Update readme. Fix where target/sparql-examples-util-0.0.1 was still …

…used, now uses target/sparql-examples-utils-*-uber.jar, so this works with any version that have been retrieved. Make sure all CLI calls are working properly (e.g. replace tester subcommand by test). Add a note explaining for these calls we expect the sparql-examples repo to be cloned in the same folder alongside sparql-examples-utils (which is kind of a logical place for it to be)

README.md

@@ -37,96 +37,103 @@ WHERE
     schema:keywords "taxa".
 ```
 
+If you want to add a label to a query please use the [schema.org keywords](https://schema.org/keywords).
+
 # Running the code
 
-If using a release
-```
+If using a release:
+```bash
 mkdir target
-wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v1.0.0/sparql-examples-util-1.0.0-uber.jar" 
-mv sparql-examples-util-1.0.0-uber.jar target
+wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.0/sparql-examples-utils-2.0.0-uber.jar" 
+mv sparql-examples-utils-2.0.0-uber.jar target
 
 # This target directory is only so that the commands in the examples match as if the code was build locally.
 # basically target/ can be remove from all examples below
 ```
-if building locally in this git repository
-```
+If building locally in this git repository:
+```bash
 mvn package
-
 ```
 
 
 # Quality Assurance (QA).
 
-To test your examples pass the folder/directory containing your exampes as an argument ('--input-directory' to the Tester command.
-e.g
+To test your examples pass the folder/directory containing your examples as an argument (`--input-directory` to the `test` subcommand, e.g.:
+
+```bash
+java -jar target/sparql-examples-utils-*-uber.jar test --input-directory=../sparql-examples/examples
 ```
-java -jar target/sparql-examples-util-1.0.0-uber.jar tester --input-directory=$HOME/git/sparql-examples/examples
+
+The queries can be executed automatically on all endpoints they apply to using an extra argument for the test `--also-run-slow-tests`. This does change the queries to add a `LIMIT 1` if no limit was set in the query.
+
+```bash
+java -jar target/sparql-examples-utils-*-uber.jar test --input-directory=../sparql-examples/examples -p MetaNetX --also-run-slow-tests
 ```
 
+> [!NOTE]
+>
+> All CLI commands provided in this readme expects you have the [`sparql-examples`](https://github.com/sib-swiss/sparql-examples) folder cloned in the same directory alongside this `sparql-examples-utils` project folder. Feel free to change them for your own example folder and path.
+
 # Conversion for upload in SPARQL endpoint
 
-To load the examples into a SPARQL endpoint they should be concatenated into one example file. Use the script `convertIntoOneTurtle.sh` provide the project name with a `-p` parameter
+Before loading the examples into a SPARQL endpoint they should be concatenated into one file, including the prefixes/namespaces definitions.
+
+Compile all query files for a specific example subfolder, into a local turtle file:
 
 ```bash
-java -jar target/sparql-examples-util-1.0.0-uber.jar convert -i examples/ -p all -f jsonld
-# Or for a specific example folder, as turtle, to a file:
-java -jar target/sparql-examples-util-1.0.0-uber.jar convert -i examples/ -p Bgee -f ttl > examples_Bgee.ttl
+java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p Bgee -f ttl > examples_Bgee.ttl
+```
+
+Or compile all subfolders as JSON-LD to the standard output:
+
+```bash
+java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p all -f jsonld
 ```
 
 ## Conversion to RQ files
 
-For easier use by other tools we can also generate [rq](https://www.w3.org/TR/2013/REC-sparql11-query-20130321/#mediaType) files. Following the syntax of [grlc](https://grlc.io/) allowing to use these queries as APIs.
+For easier use by other tools we can also generate [`.rq`](https://www.w3.org/TR/2013/REC-sparql11-query-20130321/#mediaType) files. Following the syntax of [grlc.io](https://grlc.io/) allowing to use these queries as HTTP APIs.
 ```bash
-java -jar target/sparql-examples-util-1.0.0-uber.jar convert -i examples/ -p all -r
+java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -p all -r
 ```
 
 ## Generate markdown file
 
 Generate markdown files with the query and a mermaid diagram of the queries, to be used to deploy a static website for the query examples.
 
 ```bash
-java -jar target/sparql-examples-util-*-uber.jar convert -i examples/ -m
+java -jar target/sparql-examples-utils-*-uber.jar convert -i ../sparql-examples/examples -m
 ```
 
 # Querying for queries
 
 As the SPARQL examples are themselves RDF, they can be queried for as soon as they are loaded in a SPARQL endpoint.
 ```sparql
 PREFIX sh: <http://www.w3.org/ns/shacl#>
-SELECT *
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+SELECT DISTINCT ?sq ?comment ?query
 WHERE {
-  ?ex sh:select|sh:ask|sh:construct|sh:describe ?query .
-}
+    ?sq a sh:SPARQLExecutable ;
+        rdfs:comment ?comment ;
+        sh:select|sh:ask|sh:construct|sh:describe ?query .
+} ORDER BY ?sq
 ```
 
-# Labeling queries
-
-If you want to add a label to a query please use [schema.org keyword](https://schema.org/keywords)
-
-# Testing the queries actually work
-
-The queries can be executed automatically on all endpoints they apply to using ane extra argument for the Tester `--also-run-slow-tests`. 
-
-```
-java -cp target/sparql-examples-util-1.0.0-uber.jar test --input-directory=$HOME/git/sparql-examples/examples
-```
-
-This does change the queries to add a LIMIT 1 if no limit was set in the query. Then if there is a result it is fetched.
-
 ## Finding queries that run on more than one endpoint
 
 ```bash
-java -jar target/sparql-examples-util-1.0.0-uber.jar convert --input-directory $HOME/git/sparql-examples/examples -f examples_all.ttl
+java -jar target/sparql-examples-utils-*-uber.jar convert --input-directory ../sparql-examples/examples > examples_all.ttl
 
 sparql --data examples_all.ttl "SELECT ?query (GROUP_CONCAT(?target ; separator=', ') AS ?targets) WHERE { ?query <https://schema.org/target> ?target } GROUP BY ?query HAVING (COUNT(DISTINCT ?target) > 1) "
 ```
 
 # Native executable
 
-The project is ready to be compiled by the native-image tool of the [GraalVM](https://www.graalvm.org/) project.
+The project is ready to be compiled by the native-image tool of the [GraalVM](https://www.graalvm.org/) project. 
+
 To do so set your `JAVA_HOME` to the graalvm location and user maven package -Pnative
 
-e.g. on linux with graalvm installed in your `$HOME/bin` directory
+e.g. on linux with graalvm installed in your `$HOME/bin` directory:
 ```bash
 export JAVA_HOME=$HOME/bin/graalvm-jdk-${GRAALVM_VERSION}
 mvn package -Pnative