refactor(triplestore): remove graphDB support (#2037)

* remove graphDB related scripts + clean docs * remove consistency checking * remove graphDB config * refactor twirl templates related to graphDB * remove embedded-jena-graphdb config * refactor twirl templates related to graphDB in admin routes * refactor twirl templates related to graphDB in v1 routes * remove GraphDBAPI * remove more graphDB inference related stuff * update docs * remove more graphDB stuff * PR changes * more PR changes * chore: release 20.1.0 (#2036) * commit to trigger bad gh actions Co-authored-by: DaSCH Bot <50987250+daschbot@users.noreply.github.com>
dasch-swiss · Apr 13, 2022 · bf17bcad5fd87313b797cdb6187ef7e42d6e2911 · bf17bca
1 parent 57d40f7
commit bf17bcad5fd87313b797cdb6187ef7e42d6e2911
diff --git a/README.md b/README.md
@@ -137,7 +137,7 @@ We write automated tests using [ScalaTest](https://www.scalatest.org). You can r
 
 There are three sets of automated tests:
 
-* Unit tests, route-to-route tests, and end-to-end tests are under `webapi/src/test`. To run these, type `graphdb:test` or `graphdb-free:test` (depending on which triplestore you're using) at the SBT console in the `webapi` project. To run a single test, use `graphdb:test-only *NameOfTestSpec`.
+* Unit tests, route-to-route tests, and end-to-end tests are under `webapi/src/test`. To run these, type `test` at the SBT console in the `webapi` project. To run a single test, use `testOnly *NameOfTestSpec`.
 * Integration tests, which can involve [Sipi](https://github.com/daschswiss/sipi), are under `src/it`. To run these, first start Sipi, then type `it:test` at the SBT console in the `webapi` project.
 
 Whenever you add a new feature or fix a bug, you should add one or more tests

diff --git a/docs/02-knora-ontologies/knora-base.md b/docs/02-knora-ontologies/knora-base.md
@@ -953,9 +953,6 @@ in user-created ontologies. Three types of consistency rules are enforced:
 - Constraints on the types of the subjects and objects of OWL object properties must be satisfied.
 - A datatype property may not have an empty string as an object.
 
-The implementation of consistency checking is partly triplestore-dependent; Knora may be able to provide stricter checks
-with some triplestores than with others.
-
 ### OWL Cardinalities
 
 As noted in [Resources](#resources), each subclass of

diff --git a/docs/04-publishing-deployment/configuration.md b/docs/04-publishing-deployment/configuration.md
@@ -53,10 +53,6 @@ A number of core settings is additionally configurable through system environmen
 | app.triplestore.use-https                                   | KNORA_WEBAPI_TRIPLESTORE_USE_HTTPS                              | false                |
 | app.triplestore.host                                        | KNORA_WEBAPI_TRIPLESTORE_HOST                                   | localhost            |
 | app.triplestore.auto-init                                   | KNORA_WEBAPI_TRIPLESTORE_AUTOINIT                               | false                |
-| app.triplestore.graphdb.port                                | KNORA_WEBAPI_TRIPLESTORE_GRAPHDB_PORT                           | 7200                 |
-| app.triplestore.graphdb.repository-name                     | KNORA_WEBAPI_TRIPLESTORE_GRAPHDB_REPOSITORY_NAME                | knora-test           |
-| app.triplestore.graphdb.username                            | KNORA_WEBAPI_TRIPLESTORE_GRAPHDB_USERNAME                       | admin                |
-| app.triplestore.graphdb.password                            | KNORA_WEBAPI_TRIPLESTORE_GRAPHDB_PASSWORD                       | root                 |
 | app.triplestore.fuseki.port                                 | KNORA_WEBAPI_TRIPLESTORE_FUSEKI_PORT                            | 3030                 |
 | app.triplestore.fuseki.repository-name                      | KNORA_WEBAPI_TRIPLESTORE_FUSEKI_REPOSITORY_NAME                 | knora-test           |
 | app.triplestore.fuseki.username                             | KNORA_WEBAPI_TRIPLESTORE_FUSEKI_USERNAME                        | admin                |

diff --git a/docs/04-publishing-deployment/getting-started.md b/docs/04-publishing-deployment/getting-started.md
@@ -50,9 +50,6 @@ DSP-API is designed to work with any standards-compliant
 triplestore. It is primarily tested with
 [Apache Jena Fuseki](https://jena.apache.org), an open source triplestore.
 
-Built-in support and configuration for a high-performance, proprietary
-triplestore [Ontotext GraphDB](http://ontotext.com/products/graphdb/) is
-provided but unmaintained (GraphDB must be licensed separately by the user).
 Other triplestores are planned.
 
 ## Running the DSP-Stack

diff --git a/docs/04-publishing-deployment/updates.md b/docs/04-publishing-deployment/updates.md
@@ -15,54 +15,7 @@ manual changes are needed, these will be described in the release notes, and mus
 done first.
 
 Before starting a new version of Knora, back up your repository, so you can restore it
-in case the automatic repository update fails. You can use one of these scripts
-in `webapi/scripts`:
-
-- `fuseki-dump-repository.sh` for Fuseki
-- `graphdb-dump-repository.sh` for GraphDB
-
+in case the automatic repository update fails. For Fuseki use `fuseki-dump-repository.sh`
+script located in `webapi/scripts`.
 
 For information on command-line options, run the script with no arguments.
-
-## Upgrading from a Knora Version Before 7.0.0
-
-**WARNING**: If you do not follow this procedure, your data may be
-corrupted, and Knora may not work.
-
-You must first upgrade to Knora 7.0.0, then upgrade again to the current
-version.
-
-The overall procedure is:
-
-1. Back up your repository as described above.
-
-2. Install Knora release 7.0.0, and read the general instructions in
-   `upgrade/graphdb-se/old/README.md` in that release.
-
-3. Follow the instructions in one of the subsections below for the version you are
-   upgrading from.
-
-4. Back up your repository again.
-
-5. Install the current release of Knore, and follow any manual update instructions
-   in its release notes.
-
-6. Start Knora to continue the automatic upgrade.
-
-### Upgrading from Knora 6.0.0 or 6.0.1
-
-1. Follow the instructions in `upgrade/graphdb-se/old/1263-knora-admin/README.md`.
-
-2. Follow the instructions in
-   [Upgrading from Knora 7.0.0 or Later](#upgrading-from-knora-7-0-0-or-later).
-
-### Upgrading from Knora 5.0.0 
-
-1. Follow the instructions in `upgrade/graphdb-se/old/1211-datetime/README.md`.
-
-2. Follow the instructions in `upgrade/graphdb-se/old/1230-delete-previews/README.md`.
-
-3. Follow the instructions in `upgrade/graphdb-se/old/1263-knora-admin/README.md`.
-
-4. Follow the instructions in
-   [Upgrading from Knora 7.0.0 or Later](#upgrading-from-knora-7-0-0-or-later).
diff --git a/docs/05-internals/design/api-v2/gravsearch.md b/docs/05-internals/design/api-v2/gravsearch.md
@@ -309,9 +309,7 @@ When the triplestore-specific version of the query is generated:
 
 Gravsearch also provides some virtual properties, which take advantage of forward-chaining inference
 as an optimisation if the triplestore provides it. For example, the virtual property
-`knora-api:standoffTagHasStartAncestor` is equivalent to `knora-base:standoffTagHasStartParent*`, but
-with GraphDB it is implemented using a custom inference rule (in `KnoraRules.pie`) and is therefore more
-efficient. If Knora is not using the triplestore's inference, `SparqlTransformer.transformStatementInWhereForNoInference`
+`knora-api:standoffTagHasStartAncestor` is equivalent to `knora-base:standoffTagHasStartParent*`. If Knora is not using the triplestore's inference, `SparqlTransformer.transformStatementInWhereForNoInference`
 replaces `knora-api:standoffTagHasStartAncestor` with `knora-base:standoffTagHasStartParent*`.
 
 # Optimisation of generated SPARQL

diff --git a/docs/05-internals/design/principles/consistency-checking.md b/docs/05-internals/design/principles/consistency-checking.md
@@ -5,6 +5,9 @@
 
 # Consistency Checking
 
+**Attention!** GraphDB is not supported anymore, therefore parts related 
+to it in this document are redundant.
+
 ## Requirements
 
 Knora is designed to prevent inconsistencies in RDF data,

diff --git a/docs/05-internals/design/principles/design-overview.md b/docs/05-internals/design/principles/design-overview.md
@@ -26,7 +26,7 @@ Knora is written in [Scala](http://www.scala-lang.org/), using the
 [Akka](http://akka.io/) framework for message-based concurrency. It is
 designed to work with any standards-compliant triplestore via
 the [SPARQL 1.1 Protocol](http://www.w3.org/TR/sparql11-protocol/), but is currently
-tested only with [Ontotext GraphDB](http://graphdb.ontotext.com/) (with support
+tested only with [Apache Jena Fuseki](https://jena.apache.org) (with support
 for other triplestores coming soon).
 
 ## Knora APIs

diff --git a/docs/05-internals/design/principles/store-module.md b/docs/05-internals/design/principles/store-module.md
@@ -26,14 +26,10 @@ HTTP-based triplestore support is implemented in the
 `org.knora.webapi.triplestore.http` package.
 
 An HTTP-based triplestore is one that is accessed remotely over the HTTP
-protocol. `HttpTriplestoreConnector` supports the following triplestores:
+protocol. `HttpTriplestoreConnector` supports the open source triplestore 
+- [Apache Jena Fuseki](https://jena.apache.org).
 
-   - Ontotext GraphDB
-   - Fuseki 2
-
-### GraphDB
-
-### Fuseki 2
+### Apache Jena Fuseki
 
 ## Embedded Triplestores
 

diff --git a/docs/05-internals/design/principles/triplestore-updates.md b/docs/05-internals/design/principles/triplestore-updates.md
@@ -36,16 +36,11 @@ the same data, and may eventually provide functionality to facilitate
 this coordination.)
 
 We can assume that each SPARQL update operation will run in its own
-database transaction with an isolation level of 'read committed'. This
-is what GraphDB does when it receives a SPARQL update over HTTP (see
-[GraphDB SE
-Transactions](http://graphdb.ontotext.com/documentation/standard/storage.html#transaction-control)).
+database transaction with an isolation level of 'read committed'.
 We cannot assume that it is possible to run more than one SPARQL update
-in a single database transaction. (The [SPARQL 1.1
-Protocol](http://www.w3.org/TR/sparql11-protocol/) does not provide a
-way to do this, and currently it can be done only by embedding the
-triplestore in the application and using a vendor-specific API, but we
-cannot require this in Knora.)
+in a single database transaction. The [SPARQL 1.1 Protocol](http://www.w3.org/TR/sparql11-protocol/) does not provide a way to do this, and currently it 
+can be done only by embedding the triplestore in the application and 
+using a vendor-specific API, but we cannot require this in Knora.)
 
 ### Permissions
 
@@ -253,7 +248,7 @@ Knora enforces consistency constraints using three redundant mechanisms:
 1.  By doing pre-update checks using SPARQL SELECT queries and cached
     ontology data.
 2.  By doing checks in the `WHERE` clauses of SPARQL updates.
-3.  By using GraphDB's built-in consistency checker (see
+3.  **Deprecated**: By using GraphDB's built-in consistency checker (see
     [Consistency Checking](consistency-checking.md)).
 
 We take the view that redundant consistency checks are a good thing.

diff --git a/docs/05-internals/development/docker-compose.md b/docs/05-internals/development/docker-compose.md
@@ -5,27 +5,13 @@
 
 # Starting the Knora Stack inside Docker Container
 
-To run Knora locally, we provide `docker-compose.yml` which can be used to start GraphDB, Sipi,
+To run Knora locally, we provide `docker-compose.yml` which can be used to start Fuseki, Sipi,
 Webapi running each in its own Docker container.
 
-For GraphDB it is additionally necessary to define two environment variables:
-
-``` 
-$ export KNORA_GDB_LICENSE # full path to the GraphDB-SE license file, e.g., /Users/name/GDB/GDB.license
-$ export KNORA_GDB_HOME # full path to a local folder where GraphDB should store it's data, e.g., /users/name/GDB/home
-```
-
-Per default, GraphDB-SE is started. If GraphDB-Free is needed, because there is no awailable license,
-then a third environment variable can be set to something like:
-
-```
-$ export KNORA_GDB_IMAGE=daschswiss/graphdb-free:8.3.1 
-```
-
 To run the whole stack:
 
 ```
-$ docker-compose up
+$ make stack-up
 ```
 
 For additional information please see the [Docker Compose documentation](https://docs.docker.com/compose/)
diff --git a/docs/05-internals/development/overview.md b/docs/05-internals/development/overview.md
@@ -10,8 +10,7 @@ installation of Knora. The different parts are:
 
 1. The cloned [DSP-API](https://github.com/dasch-swiss/dsp-api) Github
    repository
-1. One of the supplied triplestores in the DSP-API Github repository
-    (GraphDB-SE 8 or Fuseki 3).
+1. Fuseki - supplied triplestore in the DSP-API Github repository.
 1. Sipi by building from
     [source](https://github.com/dasch-swiss/sipi) or using the docker
     [image](https://hub.docker.com/r/daschswiss/sipi/)

diff --git a/docs/05-internals/development/testing.md b/docs/05-internals/development/testing.md
@@ -5,12 +5,6 @@
 
 # Testing
 
-Prerequisite: Before running any tests, a supported triplestore needs to
-be started and initialized through a script inside the "scripts" folder.
-For example, when using "GraphDB Free", the nedded script is
-"graphdb-free-init-knora-test-unit.sh". Please note the occurrence of
-"test-unit" in the name of the script.
-
 ## How to Write Unit Tests
 
 1)  Inside a test, at the beginning, add the following (change the paths

diff --git a/docs/07-lucene/index.md b/docs/07-lucene/index.md
@@ -6,6 +6,6 @@
 # Lucene 
 
 The Lucene full-text index provided by the triplestore is used to perform full-text searches in Knora. 
-The exact behavior can be different depending on the triplestore, e.g., GraphDB or Fuseki.
+The exact behavior can be different depending on the triplestore.
 
 * [Lucene Query Parser Syntax](lucene-query-parser-syntax.md)
diff --git a/docs/faq/index.md b/docs/faq/index.md
@@ -29,10 +29,7 @@ we recommend converting it to Knora resources, which are stored as RDF.
 
 ### Which triplestores can be used with Knora?
 
-Knora is tested with [Ontotext GraphDB SE](http://graphdb.ontotext.com/).
-Our goal is to support several triplestores, including open-source options.
-Integration with [Apache Jena Fuseki](https://jena.apache.org/documentation/fuseki2/)
-has been partly implemented, but is not currently supported.
+Knora is tested with [Apache Jena Fuseki](https://jena.apache.org/).
 
 ## Knora Ontologies