Add sbt plugin to create jar with dependences

Also update README.md with info on how to compile and run the program.

4 files changed, 69 insertions, 14 deletions

diff --git a/README.md b/README.md
index dbf0ead..55a4b01 100644
--- a/README.md
+++ b/README.md
@@ -11,19 +11,42 @@ In order to use this program you need to have [RDFox](https://www.oxfordsemantic
 RDFox is proprietary software and as such we are not able to distribute it along with our code.
 Please refer to [this link](https://www.oxfordsemantic.tech/tryrdfoxforfree) to request a free trial.
 
-This software has been developed and tested with RDFox v.4.0
+This software has been developed and tested with RDFox v.4.1
 
 ## Using the software
 
-TODO
+We assume you followed [these steps](https://docs.oxfordsemantic.tech/getting-started.html#getting-started) in order to setup RDFox on your personal machine and in particular you know the path to the `JRDFox.jar` library that comes with the distribution.
 
 ### Provide RDFox license
 
-TODO
+The [documentation](https://docs.oxfordsemantic.tech/features-and-requirements.html#license-key), describes several ways to provide the license to RDFox.
 
-### Compiling the project
+One easy way is to put your license key in a file `RDFox.lic` in `$HOME/.RDFox/`, with adeguate read permissions for the user executing the program.
 
-TODO
+### Compiling and running the project
+
+The project uses [sbt](https://www.scala-sbt.org/) to manage dependences.
+
+To compile the project run the following from the base directory:
+```
+sbt compile
+```
+
+The project uses the sbt plugin [sbt-assembly](https://github.com/sbt/sbt-assembly) to produce a fat jar with all the required dependences.
+Run the following from the base directory of the project to produce a standalone `jar` file.
+```
+sbt assembly
+```
+
+The output of the command will print the location of the produced jar. Execute it with
+```
+java -jar <path/to/fat.jar> [<option> ...]
+```
+
+Note that the fat jar file distributed with this repository excludes the RDFox as a dependency. Provided that you have the RDFox setup on your machine, you can run the program as follows
+```
+java -cp <path/to/JRDFox.jar>:<path/to/fat.jar> uk.ac.ox.cs.rsacomb.RSAComb [<option> ...]
+```
 
 ### Running tests and examples
 
diff --git a/build.sbt b/build.sbt
index 860b064..4b774e7 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,10 +1,10 @@
 import Dependencies._
 
-ThisBuild / scalaVersion          := "2.13.4"
-ThisBuild / version               := "0.1.0"
-ThisBuild / organization          := "uk.ac.ox.cs.rsacomb"
-ThisBuild / organizationName      := "Department of Computer Science - University of Oxford"
-ThisBuild / organizationHomepage  := Some(url("https://www.cs.ox.ac.uk"))
+ThisBuild / scalaVersion := "2.13.4"
+ThisBuild / version := "0.1.0"
+ThisBuild / organization := "uk.ac.ox.cs.rsacomb"
+ThisBuild / organizationName := "Department of Computer Science - University of Oxford"
+ThisBuild / organizationHomepage := Some(url("https://www.cs.ox.ac.uk"))
 
 ThisBuild / scmInfo := Some(
   ScmInfo(
@@ -23,7 +23,9 @@ ThisBuild / scmInfo := Some(
 
 ThisBuild / description := "Re-implementation of the combined approach for CQ answering over RSA ontologies."
 // ThisBuild / licenses := List("Apache 2" -> new URL("http://www.apache.org/licenses/LICENSE-2.0.txt"))
-ThisBuild / homepage := Some(url("https://github.com/KRR-Oxford/RSA-combined-approach"))
+ThisBuild / homepage := Some(
+  url("https://github.com/KRR-Oxford/RSA-combined-approach")
+)
 
 lazy val root = (project in file("."))
   .settings(
@@ -36,3 +38,29 @@ lazy val root = (project in file("."))
       graphcore
     )
   )
+
+/** Exclude RDFox from the building process
+  *
+  * @see https://github.com/sbt/sbt-assembly#excluding-jars-and-files
+  * for different ways to exclude a specific package from the building
+  * process.
+  */
+assemblyExcludedJars in assembly := {
+  val cp = (fullClasspath in assembly).value
+  cp filter { _.data.getName == "JRDFox.jar" }
+}
+
+/** See these links for more info on merging strategies in
+  * `sbt-assembly`
+  *
+  *      https://github.com/sbt/sbt-assembly#merge-strategy
+  *      https://stackoverflow.com/a/55557287
+  */
+assemblyMergeStrategy in assembly := {
+  case "module-info.class" =>
+    MergeStrategy.discard
+  case x => {
+    val oldStrategy = (assemblyMergeStrategy in assembly).value
+    oldStrategy(x)
+  }
+}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 39e8e2e..a185615 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -8,8 +8,11 @@ object Dependencies {
 
   // Libraries
   val scalatest = "org.scalatest" %% "scalatest" % scalatestVersion
-  val scalatestFlatSpec = "org.scalatest" %% "scalatest-flatspec" % scalatestVersion
-  val scalatestShouldMatchers = "org.scalatest" %% "scalatest-shouldmatchers" % scalatestVersion
-  val apibinding = "net.sourceforge.owlapi" % "owlapi-apibinding" % owlapiVersion
+  val scalatestFlatSpec =
+    "org.scalatest" %% "scalatest-flatspec" % scalatestVersion
+  val scalatestShouldMatchers =
+    "org.scalatest" %% "scalatest-shouldmatchers" % scalatestVersion
+  val apibinding =
+    "net.sourceforge.owlapi" % "owlapi-apibinding" % owlapiVersion
   val graphcore = "org.scala-graph" %% "graph-core" % scalagraphVersion
 }
diff --git a/project/plugins.sbt b/project/plugins.sbt
new file mode 100644
index 0000000..72477a2
--- /dev/null
+++ b/project/plugins.sbt
@@ -0,0 +1 @@
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.15.0")