allow ignoring SRAnonTool if explicitly specified

Author: rkm

README.md

@@ -19,7 +19,7 @@ Required arguments:
   can be found
   [here](https://github.com/johnperry/CTP/tree/master/source/files/profiles/dicom)
 - `-s` / `--sr-anon-tool`: Path to the
-  [SRAnonTool](https://github.com/SMI/SmiServices/tree/master/src/applications/SRAnonTool)
+  [SRAnonTool](https://github.com/SMI/SmiServices/tree/master/src/applications/SRAnonTool). Can be set to `false` if SR anonymisation is being performed elsewhere.
 
 Optional arguments:
 

src/main/java/uk/ac/ed/epcc/ctp_anon_cli/Program.java

@@ -61,10 +61,14 @@ public static void main(String[] args) throws ParseException {
       "Cannot find anonymisation script file"
     );
 
-    File srAnonTool = new File(Paths.get(cli.getOptionValue("s")).toString());
-    if (!srAnonTool.isFile()) throw new IllegalArgumentException(
-      "Cannot find SRAnonTool"
-    );
+    File srAnonTool = null;
+    String srAnonToolPath = cli.getOptionValue("s");
+    if (!srAnonToolPath.toLowerCase().equals("false")) {
+      srAnonTool = new File(Paths.get(srAnonToolPath).toString());
+      if (!srAnonTool.isFile()) {
+        throw new IllegalArgumentException("Cannot find SRAnonTool");
+      }
+    }
 
     List<String> files = cli.getArgList();
     boolean runAsDaemon = false;

src/main/java/uk/ac/ed/epcc/ctp_anon_cli/SmiCtpProcessor.java

@@ -129,7 +129,7 @@ public void anonymizeImpl(File inFile, File outFile) throws Exception {
     }
 
     // Structured Reports have an additional anonymisation step
-    if (!isSR) return;
+    if (!isSR || _srAnonTool == null) return;
 
     String commandArray[] = {
       _srAnonTool.getAbsolutePath(),