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  • 12:35

    umbreak on master

    Minor migration fix (#1387) (compare)

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  • 12:15

    umbreak on master

    Do not reuse source (#1386) (compare)

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    dhaneshnm edited #1383
  • 11:54

    umbreak on master

    Check project exists (#1385) *… (compare)

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    umbreak synchronize #1385
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Bogdan Roman
@bogdanromanx

@maedoc, thanks for evaluating the software, here are some answers

a few more questions: what do you use for schema dev?

currently we have no dedicated tools to help with that, mostly everyone uses their preferred IDEs

do the projects act like S3 buckets for the files?

yes and no; projects represent a bounding box for the data (both json-ld and files) and considering organisations it’s quite similar to how github organizes code in user/repository
each project currently has a single file storage location, but that will change in the upcoming v1.1 where each project can be configured with multiple storage backends (including s3); but regardless of the physical location where files are stored in terms of the API both json-ld resources and files are managed together in a project

is the Python API for putting and getting files the most efficient way to get data in & out?

if you want to use a python client, yes, but python is not necessarily the fastest runtime out there; the client merely consumes an HTTP based API so the faster the client, the faster the interaction (with a well spec’ed Nexus deployment)
if you’re looking at implementing a different client (in another language for example), the general rules of thumb are:

  • try to avoid closing connections, reusing connections removes the signifficant latency introduced by TLS negociation and the transport layer itself
  • use a connection pool and tune its size to your use
  • avoid using blocking IO
  • investigate the use of pipelining (https://en.wikipedia.org/wiki/HTTP_pipelining) the backend supports it

will there be any integration with workflow systems to run some container against data sets? (e.g. Pachyderm like)

this is something we’ve discussed several times and we find it quite interesting, but currently we haven’t had any usecases; if you have some, please let us know and we’ll see if and how we could accommodate this into our roadmap

Didac
@umbreak
@olinux now you have a way to retrieve resources using the organization and project UUIDs: https://github.com/BlueBrain/nexus/issues/598#issuecomment-492629393
pdehaye
@pdehaye

Hi all, I have been trying to follow the docs and run nexus locally using docker swarm. howeber when i do curl http://localhost/kg as a crude test i get the response curl: (52) Empty reply from server. That's no good.

The command docker service logs nexus_router returns

nexus_router.0.880pzdp27qiq@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
nexus_router.0.nsjhkv89gwbo@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout

can someone help me?

Wojtek Wajerowicz
@wwajerowicz
can you paste the logs from other services as well? kg, iam especially
pdehaye
@pdehaye
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_router
nexus_router.0.hdwdkqbbddjp@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
nexus_router.0.sw5qy7tvkx0a@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
nexus_router.0.ytiatelol8g6@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_kg
nexus_kg.1.jv58pib09wtt@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
nexus_kg.1.5s2ymlfup7im@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
nexus_kg.1.h0mroqehg646@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
nexus_kg.1.axh3kxqe37tu@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_router
nexus_router.0.hdwdkqbbddjp@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
nexus_router.0.ytiatelol8g6@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
nexus_router.0.sw5qy7tvkx0a@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_iam
nexus_iam.1.zw88t7enbr0w@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
nexus_iam.1.tp3hrawef4si@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
nexus_iam.1.e8qjcu5th6ao@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
nexus_iam.1.oggx0aq2y6ii@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
nexus_iam.1.lcb7efr3crvh@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_cassandra
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_admin
nexus_admin.1.n76qi8ydrh5g@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
nexus_admin.1.oe5ftou15c8h@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
nexus_admin.1.goglpdxcg1bv@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
nexus_admin.1.0v8htfrm17sh@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $
Henry
@hygt
hi @pdehaye it seems cassandra is not running which cause all the other services to wait before starting up
could you delete the entire stack and try again?
and check cassandra's log to see if you get any hint about what's wrong
pdehaye
@pdehaye
I think I did this right:
pdehaye@PaulOliviersMBP nexus $ docker stack rm nexus
Removing service nexus_admin
Removing service nexus_blazegraph
Removing service nexus_cassandra
Removing service nexus_elasticsearch
Removing service nexus_iam
Removing service nexus_kg
Removing service nexus_router
Removing service nexus_web
Removing network nexus_default
pdehaye@PaulOliviersMBP nexus $ docker stack ls
NAME                SERVICES            ORCHESTRATOR
pdehaye@PaulOliviersMBP nexus $ docker stack deploy nexus --compose-file=docker-compose.yaml
Creating service nexus_cassandra
failed to create service nexus_cassandra: Error response from daemon: network nexus_default not found
pdehaye@PaulOliviersMBP nexus $ docker stack deploy nexus --compose-file=docker-compose.yaml
Creating network nexus_default
Creating service nexus_cassandra
Creating service nexus_blazegraph
Creating service nexus_web
Creating service nexus_router
Creating service nexus_kg
Creating service nexus_iam
Creating service nexus_admin
Creating service nexus_elasticsearch
pdehaye@PaulOliviersMBP nexus $ curl http://localhost/kg
curl: (52) Empty reply from server
pdehaye@PaulOliviersMBP nexus $ docker services logs nexus_router
docker: 'services' is not a docker command.
See 'docker --help'
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_router
nexus_router.0.0y161th7khe5@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_kg
nexus_kg.1.3u5un9lwgx19@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_admin
nexus_admin.1.ypx66c9pf9e0@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_iam
nexus_iam.1.jgg74i5s0tab@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_cassandra
pdehaye@PaulOliviersMBP nexus $
in other words, there was this first hiccup on the restart, i tried again and somehow it went further. but then the service is still not running.
pdehaye
@pdehaye
allo allo?
pdehaye
@pdehaye
anyone here to help?
Samuel Kerrien
@samuel-kerrien
hi @pdehaye, our backend team is currently attending a conference, they will be in touch ASAP. Thanks for you patience.
pdehaye
@pdehaye
@samuel-kerrien ok, thanks. good to know. by the way I live in Geneva, so would like to meet the team when possible. got some ideas where Nexus could go.
Samuel Kerrien
@samuel-kerrien
Sounds good, we could arrange to meet for lunch next week if you can manage it ?
pdehaye
@pdehaye
@samuel-kerrien 19th? for lunch near/at Secheron?
Samuel Kerrien
@samuel-kerrien
@pdehaye best send me an email (samuel.kerrien@epfl.ch) so we can arrange something ouside of Gitter.
Ehsan
@ehsanmaag
Hi all, I was wondering if there is an easy way to list resources by Tag through Nexus web? thanks!
Mohameth François SY
@MFSY

Hi @ehsanmaag ,

I’m not aware of that capability in Nexus web or even at the REST API level. This can be a feature request. Please open an issue on the Nexus repository.

Note that listing resources in a given project by rev is available though at the REST API level. This feature can be extended to allow listing of resources by tag.

May be this feature is already in the backlog. @umbreak , @bogdanromanx what do you think ?

Bogdan Roman
@bogdanromanx
the feature is not in the backlog, please create a ticket
Sean Hill
@slhill
You can create a custom view with the parameter resourceTag=blabla and then use that view to do the searches.
Ehsan
@ehsanmaag
Thanks very much @MFSY @bogdanromanx @slhill , I think the solution Sean suggested should work. I will try it and let you know if I find anything else
Oliver Schmid
@olinux
Hi everyone,
I was wondering if the documentation for Nexus v0 is still available somewhere since https://bbp-nexus.epfl.ch/staging/docs/ is not available anymore!?
Anna
@annakristinkaufmann
Hi @olinux ! I am not sure this is the best source, but there is the v0 branch of the kg api: https://github.com/BlueBrain/nexus-kg/tree/v0/docs/src/main/paradox/api-reference
Sheetal Kaktikar
@sheetalkaktikar
Hello everyone, I am an enthusiast currently playing around with Nexus and see that it uses Blazegraph. I am trying to find a strategic roadmap for Blazegraph but cannot seem to find anything concrete online. Given the lack of clarity around the roadmap for Blazegraph, could anyone here help me understand, whether from a strategic perspective, Nexus is looking at alternatives to Blazegraph? Many thanks.
Samuel Kerrien
@samuel-kerrien
Hi Sheetal, thanks for you question ! There is indeed a lack of clarity about where BlazeGraph is going in the future. We are not actively looking for alternatives to BlazeGraph but will very likely spend time evaluating a few somewhere toward the beginning of 2020. Projects like Apache Rya have recently come to our attention and we are considering investigating it further.
Jainal Gosaliya
@jainal09
Hi @/all i was starting to learn building a knowledge graph for a project that runs on elastic search i was referring to this docs https://bluebrainnexus.io/docs/tutorial/knowledge-graph/querying-knowledge-graph-elasticsearch.html
But the github or the Google colab links in it doesn't work
Mohameth François SY
@MFSY
Hi @jainal09 . Thank you for trying this tutorial. We fixed (BlueBrain/nexus#1091) this issue sometime ago but the merge was
not successful
We’ll deploy the fix as soon as possible.
Mohameth François SY
@MFSY
@bogdanromanx just fix it.
Jainal Gosaliya
@jainal09
hey @MFSY thanks
Mohameth François SY
@MFSY
u r wecolme. let us know how it go.
ivana
@yiiifan

I think I did this right:

pdehaye@PaulOliviersMBP nexus $ docker stack rm nexus
Removing service nexus_admin
Removing service nexus_blazegraph
Removing service nexus_cassandra
Removing service nexus_elasticsearch
Removing service nexus_iam
Removing service nexus_kg
Removing service nexus_router
Removing service nexus_web
Removing network nexus_default
pdehaye@PaulOliviersMBP nexus $ docker stack ls
NAME                SERVICES            ORCHESTRATOR
pdehaye@PaulOliviersMBP nexus $ docker stack deploy nexus --compose-file=docker-compose.yaml
Creating service nexus_cassandra
failed to create service nexus_cassandra: Error response from daemon: network nexus_default not found
pdehaye@PaulOliviersMBP nexus $ docker stack deploy nexus --compose-file=docker-compose.yaml
Creating network nexus_default
Creating service nexus_cassandra
Creating service nexus_blazegraph
Creating service nexus_web
Creating service nexus_router
Creating service nexus_kg
Creating service nexus_iam
Creating service nexus_admin
Creating service nexus_elasticsearch
pdehaye@PaulOliviersMBP nexus $ curl http://localhost/kg
curl: (52) Empty reply from server
pdehaye@PaulOliviersMBP nexus $ docker services logs nexus_router
docker: 'services' is not a docker command.
See 'docker --help'
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_router
nexus_router.0.0y161th7khe5@linuxkit-025000000001    | wait-for-it.sh: waiting for kg:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_kg
nexus_kg.1.3u5un9lwgx19@linuxkit-025000000001    | wait-for-it.sh: waiting for admin:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_admin
nexus_admin.1.ypx66c9pf9e0@linuxkit-025000000001    | wait-for-it.sh: waiting for iam:8080 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_iam
nexus_iam.1.jgg74i5s0tab@linuxkit-025000000001    | wait-for-it.sh: waiting for cassandra:9042 without a timeout
pdehaye@PaulOliviersMBP nexus $ docker service logs nexus_cassandra
pdehaye@PaulOliviersMBP nexus $

Hi all, I run into the absolutely same problem, just wonder is there any solution for this?

ivana
@yiiifan
Hello everyone, I have some questions about schema. I create a scheme and try to create a resource constricted by this schema. However, when I send request as POST /v1/resources/{org_label}/{project_label}/{schema_id}, I always got an error message: {
"@context": "https://bluebrain.github.io/nexus/contexts/error.json",
"@type": "NotFound",
"reason": "The requested resource could not be found."
}
same error will also show up when I try to get this resource by @id
Let me know if I did anything wrong
ivana
@yiiifan
Also, Is there any way I can create a resource constricted by the schema on the web?
Bogdan Roman
@bogdanromanx
@yiiifan, are you using the url-encoded form for the schema id? (i.e. if a schema id is http://example.com/myschema the value in the api should be http%3A%2F%2Fexample.com%2Fmyschema)
you can also list the resources in the project to get the ids and access urls for those:
GET /v1/resources/{org}/{proj}
mukul ashok joshi
@mukulajoshi_twitter
Hi All, have been looking at the blue brain nexus for past few days. There is quite a lot of architectural similarity (CQRS) with Wikidata/Wikidata Query Service (including use of Blazegraph). Is there a way to Build/Run Nexus outside the Docker environment? Did not find any documents on how to do this. Any pointers will be useful. Thanks
Didac
@umbreak
@mukulajoshi_twitter sorry for the delay. Right now we don’t publish the artifacts in a fat JAR or similar. We are using ubernetes or Openshift to deploy our services so Docker is a combinient way to package it. Same for users testing the platform.
However for the new release 1.4 we are planning to alsos release a fat jar and provide instructions and requirements in the documentation in order to run it
mukul ashok joshi
@mukulajoshi_twitter
@umbreak thanks for the clarification. I was able to compile the source, but in absence of detailed documentation on the configuration on how to run it, was not able to progress. Look forward to the build and run documentation. Thanks
Didac
@umbreak
there are a bunch of environment variables that have to be set and several dependencies (elasticsearch, Blazegraph, Cassandra). But this should help: https://bluebrainnexus.io/docs/getting-started/running-nexus/docker-swarm/docker-compose.yaml
it is for docker but the idea is the same. If you set those environment variables directly and then run it should be the same
mukul ashok joshi
@mukulajoshi_twitter
@umbreak thanks agailn. Will go through this. For example, i can see this jar built : /nexus/service/target/scala-2.13/service_2.13-1.3.0+19-2c242f75.jar and then there is the classes folder: /nexus/service/target/scala-2.13/classes which have the conf files. So i was wondering as to where to configure? Is it in the classes folder? And then what are instructions to run, is it from the classes folder or there is some way to run the jar? Did not see any bin folder as we see in the Docker config. Thanks
mukul ashok joshi
@mukulajoshi_twitter
@umbreak see some code re-org happening in the code base. Will again go through this and rebuild to see if i can see services like kg, iam, admin. Thanks
Didac
@umbreak
Yes. I would suggest you to wait for the 1.4 release. It is scheduled for beginning of August. It will merge the admin, iam and kg services. It should provide with better performance and easier deployment
mukul ashok joshi
@mukulajoshi_twitter
@umbreak thanks for the clarification. Look forward to the 1.4 release. Thanks