Merge branch 'fix_nullpointerexception_remove_grouping' into 'develop'

Fix NullPointerException in `remove_grouping`

See merge request bioinformatics/pantools!124

CHANGELOG.md

@@ -8,6 +8,7 @@ All notable changes to Pantools will be documented in this file.
 
 ### Changed
 - `add_functions` can now specify a directory where functional databases are stored (!117).
+- parameter `-v` is now required for `change_grouping` (!124).
 
 ### Fixed
 - `msa` now works correctly with 'alt_id' properties of GO nodes (!118).

docs/source/user_guide/construct.rst

@@ -1461,16 +1461,15 @@ Options
      - Do not remove the 'is_similar' relationships between mRNA nodes.
        This does not influence the next grouping.
    * - ``--grouping-version``/``-v``
-     - Select a specific grouping version to be removed. Two additional
-       options: 'all' to remove all groupings and 'all_inactive' to
-       remove all inactive groupings.
+     - Select a specific grouping version to be removed. Should be either a
+       grouping number, 'all' for all groupings or 'all_inactive' for
+       all inactive groupings.
 
 Example commands
 """"""""""""""""
 
 .. code:: bash
 
-   $ pantools remove_grouping tomato_DB
    $ pantools remove_grouping --version=1 tomato_DB
    $ pantools remove_grouping --version=all --fast tomato_DB
    $ pantools remove_grouping --version=all_inactive tomato_DB

src/main/java/nl/wur/bif/pantools/cli/RemoveGrouping.java

@@ -26,7 +26,7 @@ public class RemoveGrouping implements Callable<Integer> {
     @GraphDatabase
     private Pantools pantools;
 
-    @Option(names = {"-v", "--grouping-version"})
+    @Option(names = {"-v", "--grouping-version"}, required = true)
     @Pattern(regexp = "[0-9]+|all|all-inactive", flags = CASE_INSENSITIVE, message = "{pattern.grouping-version}")
     String groupingVersion;