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Fix external links in documentation #4163

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Aug 15, 2023
Merged

Fix external links in documentation #4163

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ac0cdea
Fix external links in documentation
Aug 15, 2023
5df9c8a
Merge branch 'master' into fix-external-links
imsdu Aug 15, 2023
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6 changes: 6 additions & 0 deletions docs/ignore-paths.txt
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Expand Up @@ -2,6 +2,12 @@ https://bluebrain.github.io/nexus/contexts/metadata.json
https://book.validatingrdf.com/
https://dl.acm.org/.*
http://example.com/.*
https://github.com/BlueBrain/nexus/blob/master/delta/app/src/main/resources/app.conf
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Paradox is not able to validate fragments in github links anymore

https://github.com/BlueBrain/nexus/blob/master/delta/plugins/blazegraph/src/main/resources/blazegraph.conf
https://github.com/BlueBrain/nexus/blob/master/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/model/ComponentDescription.scala
https://github.com/BlueBrain/nexus-js/blob/main/packages/nexus-link/README.md
https://github.com/BlueBrain/nexus-js/blob/main/packages/nexus-sdk/README.md
https://github.com/BlueBrain/nexus-js/blob/main/packages/react-nexus/README.md
https://github.com/BlueBrain/nexus-web/blob/main/README.md.*
https://www.janelia.org
http://mouselight.janelia.org/
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2 changes: 1 addition & 1 deletion docs/src/main/paradox/docs/delta/architecture.md
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Expand Up @@ -203,7 +203,7 @@ The authorization flow is as follows:
[IRI]: https://datatracker.ietf.org/doc/html/rfc3987
[CURIE]: https://www.w3.org/TR/curie/
[LDAP]: https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol
[OpenID Connect]: https://openid.net/connect/
[OpenID Connect]: https://openid.net/developers/how-connect-works/
[OAuth 2.0]: https://datatracker.ietf.org/doc/html/rfc6749
[JSON Web Tokens]: https://jwt.io/
[Keycloak]: https://www.keycloak.org/
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2 changes: 1 addition & 1 deletion docs/src/main/paradox/docs/delta/index.md
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Expand Up @@ -32,7 +32,7 @@ Please refer to the @ref:[architecture] and @ref:[api reference] sections for mo
[api reference]: api/index.md
[in the open]: https://github.com/BlueBrain/nexus
[Apache License, version 2.0]: https://www.apache.org/licenses/LICENSE-2.0
[OpenID Connect]: https://openid.net/connect/
[OpenID Connect]: https://openid.net/developers/how-connect-works/
[OAuth 2.0]: https://datatracker.ietf.org/doc/html/rfc6749
[RDF]: https://www.w3.org/RDF/
[JSON-LD]: https://www.w3.org/TR/json-ld11/
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2 changes: 1 addition & 1 deletion docs/src/main/paradox/docs/faq.md
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Expand Up @@ -152,7 +152,7 @@ on the HTTP request, any SPARQL client should work.
### How can I create an organization as an anonymous user in the docker-compose file? What needs to be done to switch to "authenticated" mode?

By default, the permissions used - for an authenticated user - when running Nexus Delta are the ones defined on the JVM
property @link:[app.permissions.minimum](https://github.com/BlueBrain/nexus/blob/v1.4.1/delta/src/main/resources/app.conf#L213){ open=new }.
property @link:[app.permissions.minimum](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/app/src/main/resources/app.conf#L92){ open=new }.
In order to change that behaviour, please create some ACLs for the path `/`. For more details about ACLs creation,
visit the @ref:[ACLs page](delta/api/acls-api.md#create).

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2 changes: 1 addition & 1 deletion docs/src/main/paradox/docs/getting-started/running-nexus/configuration/index.md
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Expand Up @@ -32,7 +32,7 @@ A default Postgres deployment will limit the number of connections to 100, unles

@@@

Before running Nexus Delta, the @link:[expected tables](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sourcing-psql/src/main/resources/scripts/schema.ddl){ open=new } should be created.
Before running Nexus Delta, the @link:[init scripts](https://github.com/BlueBrain/nexus/tree/$git.branch$/delta/sourcing-psql/src/main/resources/scripts/postgres/init){ open=new } should be run in the lexicographical order.

It is possible to let Nexus Delta automatically create them using the following configuration parameters: `app.database.tables-autocreate=true`.

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6 changes: 3 additions & 3 deletions docs/src/main/paradox/docs/getting-started/try-nexus.md
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Expand Up @@ -10,7 +10,7 @@ Nexus consists of different products, such as:

In this tutorial, you'll learn to interact with the knowledge graph through these different tools. Nexus can be used for any kind of data although this tutorial focuses on neuroscience data.

> This tutorial is also part of the @link:[edX EPFL Simulation Neuroscience MOOC](https://www.edx.org/course/simulation-neuroscience).
> This tutorial is also part of the @link:[edX EPFL Simulation Neuroscience MOOC](https://www.edx.org/learn/biology/ecole-polytechnique-federale-de-lausanne-simulation-neuroscience/).

In @ref:[Step 0](try-nexus.md#step-0-python-setup), you'll learn to setup your Python environment if you want to run the Jupyter notebooks locally. You can skip this step if you use Binder or Google Colaboratory (preferred).

Expand Down Expand Up @@ -807,8 +807,8 @@ jupyter notebook MOOC_Content_based_Recommender_System_using_Blue_Brain_Nexus.ip

Well done! You have now completed the last part of this tutorial. To learn more, scroll down or navigate to our documentation, or start contributing to our Github repositories.

If you have reached this tutorial via the @link:[Simulation Neuroscience MOOC](https://www.edx.org/course/simulation-neuroscience),
you can now head back to the @link:[edX platform](https://www.edx.org/course/simulation-neuroscience) and complete this week assignment.
If you have reached this tutorial via the @link:[Simulation Neuroscience MOOC](https://www.edx.org/learn/biology/ecole-polytechnique-federale-de-lausanne-simulation-neuroscience/),
you can now head back to the @link:[edX platform](https://www.edx.org/learn/biology/ecole-polytechnique-federale-de-lausanne-simulation-neuroscience/) and complete this week assignment.

## Learn More

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4 changes: 2 additions & 2 deletions docs/src/main/paradox/docs/releases/v1.7-to-v1.8-migration.md
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Expand Up @@ -146,7 +146,7 @@ CREATE TABLE IF NOT EXISTS public.ignored_events(
### Create the PostgreSQL tables

Run the commands from the
@link:[Delta 1.8.x schema.ddl file](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sourcing-psql/src/main/resources/scripts/schema.ddl)
@link:[Delta 1.8.x schema scripts](https://github.com/BlueBrain/nexus/tree/$git.branch$/delta/sourcing-psql/src/main/resources/scripts/postgres/init)
to create the tables necessary for Delta operations.

## Elasticsearch and Blazegraph indices
Expand Down Expand Up @@ -196,7 +196,7 @@ This section defines the mandatory configuration to run Delta in migration mode.
#### Configuration file

A
@link:[migration configuration file](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/migration/scripts/config/migration.conf)
@link:[migration configuration file](https://github.com/BlueBrain/nexus/blob/v1.8.x/delta/migration/scripts/config/migration.conf)
needs to be made available at a path accessible by Delta 1.8, which will be references by an
@ref:[environment variable](#environment-variables).
Important fields are:
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