dcm4che-tools-common: Patch Apache CLI PosixParser to recognize '--' as end of the options mark

dcm4che-tool/dcm4che-tool-common/src/main/java/org/dcm4che3/tool/common/CLIUtils.java

@@ -54,7 +54,6 @@
 import org.apache.commons.cli.OptionGroup;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
 import org.dcm4che3.data.Tag;
 import org.dcm4che3.data.UID;
 import org.dcm4che3.data.Attributes;
@@ -341,7 +340,7 @@ public static void addPriorityOption(Options opts) {
 
     public static CommandLine parseComandLine(String[] args, Options opts, 
             ResourceBundle rb2, Class<?> clazz) throws ParseException {
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DetectEndOfOptionsPosixParser();
         CommandLine cl = parser.parse(opts, args);
         if (cl.hasOption("h")) {
             HelpFormatter formatter = new HelpFormatter();

dcm4che-tool/dcm4che-tool-common/src/main/java/org/dcm4che3/tool/common/DetectEndOfOptionsPosixParser.java

@@ -0,0 +1,64 @@
+/*
+ * Version: MPL 1.1/GPL 2.0/LGPL 2.1
+ *
+ *  The contents of this file are subject to the Mozilla Public License Version
+ *  1.1 (the "License"); you may not use this file except in compliance with
+ *  the License. You may obtain a copy of the License at
+ *  http://www.mozilla.org/MPL/
+ *
+ *  Software distributed under the License is distributed on an "AS IS" basis,
+ *  WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
+ *  for the specific language governing rights and limitations under the
+ *  License.
+ *
+ *  The Original Code is part of dcm4che, an implementation of DICOM(TM) in
+ *  Java(TM), hosted at https://github.com/gunterze/dcm4che.
+ *
+ *  The Initial Developer of the Original Code is
+ *  J4Care.
+ *  Portions created by the Initial Developer are Copyright (C) 2015-2017
+ *  the Initial Developer. All Rights Reserved.
+ *
+ *  Contributor(s):
+ *  See @authors listed below
+ *
+ *  Alternatively, the contents of this file may be used under the terms of
+ *  either the GNU General Public License Version 2 or later (the "GPL"), or
+ *  the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
+ *  in which case the provisions of the GPL or the LGPL are applicable instead
+ *  of those above. If you wish to allow use of your version of this file only
+ *  under the terms of either the GPL or the LGPL, and not to allow others to
+ *  use your version of this file under the terms of the MPL, indicate your
+ *  decision by deleting the provisions above and replace them with the notice
+ *  and other provisions required by the GPL or the LGPL. If you do not delete
+ *  the provisions above, a recipient may use your version of this file under
+ *  the terms of any one of the MPL, the GPL or the LGPL.
+ *
+ */
+
+package org.dcm4che3.tool.common;
+
+import org.apache.commons.cli.*;
+
+import java.util.Arrays;
+import java.util.Properties;
+
+/**
+ * @author Gunter Zeilinger <gunterze@gmail.com>
+ * @since Jun 2017
+ */
+public class DetectEndOfOptionsPosixParser extends PosixParser {
+
+    @Override
+    public CommandLine parse(Options opts, String[] args, Properties props, boolean stopAtNonOption)
+            throws ParseException {
+        int i = args.length;
+        while (--i >= 0 && !"--".equals(args[i]))
+            ;
+        CommandLine cl = super.parse(opts, i < 0 ? args : Arrays.copyOf(args, i), props, stopAtNonOption);
+        if (i >= 0)
+            while (++i < args.length)
+                cl.getArgList().add(args[i]);
+        return cl;
+    }
+}

dcm4che-tool/dcm4che-tool-findscu/src/main/resources/org/dcm4che3/tool/findscu/messages.properties

@@ -1,4 +1,4 @@
-usage=findscu [options] -c <aet>@<host>:<port> [dcmfile_in...]
+usage=findscu [options] -c <aet>@<host>:<port> [--] [<dicom-file>|<xml-file>...]
 try=Try `findscu --help' for more information.
 description=\n\
 The findscu application implements a Service Class User (SCU) for the \
@@ -7,7 +7,7 @@ Procedure Step, the Hanging Protocol Query/Retrieve and the Color Palette \
 Query/Retrieve Service Class. findscu only supports query functionality using \
 the C-FIND message. It sends query keys to an Service Class Provider (SCP) \
 and waits for responses. Query keys can be specified in DICOM binary file(s) \
-dcmfile_in or xml file(s) dcmfile_in.xml or by options -m and -r. \
+or DICOM XML file(s) -- <dicom-file>|<xml-file>... or by options -m and -r. \
 For reference, sample files (patient.xml, study.xml, series.xml, instance.xml, mwl.xml) \
 with query keys on PATIENT, STUDY, SERIES, IMAGE and MWL levels \
 are provided in etc/findscu folder. \n\-\n\
@@ -17,7 +17,7 @@ Example 1: findscu -c DCMQRSCP@localhost:11112 -m PatientName=Doe^John -m StudyD
 -m ModalitiesInStudy=CT\n\
 => Query Query/Retrieve Service Class Provider DCMQRSCP listening on local port 11112 for CT Studies \
 for Patient John Doe since 2011-05-10 \n\-\n\
-Example 2: findscu -c DCMQRSCP@localhost:11112 /etc/findscu/study.xml \n\
+Example 2: findscu -c DCMQRSCP@localhost:11112 -- /etc/findscu/study.xml \n\
 => Query Query/Retrieve Service Class Provider DCMQRSCP listening on local port 11112 with query keys \
 provided in /etc/findscu/study.xml file
 model=specifies Information Model. Supported names: PatientRoot, StudyRoot, PatientStudyOnly, \

dcm4che-tool/dcm4che-tool-movescu/src/main/resources/org/dcm4che3/tool/movescu/messages.properties

@@ -1,12 +1,12 @@
-usage=movescu [options] -c <aet>@<host>:<port> --dest <aet> [dcmfile_in...]
+usage=movescu [options] -c <aet>@<host>:<port> --dest <aet> [--] [<dicom-file>...]
 try=Try `movescu --help' for more information.
 description=\n\
 The movescu application implements a Service Class User (SCU) for the Query/Retrieve, the \
 Composite Instance Root Retrieve, the Composite Instance Retrieve Without Bulk Data, the \
 Hanging Protocol Query/Retrieve and the Color Palette Query/Retrieve Service Class. movescu \
 only supports retrieve functionality using the C-MOVE message. It sends matching keys to an \
 Service Class Provider (SCP) and waits for responses. Matching keys can be specified in \
-DICOM file(s) dcmfile_in or by options -m.\n\-\n\
+DICOM file(s) -- <dicom-file>... or by options -m.\n\-\n\
 Options:
 example=-\n\
 Examples:\n\