BlueBrain Nexus Platform, migrated to: https://github.com/BlueBrain/nexus/discussions
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
please also be aware that there’s an open issue that affects the v1.4.0 release: BlueBrain/nexus#1471
@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
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?
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
@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
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
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.
@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
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?
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?
"reason": "The supplied authentication is not authorized to access this resource."). Can you see anything that is wrong with my created ACLs?
When you did the first PATCH on
/ you should have done it for the identity:"realm": "nexusdev",
"subject": "user1"
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
/userinfoendpoint 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.
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!
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
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
@bogdanromanx
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
@niksub minikube documentation is at: https://bluebrainnexus.io/docs/getting-started/running-nexus.html#run-nexus-locally-with-minikube
the correct yaml file would be: https://bluebrainnexus.io/docs/getting-started/running-nexus/minikube/delta.yaml
Trying to use Nexus with manual build (outside docker). Using Nexus Release 1.4.2 for Delta and Nexus-Web. Have manually installed and started Cassandra, ElasticSearch, Blazegraph. Trying to use Keycloak both as Broker and Identity Provider with Client set to the Nexus-Web. Have created a Realm in Delta using the Delta API with OpenIDConfig of the Realm created in Keycloak. And then started Nexus-Web with API Endpoint of Delta API. When I access the Nexus-Web page, the login menu drop down does not result in creating the button for the Identity Provider login. Tried setting the Client ID in the command line of Nexus-Web, but that also does not change anything. Is there anything missing or wrong in either the Keycloak setup or starting of Nexus-Web or any other API update for Delta? Any pointers will be much appreciated. Thanks
3 replies
Nexus Web displays the login options based on the response from that request
@umbreak thanks. Yes, initially was not passing the API_Endpoint which showed requests failing in the Dev Tools Network tab. Then after passing the API_Endpoint can see this response when the /v1/realms gets invoked: *{"@context":["https://bluebrain.github.io/nexus/contexts/resource.json","https://bluebrain.github.io/nexus/contexts/iam.json","https://bluebrain.github.io/nexus/contexts/search.json"],"_total":1,"_results":[{"@id":"http://127.0.0.1:8080/v1/realms/keycloak","@type":"Realm","name":"Nexus Keycloak","openIdConfig":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/.well-known/openid-configuration","_label":"keycloak","_grantTypes":["password","clientCredentials","refreshToken","authorizationCode","implicit"],"_issuer":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus","_authorizationEndpoint":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/protocol/openid-connect/auth","_tokenEndpoint":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/protocol/openid-connect/token","_userInfoEndpoint":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/protocol/openid-connect/userinfo","_revocationEndpoint":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/protocol/openid-connect/revoke","_endSessionEndpoint":"http://127.0.0.1:8180/auth/realms/blue-brain-nexus/protocol/openid-connect/logout","_rev":1,"_deprecated":false,"_createdAt":"2021-01-13T13:51:05.704Z","_createdBy":"http://127.0.0.1:8080/v1/anonymous","_updatedAt":"2021-01-13T13:51:05.704Z","_updatedBy":"http://127.0.0.1:8080/v1/anonymous"}]}*. I kind of tried to compare this with the response seen in the Sandbox environment, but did not see any glaring differences, though i could be wrong. Would be useful if you can give a look over and see if there anything patently wrong in the above response. Thanks