so_terms missing during buildDB

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so_terms missing during buildDB

Sam Hokin-3
This is new, and I presume resulted from a system upgrade from Fedora 32 to 33 which updated Java and other things.

Execution failed for task ':dbmodel:createSoModel'.
 > Could not find file containing SO terms to add to the model, check the dbmodel/build.gradle file. Property was:
/home/shokin/.gradle/daemon/6.3/dbmodel/resources/so_terms

Any ideas? This is reproduced when I use the current build.gradle from FlyMine.
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Re: so_terms missing during buildDB

Daniela Butano-2
Hi Sam,
the createSoModel gradle task, calls the SOToModelTask java class
passing the soTermListFile file that we set in
{mine_instance}/dbmodel/build.gradle
dbModelConfig {
     .....
     .....
     soTermListFilePath = "dbmodel/resources/so_terms"
     soAdditionFilePath = "dbmodel/build/so_additions.xml"
}
I am not sure why SOToModelTask receive in input
/home/shokin/.gradle/daemon/6.3/dbmodel/resources/so_terms (I deduce
from here
https://github.com/intermine/intermine/blob/dev/bio/core/src/main/java/org/intermine/bio/task/SOToModelTask.java#L67)
instead of dbmodel/build/so_additions.xml.
I hope this can give you some clues....
Daniela

> This is new, and I presume resulted from a system upgrade from Fedora
> 32 to 33 which updated Java and other things.
>
> Execution failed for task ':dbmodel:createSoModel'.
>> Could not find file containing SO terms to add to the model, check the
>> dbmodel/build.gradle file. Property was:
>> /home/shokin/.gradle/daemon/6.3/dbmodel/resources/so_terms
>
> Any ideas? This is reproduced when I use the current build.gradle from
> FlyMine.
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: so_terms missing during buildDB

Sam Hokin-3
Hrm, that got me going. This works:

     soTermListFilePath = "/home/shokin/beanmine/dbmodel/resources/so_terms"
     soAdditionFilePath = "/home/shokin/beanmine/dbmodel/build/so_additions.xml"

So for some reason, gradle isn't using the working directory (/home/shokin/beanmine) as the root of those file paths in the normal
dbmodel/build.gradle any more. I have no idea why. This is true for all my mines, and I set my wrapper to use gradle version 4.9,
same result. This was with the gradle binary being 6.3, which I've been using for a long time. So then I switched to the 4.9 gradle
binary and still had the same error.

Something has changed mysteriously on my system that has made gradle use a different default file path root for those settings. This
is the just-out Fedora 33, but I'm using gradle binaries from gradle.org. Very weird. But easy enough to put full file paths in
those settings. Annoying, though.

On 11/10/20 10:00 AM, [hidden email] wrote:
> dbModelConfig {
>      .....
>      .....
>      soTermListFilePath = "dbmodel/resources/so_terms"
>      soAdditionFilePath = "dbmodel/build/so_additions.xml"
> }
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Re: so_terms missing during buildDB

Sam Hokin-3
In reply to this post by Daniela Butano-2
FWIW, this also works:

dbModelConfig {
     mineName = "beanmine"
     objectStoreName = "os.production"
     modelName = "genomic"
     defaultInterminePropertiesFile = "default.intermine.production.properties"
     userProfileObjectStoreName = "os.userprofile-production"
     userProfileModelName = "userprofile"
     soTermListFilePath = "$rootDir/dbmodel/resources/so_terms"
     soAdditionFilePath = "$rootDir/dbmodel/build/so_additions.xml"
}

So my gradle has decided to use something other than $rootDir as the default root. Bizarre.

On 11/10/20 10:00 AM, [hidden email] wrote:
> dbModelConfig {
>      .....
>      .....
>      soTermListFilePath = "dbmodel/resources/so_terms"
>      soAdditionFilePath = "dbmodel/build/so_additions.xml"
> }
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Re: so_terms missing during buildDB

Daniela Butano-2
Sam,
i remember that someone else had similar issues....(from our
gsoc/gsod/outreachy candidates) but I do not remember what was the
cause..unfortunally.
I think it would be better to investigate a bit more and try to have the
build working with the original configuration
Daniela

> FWIW, this also works:
>
> dbModelConfig {
>     mineName = "beanmine"
>     objectStoreName = "os.production"
>     modelName = "genomic"
>     defaultInterminePropertiesFile =
> "default.intermine.production.properties"
>     userProfileObjectStoreName = "os.userprofile-production"
>     userProfileModelName = "userprofile"
>     soTermListFilePath = "$rootDir/dbmodel/resources/so_terms"
>     soAdditionFilePath = "$rootDir/dbmodel/build/so_additions.xml"
> }
>
> So my gradle has decided to use something other than $rootDir as the
> default root. Bizarre.
>
> On 11/10/20 10:00 AM, [hidden email] wrote:
>> dbModelConfig {
>>      .....
>>      .....
>>      soTermListFilePath = "dbmodel/resources/so_terms"
>>      soAdditionFilePath = "dbmodel/build/so_additions.xml"
>> }

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Re: so_terms missing during buildDB

Sam Hokin-3
I agree, gradle is _supposed_ to use the projectDir as the file root. So something is amiss that is messing up gradle's normal behavior.

On 11/10/20 11:17 AM, [hidden email] wrote:
> Sam,
> i remember that someone else had similar issues....(from our gsoc/gsod/outreachy candidates) but I do not remember what was the
> cause..unfortunally.
> I think it would be better to investigate a bit more and try to have the build working with the original configuration
> Daniela
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