Merge branch 'master' into 3284-allow-to-provision-acls-startup

build.sbt

@@ -20,7 +20,7 @@ val akkaHttpCirceVersion       = "1.39.2"
 val akkaCorsVersion            = "1.2.0"
 val akkaVersion                = "2.6.21"
 val alpakkaVersion             = "3.0.4"
-val awsSdkVersion              = "2.29.2"
+val awsSdkVersion              = "2.29.9"
 val betterMonadicForVersion    = "0.3.1"
 val caffeineVersion            = "3.1.8"
 val catsEffectVersion          = "3.5.5"
@@ -37,7 +37,7 @@ val fs2Version                 = "3.11.0"
 val fs2AwsVersion              = "6.1.3"
 val googleAuthClientVersion    = "1.36.0"
 val handleBarsVersion          = "4.4.0"
-val hikariVersion              = "6.0.0"
+val hikariVersion              = "6.1.0"
 val jenaVersion                = "4.10.0"
 val jsonldjavaVersion          = "0.13.6"
 val kamonVersion               = "2.7.5"
@@ -48,7 +48,7 @@ val logbackVersion             = "1.5.12"
 val magnoliaVersion            = "1.1.10"
 val munitVersion               = "1.0.2"
 val munitCatsEffectVersion     = "2.0.0"
-val nimbusJoseJwtVersion       = "9.42"
+val nimbusJoseJwtVersion       = "9.46"
 val postgresJdbcVersion        = "42.7.4"
 val pureconfigVersion          = "0.17.7"
 val scalaTestVersion           = "3.2.19"
@@ -713,6 +713,7 @@ lazy val ship = project
     compositeViewsPlugin % "compile->compile",
     elasticsearchPlugin  % "compile->compile",
     storagePlugin        % "compile->compile;test->test",
+    searchPlugin,
     tests                % "test->compile;test->test"
   )
   .settings(

delta/plugins/storage/src/main/resources/storage.conf

@@ -44,7 +44,8 @@ plugins.storage {
       show-location = true
       # the default maximum allowed file size (in bytes) for uploaded files. 10 GB 
       default-max-file-size = 10737418240
-      default-bucket = "nexus-delta-production"
+      default-bucket = "default-bucket-override-me"
+      default-bucket = ${?DEFAULT_BUCKET}
     }
     # Remote disk storage configuration
     remote-disk {

docs/src/main/paradox/docs/delta/api/files-api.md

@@ -467,7 +467,7 @@ Request (metadata)
 Response  (metadata)
 :   @@snip [fetched-metadata.json](assets/files/fetched-metadata.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch tags

docs/src/main/paradox/docs/delta/api/projects-api.md

@@ -253,7 +253,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/projects/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the project will be returned.
 
 ## Fetch (specific version)

docs/src/main/paradox/docs/delta/api/resolvers-api.md

@@ -210,7 +210,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/resolvers/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/resources-api.md

@@ -327,7 +327,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/resources/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/schemas-api.md

@@ -247,7 +247,7 @@ Request
 Response
 :   @@snip [schema-fetched.json](assets/schemas/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/search-api.md

@@ -15,7 +15,7 @@ The search plugin relies on @ref:[composite views](./views/composite-view-api.md
   indices to which user has access to, i.e. has `views/query` permission.
 
 For instructions on how to configure global search in Nexus and how it works please visit the
-@ref:[Search configuration](../../getting-started/running-nexus/search-configuration.md) page.
+@ref:[Search configuration](../../running-nexus/search-configuration.md) page.
 
 @@@ note { .tip title="Api Mapping" }
 

docs/src/main/paradox/docs/delta/api/storages-api.md

@@ -221,7 +221,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/storages/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/supervision-api.md

@@ -64,7 +64,7 @@ and the number of triples per individual view.
 The unassigned part allows to spot orphan namespaces, that is to say namespaces which may not have been properly deleted
 when a view got modified or deprecated.
 
-This is an indicator which helps to scale correctly the @ref:[Blazegraph instance](../../getting-started/running-nexus/blazegraph.md).
+This is an indicator which helps to scale correctly the @ref:[Blazegraph instance](../../running-nexus/blazegraph.md).
 
 ```
 GET /v1/supervision/blazegraph

docs/src/main/paradox/docs/delta/api/views/composite-sink.md

@@ -16,7 +16,7 @@ selected via configuration.
 
 By default, Nexus Delta will use the Single Composite Sink. This sink performs one query to the Blazegraph common namespace for each resource in the project. The queries are done in chronological order (by the `updatedAt` time of the resources).
 
-We recommend reading through the @ref:[search configuration example use case](../../../getting-started/running-nexus/search-configuration.md#example-use-case) and the @ref[Composite View API reference](composite-view-api.md) to learn more about Composite Views.
+We recommend reading through the @ref:[search configuration example use case](../../../running-nexus/search-configuration.md#example-use-case) and the @ref[Composite View API reference](composite-view-api.md) to learn more about Composite Views.
 
 ## Batch Composite Sink
 

docs/src/main/paradox/docs/delta/api/views/composite-view-api.md

@@ -500,7 +500,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/composite/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/views/elasticsearch-view-api.md

@@ -332,7 +332,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/elasticsearch/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 Note that for retro-compatibility purposes, fetching an elasticsearch view returns legacy fields.

docs/src/main/paradox/docs/delta/api/views/sparql-view-api.md

@@ -211,7 +211,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/blazegraph/sparql/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/plugins/index.md

@@ -77,7 +77,7 @@ The plugin can also define instances of following traits/classes, which will be
   - @link:[EventMetricEncoder](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/model/metrics/EventMetricEncoder.scala){ open=new } - enables Delta to convert a database event to an event metric
   - @link:[MetadataContextValue](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/model/MetadataContextValue.scala){ open=new } - registers metadata context of this plugin into global metadata context 
   - @link:[RemoteContextResolution](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/context/RemoteContextResolution.scala){ open=new } - enables Delta to resolve static contexts defined by the plugin
-  - @link:[ServiceDependency](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/ServiceDependency.scala){ open=new } - allows the plugin to define dependencies which will be displayed in `/version` endpoint.
+  - @link:[ServiceDependency](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/kernel/src/main/scala/ch/epfl/bluebrain/nexus/delta/kernel/dependency/ServiceDependency.scala){ open=new } - allows the plugin to define dependencies which will be displayed in `/version` endpoint.
   - @link:[ApiMappings](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/projects/model/ApiMappings.scala){ open=new } - allows the plugin to define default API mappings used to shorten URLs
   - @link:[ResourceToSchemaMappings](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/sdk/src/main/scala/ch/epfl/bluebrain/nexus/delta/sdk/model/ResourceToSchemaMappings.scala){ open=new } - allows the plugin to define mapping from the resource type to schema, which can be used to interact with resources created by the plugin through `/resources` endpoints.
 

docs/src/main/paradox/docs/faq.md

@@ -17,8 +17,8 @@ There are many ways to run Nexus. Our public Sandbox is running @link:[here](htt
 and you can use it to test Nexus on small, non-sensitive data. Our @ref:[tutorial](getting-started/try-nexus.md) can 
 help you to run Nexus step by step.
 
-Meanwhile if you want to run it locally you can do so using @ref:[Docker](getting-started/running-nexus/index.md#docker). You can also deploy Nexus 
-@ref:[“on premise”](getting-started/running-nexus/index.md#on-premise-cloud-deployment), as a single instance or as a cluster. 
+Meanwhile if you want to run it locally you can do so using @ref:[Docker](running-nexus/index.md#docker). You can also deploy Nexus 
+@ref:[“on premise”](running-nexus/index.md#on-premise-cloud-deployment), as a single instance or as a cluster. 
 Blue Brain Nexus has also been deployed and tested on AWS using @link:[Kubernetes](https://kubernetes.io/){ open=new }.
 
 ### How can I try Blue Brain Nexus without installing it? 
@@ -75,7 +75,7 @@ There are several channels provided to address different issues:
 
 On macOS and Windows, Docker effectively runs containers inside a VM created by the system hypervisor. Nexus requires 
 at least 2 CPUs and 8 GB of memory in total. You can increase the limits in Docker settings in the menu 
-_Preferences > Advanced_. More details are in the dedicated @ref:[page](getting-started/running-nexus/index.md).
+_Preferences > Advanced_. More details are in the dedicated @ref:[page](running-nexus/index.md).
 
 ### What is JSON-LD?
 

docs/src/main/paradox/docs/getting-started/index.md

@@ -3,7 +3,6 @@
 - @ref:[Understanding Knowledge Graphs](understanding-knowledge-graphs.md)
 - @ref:[Neuroscience Tutorial](try-nexus.md)
 - @ref:[MovieLens Tutorial](try-nexus-movielens.md)
-- @ref:[Running Nexus](running-nexus/index.md)
 
 @@@
 
@@ -13,4 +12,4 @@ The Nexus ecosystem is a data catalog with several technologies and techniques u
 
 One of the powerful ways to query data is through the Knowledge Graph built in Nexus. For that reason we encourage you to get familiar with these concepts reading @ref:[Understanding Knowledge Graphs](understanding-knowledge-graphs.md).
 
-The next steps would be to either try Nexus using the @ref:[Sandbox](try-nexus.md) deployment or @ref:[run Nexus locally](running-nexus/index.md).
+The next steps would be to either try Nexus using the @ref:[Sandbox](try-nexus.md) deployment or @ref:[run Nexus locally](../running-nexus/index.md).

docs/src/main/paradox/docs/getting-started/try-nexus.md

@@ -116,7 +116,7 @@ You will need the names of the organisation and project for the next parts of th
 
 ### 1.2. Running your Own Instance of Nexus
 
-We do not recommend to setup your own instance for this tutorial. If you are interested to install your own instance, @ref:[check our guide](./running-nexus/index.md).
+We do not recommend to setup your own instance for this tutorial. If you are interested to install your own instance, @ref:[check our guide](../running-nexus/index.md).
 
 ## Step 2: Download and Register Data from a Single Source
 

docs/src/main/paradox/docs/index.md

@@ -2,8 +2,8 @@
 
 - [Versions](versions.md)
 - [Quick Start Guide](getting-started/index.md)
+- [Running Nexus](running-nexus/index.md)
 - [Releases](releases/index.md)
-- [Roadmap](roadmap.md)
 - [Nexus Fusion](fusion/index.md)
 - [Nexus Forge](forge.md)
 - [Nexus Delta](delta/index.md)
@@ -67,14 +67,10 @@ Do you know know what a knowledge graph is? Or want to deepen your understanding
 Want to get started with Nexus right away? We provide a @ref:[tutorial](getting-started/try-nexus.md) that uses our 
 @link:[sandbox](https://sandbox.bluebrainnexus.io/){ open=new } environment to let you try the functionalities.
 
-Ready to deploy your own instance of Nexus? Follow our @ref:[guide](getting-started/running-nexus/index.md).
+Ready to deploy your own instance of Nexus? Follow our @ref:[guide](running-nexus/index.md).
 
 ## Versions
 
 Looking for docs for another release of Nexus ?
 
 @ref:[List of versions](versions.md)
-
-## Roadmap
-
-Curious about our upcoming features? Read our @ref:[open Roadmap](roadmap.md) to find out more.

docs/src/main/paradox/docs/releases/v1.11-release-notes.md

@@ -14,19 +14,25 @@ For the detailed list of updates in this release, see the @link:[list of address
 This feature allows to reduce the pressure on the primary store by changing the way indexing routines for views (but also graph-analytics) 
 behaves when they have processed all available data.
 
-More @ref:[here](../delta/api/views/index.md#passivation)
+@ref:[More here](../delta/api/views/index.md#passivation)
 
 ### Conditional requests
 
-Nexus now supports conditional requests
+Nexus now supports conditional requests.
 
-More @ref[here](../delta/api/conditional-requests.md)
+@ref[More here](../delta/api/conditional-requests.md)
+
+### Realm provisioning
+
+Nexus now allows to provision realms at start up so as to simplify automated deployments.
+
+@ref[More here](../running-nexus/configuration/index.md#realm-provisioning)
 
 ### Remote storage server
 
 The remote storage server part has been removed.
 
-The client is deprecated and remains with @link:[the remote storage in 1.10](https://hub.docker.com/r/bluebrain/nexus-storage/tags).
+The client is deprecated and remains compatible with @link:[the remote storage in 1.10](https://hub.docker.com/r/bluebrain/nexus-storage/tags).
 
 ## Nexus Fusion
 

docs/src/main/paradox/docs/releases/v1.6-release-notes.md

@@ -12,7 +12,7 @@ visit the @ref:[migration instructions](v1.5-to-v1.6-migration.md) for the neces
 
 ## Nexus Delta
 
-The main goal of this release is to allow users to search across multiple projects through @ref:[global search](../getting-started/running-nexus/search-configuration.md)
+The main goal of this release is to allow users to search across multiple projects through @ref:[global search](../running-nexus/search-configuration.md)
 
 Secondary goals include:
 
@@ -47,14 +47,14 @@ Global search is composed of 2 parts:
 - A Delta plugin which allows to index and query resources according to a given configuration
 - A matching plugin in Fusion allows to query the endpoints provided by Delta to filter/sort results and customize how these results are displayed to the users
 
-More details about search and how to configure it is provided @ref:[here](../getting-started/running-nexus/search-configuration.md)
+More details about search and how to configure it is provided @ref:[here](../running-nexus/search-configuration.md)
 
 Please note that this first version is experimental in both Delta and Fusion and that improvements and possibly breaking
 changes may be introduced in the upcoming releases.
 
 ### Secure the Delta Elasticsearch client
 
-With 1.6, it is now possible to define credentials to query a secured Elasticsearch cluster: @ref:[Elasticsearch configuration](../getting-started/running-nexus/configuration/index.md#elasticsearch-views-plugin-configuration).
+With 1.6, it is now possible to define credentials to query a secured Elasticsearch cluster: @ref:[Elasticsearch configuration](../running-nexus/configuration/index.md#elasticsearch-views-plugin-configuration).
 
 ### Dedicated Blazegraph client for user-defined queries
 
@@ -82,7 +82,7 @@ The RDF parser allowing to validate incoming data can now be @link:[configured](
 
 When enabled, a dedicated project is created for the current user on its first access to the Nexus platform.
 
-How to enable and configure it is detailed @ref:[here](../getting-started/running-nexus/configuration/index.md#automatic-project-provisioning)
+How to enable and configure it is detailed @ref:[here](../running-nexus/configuration/index.md#automatic-project-provisioning)
 
 ### Deletion of projects
 

docs/src/main/paradox/docs/releases/v1.7-release-notes.md

@@ -90,7 +90,7 @@ This change implies a @ref:[migration when updating Nexus Delta to 1.7](v1.6-to-
 
 Besides JVM properties and environment variables, Delta configuration can now be defined via a external file.
 
-@ref:[Read More about Delta configuration](../getting-started/running-nexus/configuration/index.md)
+@ref:[Read More about Delta configuration](../running-nexus/configuration/index.md)
 
 ### Deleting tags on resources
 

docs/src/main/paradox/docs/releases/v1.7-to-v1.8-migration.md

@@ -248,7 +248,7 @@ The following environment variables need to be set when launching Delta v1.8 in
 | S3 storage enabling         | plugins.storage.storages.amazon.enabled              | true/false            |
 
 For more information on the configuration of Delta, please refer to the
-@ref:[Nexus configuration page](../getting-started/running-nexus/configuration/index.md).
+@ref:[Nexus configuration page](../running-nexus/configuration/index.md).
 
 ## Migrating events from Cassandra to PostgreSQL
 

docs/src/main/paradox/docs/releases/v1.8-to-v1.9-migration.md

@@ -61,5 +61,5 @@ Currently, both remote storages and composite views with remote sources can hold
 
 A remote storage might currently have a token stored in the storage definition. In 1.9, this should be moved to `plugins.storage.storages.remote-disk.credentials`.
 
-A composite view might currently have a token stored in the view definition. In 1.9, this should be moved to `plugins.composite-views.remote-source-credentials`, as shown @ref:[here](../getting-started/running-nexus/configuration/index.md#composite-views-plugin-configuration)
+A composite view might currently have a token stored in the view definition. In 1.9, this should be moved to `plugins.composite-views.remote-source-credentials`, as shown @ref:[here](../running-nexus/configuration/index.md#composite-views-plugin-configuration)