BlueBrain/nexus

BlueBrain Nexus Platform, migrated to: https://github.com/BlueBrain/nexus/discussions

mukul ashok joshi

@mukulajoshi_twitter

Hi All, while executing "dist" via sbt on the source code, am getting this error : java.io.IOException: Cannot run program "cargo" (in directory "D:\nexus\storage\permissions-fixer"): CreateProcess error=2, The system cannot find the file specified. Has anyone faced this issue or is this something specific to windows?

mukul ashok joshi

@mukulajoshi_twitter

Hmmm it seems Cargo is part of the Rust language..So Cargo needs to be on the PATH?..will check whether solves the issue..

Bogdan Roman

@bogdanromanx

@mukulajoshi_twitter part of the build is a rust command line application that can be used to apply permission changes to files in certain deployment scenarios (remote storage)

yes, cargo would need to be on the path

but this is something that you can skip if it’s not of interest by excluding this module from the build

may I ask, what are you trying to achieve?

mukul ashok joshi

@mukulajoshi_twitter

@bogdanromanx thanks for the reply. At this point i am just trying to get nexus running outside a docker environment. For this i was trying to create the dist via sbt. Yes now after having been able to do the dist, i am able to run the delta and there does not seem to be a need for the storage module at this point. Thanks again.

Bogdan Roman

@bogdanromanx

great, np

are you using the universal packager build the dist? (delta/universal:packageBin)?

Bogdan Roman

@bogdanromanx

so without any modifications to the build, if you run: sbt delta/universal:packageBin the build will produce a zip file containing the service dependencies and run script in delta/target/universal

Bogdan Roman

@bogdanromanx

please also be aware that there’s an open issue that affects the v1.4.0 release: BlueBrain/nexus#1471

mukul ashok joshi

@mukulajoshi_twitter

@bogdanromanx thanks for the additional information! I did some workaround to get the dist for the storage (by commenting out the cargo and manually creating the fixer folder, since the scripts are unix specific and do not work on windows), since i did not know about the universal packager. Next time will use the delta specific universal packager, if there is no need for storage. Currently trying to figure out how to get the login for the nexus-web (fusion), which seems to depend on realms/identities. Any pointers on this as well will be useful. Once the creation of organization/projects is possible, then probably the open issue will come in picture. Also any writeups on how shacl is used in nexus will be useful (how it is uploaded and then used for validation). Thanks again

Bogdan Roman

@bogdanromanx

with respect to the login, there are quite a few options on the table, but it depends on how you’d like to set it up

are you planning on using LDAP? or something different?

either way, I would recommend using Keycloak to mediate access between Nexus and your Identity Provider of choice (LDAP, FB, Google, Github etc.)

with respect to the Nexus configuration, it’s a matter of creating a realm pointing to the openid config discovery document and then granting the appropriate permissions

@MFSY, do we have any documentation on how to create shacl based schemas?

Bogdan Roman

@bogdanromanx

shacl based validation in Nexus is offered through the use of schemas; a schema is a resource in a project; you can have many schemas and they have the same lifecycle as any other resources

there are some examples here: https://bluebrainnexus.io/docs/delta/api/current/kg-schemas-api.html

once you’ve created a schema, you can create resources that are constrained by that schema using the normal resource api: https://bluebrainnexus.io/docs/delta/api/current/kg-resources-api.html

validation happens when a resource is created or updated; if validation succeeds, the operation will succeed, otherwise the operation will be rejected by the system

mukul ashok joshi

@mukulajoshi_twitter

@bogdanromanx thanks! Really helpful pointers. Will get started on these and hopefully will be able to create/browse the data as a graph. Also how does the data go from Cassandra (write) to Elastic/Blazegraph (read)? Is that also done when the data is created? Or there is some other process for it? Thanks again

Bogdan Roman

@bogdanromanx

the system does that automatically; we call these processes projections

there’s some information on that here: https://bluebrainnexus.io/docs/delta/architecture.html#anatomy

the processes are controlled (configured) through the use of resources of type View

there are quite a few variations of these resources, explained here: https://bluebrainnexus.io/docs/delta/api/current/views/index.html

happy to be able to help

Is that also done when the data is created?

it’s done for each change in the system through asynchronous processes immediately after data is created, updated or deprecated

mukul ashok joshi

@mukulajoshi_twitter

@bogdanromanx thanks again for the detailed replies. These are really helpful insights!

Bogdan Roman

@bogdanromanx

👍

Paul Pawletta

@PaulPawletta

Hi everyone. Is there a better way to create resources against a schema except from sending a "POST /v1/resources/{org_label}/{project_label}/{schema_id}"? I couldn't find any functionalities in Nexus Fusion or Nexus Forge. My use case would be e.g. that I have a pandas dataframe and I want to upload or validate it against the uploaded schema in Nexus Delta.

Alejandra Garcia Rojas M

@alegrm

@PaulPawletta you can use the Nexus Forge to convert a data frame to a Resource object in the Forge, and then you can validate the Resource with the Forge too, but notice that you need to configure the Forge Model to have access to the Shacl Model you want to validate that against. Check the notebook 7 and 11 in https://github.com/BlueBrain/nexus-forge/tree/master/examples/notebooks/getting-started, and the doc of the Forge configuration here https://nexus-forge.readthedocs.io/en/latest/interaction.html#forge

Paul Pawletta

@PaulPawletta

@alegrm Thank you! Notebook 11 was exactly what I was looking for.

Paul Pawletta

@PaulPawletta

Hi all. I'm running Nexus and Keycloak using docker swarm and I'm trying to set up ACLs for users. After creating a realm I'm able to create ACL for /org1 (still keeping all the rights for Annonymous at root - / ). Now when I try to modify the ACL at root using PATCH, I'm ending up removing all ACLs including Annonymous and the created ACLs for /org1. So I'm loosing all the permissions to do anything inside Nexus. How should I modify the ACLs at root level?

Didac

@umbreak

As soon as you replace the ACLs for /, the previous Anonymous ACLs get overriden, yes. So whenever you change the ACLs, make sure you set an identity that you can login from

Paul Pawletta

@PaulPawletta

response.jsonld

This is the response I'm receiving from http://localhost/v1/acls/org1?ancestors=true&self=false

And I'm not able to create anything now with my users from group1 (AuthorizationFailed -
"reason": "The supplied authentication is not authorized to access this resource."). Can you see anything that is wrong with my created ACLs?

Paul Pawletta

@PaulPawletta

In Nexus-Web I can login with my users from group1, but I loose all functionalities for reading and writing.

Didac

@umbreak

what do you get as a response from the identities endpoint when using your TOKEN?

curl -s -H "Authorization: Bearer $TOKEN" "https://{host}/v1/identities

Paul Pawletta

@PaulPawletta

Didac

@umbreak

as you can see, there is nothing like group1 in this list, and you set ACLs in / for group1

When you did the first PATCH on / you should have done it for the identity:

"realm": "nexusdev",
"subject": "user1"

Paul Pawletta

@PaulPawletta

Thanks @umbreak that works! I guess my error is then related to how I configure the groups in keycloak

Didac

@umbreak

Yes. I guess the groups are not linked to the users correctly. When dealing with groups you have 2 options:

Adding the group information directly into the token. This is the most performant option if you don’t have too many groups in application. Otherwise don’t use it since the token is gonna get pretty big.
Using the /userinfo endpoint to fetch the group information.

I believe keycloack supports both, but I’m not well aware of the details. If you need some help with keycloak I could probably ask someone else on the team to help you. Let us know.

Paul Pawletta

@PaulPawletta

Exactly. The problem was the missing group information. Now it works with group ACLs. Thanks @umbreak ,we probably need help in the future for a proper production setup. For now I'm just playing :)

Paul Pawletta

@PaulPawletta

Hi everyone, we are planning on using BBN as a KG for our metadata at Charite Berlin. We envision a similar version to EBRAINS KG.
Right now, I'm looking for existing SHACL shapes that we could use and extend. I know about Neuroshapes, but it seems to me the metadata model for EBRAINS KG is more close to openMINDS v1. So my questions are:

Are there any other SHACL constraints besides from Neuroshapes? e.g. Does anyone know what is used by EBRAINS KG?
How is Neuroshapes related to openMINDS?
Specifically is there SHACL shape that resembles a dataset as defined by openMINDS?

Thanks!

Anna

@annakristinkaufmann

Hi Paul!

Thanks a lot for getting in touch!

Regarding your questions:

and 2. Unfortunately, we don't know details about the EBRAINS data model. Maybe best to get in touch with them directly!
Maybe have a look at the neuroshapes dataset schema: https://github.com/INCF/neuroshapes/blob/8f3ce6d1de892990bab4f36179300ba485341d80/shapes/neurosciencegraph/datashapes/core/dataset/schema.json which extends the neuroshapes minds schema: https://github.com/INCF/neuroshapes/blob/8f3ce6d1de892990bab4f36179300ba485341d80/shapes/neurosciencegraph/commons/minds/schema.json

niksub

@niksub

Hello. I'm trying to install nexus on minikube, but got error because file missing - 404 https://bluebrainnexus.io/docs/getting-started/running-nexus/minikube/kg.yaml

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