.



If so, you need to



ALTER TABLE gene OWNER TO <new owner>;



(and so on for ALL tables. There's a way to do this by updating system tables. But that is riskier. It's safer to type \dt to print the tables, capture that in a file and use that to generate a file of SQL commands.)



After doing this, make sure you can select from the table. Connect with psql using the webapp's credentials and type:



select count(*) from gene;



The webapp also needs to create temporary tables when it is running. Be sure that you can do this with the commands:



create table foo (id int);



If that is successful:



drop table foo;



Joe

On 01/26/2018 11:45 AM, Zacher, Stacy wrote:

> Hi again:

>

> We did change the owner to a new user, updated the ratmine.properties file but when the developer tries to redeploy the app, that is where we are getting errrors.

> He indicated:

>

> "I am getting the error when trying to run acceptance tests or when trying to deploy the web app.

>

> For the webapp, from the webapp directory $ ant default remove-webapp

> deploy-webapp

>

>  From tests, from the integrate directory $ ant acceptance-tests "

>

>> Here is the error the developer is getting:

>>

>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:

>> org.postgresql.util.PSQLException: ERROR: permission denied for

>> relation intermine_metadata

>>

> Since the developer is on loan to us, I'm trying to troubleshoot this for him along with the systems administrator.

>

> If you have any ideas, please let me know. Thanks again for your assistance.

>

> Stacy

>

> -----Original Message-----

> From: Zacher, Stacy

> Sent: Friday, January 26, 2018 12:50 PM

> To: 'Julie Sullivan'; [hidden email]

> Subject: RE: [InterMine Dev] Error

>

> Thank you very much Julie! I will try this.

>

>

>

> -----Original Message-----

> From: Julie Sullivan [mailto:[hidden email]]

> Sent: Friday, January 26, 2018 2:43 AM

> To: Zacher, Stacy; [hidden email]

> Subject: Re: [InterMine Dev] Error

>

> ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.

> ________________________________

>

> Hi Stacy

>

> Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

>

> intermine.readthedocs.io/en/latest/webapp/properties/intermine-propert

> ies/

>

> If you have more troubles, I am happy to skype! You can also pop onto

> our discord server: chat.intermine.org

>

> Cheers

> Julie

>

> On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

>> Hello:

>>

>> Our developer is getting an error when trying to get intermine up and

>> running on a server that we just rebuilt.   Originally these databases

>> were built years ago and whoever built intermine chose the postgres

>> superuser to own all the databases. If possible, we would like to

>> appoint a different database owner instead of postgres.

>>

>> Is that possible or will intermine not cooperate?   Is it a matter of

>> just altering the database and selecting a new owner or would other

>> permissions in postgres need to be changed as well.

>>

>>

>> Here is the error the developer is getting:

>>

>> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:

>> org.postgresql.util.PSQLException: ERROR: permission denied for

>> relation intermine_metadata

>>

>> Any assistance would be appreciate.

>>

>>

>> Thanks!

>>

>> *Stacy Zacher*

>>

>> Database Administrator | Information Services

>>

>> *Medical College of Wisconsin*

>>

>> [hidden email] <mailto:[hidden email]>

>>

>> 414-955-5654

>>

>>

>>

>> _______________________________________________

>> dev mailing list

>> [hidden email]

>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.

>> o

>> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYP

>> Q

>> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5Yd

>> AwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=

>>

> _______________________________________________

> dev mailing list

> [hidden email]

> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o

> rg_mailman_listinfo_dev&d=DwICaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ

> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=_g3UPSfxPccS7ZTTQFXwII1khmH8rd2ozf

> WG_vru-y8&s=-reAJcqbNawCYMPxZNFxIw2ISgEVToOlZIVDTfxhMS8&e=



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Re: Error

Zacher, Stacy
In reply to this post by Julie Sullivan-2
Hi:

We have attempted to copy our postgres environment for intermine to a new server.  Everything appears to have been copied over, and postgres starts etc. but when we run  

ant -Daction=create-search-index -v

it errors out after about 42 minutes with the errors below.  
Esp Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028


Does anyone have any idea what we might need to do to resolve this?  I'm not the person deploying it - I am the database administrator.
Thanks for any assistance.  

postprocess:
[postprocess] Found 9 post-processes
[postprocess] Performing postprocess: create-search-index
[postprocess] Creating lucene index for keyword search...


BUILD FAILED
/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:435)
        at org.apache.tools.ant.Target.performTasks(Target.java:456)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
        at org.apache.tools.ant.Main.runBuild(Main.java:851)
        at org.apache.tools.ant.Main.startAnt(Main.java:235)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
        ... 17 more
Caused by: Operation was:create-search-index
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)
        ... 22 more
Caused by: java.lang.RuntimeException: Index creation failed:
        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)
        at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)
        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)
        ... 22 more
Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
        at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)
        at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)
        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)
        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)
        at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)
        at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)
        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)
        ... 24 more

Total time: 42 minutes 59 seconds


-----Original Message-----
From: Zacher, Stacy
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; [hidden email]
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [mailto:[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

> Hello:
>
> Our developer is getting an error when trying to get intermine up and
> running on a server that we just rebuilt.   Originally these databases
> were built years ago and whoever built intermine chose the postgres
> superuser to own all the databases. If possible, we would like to
> appoint a different database owner instead of postgres.
>
> Is that possible or will intermine not cooperate?   Is it a matter of
> just altering the database and selecting a new owner or would other
> permissions in postgres need to be changed as well.
>
>
> Here is the error the developer is getting:
>
> /data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
> org.postgresql.util.PSQLException: ERROR: permission denied for
> relation intermine_metadata
>
> Any assistance would be appreciate.
>
>
> Thanks!
>
> *Stacy Zacher*
>
> Database Administrator | Information Services
>
> *Medical College of Wisconsin*
>
> [hidden email] <mailto:[hidden email]>
>
> 414-955-5654
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.intermine.o
> rg_mailman_listinfo_dev&d=DwID-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQ
> kjgspw4Y&r=gOVZb7TNzY8wrQkgFJZGpQ&m=yOv5d_-6ptmUn-N05T8asaaDgH4ALI5YdAwIaOQPS90&s=uSdBNH7bDUjNLht-zL0FlGw_A1QIKqCEk8Nw8xjMvRs&e=
>
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Re: Error

Paulo Nuin
Hi

I would run all the post-processing in the same machine as the “regular” build and use pg_dump to dump it to a SQL file then load in your production. The index is saved in the same DB as your genomic data.

Cheers
Paulo



On Sep 19, 2018, at 2:58 PM, Zacher, Stacy <[hidden email]> wrote:

Hi:

We have attempted to copy our postgres environment for intermine to a new server.  Everything appears to have been copied over, and postgres starts etc. but when we run  

ant -Daction=create-search-index -v

it errors out after about 42 minutes with the errors below.  
Esp Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028


Does anyone have any idea what we might need to do to resolve this?  I'm not the person deploying it - I am the database administrator.
Thanks for any assistance.  

postprocess:
[postprocess] Found 9 post-processes
[postprocess] Performing postprocess: create-search-index
[postprocess] Creating lucene index for keyword search...


BUILD FAILED
/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
       at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:435)
       at org.apache.tools.ant.Target.performTasks(Target.java:456)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
       at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
       at org.apache.tools.ant.Main.runBuild(Main.java:851)
       at org.apache.tools.ant.Main.startAnt(Main.java:235)
       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
       ... 17 more
Caused by: Operation was:create-search-index
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)
       ... 22 more
Caused by: java.lang.RuntimeException: Index creation failed:
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)
       at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)
       ... 22 more
Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
       at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)
       at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)
       at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)
       at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)
       ... 24 more

Total time: 42 minutes 59 seconds


-----Original Message-----
From: Zacher, Stacy 
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; [hidden email]
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; [hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:
Hello:

Our developer is getting an error when trying to get intermine up and
running on a server that we just rebuilt.   Originally these databases
were built years ago and whoever built intermine chose the postgres 
superuser to own all the databases. If possible, we would like to 
appoint a different database owner instead of postgres.

Is that possible or will intermine not cooperate?   Is it a matter of
just altering the database and selecting a new owner or would other 
permissions in postgres need to be changed as well.


Here is the error the developer is getting:

/data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
org.postgresql.util.PSQLException: ERROR: permission denied for 
relation intermine_metadata

Any assistance would be appreciate.


Thanks!

*Stacy Zacher*

Database Administrator | Information Services

*Medical College of Wisconsin*

[hidden email] <[hidden email]>

414-955-5654



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Re: Error

Zacher, Stacy

Hi Paulo:

Thank you for your rely, we will try that.

Best regards,
Stacy

 

 

From: Paulo Nuin [mailto:[hidden email]]
Sent: Wednesday, September 19, 2018 4:17 PM
To: Zacher, Stacy
Cc: Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

 

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.


Hi

 

I would run all the post-processing in the same machine as the “regular” build and use pg_dump to dump it to a SQL file then load in your production. The index is saved in the same DB as your genomic data.

 

Cheers

Paulo

 

 



On Sep 19, 2018, at 2:58 PM, Zacher, Stacy <[hidden email]> wrote:

 

Hi:

We have attempted to copy our postgres environment for intermine to a new server.  Everything appears to have been copied over, and postgres starts etc. but when we run  

ant -Daction=create-search-index -v

it errors out after about 42 minutes with the errors below.  
Esp Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028


Does anyone have any idea what we might need to do to resolve this?  I'm not the person deploying it - I am the database administrator.
Thanks for any assistance.  

postprocess:
[postprocess] Found 9 post-processes
[postprocess] Performing postprocess: create-search-index
[postprocess] Creating lucene index for keyword search...


BUILD FAILED
/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
       at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:435)
       at org.apache.tools.ant.Target.performTasks(Target.java:456)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
       at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
       at org.apache.tools.ant.Main.runBuild(Main.java:851)
       at org.apache.tools.ant.Main.startAnt(Main.java:235)
       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
       ... 17 more
Caused by: Operation was:create-search-index
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)
       ... 22 more
Caused by: java.lang.RuntimeException: Index creation failed:
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)
       at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)
       ... 22 more
Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
       at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)
       at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)
       at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)
       at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)
       ... 24 more

Total time: 42 minutes 59 seconds


-----Original Message-----
From: Zacher, Stacy 
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; 
[hidden email]
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [
[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; 
[hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

Hello:

Our developer is getting an error when trying to get intermine up and
running on a server that we just rebuilt.   Originally these databases
were built years ago and whoever built intermine chose the postgres 
superuser to own all the databases. If possible, we would like to 
appoint a different database owner instead of postgres.

Is that possible or will intermine not cooperate?   Is it a matter of
just altering the database and selecting a new owner or would other 
permissions in postgres need to be changed as well.


Here is the error the developer is getting:

/data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
org.postgresql.util.PSQLException: ERROR: permission denied for 
relation intermine_metadata

Any assistance would be appreciate.


Thanks!

*Stacy Zacher*

Database Administrator | Information Services

*Medical College of Wisconsin*

[hidden email] <[hidden email]>

414-955-5654



_______________________________________________
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Re: Error

Zacher, Stacy
In reply to this post by Paulo Nuin

PS,

Do you know what this error is caused by?

 

Last time we moved the databases to a new server, we didn’t see this error at all:

I’m not sure what large object 2518028 is supposed to be to review who the “owner” is!

 

Thanks


Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028

 

 

-init-task-xml:

 

postprocess:

[postprocess] Found 9 post-processes

[postprocess] Performing postprocess: create-search-index

[postprocess] Creating lucene index for keyword search...

 

BUILD FAILED

/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)

        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)

        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:498)

        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)

        at org.apache.tools.ant.Task.perform(Task.java:348)

        at org.apache.tools.ant.Target.execute(Target.java:435)

        at org.apache.tools.ant.Target.performTasks(Target.java:456)

        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)

        at org.apache.tools.ant.Project.executeTarget(Project.java:1364)

        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)

        at org.apache.tools.ant.Project.executeTargets(Project.java:1248)

        at org.apache.tools.ant.Main.runBuild(Main.java:851)

        at org.apache.tools.ant.Main.startAnt(Main.java:235)

        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)

        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Caused by: java.lang.reflect.InvocationTargetException

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:498)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)

        ... 17 more

Caused by: Operation was:create-search-index

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)

        ... 22 more

Caused by: java.lang.RuntimeException: Index creation failed:

        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)

        at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)

        ... 22 more

Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028

        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

        at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)

        at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)

        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)

        at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)

        at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)

        at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)

        at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)

        ... 24 more

 

Total time: 18 minutes 3 seconds

 

From: Zacher, Stacy
Sent: Wednesday, September 19, 2018 4:19 PM
To: 'Paulo Nuin'
Cc: Julie Sullivan; [hidden email]
Subject: RE: [InterMine Dev] Error

 

Hi Paulo:

Thank you for your rely, we will try that.

Best regards,
Stacy

 

 

From: Paulo Nuin [[hidden email]]
Sent: Wednesday, September 19, 2018 4:17 PM
To: Zacher, Stacy
Cc: Julie Sullivan; [hidden email]
Subject: Re: [InterMine Dev] Error

 

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.


Hi

 

I would run all the post-processing in the same machine as the “regular” build and use pg_dump to dump it to a SQL file then load in your production. The index is saved in the same DB as your genomic data.

 

Cheers

Paulo

 

 

 

On Sep 19, 2018, at 2:58 PM, Zacher, Stacy <[hidden email]> wrote:

 

Hi:

We have attempted to copy our postgres environment for intermine to a new server.  Everything appears to have been copied over, and postgres starts etc. but when we run  

ant -Daction=create-search-index -v

it errors out after about 42 minutes with the errors below.  
Esp Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028


Does anyone have any idea what we might need to do to resolve this?  I'm not the person deploying it - I am the database administrator.
Thanks for any assistance.  

postprocess:
[postprocess] Found 9 post-processes
[postprocess] Performing postprocess: create-search-index
[postprocess] Creating lucene index for keyword search...


BUILD FAILED
/rgd/intermine/git_ratmine/intermine/imbuild/postprocess.xml:31: error running PostProcessTask (action: create-search-index)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:149)
       at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:122)
       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
       at org.apache.tools.ant.Task.perform(Task.java:348)
       at org.apache.tools.ant.Target.execute(Target.java:435)
       at org.apache.tools.ant.Target.performTasks(Target.java:456)
       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
       at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
       at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
       at org.apache.tools.ant.Main.runBuild(Main.java:851)
       at org.apache.tools.ant.Main.startAnt(Main.java:235)
       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:498)
       at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:147)
       ... 17 more
Caused by: Operation was:create-search-index
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:228)
       ... 22 more
Caused by: java.lang.RuntimeException: Index creation failed:
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:507)
       at org.intermine.web.task.CreateSearchIndexTask.execute(CreateSearchIndexTask.java:115)
       at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:202)
       ... 22 more
Caused by: org.postgresql.util.PSQLException: ERROR: must be owner of large object 2518028
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
       at org.postgresql.core.v3.QueryExecutorImpl.receiveFastpathResult(QueryExecutorImpl.java:686)
       at org.postgresql.core.v3.QueryExecutorImpl.fastpathCall(QueryExecutorImpl.java:537)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:100)
       at org.postgresql.fastpath.Fastpath.fastpath(Fastpath.java:145)
       at org.postgresql.largeobject.LargeObjectManager.delete(LargeObjectManager.java:336)
       at org.intermine.modelproduction.MetadataManager.deleteLargeBinary(MetadataManager.java:367)
       at org.intermine.api.lucene.KeywordSearch.saveIndexToDatabase(KeywordSearch.java:415)
       ... 24 more

Total time: 42 minutes 59 seconds


-----Original Message-----
From: Zacher, Stacy 
Sent: Friday, January 26, 2018 12:50 PM
To: 'Julie Sullivan'; 
[hidden email]
Subject: RE: [InterMine Dev] Error

Thank you very much Julie! I will try this.  



-----Original Message-----
From: Julie Sullivan [
[hidden email]]
Sent: Friday, January 26, 2018 2:43 AM
To: Zacher, Stacy; 
[hidden email]
Subject: Re: [InterMine Dev] Error

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Stacy

Yes! You can change the owner of the database in postgres, then update the credentials in your ratmine.properties file. You'll have to redeploy your webapp to apply these changes however.

intermine.readthedocs.io/en/latest/webapp/properties/intermine-properties/

If you have more troubles, I am happy to skype! You can also pop onto our discord server: chat.intermine.org

Cheers
Julie

On 01/25/2018 11:35 PM, Zacher, Stacy wrote:

Hello:

Our developer is getting an error when trying to get intermine up and
running on a server that we just rebuilt.   Originally these databases
were built years ago and whoever built intermine chose the postgres 
superuser to own all the databases. If possible, we would like to 
appoint a different database owner instead of postgres.

Is that possible or will intermine not cooperate?   Is it a matter of
just altering the database and selecting a new owner or would other 
permissions in postgres need to be changed as well.


Here is the error the developer is getting:

/data/intermine/git_ratmine/intermine/imbuild/objectstore.xml:98:
org.postgresql.util.PSQLException: ERROR: permission denied for 
relation intermine_metadata

Any assistance would be appreciate.


Thanks!

*Stacy Zacher*

Database Administrator | Information Services

*Medical College of Wisconsin*

[hidden email] <[hidden email]>

414-955-5654



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