Persistent organism names in organism drop down

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Persistent organism names in organism drop down

Matthew Nicotra
Hi,

In the process of setting up Apollo to run on our server, I created a number of "test" organisms, some of which I deleted via the admin interface within the annotator and others I deleted by simply deleting their data directory within the common_data_directory. Now I can't get rid of these "ghost" organisms. I have even tried undeploying Apollo, deleting the tomcat installation directory (/opt/tomcat) and then reinstalling Tomcat, rebuilding Apollo, and redeploying it. The organism names are still there. I assume there is a configuration file somewhere that I can't find. 

Would anyone be able to help me locate it?

I am running Apollo 2.6.0 on Tomcat 9 on Ubuntu 18.04 LTS. Everything else appears to be functioning normally.

Thanks,

Matt

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Re: Persistent organism names in organism drop down

nathandunn

Matt,

There is an apollo-config.groovy file you should configure (based on the samples-**apollo.groovy files). 

If you can’t find that, then by default it creates an h2 database based on the default configuration here: 


And the default datasources file here:


For the dev instance you see the line:

url = "jdbc:h2:AnnotationDatabase:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

As such it creates a file AnnotationDatabase.XXX (I can’t remember what the suffixes are).


You can see from the “production” environment the line:

url = "

Which I thought would break.   Apparently not. 


What I would do:

1 - "ls -ltrc" in the tomcat home user directory and see if anything obvious arises. 
2 - copy sample-h2-apollo-config.groovy (if that’s what you want to use) to apollo-config.groovy and explicitly set your h2 database location.  

Redeploy and it should work.   I would try and pick a writeable absolute path if  you write to file (or you could use postrgesql etc.). 



Nathan


On Jun 9, 2020, at 11:56 AM, Matthew Nicotra <[hidden email]> wrote:

Hi,

In the process of setting up Apollo to run on our server, I created a number of "test" organisms, some of which I deleted via the admin interface within the annotator and others I deleted by simply deleting their data directory within the common_data_directory. Now I can't get rid of these "ghost" organisms. I have even tried undeploying Apollo, deleting the tomcat installation directory (/opt/tomcat) and then reinstalling Tomcat, rebuilding Apollo, and redeploying it. The organism names are still there. I assume there is a configuration file somewhere that I can't find. 

Would anyone be able to help me locate it?

I am running Apollo 2.6.0 on Tomcat 9 on Ubuntu 18.04 LTS. Everything else appears to be functioning normally.

Thanks,

Matt

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Re: Persistent organism names in organism drop down

Matthew Nicotra

Following up on this. It appears that the reason I couldn't delete the organism was because several users still had permissions set for the organism. After unchecking all permissions for the organism in the user settings (in the Annotator panel), I was able to delete the organism in the web interface. 

 

Hope this helps others if they have a similar issue. 

 

 

From: Nathan Dunn <[hidden email]>
Date: Tuesday, June 9, 2020 at 6:29 PM
To: "Nicotra, Matthew L" <[hidden email]>
Cc: apollo <[hidden email]>
Subject: Re: [apollo] Persistent organism names in organism drop down

 

 

Matt,

 

There is an apollo-config.groovy file you should configure (based on the samples-**apollo.groovy files). 

 

If you can’t find that, then by default it creates an h2 database based on the default configuration here: 

 

 

And the default datasources file here:

 

 

For the dev instance you see the line:

 

url = "jdbc:h2:AnnotationDatabase:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

As such it creates a file AnnotationDatabase.XXX (I can’t remember what the suffixes are).

 

 

You can see from the “production” environment the line:

 

url = “"

Which I thought would break.   Apparently not. 

 

 

What I would do:

 

1 - "ls -ltrc" in the tomcat home user directory and see if anything obvious arises. 

2 - copy sample-h2-apollo-config.groovy (if that’s what you want to use) to apollo-config.groovy and explicitly set your h2 database location.  

 

Redeploy and it should work.   I would try and pick a writeable absolute path if  you write to file (or you could use postrgesql etc.). 

 

 

 

Nathan

 



On Jun 9, 2020, at 11:56 AM, Matthew Nicotra <[hidden email]> wrote:

 

Hi,

 

In the process of setting up Apollo to run on our server, I created a number of "test" organisms, some of which I deleted via the admin interface within the annotator and others I deleted by simply deleting their data directory within the common_data_directory. Now I can't get rid of these "ghost" organisms. I have even tried undeploying Apollo, deleting the tomcat installation directory (/opt/tomcat) and then reinstalling Tomcat, rebuilding Apollo, and redeploying it. The organism names are still there. I assume there is a configuration file somewhere that I can't find. 

 

Would anyone be able to help me locate it?

 

I am running Apollo 2.6.0 on Tomcat 9 on Ubuntu 18.04 LTS. Everything else appears to be functioning normally.

 

Thanks,

 

Matt



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