docs: update README.md

README.md

@@ -13,13 +13,13 @@ A hybrid architecture for conjunctive query answering overover OWL 2 DL.
 <a href="https://github.com/KRR-Oxford/ACQuA/issues">Report bug</a>
 <br/><br/>
 <a href="https://github.com/KRR-Oxford/ACQuA/releases/latest">
-    <img src="https://img.shields.io/github/release/KRR-Oxford/RSAComb.svg?style=for-the-badge" alt="Release badge">
+    <img src="https://img.shields.io/github/release/KRR-Oxford/ACQuA.svg?style=for-the-badge" alt="Release badge">
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+    <img src="https://img.shields.io/github/issues/KRR-Oxford/ACQuA.svg?style=for-the-badge" alt="Issues badge">
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@@ -41,29 +41,35 @@ If the bounds don’t coincide, then the “gap” answers are checked using the
 
 This reference implementation combines [RSAComb], [PAGOdA], and [HermiT], but these tools can be potentially subtituted or augmented with more capable ones to improve the overall performance of the system.
 
-> ACQuA is still in its preliminary stage of development and might contain bugs.
+> *Disclaimer:* ACQuA is still in its preliminary stage of development and might contain bugs.
 
 ## Preliminaries
 
 RSAComb uses a recent version of [RDFox] under the hood to offload part of the computation.
 
-In order to run ACQuA you need to have [RDFox](https://www.oxfordsemantic.tech/product) available in your system, along with *a valid license*.
+In order to run ACQuA you need to have RDFox available in your system, along with *a valid license*.
 RDFox is proprietary software and as such we are not able to distribute it along with our code.
-This software has been developed and tested with RDFox v5.5
+This software has been developed and tested with **RDFox v5.5**.
+
+### Requirements
+
+- Maven
+- [RSAComb] v1.1.0
+- RDFox v5.5
 
 ### Installing RDFox
 
 We refer to the [official documentation](https://docs.oxfordsemantic.tech/getting-started.html#getting-started) for a step-by-step guide on how to setup RDFox on your personal machine.
 In particular, you will need to know the path to the RDFox Java API (usually called `JRDFox.jar`) that comes with the distribution.
 
 Alternatively, run the following commands (on a Linux x86 machine) from the root of the project to install RDFox locally.
-Download links for other versions, operating systems, and architectures can be found [here](https://www.oxfordsemantic.tech/downloads).
+Download links for other versions, operating systems, and architectures can be found [here][RDFox].
 
 ```{.bash}
 mkdir -p lib && pushd lib
 wget https://rdfox-distribution.s3.eu-west-2.amazonaws.com/release/v5.5/RDFox-linux-x86_64-5.5.zip
-unzip RDFox-linux-x86_64-5.2.1.zip
-ln -s RDFox-linux-x86_64-5.2.1.zip/lib/JRDFox.jar
+unzip RDFox-linux-x86_64-5.5.zip
+ln -s RDFox-linux-x86_64-5.5/lib/JRDFox.jar
 popd
 ```
 
@@ -76,16 +82,40 @@ One easy way is to put your license key in a file `RDFox.lic` in `$HOME/.RDFox/`
 
 ## Using the software
 
-`TODO`
+The project is managed using Maven.
+You can compile the code using the following command
 
-### Running tests
+```{#acqua-compile .sh}
+mvn compile
+```
 
-`TODO`
+To build a JAR file, package the project as follows
 
-```
-mvn compile
+```{#acqua-package .sh}
 mvn package
-java -cp ... uk.ac.ox.cs.acqua.Acqua [OPTIONs]
+```
+
+To run ACQuA from the command line you can use the following command
+
+```{#acqua-run .sh}
+java -cp target/acqua-0.2.0-jar-with-dependencies.jar:<path/to/JRDFox.jar>:<path/to/RSAComb.jar> uk.ac.ox.cs.acqua.Acqua [OPTION ...]
+```
+
+where `path/to/RSAComb.jar` and `path/to/JRDFox.jar` are the paths in your system for `RSAComb.jar` and `JRDFox.jar`, respectively.
+For example to get a help message from the CLI use
+
+```{#acqua-help .sh}
+java -cp target/acqua-0.2.0-jar-with-dependencies.jar:<path/to/JRDFox.jar>:<path/to/RSAComb.jar> uk.ac.ox.cs.acqua.Acqua --help
+```
+
+To run an example shipping with the distribution you can try
+
+```{#acqua-test .sh}
+java -cp target/acqua-0.2.0-jar-with-dependencies.jar:<path/to/JRDFox.jar>:<path/to/RSAComb.jar> \
+    uk.ac.ox.cs.acqua.Acqua \
+    -o tests/lubm/univ-bench.owl \
+    -d tests/lubm/data/lubm1.ttl \
+    -q tests/lubm/queries.sparql
 ```
 
 ## References
@@ -97,8 +127,8 @@ java -cp ... uk.ac.ox.cs.acqua.Acqua [OPTIONs]
 ## Acknowledgements
 
 - OWLAPI [[2]](#references)
-- [RDFox](https://www.oxfordsemantic.tech/product)
-- [PAGOdA]()
+- [RDFox]
+- [PAGOdA]
 
 ## Credits
 
@@ -112,6 +142,9 @@ From the [Knowledge Representation and Reasoning research group](https://www.cs.
 
 This project is licensed under the [Apache License 2.0](LICENSE).
 
-## TODOs
+<!-- References -->
 
-- [ ] Better integration between ACQuA, RDFox and PAGOdA configuration parameters.
+[RSAComb]: https://github.com/KRR-Oxford/RSAComb
+[RDFox]: https://www.oxfordsemantic.tech/product
+[PAGOdA]: http://www.cs.ox.ac.uk/isg/tools/PAGOdA
+[HermiT]: http://www.hermit-reasoner.com/