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saved list showing 0 objects

Steven Neuhauser

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

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Re: saved list showing 0 objects

Steven Neuhauser

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [mailto:[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

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Re: saved list showing 0 objects

Paulo Nuin
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

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Re: saved list showing 0 objects

Daniela Butano-2

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela


On 19/04/17 22:48, Paulo Nuin wrote:
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

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Re: saved list showing 0 objects

Joel Richardson-2
Hi Daniela,

Thanks, this is very helpful. 
In the description of the bagvalues table, the value column is "identifier originally typed in by user”.
For lists created from a query result, what value is used? For genes and such I would guess it’s the primaryIdentifier. But is that determined by declared class keys?

Joel
-- 
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435

From: dev <[hidden email]> on behalf of Daniela Butano <[hidden email]>
Date: Thursday, April 20, 2017 at 5:05 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [InterMine Dev] saved list showing 0 objects

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela


On 19/04/17 22:48, Paulo Nuin wrote:
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

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Re: saved list showing 0 objects

Steven Neuhauser
In reply to this post by Daniela Butano-2

Hi Daniela,


For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.


Can I change the intermine_state to NOT_CURRENT and restart the webapp?


Thanks,

Steve


From: dev <[hidden email]> on behalf of Daniela Butano <[hidden email]>
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela


On 19/04/17 22:48, Paulo Nuin wrote:
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

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Re: saved list showing 0 objects

Daniela Butano-2

Steve,

do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?


On 20/04/17 14:40, Steven Neuhauser wrote:

Hi Daniela,


For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.


Can I change the intermine_state to NOT_CURRENT and restart the webapp?


Thanks,

Steve


From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela


On 19/04/17 22:48, Paulo Nuin wrote:
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

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Re: saved list showing 0 objects

Paulo Nuin
In reply to this post by Steven Neuhauser
Hi

We had a similar problem with our instance, and a development build with the latest version of InterMine solved the problem, we didn’t need to change the state of the list. Manually extracting the list shouldn’t be to hard, and it can be imported again.  The whole list is on the table bag values, and it can be linked to the column id in the savedbag.

Cheers
Paulo


On Apr 20, 2017, at 7:40 AM, Steven Neuhauser <[hidden email]> wrote:

Hi Daniela,

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.
There are a few that are TO_UPGRADE.
The lists that show 0 values are marked as CURRENT.

Can I change the intermine_state to NOT_CURRENT and restart the webapp? 

Thanks,
Steve

From: dev <[hidden email]> on behalf of Daniela Butano <[hidden email]>
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Hi Steve,
as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).
If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).
Let me know if this is not the case.
Cheers,
Daniela

On 19/04/17 22:48, Paulo Nuin wrote:
Hi

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

Cheers
Paulo


On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________
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[hidden email]
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[hidden email]
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Re: saved list showing 0 objects

Steven Neuhauser
In reply to this post by Daniela Butano-2

Hi Daniela,

 

This is happening on our public site. There is only one mousemine instance using this database.

Maybe I should try redeploying the webapp as Paulo suggested.

 

Steve.

 

From: Daniela Butano [mailto:[hidden email]]
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Steve,

do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?

 

On 20/04/17 14:40, Steven Neuhauser wrote:

Hi Daniela,

 

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.

 

Can I change the intermine_state to NOT_CURRENT and restart the webapp?

 

Thanks,

Steve


From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela

 

On 19/04/17 22:48, Paulo Nuin wrote:

Hi

 

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

 

Cheers

Paulo

 

 

On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

 

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

---

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[hidden email]
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Re: saved list showing 0 objects

Daniela Butano-2

Hi Steve

in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)


I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.

If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....


Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.

select * from intermine_metadata where key='serialNumber';


After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.


cheers,

daniela





On 20/04/17 17:03, Steven Neuhauser wrote:

Hi Daniela,

 

This is happening on our public site. There is only one mousemine instance using this database.

Maybe I should try redeploying the webapp as Paulo suggested.

 

Steve.

 

From: Daniela Butano [[hidden email]]
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Steve,

do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?

 

On 20/04/17 14:40, Steven Neuhauser wrote:

Hi Daniela,

 

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.

 

Can I change the intermine_state to NOT_CURRENT and restart the webapp?

 

Thanks,

Steve


From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela

 

On 19/04/17 22:48, Paulo Nuin wrote:

Hi

 

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

 

Cheers

Paulo

 

 

On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

 

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

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Re: saved list showing 0 objects

Paulo Nuin
Hi all

As I mentioned before, this happened to us on updating from an older version to 1.7.1 (we discussed this on Discord, Daniela) and just a build/redeploy with 1.7.1 solved the problem, and we have at least two instances pointing to the same profile database at the same time, with cases of different backend and front-end versions. 

My guess is that something on the update from one version to another might have erroneously changed the version number in the profile database and this prevents the status to change in all the lists. 

If the number of non-upgradeable lists is small, I would manually/scripting extract them from the profile database and re-add on the web interface. 

Cheers
Paulo


On Apr 20, 2017, at 11:13 AM, Daniela Butano <[hidden email]> wrote:

Hi Steve
in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)

I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.
If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....

Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.
select * from intermine_metadata where key='serialNumber';

After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.

cheers,
daniela




On 20/04/17 17:03, Steven Neuhauser wrote:
Hi Daniela,
 
This is happening on our public site. There is only one mousemine instance using this database.
Maybe I should try redeploying the webapp as Paulo suggested.
 
Steve.
 
From: Daniela Butano [[hidden email]] 
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Steve,
do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?
 
On 20/04/17 14:40, Steven Neuhauser wrote:
Hi Daniela,
 
For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.
There are a few that are TO_UPGRADE.
The lists that show 0 values are marked as CURRENT.
 
Can I change the intermine_state to NOT_CURRENT and restart the webapp? 
 
Thanks,
Steve

From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Hi Steve,
as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).
If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).
Let me know if this is not the case.
Cheers,
Daniela
 
On 19/04/17 22:48, Paulo Nuin wrote:
Hi 
 
Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.
 
Cheers
Paulo
 
 
On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:
 
Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
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Re: saved list showing 0 objects

Daniela Butano-2
Hi Paulo,
I don't know the reasons why you have 2 instances pointing to the same userprofile db but be aware that this causes more upgrading in the user lists.
Every time you restart alternatively the 2 instances (that I suppose have different serialNumbers each others), intermine_state of the lists will be set to NOT_CURRENT!!!
This is a possible scenario.

Initial state:
Application1 with serialNumber1 = serialNumber1 in userprofile
Application2 with serialNumber2 != serialNumber1 in userprofile
When you restart Application2 -> serialNumber2 will be set in the userprofile, all lists will be set to NOT_CURRENT. When the user logs in -> upgrading list process starts.
Now if you restart Application1 -> serialNumber1 will be set to the userprofile, (and again as before) all lists will be set to NOT_CURRENT. When the user logs in -> upgrading list process starts.
Having two instances, pointing to the same userprofile, also causes the problem of saved lists showing 0 objects. (see following email)!!!

Daniela  

On 20/04/17 19:18, Paulo Nuin wrote:
Hi all

As I mentioned before, this happened to us on updating from an older version to 1.7.1 (we discussed this on Discord, Daniela) and just a build/redeploy with 1.7.1 solved the problem, and we have at least two instances pointing to the same profile database at the same time, with cases of different backend and front-end versions. 

My guess is that something on the update from one version to another might have erroneously changed the version number in the profile database and this prevents the status to change in all the lists. 

If the number of non-upgradeable lists is small, I would manually/scripting extract them from the profile database and re-add on the web interface. 

Cheers
Paulo


On Apr 20, 2017, at 11:13 AM, Daniela Butano <[hidden email]> wrote:

Hi Steve
in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)

I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.
If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....

Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.
select * from intermine_metadata where key='serialNumber';

After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.

cheers,
daniela




On 20/04/17 17:03, Steven Neuhauser wrote:
Hi Daniela,
 
This is happening on our public site. There is only one mousemine instance using this database.
Maybe I should try redeploying the webapp as Paulo suggested.
 
Steve.
 
From: Daniela Butano [[hidden email]] 
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Steve,
do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?
 
On 20/04/17 14:40, Steven Neuhauser wrote:
Hi Daniela,
 
For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.
There are a few that are TO_UPGRADE.
The lists that show 0 values are marked as CURRENT.
 
Can I change the intermine_state to NOT_CURRENT and restart the webapp? 
 
Thanks,
Steve

From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Hi Steve,
as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).
If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).
Let me know if this is not the case.
Cheers,
Daniela
 
On 19/04/17 22:48, Paulo Nuin wrote:
Hi 
 
Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.
 
Cheers
Paulo
 
 
On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:
 
Confusingly, in two places I used “tables” where it should read “lists”
 
Steve
 
From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects
 
Hi All,
 
We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.
 
We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.
 
The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.
 
Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?
 
Thanks,
Steve
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Re: saved list showing 0 objects

Daniela Butano-2
In reply to this post by Daniela Butano-2

Hi Steve,


the only reason for a list with intermine_state=CURRENT showing 0 items, it's because the osbag_int table in the production db is empty for that list.

So if you query the production db:

select * from osbag_int where bagid={osbid field from the savedbag table, in userprofile};

you have 0 in return.

Please confirm me.


The osbag_id table is updated every time we create, update, delete a list. This table stores the intermine IDs (in the value field).

(If the database is rebuilt, the IDs change and the information in this table becomes incorrect. The lists require an upgrade for them to be updated with the new, correct InterMine object IDs. For this reason we run the upgrade process).

The upgrade process updates:

* osbid field in the savedbag table (in the userprofile)

* osbag_id table with the new osbid and the intermine IDs (in the production)


For some reasons, the osbag_int table (in production) is not sync anymore with the osbag_id values in the userprofile and we have to understand why. :)


I HAVE BEEN ABLE TO REPRODUCE THE PROBLEM but only with 2 applications pointing to the same userprofile. Thsi explain Paulo's problem.

I know that it's not your case, but maybe help you to understand deeper and figure out which might be "your" scenario...


Application1 with serialNumber1 != serialNumber2 in userprofile

Application2 with serialNumber2 = serialNumber2 in userprofile


Restart Application1 -> serialNumber1 will be set in the userprofile.

User daniela creates list1 using the Application2. When the list is created list1 is set to CURRENT, and the osbag_int table is updated, but in the Application2 not in Application1!!!


Restart Application1.The serialNumbers are the same: serialNumber1 in the Application1, serialNumebr1 in the userprofile.

User daniela logs in the Application1. No need to run the upgrade process, the list1 is still CURRENT.

The list shows 0 items because osbag_int table, in the Application1 doesn't contain the  intermine IDs for the list1 (Application2 does)


This is just an example.

I will try to figure out if there might be other cases.

Please, Steve let me know if you can figure out other scenarios.


Cheers,

Daniela



On 20/04/17 18:13, Daniela Butano wrote:

Hi Steve

in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)


I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.

If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....


Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.

select * from intermine_metadata where key='serialNumber';


After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.


cheers,

daniela





On 20/04/17 17:03, Steven Neuhauser wrote:

Hi Daniela,

 

This is happening on our public site. There is only one mousemine instance using this database.

Maybe I should try redeploying the webapp as Paulo suggested.

 

Steve.

 

From: Daniela Butano [[hidden email]]
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Steve,

do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?

 

On 20/04/17 14:40, Steven Neuhauser wrote:

Hi Daniela,

 

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.

 

Can I change the intermine_state to NOT_CURRENT and restart the webapp?

 

Thanks,

Steve


From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela

 

On 19/04/17 22:48, Paulo Nuin wrote:

Hi

 

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

 

Cheers

Paulo

 

 

On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

 

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

---

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[hidden email]
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Re: saved list showing 0 objects

Steven Neuhauser

Hi Daniela,


 We just released an update to our database and an updated war file.

 When that happened it updated all the superuser's lists and they now have the correct counts.

 

 I don't know how it got into the state it was in.


Steve


From: Daniela Butano <[hidden email]>
Sent: Friday, April 21, 2017 8:27 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 

Hi Steve,


the only reason for a list with intermine_state=CURRENT showing 0 items, it's because the osbag_int table in the production db is empty for that list.

So if you query the production db:

select * from osbag_int where bagid={osbid field from the savedbag table, in userprofile};

you have 0 in return.

Please confirm me.


The osbag_id table is updated every time we create, update, delete a list. This table stores the intermine IDs (in the value field).

(If the database is rebuilt, the IDs change and the information in this table becomes incorrect. The lists require an upgrade for them to be updated with the new, correct InterMine object IDs. For this reason we run the upgrade process).

The upgrade process updates:

* osbid field in the savedbag table (in the userprofile)

* osbag_id table with the new osbid and the intermine IDs (in the production)


For some reasons, the osbag_int table (in production) is not sync anymore with the osbag_id values in the userprofile and we have to understand why. :)


I HAVE BEEN ABLE TO REPRODUCE THE PROBLEM but only with 2 applications pointing to the same userprofile. Thsi explain Paulo's problem.

I know that it's not your case, but maybe help you to understand deeper and figure out which might be "your" scenario...


Application1 with serialNumber1 != serialNumber2 in userprofile

Application2 with serialNumber2 = serialNumber2 in userprofile


Restart Application1 -> serialNumber1 will be set in the userprofile.

User daniela creates list1 using the Application2. When the list is created list1 is set to CURRENT, and the osbag_int table is updated, but in the Application2 not in Application1!!!


Restart Application1.The serialNumbers are the same: serialNumber1 in the Application1, serialNumebr1 in the userprofile.

User daniela logs in the Application1. No need to run the upgrade process, the list1 is still CURRENT.

The list shows 0 items because osbag_int table, in the Application1 doesn't contain the  intermine IDs for the list1 (Application2 does)


This is just an example.

I will try to figure out if there might be other cases.

Please, Steve let me know if you can figure out other scenarios.


Cheers,

Daniela



On 20/04/17 18:13, Daniela Butano wrote:

Hi Steve

in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)


I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.

If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....


Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.

select * from intermine_metadata where key='serialNumber';


After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.


cheers,

daniela





On 20/04/17 17:03, Steven Neuhauser wrote:

Hi Daniela,

 

This is happening on our public site. There is only one mousemine instance using this database.

Maybe I should try redeploying the webapp as Paulo suggested.

 

Steve.

 

From: Daniela Butano [[hidden email]]
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Steve,

do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?

 

On 20/04/17 14:40, Steven Neuhauser wrote:

Hi Daniela,

 

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.

There are a few that are TO_UPGRADE.

The lists that show 0 values are marked as CURRENT.

 

Can I change the intermine_state to NOT_CURRENT and restart the webapp?

 

Thanks,

Steve


From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Hi Steve,

as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).

If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).

Let me know if this is not the case.

Also have a look a this section https://github.com/intermine/im-docs/blob/master/docs/webapp/lists/list-upgrade.rst#upgrading-to-a-new-release (just updated with few more details).

Cheers,

Daniela

 

On 19/04/17 22:48, Paulo Nuin wrote:

Hi

 

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

 

Cheers

Paulo

 

 

On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

 

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.

Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,

Steve

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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[hidden email]
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Re: saved list showing 0 objects

Paulo Nuin
Hi

Glad that you got it solved. Our error was the first time it happened too, in many updates.

Cheers
Paulo


On Apr 21, 2017, at 8:58 AM, Steven Neuhauser <[hidden email]> wrote:

Hi Daniela,

 We just released an update to our database and an updated war file. 
 When that happened it updated all the superuser's lists and they now have the correct counts.

 

 I don't know how it got into the state it was in.

Steve

From: Daniela Butano <[hidden email]>
Sent: Friday, April 21, 2017 8:27 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects
 
Hi Steve,

the only reason for a list with intermine_state=CURRENT showing 0 items, it's because the osbag_int table in the production db is empty for that list.
So if you query the production db: 
select * from osbag_int where bagid={osbid field from the savedbag table, in userprofile};
you have 0 in return.
Please confirm me.

The osbag_id table is updated every time we create, update, delete a list. This table stores the intermine IDs (in the value field). 
(If the database is rebuilt, the IDs change and the information in this table becomes incorrect. The lists require an upgrade for them to be updated with the new, correct InterMine object IDs. For this reason we run the upgrade process).
The upgrade process updates:
* osbid field in the savedbag table (in the userprofile)
* osbag_id table with the new osbid and the intermine IDs (in the production)

For some reasons, the osbag_int table (in production) is not sync anymore with the osbag_id values in the userprofile and we have to understand why. :)

I HAVE BEEN ABLE TO REPRODUCE THE PROBLEM but only with 2 applications pointing to the same userprofile. Thsi explain Paulo's problem.
I know that it's not your case, but maybe help you to understand deeper and figure out which might be "your" scenario...

Application1 with serialNumber1 != serialNumber2 in userprofile
Application2 with serialNumber2 = serialNumber2 in userprofile 

Restart Application1 -> serialNumber1 will be set in the userprofile.
User daniela creates list1 using the Application2. When the list is created list1 is set to CURRENT, and the osbag_int table is updated, but in the Application2 not in Application1!!!

Restart Application1.The serialNumbers are the same: serialNumber1 in the Application1, serialNumebr1 in the userprofile. 
User daniela logs in the Application1. No need to run the upgrade process, the list1 is still CURRENT.
The list shows 0 items because osbag_int table, in the Application1 doesn't contain the  intermine IDs for the list1 (Application2 does)

This is just an example.
I will try to figure out if there might be other cases.
Please, Steve let me know if you can figure out other scenarios.

Cheers,
Daniela


On 20/04/17 18:13, Daniela Butano wrote:
Hi Steve
in general I don't like to change/update manually the database. Too risky ..and I'm not so brave ;)

I have tried to re-produce the problem with no success. Actually, the only time I was able to reproduce it,  it was when I had two different applications pointing to the same userprofile, but it's not your case...at in any case i was able to reproduce only once :(.
If you give me another day I will try to investigate a bit more! There is clearly a bug somewhere....

Another way to force the upgrading process (but this requires a manual "less invasive" change to the userprofile) it's changing the serialNumber in the userprofile db.
select * from intermine_metadata where key='serialNumber';

After changing it, you should restart the webapp.  It should work, but please first backup twice ;) the db.

cheers,
daniela




On 20/04/17 17:03, Steven Neuhauser wrote:
Hi Daniela,

 

This is happening on our public site. There is only one mousemine instance using this database.
Maybe I should try redeploying the webapp as Paulo suggested.

 

Steve.

 

From: Daniela Butano [[hidden email]] 
Sent: Thursday, April 20, 2017 11:40 AM
To: Steven Neuhauser; [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Steve,
do you have another intermine instance (maybe test enviroment) pointing to the same userporfile database?

 

On 20/04/17 14:40, Steven Neuhauser wrote:
Hi Daniela,

 

For almost all the superuser's lists in the savedbag table the intermine_state is CURRENT.
There are a few that are TO_UPGRADE.
The lists that show 0 values are marked as CURRENT.

 

Can I change the intermine_state to NOT_CURRENT and restart the webapp? 

 

Thanks,
Steve

From: dev [hidden email] on behalf of Daniela Butano [hidden email]
Sent: Thursday, April 20, 2017 5:05 AM
To: [hidden email]
Subject: Re: [InterMine Dev] saved list showing 0 objects

 

Hi Steve,
as Paulo suggested, first have a look at the intermine_state in the savedbag table (userprofile db).
If a list shows '0 values', the intermine_state should be NOT_CURRENT (if the user hasn't logged in yet) or TO_UPGRADE (if the user has logged in, but the system hasn't be able to automatically upgrade it).
Let me know if this is not the case.
Cheers,
Daniela

 

On 19/04/17 22:48, Paulo Nuin wrote:
Hi 

 

Are you able to access the profile DB on a SQL console? If so, you can verify the state of the lists and their contents.

 

Cheers
Paulo

 

 

On Apr 19, 2017, at 2:37 PM, Steven Neuhauser <[hidden email]> wrote:

 

Confusingly, in two places I used “tables” where it should read “lists”

 

Steve

 

From: dev [[hidden email]] On Behalf Of Steven Neuhauser
Sent: Wednesday, April 19, 2017 4:30 PM
To: [hidden email]
Subject: [InterMine Dev] saved list showing 0 objects

 

Hi All,

 

We just noticed that all the lists saved by the superuser showed ‘0 values’ in the Number Of Objects column on the MyMine Lists tab.
Some tables lists are in the “Lists to upgrade” table but most are not.

 

We think the same thing might be happening to other users as we have had some users wondering why their lists were gone.

 

The superuser’s tables lists can be upgraded and saved by using the bagUpgrade.do URL and providing the table name, this seems to fix them.

 

Any ideas what might have happened? It seems like some automagic upgrade of lists did not take place?

 

Thanks,
Steve
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