update issue from 2.3 to 2.4

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update issue from 2.3 to 2.4

Prashant S Hosmani
Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN  apollo.TrackService  - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService  - Unable to write to directory apollo_data. Assertion failed: 

assert testDirectory.mkdirs()
       |             |
       apollo_data   false
```




Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA

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Re: update issue from 2.3 to 2.4

nathandunn


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.  

Nathan


> On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:
>
> Hi All,
>
> We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?
>
> ```
> 2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN  apollo.TrackService  - Unable to write to the database directory, so checking the config file
> 2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService  - Unable to write to directory apollo_data. Assertion failed:
>
> assert testDirectory.mkdirs()
>        |             |
>        apollo_data   false
> ```
>
>
> <Attachment.png>
>
> Thank you,
> Prashant
>
>
> Prashant Hosmani
> Sol Genomics Network
> Boyce Thompson Institute, Ithaca, NY, USA

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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA

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Re: update issue from 2.3 to 2.4

nathandunn

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA


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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA


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Re: update issue from 2.3 to 2.4

nathandunn

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA



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Re: update issue from 2.3 to 2.4

nathandunn


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA




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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error



Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA




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Re: update issue from 2.3 to 2.4

nathandunn

Did you update the path here and click on “Update Common Data Path”?


Nathan


On Aug 6, 2019, at 11:09 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error
<Attachment.png>


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA





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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
Yes! and popup comes back again.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:31 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you update the path here and click on “Update Common Data Path”?

<PastedGraphic-1.png>

Nathan


On Aug 6, 2019, at 11:09 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error
<Attachment.png>


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA





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Re: update issue from 2.3 to 2.4

nathandunn

1 - The popup comes back up with the older path (apollo_data) and not the newer one (/opt/apollo/temporary_data)?


2a - What does the server log say when you try to update the path in 1?   

3 - What happens if you type:

ls -ltrca /opt/apollo/temporary_data

4 - What happens if you go nuclear and type:

sudo chmod -R 777 /opt/apollo/temporary_data

And then repeat step 1? 

 

Nathan


On Aug 6, 2019, at 11:38 AM, Prashant S Hosmani <[hidden email]> wrote:

Yes! and popup comes back again.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:31 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you update the path here and click on “Update Common Data Path”?

<PastedGraphic-1.png>

Nathan


On Aug 6, 2019, at 11:09 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error
<Attachment.png>


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






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Re: update issue from 2.3 to 2.4

Prashant S Hosmani
Hi Nathan,

It works! Thanks

After going “nuclear” it works.  Also see update in postgres

apollo-production=# select * from application_preference;
   id    | version |         name          |           value            
---------+---------+-----------------------+----------------------------
 1348807 |       1 | common_data_directory | /opt/apollo/temporary_data
(1 row)



Regards,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:56 PM -0400, Nathan Dunn <[hidden email]>, wrote:

1 - The popup comes back up with the older path (apollo_data) and not the newer one (/opt/apollo/temporary_data)?


2a - What does the server log say when you try to update the path in 1?   

3 - What happens if you type:

ls -ltrca /opt/apollo/temporary_data

4 - What happens if you go nuclear and type:

sudo chmod -R 777 /opt/apollo/temporary_data

And then repeat step 1? 

 

Nathan


On Aug 6, 2019, at 11:38 AM, Prashant S Hosmani <[hidden email]> wrote:

Yes! and popup comes back again.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:31 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you update the path here and click on “Update Common Data Path”?

<PastedGraphic-1.png>

Nathan


On Aug 6, 2019, at 11:09 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error
<Attachment.png>


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA






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Reply | Threaded
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Re: update issue from 2.3 to 2.4

nathandunn

Cheers. 

Glad it worked.   Thanks for sticking with it. 

Nathan


On Aug 6, 2019, at 12:08 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

It works! Thanks

After going “nuclear” it works.  Also see update in postgres

apollo-production=# select * from application_preference;
   id    | version |         name          |           value            
---------+---------+-----------------------+----------------------------
 1348807 |       1 | common_data_directory | /opt/apollo/temporary_data
(1 row)



Regards,
Prashant

--
Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:56 PM -0400, Nathan Dunn <[hidden email]>, wrote:

1 - The popup comes back up with the older path (apollo_data) and not the newer one (/opt/apollo/temporary_data)?


2a - What does the server log say when you try to update the path in 1?   

3 - What happens if you type:

ls -ltrca /opt/apollo/temporary_data

4 - What happens if you go nuclear and type:

sudo chmod -R 777 /opt/apollo/temporary_data

And then repeat step 1? 

 

Nathan


On Aug 6, 2019, at 11:38 AM, Prashant S Hosmani <[hidden email]> wrote:

Yes! and popup comes back again.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 2:31 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you update the path here and click on “Update Common Data Path”?

<PastedGraphic-1.png>

Nathan


On Aug 6, 2019, at 11:09 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

ls -ltrca /opt/apollo/temporary_data
still empty!
popup comes back with same error
<Attachment.png>


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 1:46 PM -0400, Nathan Dunn <[hidden email]>, wrote:


On Aug 6, 2019, at 9:27 AM, Prashant S Hosmani <[hidden email]> wrote:

I have created  (/opt/apollo/temporary_data) directory. I changed permissions for this folder with postgres database user and also tried with production user. 


Great.  

When you type:

ls -ltrca /opt/apollo/temporary_data

What do you see? 

What do you see on the screen and in the logs when you restart the server?

I have working apollo with 2.3.1 running with several organism (>30). Only update to 2.4 causing this issue.

That is expected with this situation.   Once you specify the temporary directory, it all should work. 

Nathan


Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 6, 2019, 11:00 AM -0400, Nathan Dunn <[hidden email]>, wrote:

You will likely have to create that directory:

 /opt/apollo/temporary_data

If you execute the commands, what do you see?

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data
ls -ltrca /opt/apollo/temporary_data

Does it work after the directory has been created for you?

Nathan


On Aug 6, 2019, at 7:25 AM, Prashant S Hosmani <[hidden email]> wrote:

Hi Nathan,

I tried restarting server.

Looks like database directory has not been set properly-

apollo-production=# select * from application_preference ;
 id | version | name | value 
----+---------+------+-------
(0 rows)

Also the /opt/apollo/temporary_data is empty.

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 5:42 PM -0400, Nathan Dunn <[hidden email]>, wrote:

Did you try restarting the server? 

Also, if you look for the directory, what do you see?

ls -ltrca /opt/apollo/temporary_data


Also, can you confirm that the database directory has been set properly.

This is what I see on my local dev box:

psql apollo-db ; 
psql (11.2, server 9.6.11)
Type "help" for help.

apollo-db=# select * from application_preference ; 
  id   | version |         name          |         value         
-------+---------+-----------------------+-----------------------
 16511 |       0 | common_data_directory | /opt/temporary/apollo
(1 row)


Nathan


On Aug 5, 2019, at 2:00 PM, Prashant S Hosmani <[hidden email]> wrote:

Hello Nathan,

Thank you for quick response. I tried that and popup still comes up without any change. Anything else I should try?

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA
On Aug 5, 2019, 3:32 PM -0400, Nathan Dunn <[hidden email]>, wrote:


You need to create a local directory writable by your server and pass in that variable.

e.g.,

sudo mkdir -p /opt/apollo/temporary_data
sudo chmod 755 /opt/apollo/temporary_data


And pass in:

/opt/apollo/temporary_data

To the popup you’re seeing.

Nathan


On Aug 5, 2019, at 12:21 PM, Prashant S Hosmani <[hidden email]> wrote:

Hi All,

We have issue with the updating Apollo from 2.3.1 to 2.4.1. The issue is creating apollo_data directory as shown in this image. I checked catalina.out to see more information about the error. Is there a change in config which is recommended before updating to 2.4?

```
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] WARN apollo.TrackService - Unable to write to the database directory, so checking the config file
2019-08-05 14:48:49,019 [http-bio-8080-exec-141] ERROR apollo.TrackService - Unable to write to directory apollo_data. Assertion failed:

assert testDirectory.mkdirs()
| |
apollo_data false
```


<Attachment.png>

Thank you,
Prashant


Prashant Hosmani
Sol Genomics Network
Boyce Thompson Institute, Ithaca, NY, USA







--
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].