[InterMine Dev] doc on primary keys

Joe Carlson jwcarlson at lbl.gov
Thu Apr 28 19:23:51 BST 2016

Thanks, Julie.

The reason I was doing the close reading is that I noticed that I had 
messed up something when building a mine. It was going extremely slow 
and I was puzzled. During the integration step, things were getting 
queried based on a secondaryIdentifier even though I had never specified 
that in any (known) key properties file.

I later realized it was an ant thing. (Thus reinforcing my general 
formiphobia.) I had played around with using the secondaryidentifier as 
the key field in one of my loaders. But then later decided against it. 
Even though I had changed the key properties file in my 
<source>/resources/ directory, the version in <source>/build was not 
regenerated with the next build. Running an 'ant clean' solved this 
issue. but it looks like there are some dependencies not captured in the 
build files.


On 04/28/2016 01:34 AM, Julie Sullivan wrote:
> On 27/04/16 20:05, Joe Carlson wrote:
>> I’ve been looking at the documentation on primary keys
>> http://intermine.readthedocs.org/en/latest/database/database-building/primary-keys/ 
>> Is this up to date?
> Yes
>> I’ve been wondering exactly what was the purpose of 
>> genomic_keyDefs.properties in
> <mine>/dbmodel/resources/. From what I see in the doc, this file must 
> contain the
> description of all keys that will be used by any of the data loaders. 
> And the key
>  properties files in bio/source/<sourcename>/resources/ refer to these 
> keys by key
>  name with the syntax Classname = keyname. Is this just an older way 
> of doing it a
> nd has been replaced by the form Classname.keyname=field1, field2 in 
> the individual
>  loaders?
> Yes, exactly. We thought it was easier to define keys in each data 
> source so we added the new way. However some people disagreed and 
> wanted to keep the old way, so we left both.
>>   I see that the doc says the central key file is an older way of 
>> defining keys.
> If I have no cases of specifying keys by name in the any of my 
> sources, does the
> genomic_keyDefs.properties file used anywhere?
> No. If you've defined keys in each data source that central keys file 
> is not used for integration.
>> Thanks,
>> Joe
>> _______________________________________________
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>> dev at lists.intermine.org
>> https://lists.intermine.org/mailman/listinfo/dev

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