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  • May 18 12:52
    bbpgithubaudit opened #212
  • Apr 29 08:06

    MFSY on master

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    bbpgithubaudit opened #48
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  • Sep 27 2021 13:53
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Anna
@annakristinkaufmann
Let me know if the same happens on staging
genric
@genric
they don't have the target class
so I don't actually know how it selects the shape for validation
do you plan to load all incf/neuroshapes to staging?
Anna
@annakristinkaufmann
As I understood it, you would still put your own schemas with the respective targetClass declaration but in your schema, you import the respective incf/neuroshapes schemas. @MFSY would probably be a better person to help you out on this
genric
@genric
ok, let's try this tomorrow
genric
@genric
yep, got same error on hbp nexus: 'violations': ['No data was selected for validation']}
Mohameth François SY
@MFSY
Hi
Can you provide us with the identifier of the schema you want to use
?
and why the context of the data is so long ?
The one you point to above is no longer accessible.
genric
@genric
Hi
SubCellularModelScriptShape
Mohameth François SY
@MFSY
I got an ‘Application is not available’. I think dev is no longer available
I suggest you work in staging
genric
@genric
yep
there are no incf schemas in staging
who should load them there?
at the moment I'm trying hbp nexus
Oliver Schmid
@olinux

This schema is in a protected area but only imports https://nexus.humanbrainproject.org/v0/schemas/neurosciencegraph/simulation/modelscript/v0.1.0

I think the problem is (as you've mentioned) that the schema you're referencing to does not contain the targetClass definition. It therefore doesn't match any shapes and the reported error is correct. I think the only way to solve this is to change the schem

genric
@genric
yep, I'm half way making those changes :) just wanted to be sure I'm on the right track
Oliver Schmid
@olinux
Ok. Please make sure, you create a new version of the schema - otherwise we will not be able to reimport it to the HBP nexus (since the old one is already published)
genric
@genric
well :) I was hoping to avoid that
would it be possible to wipe those? Or there is already data there?
Mohameth François SY
@MFSY

This is how modelScript was modelled during the Hackathon:

  • Entities of type nsg:MEModel (in neurosciencegraph/simulation/memodel) or nsg:SubCellularModel (in /neurosciencegraph/simulation/subcellularmodel) have a nsg:modelScript which should respectively conform to neurosciencegraph/simulation/modelscript/v0.1.0/shapes/EModelScriptShape and neurosciencegraph/simulation/modelscript/v0.1.0/shapes/SubCellularModelScriptShape.

We omit to propose a way to submit entities of type nsg:ModelScript. We’ll need to update the schemas and bumped the version

sorry @genric
genric
@genric
I'm not too much in favor of having versions diverge in the simulation domain
Mohameth François SY
@MFSY
Me neither. We just need to bump all the versions of the different schemas at the same time.
genric
@genric
ok, I'll make a pull request soon
Oliver Schmid
@olinux
Hm - I get your point, but since Nexus does not allow us to "unpublish" a schema (for good reasons) it only works that way. I'm not really sure if updating the version number for the whole domain is a good idea - you will create new versions for many schemas that stay identical. This requires an unnecessary data migration (I'm aware that as long as the input source is a single script, this is not too painful - but as soon as there are multiple sources providing data it will be). For me, this is a typical minor-version/bugfix change -> v0.1.1.
@genric to really answer question: We potentially could wipe it for now (since we have everything reproducible) - but I'm sure, similar issues will arise at some point when it's not possible to wipe anymore and I think we should discuss and practice this... :)
Oliver Schmid
@olinux
since we're using semantic versioning, it could be interesting though to have an alias for schemas in nexus -> so you could upload/read from v0.1.LATEST ;)
genric
@genric
Well, there pros/cons to have version bump in lockstep for domains or have only patch bump for specific ones
My hope was that I try these schemas in sort of sandbox env before stabilizing them and publishing to prod
Oliver Schmid
@olinux
Ok - What we can do is to provide the "non-tested" schemas in our integration environment first - but that would mean that we would have some kind of staging in the INCF gitrepo - like having a branch "integration" where they live until it's sure they are working, and then moved to master (where they are fetched for the production instances)
genric
@genric
but unless they are published there is no way to try them :) workbench tests are good but I think they don't cover all possibilities
Oliver Schmid
@olinux
This would also mean that we would wipe and re-instantiate the integration environment on a regular base.
genric
@genric
this sound great, it will minimize the version bumping
nevertheless we need to discuss versioning strategies
Oliver Schmid
@olinux
@MFSY what do you think about having some staging in INCF? I think it's crucial because we have to be sure that a schema in master is final.
@genric - I agree - this is a complex topic and it would be good to have a common understanding
Mohameth François SY
@MFSY
Let have a meeting and discuss all of this. I set up one.
Oliver Schmid
@olinux
:thumbsup: thanks!
Andrew Davison
@apdavison
I'm unclear how things work with the various OntologyTermShapes. For example, with the SexOntologyTermShape, I guess somewhere there should be something that specifies the possible values for validation, e.g. "male", "female", but I don't see where that is.
Mohameth François SY
@MFSY

Hi @apdavison ,

I’ve opened while ago an issue on INCF/neuroshapes describing (proposing actually) a way to handle ontologies

INCF/neuroshapes#53
The idea is as follows:
  • we should provide relevant defaults for people to use. I think of ontology terms from NIFSTD (We can add relevant ontologies that HBP and BBP are using)
  • we should allow users to use their own ontology term
  • we should allow users that don’t have ontology terms ot still be able to use the schemas