Optimize imports and reformat everything with IntelliJ defaults. (#458)

* Optimize imports and reformat everything with IntelliJ defaults. * Fix test to use correct root type for complexes. * Fix lookup test for new protein complex classification.
geneontology · Feb 23, 2022 · 11b6ec8 · 11b6ec8
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diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -9,7 +9,7 @@ on:
       - master
       - dev
   pull_request:
-    branches: 
+    branches:
       - master
       - dev
 
@@ -19,11 +19,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 11
-      uses: actions/setup-java@v2
-      with:
-        java-version: '11'
-        distribution: 'adopt'
-    - name: Build with Maven
-      run: mvn test
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+      - name: Build with Maven
+        run: mvn test
diff --git a/INSTRUCTIONS.md b/INSTRUCTIONS.md
@@ -1,24 +1,24 @@
 <!-- MarkdownTOC -->
 
 - [About this document](#about-this-document)
-	- [Building the server](#building-the-server)
-		- [Prerequisites to build the code](#prerequisites-to-build-the-code)
-		- [Building the Minerva Server](#building-the-minerva-server)
-	- [Running the Minerva Server](#running-the-minerva-server)
-		- [Prerequisites](#prerequisites)
-		- [Start the MolecularModelManager server from the command line](#start-the-molecularmodelmanager-server-from-the-command-line)
-		- [Start Server via Eclipse:](#start-server-via-eclipse)
-	- [Running Tests](#running-tests)
-		- [Failing Tests](#failing-tests)
-		- [Quick Test via `curl`](#quick-test-via-curl)
-		- [Sonarqube](#Sonarqube)
-	- [Obtaining `owl-models` and `go-lego.owl`](#obtaining-owl-models-and-go-legoowl)
-		- [Useful source files for learning](#useful-source-files-for-learning)
-	- [Using the Blazegraph model store](#using-the-blazegraph-model-store)
-		- [Create a new Blazegraph journal from a directory of existing model files](#create-a-new-blazegraph-journal-from-a-directory-of-existing-model-files)
-		- [Dump model files from a Blazegraph journal that is not in use](#dump-model-files-from-a-blazegraph-journal-that-is-not-in-use)
-		- [Start the Minerva Server with configuration for Blazegraph journal and model dump folder](#start-the-minerva-server-with-configuration-for-blazegraph-journal-and-model-dump-folder)
-		- [Request an OWL dump of all models from a running Minerva Server](#request-an-owl-dump-of-all-models-from-a-running-minerva-server)
+    - [Building the server](#building-the-server)
+        - [Prerequisites to build the code](#prerequisites-to-build-the-code)
+        - [Building the Minerva Server](#building-the-minerva-server)
+    - [Running the Minerva Server](#running-the-minerva-server)
+        - [Prerequisites](#prerequisites)
+        - [Start the MolecularModelManager server from the command line](#start-the-molecularmodelmanager-server-from-the-command-line)
+        - [Start Server via Eclipse:](#start-server-via-eclipse)
+    - [Running Tests](#running-tests)
+        - [Failing Tests](#failing-tests)
+        - [Quick Test via `curl`](#quick-test-via-curl)
+        - [Sonarqube](#Sonarqube)
+    - [Obtaining `owl-models` and `go-lego.owl`](#obtaining-owl-models-and-go-legoowl)
+        - [Useful source files for learning](#useful-source-files-for-learning)
+    - [Using the Blazegraph model store](#using-the-blazegraph-model-store)
+        - [Create a new Blazegraph journal from a directory of existing model files](#create-a-new-blazegraph-journal-from-a-directory-of-existing-model-files)
+        - [Dump model files from a Blazegraph journal that is not in use](#dump-model-files-from-a-blazegraph-journal-that-is-not-in-use)
+        - [Start the Minerva Server with configuration for Blazegraph journal and model dump folder](#start-the-minerva-server-with-configuration-for-blazegraph-journal-and-model-dump-folder)
+        - [Request an OWL dump of all models from a running Minerva Server](#request-an-owl-dump-of-all-models-from-a-running-minerva-server)
 
 <!-- /MarkdownTOC -->
 
@@ -30,8 +30,8 @@ This is a quick overview on how to setup a Java server for the MolecularModelMan
 
 ### Prerequisites to build the code
 
- * Java (JDK 1.8 or later) as compiler
- * Maven (3.0.x) Build-Tool
+* Java (JDK 1.8 or later) as compiler
+* Maven (3.0.x) Build-Tool
 
 ### Building the Minerva Server
 
@@ -79,8 +79,8 @@ start-m3-server.sh -c go-trunk/ontology/extensions/catalog-v001.xml \
 
 ### Automatically create a catalog file pointing to local copies of the imported ontologies
 
-If you have [ROBOT](http://robot.obolibrary.org) installed, you can easily create a local mirror of an OWL imports chain, so that large 
-imported ontologies don't need to be repeatedly downloaded while you are developing locally:
+If you have [ROBOT](http://robot.obolibrary.org) installed, you can easily create a local mirror of an OWL imports
+chain, so that large imported ontologies don't need to be repeatedly downloaded while you are developing locally:
 
 `robot mirror --input my-ontology.owl --directory my-cache --output my-catalog.xml`
 
@@ -102,7 +102,6 @@ https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-e
 
 [Maven CLI](http://maven.apache.org/ref/3.3.9/maven-embedder/cli.html)
 
-
 ### Quick Test via `curl`
 
 This assumes you are in the `minerva/` directory, which is the parent of `minerva-server/`.
@@ -113,7 +112,8 @@ curl localhost:6800/`cat minerva-server/src/test/resources/server-test/long-get.
 
 ### Sonarqube
 
-Run sonarqube server locally using docker and ensure it is up and running by visiting [http://localhost:9000](http://localhost:9000)
+Run sonarqube server locally using docker and ensure it is up and running by
+visiting [http://localhost:9000](http://localhost:9000)
 
 ```
 docker run -d --rm --name sonarqube -p 9000:9000 sonarqube:7.9.6-community
@@ -131,15 +131,17 @@ For static analysis and code coverage:
 mvn clean package sonar:sonar 
 ```
 
-Stopping sonarqube docker container. This would automatically remove the container since the <i>--rm</i> option was used above.
+Stopping sonarqube docker container. This would automatically remove the container since the <i>--rm</i> option was used
+above.
 
 ```
 docker stop sonarqube
 ```
 
 ## Obtaining `owl-models` and `go-lego.owl`
 
-See [Monarch Ontology](https://github.com/monarch-initiative/monarch-ontology) and use the instructions there to generate a `catalog-v001.xml`.
+See [Monarch Ontology](https://github.com/monarch-initiative/monarch-ontology) and use the instructions there to
+generate a `catalog-v001.xml`.
 
 - ftp://ftp.geneontology.org/pub/go//experimental/lego/server/owl-models
 - ftp://ftp.geneontology.org/pub/go//ontology/extensions/go-lego.owl
@@ -148,7 +150,6 @@ See [Monarch Ontology](https://github.com/monarch-initiative/monarch-ontology) a
 
 - `/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java`
 
-
 ## Using the Blazegraph model store
 
 ### Create a new Blazegraph journal from a directory of existing model files
@@ -163,7 +164,8 @@ See [Monarch Ontology](https://github.com/monarch-initiative/monarch-ontology) a
 
 `java "-Xmx$MINERVA_MEMORY" -jar minerva-server.jar -c catalog-v001.xml -g http://purl.obolibrary.org/obo/go/extensions/go-lego.owl -f blazegraph.jnl --export-folder exported-models --port 9999 --use-request-logging --slme-elk --skip-class-id-validation --set-important-relation-parent http://purl.obolibrary.org/obo/LEGOREL_0000000`
 
-Note the options `-f blazegraph.jnl` for specifying the journal file and `--export-folder exported-models` for specifying where to write OWL models in response to a `export-all` operation request.
+Note the options `-f blazegraph.jnl` for specifying the journal file and `--export-folder exported-models` for
+specifying where to write OWL models in response to a `export-all` operation request.
 
 ### Request an OWL dump of all models from a running Minerva Server
 
@@ -173,9 +175,13 @@ This will output to the folder configured in the startup arguments.
 
 ### Run a SPARQL Update against the triples in the database
 
-*This should be handled with care since direct changes to triples will bypass any validations that typically occur when data are edited via the standard Minerva server API.*
+*This should be handled with care since direct changes to triples will bypass any validations that typically occur when
+data are edited via the standard Minerva server API.*
 
-[SPARQL Update](http://www.w3.org/TR/sparql11-update/) is useful for various bulk maintenance operations that may periodically be necessary, e.g. updating all uses of an obsolete property to the current preferred IRI. Before running the update, the server should be stopped, since the Blazegraph journal can only be used from one Java process at a time. Then simply run the command like this:
+[SPARQL Update](http://www.w3.org/TR/sparql11-update/) is useful for various bulk maintenance operations that may
+periodically be necessary, e.g. updating all uses of an obsolete property to the current preferred IRI. Before running
+the update, the server should be stopped, since the Blazegraph journal can only be used from one Java process at a time.
+Then simply run the command like this:
 
 ```bash
 java -jar minerva-cli.jar --sparql-update -j blazegraph.jnl -f update.rq
@@ -199,8 +205,11 @@ WHERE {
 
 ## SPARQL endpoint service
 
-Minerva provides a read-only SPARQL query service at the `/sparql` path. Using GET, a URL-encoded query can be submitted as a value for the `query` parameter. Alternatively, POST can be used to submit form data with a `query` parameter, or to submit a SPARQL query directly, using the `application/sparql-query` MIME type.
+Minerva provides a read-only SPARQL query service at the `/sparql` path. Using GET, a URL-encoded query can be submitted
+as a value for the `query` parameter. Alternatively, POST can be used to submit form data with a `query` parameter, or
+to submit a SPARQL query directly, using the `application/sparql-query` MIME type.
 
 ### SPARQL endpoint configuration
 
-The only configurable aspect of the SPARQL endpoint is the query timeout. This can be set with a command-line option to the Minerva server at startup: `--sparql-endpoint-timeout 10`. The value is the time in seconds; the default is `10`.
+The only configurable aspect of the SPARQL endpoint is the query timeout. This can be set with a command-line option to
+the Minerva server at startup: `--sparql-endpoint-timeout 10`. The value is the time in seconds; the default is `10`.
diff --git a/README.md b/README.md
@@ -8,18 +8,16 @@ To build and launch a server, see [INSTRUCTIONS.md](INSTRUCTIONS.md)
 
 ## About
 
-Minerva is a wrapper and server for the OWL API and a triplestore (currently
-blazegraph) that serves as the
-back end for Noctua. It communicates with Noctua via Barista. It gains
-its knowledge of the world through a Golr instance.
+Minerva is a wrapper and server for the OWL API and a triplestore (currently blazegraph) that serves as the back end for
+Noctua. It communicates with Noctua via Barista. It gains its knowledge of the world through a Golr instance.
 
 For specifications, see [specs/](specs)
 
 ## Code
 
- * minerva-core : core logic
- * minerva-json : conversion to and from the JSON-LD esque transport and model exchange format 
- * minerva-converter : converter to/from other formats. Primarily GAF/GPAD
- * minerva-lookup : To be deprecated? Non-generic functions for looking up genes in golr
- * minerva-server : JAX-RS server
- * minerva-cli : command line interface
+* minerva-core : core logic
+* minerva-json : conversion to and from the JSON-LD esque transport and model exchange format
+* minerva-converter : converter to/from other formats. Primarily GAF/GPAD
+* minerva-lookup : To be deprecated? Non-generic functions for looking up genes in golr
+* minerva-server : JAX-RS server
+* minerva-cli : command line interface
diff --git a/configuration.md b/configuration.md
@@ -1,7 +1,11 @@
 # Configurable Minerva options
+
 This document covers some of the configurable aspects of Minerva.
 
 ## Model ID prefix
-The model ID prefix is used when constructing IRIs to name new models and individuals (which are based on their containing model ID). The default is `http://model.geneontology.org/`, however this can be changed via a command-line argument for most CLI commands and the server startup. E.g. `--model-id-prefix 'http://model.myproject.org/'`. 
+
+The model ID prefix is used when constructing IRIs to name new models and individuals (which are based on their
+containing model ID). The default is `http://model.geneontology.org/`, however this can be changed via a command-line
+argument for most CLI commands and the server startup. E.g. `--model-id-prefix 'http://model.myproject.org/'`.
 
 *TODO: check consistency of argument names across CLI commands.*