WARN org.intermine.api.config.ClassKeyHelper - No key defined for [insert entity here]

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WARN org.intermine.api.config.ClassKeyHelper - No key defined for [insert entity here]

Sam Hokin-3
Hi, devs. I've been doing some cleanup of my InterMine instance, looking for error messages and such. One glaring thing is a Tomcat
warning that is issued for every entity in the model:

  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for InterMineObject
1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for InterMineObject
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for OntologyAnnotation
1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for OntologyAnnotation
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for Ontology
1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for Ontology
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for GeneFamily
1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for GeneFamily
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for SequenceVariant
1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for SequenceVariant
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for Location
1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for Location
...

It doesn't seem to be harming the operation of the mine, as far as I can tell, but I'm wondering what is going on with these
warnings. Normally I'd prefer to not have a stream of warnings issued on startup of web app. But maybe that's just me. This is
running the origin/dev branch, as of:

commit ad3093e42ac4b6eead025c8f16dfc93d36443b6f
Author: julie-sullivan <[hidden email]>
Date:   Thu Jan 14 11:05:22 2016 +0000


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Re: WARN org.intermine.api.config.ClassKeyHelper - No key defined for [insert entity here]

Justin Clark-Casey
Hi Sam.  I agree that this really shouldn't happen.  When components start spewing out a bunch of warnings that can't be fixed then people start to ignore all
warnings, both useful and useless.

Just so I can get some context, is this right after lines such as

458 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Production database has serialNumber "-3659290225288146967"
458 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Userprofile database has serialNumber "-3659290225288146967"
469 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - initializeTrackers: trackerList
isorg.intermine.api.tracker.TemplateTracker,org.intermine.api.tracker.ListTracker,org.intermine.api.tracker.LoginTracker,org.intermine.api.tracker.QueryTracker,org.intermine.api.tracker.KeySearchTracker
472 [localhost-startStop-1] INFO org.intermine.api.tracker.TemplateTracker  - Creating new org.intermine.api.tracker.TemplateTracker tracker
475 [localhost-startStop-1] INFO org.intermine.api.tracker.ListTracker  - Creating new org.intermine.api.tracker.ListTracker tracker
477 [localhost-startStop-1] INFO org.intermine.api.tracker.LoginTracker  - Creating new org.intermine.api.tracker.LoginTracker tracker
479 [localhost-startStop-1] INFO org.intermine.api.tracker.QueryTracker  - Creating new org.intermine.api.tracker.QueryTracker tracker
481 [localhost-startStop-1] INFO org.intermine.api.tracker.KeySearchTracker  - Creating new org.intermine.api.tracker.KeySearchTracker tracker
484 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for InterMineObject
484 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for PromoterEvidenceCode
...

?  If it's somewhere else then it would be useful to see more of your log file, just so I can be sure we're looking at the same kind of thing.

Regards,

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 15/01/16 17:32, Sam Hokin wrote:

> Hi, devs. I've been doing some cleanup of my InterMine instance, looking for error messages and such. One glaring thing is a Tomcat warning that is issued for
> every entity in the model:
>
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for InterMineObject
> 1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for InterMineObject
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for OntologyAnnotation
> 1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for OntologyAnnotation
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for Ontology
> 1517 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for Ontology
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for GeneFamily
> 1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for GeneFamily
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for SequenceVariant
> 1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for SequenceVariant
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for Location
> 1518 [localhost-startStop-1] WARN org.intermine.api.config.ClassKeyHelper  - No key defined for Location
> ...
>
> It doesn't seem to be harming the operation of the mine, as far as I can tell, but I'm wondering what is going on with these warnings. Normally I'd prefer to
> not have a stream of warnings issued on startup of web app. But maybe that's just me. This is running the origin/dev branch, as of:
>
> commit ad3093e42ac4b6eead025c8f16dfc93d36443b6f
> Author: julie-sullivan <[hidden email]>
> Date:   Thu Jan 14 11:05:22 2016 +0000
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: WARN org.intermine.api.config.ClassKeyHelper - No key defined for [insert entity here]

Sam Hokin-3
Yeah, Justin, pretty much what you posted. Here's a bunch of INFO lines leading up to the first ClassKeyHelper WARN:

  INFO [localhost-startStop-1] (ObjectStoreAbstractImpl.java:100) - Creating new
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "userprofile"
1351 [localhost-startStop-1] INFO org.intermine.objectstore.ObjectStoreAbstractImpl  - Creating new
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "userprofile"
  INFO [localhost-startStop-1] (ObjectStoreAbstractImpl.java:100) - Creating new
org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl with sequence = {}, model = "userprofile"
1353 [localhost-startStop-1] INFO org.intermine.objectstore.ObjectStoreAbstractImpl  - Creating new
org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl with sequence = {}, model = "userprofile"
  INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:929) - Generating cached metadata for table UserProfile
1437 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata
for table UserProfile
  INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:634) - Generating cached metadata for ClassDescriptor
org.intermine.model.userprofile.UserProfile
1438 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata
for ClassDescriptor org.intermine.model.userprofile.UserProfile
  INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:929) - Generating cached metadata for table InterMineObject
1438 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata
for table InterMineObject
  INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:634) - Generating cached metadata for ClassDescriptor
org.intermine.model.InterMineObject
1439 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata
for ClassDescriptor org.intermine.model.InterMineObject
  INFO [localhost-startStop-1] (PrecomputedTableManager.java:513) - Loaded 0 precomputed table descriptions (plus 0 failed) in 1 ms
1458 [localhost-startStop-1] INFO org.intermine.sql.precompute.PrecomputedTableManager  - Loaded 0 precomputed table descriptions
(plus 0 failed) in 1 ms
  INFO [localhost-startStop-1] (InitialiserPlugin.java:1072) - Production database has serialNumber "3728587695285563088"
1475 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Production database has serialNumber
"3728587695285563088"
  INFO [localhost-startStop-1] (InitialiserPlugin.java:1073) - Userprofile database has serialNumber "3728587695285563088"
1475 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Userprofile database has serialNumber
"3728587695285563088"
  INFO [localhost-startStop-1] (InitialiserPlugin.java:1005) - initializeTrackers: trackerList
isorg.intermine.api.tracker.TemplateTracker,org.intermine.api.tracker.ListTracker,org.intermine.api.tracker.LoginTrac
ker,org.intermine.api.tracker.QueryTracker,org.intermine.api.tracker.KeySearchTracker
1492 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - initializeTrackers: trackerList
isorg.intermine.api.tracker.TemplateTracker,org.intermine.api.tracker.ListTracker,org.intermine.api
.tracker.LoginTracker,org.intermine.api.tracker.QueryTracker,org.intermine.api.tracker.KeySearchTracker
  INFO [localhost-startStop-1] (TemplateTracker.java:54) - Creating new org.intermine.api.tracker.TemplateTracker tracker
1496 [localhost-startStop-1] INFO org.intermine.api.tracker.TemplateTracker  - Creating new
org.intermine.api.tracker.TemplateTracker tracker
  INFO [localhost-startStop-1] (ListTracker.java:46) - Creating new org.intermine.api.tracker.ListTracker tracker
1502 [localhost-startStop-1] INFO org.intermine.api.tracker.ListTracker  - Creating new org.intermine.api.tracker.ListTracker tracker
  INFO [localhost-startStop-1] (LoginTracker.java:43) - Creating new org.intermine.api.tracker.LoginTracker tracker
1506 [localhost-startStop-1] INFO org.intermine.api.tracker.LoginTracker  - Creating new org.intermine.api.tracker.LoginTracker tracker
  INFO [localhost-startStop-1] (QueryTracker.java:40) - Creating new org.intermine.api.tracker.QueryTracker tracker
1509 [localhost-startStop-1] INFO org.intermine.api.tracker.QueryTracker  - Creating new org.intermine.api.tracker.QueryTracker tracker
  INFO [localhost-startStop-1] (KeySearchTracker.java:44) - Creating new org.intermine.api.tracker.KeySearchTracker tracker
1512 [localhost-startStop-1] INFO org.intermine.api.tracker.KeySearchTracker  - Creating new
org.intermine.api.tracker.KeySearchTracker tracker
  WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for InterMineObject


On 01/18/2016 09:49 AM, Justin Clark-Casey wrote:
> Hi Sam.  I agree that this really shouldn't happen.  When components start spewing out a bunch of warnings that can't be fixed
> then people start to ignore all warnings, both useful and useless.
>
> Just so I can get some context, is this right after lines such as....

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Re: WARN org.intermine.api.config.ClassKeyHelper - No key defined for [insert entity here]

Justin Clark-Casey
Yeah, these warnings were being printed for any class in the model that did not have a key defined in <mine>/class_keys.properties.

This file tells the webapp the key to uniquely determine objects which enables them to be used in list upload.  It also boosts their search ranking.  I
added/cleaned up the tiny bit of documentation on this at [1].

I think the warnings are more harmful than useful since I don't think it would make any sense to define keys for certain objects (e.g. InterMineObject and
things like OntologyAnnotation).  So I have removed the warning as of [2]. Please say if you think this is the wrong move.

[1] http://intermine.readthedocs.org/en/latest/webapp/properties/class-keys/
[2] https://github.com/intermine/intermine/commit/0a9481e75a7de2d0c3855bc5aac7524760a2cc25

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 18/01/16 16:57, Sam Hokin wrote:

> Yeah, Justin, pretty much what you posted. Here's a bunch of INFO lines leading up to the first ClassKeyHelper WARN:
>
>   INFO [localhost-startStop-1] (ObjectStoreAbstractImpl.java:100) - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence =
> {}, model = "userprofile"
> 1351 [localhost-startStop-1] INFO org.intermine.objectstore.ObjectStoreAbstractImpl  - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
> with sequence = {}, model = "userprofile"
>   INFO [localhost-startStop-1] (ObjectStoreAbstractImpl.java:100) - Creating new org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl with
> sequence = {}, model = "userprofile"
> 1353 [localhost-startStop-1] INFO org.intermine.objectstore.ObjectStoreAbstractImpl  - Creating new
> org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl with sequence = {}, model = "userprofile"
>   INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:929) - Generating cached metadata for table UserProfile
> 1437 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata for table UserProfile
>   INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:634) - Generating cached metadata for ClassDescriptor
> org.intermine.model.userprofile.UserProfile
> 1438 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata for ClassDescriptor
> org.intermine.model.userprofile.UserProfile
>   INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:929) - Generating cached metadata for table InterMineObject
> 1438 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata for table InterMineObject
>   INFO [localhost-startStop-1] (ObjectStoreWriterInterMineImpl.java:634) - Generating cached metadata for ClassDescriptor org.intermine.model.InterMineObject
> 1439 [localhost-startStop-1] INFO org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl  - Generating cached metadata for ClassDescriptor
> org.intermine.model.InterMineObject
>   INFO [localhost-startStop-1] (PrecomputedTableManager.java:513) - Loaded 0 precomputed table descriptions (plus 0 failed) in 1 ms
> 1458 [localhost-startStop-1] INFO org.intermine.sql.precompute.PrecomputedTableManager  - Loaded 0 precomputed table descriptions (plus 0 failed) in 1 ms
>   INFO [localhost-startStop-1] (InitialiserPlugin.java:1072) - Production database has serialNumber "3728587695285563088"
> 1475 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Production database has serialNumber "3728587695285563088"
>   INFO [localhost-startStop-1] (InitialiserPlugin.java:1073) - Userprofile database has serialNumber "3728587695285563088"
> 1475 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - Userprofile database has serialNumber "3728587695285563088"
>   INFO [localhost-startStop-1] (InitialiserPlugin.java:1005) - initializeTrackers: trackerList
> isorg.intermine.api.tracker.TemplateTracker,org.intermine.api.tracker.ListTracker,org.intermine.api.tracker.LoginTrac
> ker,org.intermine.api.tracker.QueryTracker,org.intermine.api.tracker.KeySearchTracker
> 1492 [localhost-startStop-1] INFO org.intermine.web.struts.InitialiserPlugin  - initializeTrackers: trackerList
> isorg.intermine.api.tracker.TemplateTracker,org.intermine.api.tracker.ListTracker,org.intermine.api
> .tracker.LoginTracker,org.intermine.api.tracker.QueryTracker,org.intermine.api.tracker.KeySearchTracker
>   INFO [localhost-startStop-1] (TemplateTracker.java:54) - Creating new org.intermine.api.tracker.TemplateTracker tracker
> 1496 [localhost-startStop-1] INFO org.intermine.api.tracker.TemplateTracker  - Creating new org.intermine.api.tracker.TemplateTracker tracker
>   INFO [localhost-startStop-1] (ListTracker.java:46) - Creating new org.intermine.api.tracker.ListTracker tracker
> 1502 [localhost-startStop-1] INFO org.intermine.api.tracker.ListTracker  - Creating new org.intermine.api.tracker.ListTracker tracker
>   INFO [localhost-startStop-1] (LoginTracker.java:43) - Creating new org.intermine.api.tracker.LoginTracker tracker
> 1506 [localhost-startStop-1] INFO org.intermine.api.tracker.LoginTracker  - Creating new org.intermine.api.tracker.LoginTracker tracker
>   INFO [localhost-startStop-1] (QueryTracker.java:40) - Creating new org.intermine.api.tracker.QueryTracker tracker
> 1509 [localhost-startStop-1] INFO org.intermine.api.tracker.QueryTracker  - Creating new org.intermine.api.tracker.QueryTracker tracker
>   INFO [localhost-startStop-1] (KeySearchTracker.java:44) - Creating new org.intermine.api.tracker.KeySearchTracker tracker
> 1512 [localhost-startStop-1] INFO org.intermine.api.tracker.KeySearchTracker  - Creating new org.intermine.api.tracker.KeySearchTracker tracker
>   WARN [localhost-startStop-1] (ClassKeyHelper.java:84) - No key defined for InterMineObject
>
>
> On 01/18/2016 09:49 AM, Justin Clark-Casey wrote:
>> Hi Sam.  I agree that this really shouldn't happen.  When components start spewing out a bunch of warnings that can't be fixed
>> then people start to ignore all warnings, both useful and useless.
>>
>> Just so I can get some context, is this right after lines such as....
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev