default build procedure does not work as expected

[hmenager]

If I clone the repo as is, and type as instructed "mvn clean package" I get:

[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building bubastis 1.1.1
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bubastis ---
[INFO] Deleting /home/hmenager/bubastis/target
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bubastis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/hmenager/bubastis/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ bubastis ---
[INFO] Compiling 10 source files to /home/hmenager/bubastis/target/classes
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bubastis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/hmenager/bubastis/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ bubastis ---
[INFO] Compiling 1 source file to /home/hmenager/bubastis/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ bubastis ---
[INFO] Surefire report directory: /home/hmenager/bubastis/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running uk.ac.ebi.efo.bubastis.DriverTest
test one url and one local file
Parsing failed.  Reason: Ontology 1 is neither a file nor a URL
test two local files
Parsing failed.  Reason: Ontology 1 is neither a file nor a URL
test two local files with differences
Parsing failed.  Reason: Ontology 1 is neither a file nor a URL
test one url and one local file
Parsing failed.  Reason: Ontology 1 is neither a file nor a URL
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec - in uk.ac.ebi.efo.bubastis.DriverTest

Results :

Tests run: 4, Failures: 0, Errors: 0, Skipped: 0

[INFO] 
[INFO] --- maven-war-plugin:2.2:war (default-war) @ bubastis ---
[INFO] Packaging webapp
[INFO] Assembling webapp [bubastis] in [/home/hmenager/bubastis/target/bubastis]
[INFO] Processing war project
[INFO] Copying webapp resources [/home/hmenager/bubastis/src/main/webapp]
[INFO] Webapp assembled in [72 msecs]
[INFO] Building war: /home/hmenager/bubastis/target/bubastis.war
[INFO] WEB-INF/web.xml already added, skipping
[INFO] 
[INFO] --- maven-assembly-plugin:2.4:single (make-assembly) @ bubastis ---
[INFO] Building jar: /home/hmenager/bubastis/target/bubastis_1_2.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.253 s
[INFO] Finished at: 2017-07-03T22:14:16+02:00
[INFO] Final Memory: 31M/271M
[INFO] ------------------------------------------------------------------------

Then trying to launch it:

$ java -jar target/bubastis_1_2.jar 
Error: Could not find or load main class uk.ac.ebi.efo.bubastis.Driver

If I however tweak pom.xml to change the packaging, like this:

diff --git a/pom.xml b/pom.xml
index 5adc2d0..b10f9b2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
     <groupId>uk.ac.ebi.fgpt</groupId>
     <artifactId>bubastis</artifactId>
     <version>1.1.1</version>
-    <packaging>war</packaging>
+    <packaging>jar</packaging>^M
 
     <name>bubastis</name>
     <url>http://www.ebi.ac.uk/efo/bubastis</url>

and then launch the same command line, the Driver class is indeed found in the jarfile (bubastis_1_2.jar, not bubastis.jar which isn't functional). I'm pretty sure this isn't the right way to get a functional bubastis jarfile, as I haven't dealt with java for a long long time, but there is probably a way to fix this.

cc @joncison, fixing this would improve a lot the edam release process!