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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:42:15 UTC

[8/8] incubator-taverna-commandline git commit: temporarily empty repository

temporarily empty repository

.. as Software Grant is not yet formally on file


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/d57ed128
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/d57ed128
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/d57ed128

Branch: refs/heads/master
Commit: d57ed128cd36e12f5cc1e3304f67bd5c10f0735c
Parents: e25a5dc
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 17 20:41:52 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 17 20:41:52 2015 +0000

----------------------------------------------------------------------
 .gitignore                                      |  24 -
 .travis.yml                                     |   1 -
 README.md                                       |   6 -
 pom.xml                                         |  40 --
 taverna-commandline-api/pom.xml                 |  12 -
 .../exceptions/ArgumentsParsingException.java   |  34 -
 .../CommandLineMasterPasswordException.java     |  34 -
 .../DatabaseConfigurationException.java         |  43 --
 .../exceptions/InputMismatchException.java      |  61 --
 .../exceptions/InvalidOptionException.java      |  30 -
 .../exceptions/OpenDataflowException.java       |  44 --
 .../exceptions/ReadInputException.java          |  35 -
 .../exceptions/SaveResultsException.java        |  34 -
 .../commandline/options/CommandLineOptions.java | 119 ----
 taverna-commandline-common/pom.xml              |  88 ---
 .../CommandLineMasterPasswordProvider.java      | 184 ------
 .../taverna/t2/commandline/CommandLineTool.java | 437 -------------
 .../data/DatabaseConfigurationHandler.java      | 154 -----
 .../t2/commandline/data/ErrorValueHandler.java  |  72 ---
 .../t2/commandline/data/InputsHandler.java      | 280 --------
 .../t2/commandline/data/SaveResultsHandler.java |  87 ---
 .../taverna-commandline-common-context-osgi.xml |  22 -
 .../taverna-commandline-common-context.xml      |  21 -
 .../main/resources/database-defaults.properties |  11 -
 .../src/main/resources/help.txt                 |  87 ---
 .../TestDatabaseConfigurationHandler.java       |  21 -
 taverna-commandline-launcher/pom.xml            |  83 ---
 .../commandline/CommandLineOptionsImpl.java     | 445 -------------
 .../taverna/commandline/TavernaCommandLine.java | 143 ----
 .../src/main/resources/help.txt                 |  87 ---
 .../TestCommandLineOptionsHandler.java          | 267 --------
 taverna-commandline-product/pom.xml             | 529 ---------------
 .../main/assembly/dependencies-component.xml    |  21 -
 .../src/main/assembly/developer-assembly.xml    |  13 -
 .../src/main/assembly/nightly-assembly.xml      |  15 -
 .../src/main/assembly/release-assembly.xml      |  15 -
 .../src/main/etc/conf/log4j.properties          |  14 -
 .../src/main/etc/conf/logging.properties        |  10 -
 .../src/main/etc/conf/taverna.app.properties    |   2 -
 .../src/main/etc/executeworkflow.bat            |  17 -
 .../src/main/etc/executeworkflow.sh             |  25 -
 taverna-commandline-tests/pom.xml               |  71 --
 .../commandline/TavernaCommandLineTest.java     | 485 --------------
 .../taverna/commandline/WorkflowTestRunner.java |  70 --
 .../taverna/commandline/WorkflowTestSuite.java  |  79 ---
 .../biomartandembossanalysis.url                |   1 -
 .../biomartandembossanalysis/ignorePort         |   1 -
 .../biomoby_tutorial_workflow.url               |   1 -
 .../biomoby_tutorial_workflow/ignorePort        |   1 -
 .../biomoby_tutorial_workflow/inputs/id         |   1 -
 .../biomoby_tutorial_workflow/inputs/namespace  |   1 -
 .../demonstration_of_configurable_iteration.url |   1 -
 .../ebi_interproscan_newservices.url            |   1 -
 .../ebi_interproscan_newservices/ignorePort     |   1 -
 .../ebi_interproscan_newservices/inputs/email   |   1 -
 .../inputs/sequence                             |   8 -
 .../example_of_conditional_invocation.url       |   1 -
 .../inputs/condition                            |   1 -
 .../example_of_explicit_looping.url             |   1 -
 .../example_of_explicit_looping/inputs/end      |   1 -
 .../example_of_explicit_looping/inputs/start    |   1 -
 .../example_of_explicit_looping/inputs/step     |   1 -
 ...e_workflow_for_rest_and_xpath_activities.url |   1 -
 .../Name_Of_Location_for_Weather_Forecast       |   1 -
 .../fetch_dragon_images_from_biomoby.url        |   1 -
 .../fetch_pdb_flatfile_from_rcsb_server.url     |   1 -
 .../inputs/pdbID                                |   1 -
 .../fetch_today_s_xkcd_comic.url                |   1 -
 .../myexperiment/gbseq_test/gbseq_test.url      |   1 -
 .../myexperiment/hello_anyone/hello_anyone.url  |   1 -
 .../myexperiment/hello_anyone/inputs/name       |   1 -
 .../myexperiment/hello_world/hello_world.url    |   1 -
 .../pipelined_list_iteration/inputs/input       |   1 -
 .../pipelined_list_iteration.url                |   1 -
 .../retrieve_sequence_in_embl_format.url        |   1 -
 .../secure_rest_service_call_example.url        |   1 -
 .../secure_web_service_call_example.url         |   1 -
 .../spreadsheed_data_import_example.url         |   1 -
 .../unix_external_tools_with_zip_and_unzip.url  |   1 -
 .../unix_numerically_adding_two_values/inputs/a |   1 -
 .../unix_numerically_adding_two_values/inputs/b |   1 -
 .../unix_numerically_adding_two_values.url      |   1 -
 ...ix_tool_service_using_string_replacement.url |   1 -
 .../src/test/resources/security/t2keystore.ubr  | Bin 3312 -> 0 bytes
 .../test/resources/security/t2truststore.ubr    | Bin 213408 -> 0 bytes
 .../resources/security/taverna-keystore.ubr     | Bin 3312 -> 0 bytes
 .../resources/security/taverna-truststore.ubr   | Bin 213408 -> 0 bytes
 .../workflows/apiconsumer/apiconsumer.t2flow    | 178 -----
 .../resources/workflows/apiconsumer/inputs/in   |   1 -
 .../workflows/beanshell/beanshell.t2flow        | 137 ----
 .../resources/workflows/beanshell/inputs/in     |   1 -
 .../resources/workflows/biomart/biomart.t2flow  |  30 -
 .../workflows/dataflow/dataflow.t2flow          | 217 -------
 .../test/resources/workflows/dataflow/inputs/in |   1 -
 .../resources/workflows/in-out/in-out.t2flow    |  12 -
 .../test/resources/workflows/in-out/inputs/in   |   1 -
 .../resources/workflows/iteration/inputs/in     |   1 -
 .../workflows/iteration/iteration.t2flow        | 474 --------------
 .../resources/workflows/localworker/inputs/in   |   1 -
 .../workflows/localworker/localworker.t2flow    |  67 --
 .../test/resources/workflows/rest/rest.t2flow   | 154 -----
 .../secure-basic-authentication-https.t2flow    |  74 ---
 .../secure-basic-authentication.t2flow          |  74 ---
 ...cure-client-cert-authentication-https.t2flow | 162 -----
 .../secure-digest-authentication-https.t2flow   | 107 ---
 .../secure-digest-authentication.t2flow         | 129 ----
 .../secure-ws-https/secure-ws-https.t2flow      | 180 ------
 .../workflows/secure-ws/secure-ws.t2flow        | 180 ------
 .../workflows/secure-wsdl/secure-wsdl.t2flow    | 131 ----
 .../resources/workflows/soaplab/soaplab.t2flow  |  84 ---
 .../spreadsheetimport/spreadsheetimport.t2flow  | 646 -------------------
 .../stringconstant/stringconstant.t2flow        |  32 -
 .../test/resources/workflows/tool/tool.t2flow   | 158 -----
 .../test/resources/workflows/wsdl/wsdl.t2flow   |  22 -
 .../resources/workflows/xmlSplitter/inputs/age  |   1 -
 .../workflows/xmlSplitter/inputs/firstName      |   1 -
 .../workflows/xmlSplitter/inputs/lastName       |   1 -
 .../workflows/xmlSplitter/xmlSplitter.t2flow    | 339 ----------
 .../test/resources/workflows/xpath/xpath.t2flow | 127 ----
 119 files changed, 8140 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index bcd653c..0000000
--- a/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# Apache Taverna Commandline
-
-[![Build Status](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline.svg)](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline)
-
-After building, see taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT-dev/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT/ or equivalent
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 0355623..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>org.apache.taverna</groupId>
-		<artifactId>taverna-parent</artifactId>
-		<version>1-incubating-SNAPSHOT</version>
-	</parent>
-	<groupId>org.apache.taverna.commandline</groupId>
-	<artifactId>taverna-commandline</artifactId>
-	<version>3.1.0.incubating-SNAPSHOT</version>
-	<packaging>pom</packaging>
-	<name>Apache Taverna Command Line</name>
-  <properties>
-    <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
-    <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
-    <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
-    <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
-  </properties>
-	<modules>
-    <module>taverna-commandline-api</module>
-    <module>taverna-commandline-common</module>
-    <module>taverna-commandline-launcher</module>
-    <module>taverna-commandline-product</module>
-    <!--
-    <module>taverna-commandline-tests</module>
-    -->
-  </modules>
-  <repositories>
-    <repository>
-      <id>taverna-incubating</id>
-      <name>Apache Taverna incubating Repository</name>
-        <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
-      <releases>
-        <enabled>false</enabled>
-      </releases>
-      <snapshots />
-    </repository>
-  </repositories>
-</project>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
deleted file mode 100644
index 98ae247..0000000
--- a/taverna-commandline-api/pom.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>org.apache.taverna.commandline</groupId>
-		<artifactId>taverna-commandline</artifactId>
-		<version>3.1.0.incubating-SNAPSHOT</version>
-	</parent>
-	<packaging>bundle</packaging>
-	<artifactId>taverna-commandline-api</artifactId>
-	<name>Apache Taverna Commandline API</name>
-</project>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
deleted file mode 100644
index eb21cd7..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@SuppressWarnings("serial")
-public class ArgumentsParsingException extends Exception {
-
-	public ArgumentsParsingException(String message) {
-		super(message);
-	}
-	
-	public ArgumentsParsingException(String message, Throwable cause) {
-		super(message, cause);
-	}
-}
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
deleted file mode 100644
index 0714275..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@SuppressWarnings("serial")
-public class CommandLineMasterPasswordException extends Exception {
-
-	public CommandLineMasterPasswordException(String message) {
-		super(message);
-	}
-	
-	public CommandLineMasterPasswordException(String message, Throwable cause) {
-		super(message, cause);
-	}
-}
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
deleted file mode 100644
index 616fb70..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class DatabaseConfigurationException extends Exception {
-	
-	private static final long serialVersionUID = -4128248547532355697L;
-
-	public DatabaseConfigurationException() {
-
-	}
-
-	public DatabaseConfigurationException(String message) {
-		super(message);
-	}
-
-	public DatabaseConfigurationException(Throwable cause) {
-		super(cause);
-	}
-
-	public DatabaseConfigurationException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
deleted file mode 100644
index da03891..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-import java.util.Set;
-
-public class InputMismatchException extends InvalidOptionException {	
-	
-	private static final long serialVersionUID = -5368068332397293706L;
-	private final Set<String> expectedInputNames;
-	private final Set<String> providedInputNames;
-	
-	public InputMismatchException(String msg, Set<String> expectedInputNames, Set<String> providedInputNames) {
-		super(msg);
-		this.expectedInputNames = expectedInputNames;
-		this.providedInputNames = providedInputNames;				
-	}
-
-	public String getMessage() {
-		String result = super.getMessage();
-		
-		if (expectedInputNames != null){
-			result += "\n" + expectedInputNames.size() + " inputs were expected";
-			if (expectedInputNames.size()>0) result += " which are:\n";
-			for (String name : expectedInputNames) {
-				result += "'"+name+"' ";			
-			}			
-		}
-		
-		if (providedInputNames != null){
-			result += "\n" + providedInputNames.size()
-					+ " inputs were provided";
-			if (providedInputNames.size() > 0)
-				result += " which are:\n";
-			for (String name : providedInputNames) {
-				result += "'" + name + "' ";
-			}
-		}
-		return result;
-	}
-	
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
deleted file mode 100644
index c07a19f..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class InvalidOptionException extends Exception {
-
-	private static final long serialVersionUID = 2467409785164223258L;
-
-	public InvalidOptionException(String message) {
-		super(message);
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
deleted file mode 100644
index 664ab71..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class OpenDataflowException extends Exception {
-
-	
-	private static final long serialVersionUID = 4778578311101082197L;
-
-	public OpenDataflowException() {
-		
-	}
-
-	public OpenDataflowException(String message) {
-		super(message);	
-	}
-
-	public OpenDataflowException(Throwable cause) {
-		super(cause);
-	}
-
-	public OpenDataflowException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
deleted file mode 100644
index 226d6ea..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class ReadInputException extends Exception {
-		
-	private static final long serialVersionUID = -3494432791254643055L;
-
-	public ReadInputException(String msg) {
-		super(msg); 
-	}
-	
-	public ReadInputException(String msg, Throwable e) {
-		super(msg,e); 
-	}
-	
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
deleted file mode 100644
index 7ad460d..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-@SuppressWarnings("serial")
-public class SaveResultsException extends Exception {
-
-	public SaveResultsException(String message) {
-		super(message);
-	}
-	
-	public SaveResultsException(String message, Throwable cause) {
-		super(message, cause);
-	}
-}
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
deleted file mode 100644
index dd8e20f..0000000
--- a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2013 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.options;
-
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-
-/**
- *
- *
- * @author David Withers
- */
-public interface CommandLineOptions {
-
-	public static final String CREDENTIAL_MANAGER_DIR_OPTION = "cmdir";
-	public static final String CREDENTIAL_MANAGER_PASSWORD_OPTION = "cmpassword";
-
-	public boolean askedForHelp();
-
-	public boolean isProvenanceEnabled();
-
-	public void displayHelp();
-
-	public void displayHelp(boolean showFullText);
-
-	public String[] getArgs();
-
-	/**
-	 *
-	 * @return the port that the database should run on
-	 */
-	public String getDatabasePort();
-
-	/**
-	 *
-	 * @return a path to a properties file that contains database configuration
-	 *         settings
-	 */
-	public String getDatabaseProperties();
-
-	/**
-	 * Returns an array that alternates between a portname and path to a file
-	 * containing the input values. Therefore the array will always contain an
-	 * even number of elements
-	 *
-	 * @return an array of portname and path to files containing individual
-	 *         inputs.
-	 */
-	public String[] getInputFiles();
-
-	public String[] getInputValues();
-
-	public String getLogFile();
-
-	/**
-	 *
-	 * @return the directory to write the results to
-	 */
-	public String getOutputDirectory();
-
-	public boolean getStartDatabase();
-
-	/**
-	 * @return the directory with Credential Manager's files
-	 */
-	public String getCredentialManagerDir();
-
-	public boolean getStartDatabaseOnly() throws InvalidOptionException;
-
-	public String getWorkflow() throws InvalidOptionException;
-
-	public boolean hasDelimiterFor(String inputName);
-
-	public boolean hasInputFiles();
-
-	public boolean hasInputValues();
-
-	public boolean hasLogFile();
-
-	public boolean hasOption(String option);
-	
-	public boolean hasSaveResultsToBundle() ;
-
-	public String inputDelimiter(String inputName);
-
-	public boolean isClientServer();
-
-	public boolean isEmbedded();
-
-	public boolean isInMemory();
-
-	/**
-	 * Save the results to a directory if -outputdir has been explicitly defined,
-	 * or if -outputdoc has not been defined.
-	 *
-	 * @return boolean
-	 */
-	public boolean saveResultsToDirectory();
-
-	public String saveResultsToBundle();
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
deleted file mode 100644
index 17c6a42..0000000
--- a/taverna-commandline-common/pom.xml
+++ /dev/null
@@ -1,88 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>org.apache.taverna.commandline</groupId>
-		<artifactId>taverna-commandline</artifactId>
-		<version>3.1.0.incubating-SNAPSHOT</version>
-	</parent>
-	<artifactId>taverna-commandline-common</artifactId>
-	<packaging>bundle</packaging>
-	<name>Apache Taverna Commandline Common</name>
-	<dependencies>
-		<dependency>
-			<groupId>${project.parent.groupId}</groupId>
-			<artifactId>taverna-commandline-api</artifactId>
-			<version>${project.parent.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.apache.taverna.engine</groupId>
-			<artifactId>taverna-run-api</artifactId>
-			<version>${taverna.engine.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.taverna.engine</groupId>
-			<artifactId>taverna-database-configuration-api</artifactId>
-			<version>${taverna.engine.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.apache.taverna.language</groupId>
-			<artifactId>taverna-scufl2-api</artifactId>
-			<version>${taverna.language.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.taverna.language</groupId>
-			<artifactId>taverna-scufl2-validation</artifactId>
-			<version>${taverna.language.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.taverna.language</groupId>
-			<artifactId>taverna-scufl2-validation-structural</artifactId>
-			<version>${taverna.language.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.taverna.language</groupId>
-			<artifactId>taverna-scufl2-validation-correctness</artifactId>
-			<version>${taverna.language.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.taverna.language</groupId>
-			<artifactId>taverna-databundle</artifactId>
-			<version>${taverna.language.version}</version>
-		</dependency>
-
-<!--
-		<dependency>
-			<groupId>org.apache.taverna.engine</groupId>
-			<artifactId>provenanceconnector</artifactId>
-			<version>${taverna.engine.version}</version>
-		</dependency>
- -->
-		<dependency>
-			<groupId>org.apache.taverna.engine</groupId>
-			<artifactId>taverna-credential-manager</artifactId>
-			<version>${taverna.engine.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-			<version>${commons.io.version}</version>
-		</dependency>
-
-		<!-- <dependency> <groupId>uk.org.mygrid.resources.mimeutil</groupId> <artifactId>mime-util</artifactId>
-			<version>2.1.2-2</version> </dependency> -->
-
-		<!-- TEST -->
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>${junit.version}</version>
-			<scope>test</scope>
-		</dependency>
-
-	</dependencies>
-
-</project>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
deleted file mode 100644
index 048e582..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
+++ /dev/null
@@ -1,184 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2008-2010 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.io.BufferedReader;
-import java.io.Console;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-
-import net.sf.taverna.t2.commandline.exceptions.CommandLineMasterPasswordException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider;
-
-import org.apache.log4j.Logger;
-
-/**
- * An implementation of {@link MasterPasswordProvider} that reads Credential Manager's
- * master password from stdin (pipe or terminal) is -cmpassword option is present in command
- * line arguments. Otherwise it tries to read it from a special file password.txt in a special
- * directory specified by -cmdir option, if present.
- *
- * @author Alex Nenadic
- */
-public class CommandLineMasterPasswordProvider implements MasterPasswordProvider {
-
-	private static final String CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION = "cmpassword";
-	private static final String CREDENTIAL_MANAGER_DIRECTORY_OPTION = "cmdir";
-
-	private static Logger logger = Logger.getLogger(CommandLineMasterPasswordProvider.class);
-
-	private String masterPassword = null;
-	private int priority = 200;
-
-	private boolean finishedReadingPassword = false;
-	private final CommandLineOptions commandLineOptions;
-
-	public CommandLineMasterPasswordProvider(CommandLineOptions commandLineOptions) {
-		this.commandLineOptions = commandLineOptions;
-	}
-
-	@Override
-	public String getMasterPassword(boolean firstTime) {
-		if (!finishedReadingPassword) {
-			// -cmpassword option was present in the command line arguments
-			if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION)) {
-				// Try to read the password from stdin (terminal or pipe)
-				try {
-					masterPassword = getCredentialManagerPasswordFromStdin();
-				} catch (CommandLineMasterPasswordException e) {
-					masterPassword = null;
-				}
-			}
-			// -cmpassword option was not present in the command line arguments
-			// and -cmdir option was there - try to get the master password from
-			// the "special" password file password.txt inside the Cred. Manager directory.
-			else {
-				if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
-					// Try to read the password from a special file located in
-					// Credential Manager directory (if the dir was not null)
-					try {
-						masterPassword = getCredentialManagerPasswordFromFile();
-					} catch (CommandLineMasterPasswordException ex) {
-						masterPassword = null;
-					}
-				}
-			}
-			finishedReadingPassword = true; // we do not want to attempt to read from stdin several
-											// times
-		}
-		return masterPassword;
-	}
-
-	public void setMasterPassword(String masterPassword) {
-		this.masterPassword = masterPassword;
-		finishedReadingPassword = true;
-	}
-
-	@Override
-	public int getProviderPriority() {
-		return priority;
-	}
-
-	private String getCredentialManagerPasswordFromStdin()
-			throws CommandLineMasterPasswordException {
-
-		String password = null;
-
-		Console console = System.console();
-
-		if (console == null) { // password is being piped in, not entered in the terminal by user
-			BufferedReader buffReader = null;
-			try {
-				buffReader = new BufferedReader(new InputStreamReader(System.in));
-				password = buffReader.readLine();
-			} catch (IOException ex) {
-				// For some reason the error of the exception thrown
-				// does not get printed from the Launcher so print it here as
-				// well as it gives more clue as to what is going wrong.
-				logger.error(
-						"An error occured while trying to read Credential Manager's password that was piped in: "
-								+ ex.getMessage(), ex);
-				throw new CommandLineMasterPasswordException(
-						"An error occured while trying to read Credential Manager's password that was piped in: "
-								+ ex.getMessage(), ex);
-			} finally {
-				try {
-					buffReader.close();
-				} catch (Exception ioe1) {
-					// Ignore
-				}
-			}
-		} else { // read the password from the terminal as entered by the user
-			try {
-				// Block until user enters password
-				char passwordArray[] = console.readPassword("Password for Credential Manager: ");
-				if (passwordArray != null) { // user did not abort input
-					password = new String(passwordArray);
-				} // else password will be null
-
-			} catch (Exception ex) {
-				// For some reason the error of the exception thrown
-				// does not get printed from the Launcher so print it here as
-				// well as it gives more clue as to what is going wrong.
-				logger.error(
-						"An error occured while trying to read Credential Manager's password from the terminal: "
-								+ ex.getMessage(), ex);
-				throw new CommandLineMasterPasswordException(
-						"An error occured while trying to read Credential Manager's password from the terminal: "
-								+ ex.getMessage(), ex);
-			}
-		}
-		return password;
-	}
-
-	private String getCredentialManagerPasswordFromFile() throws CommandLineMasterPasswordException {
-		String password = null;
-		if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
-			String cmDir = commandLineOptions.getCredentialManagerDir();
-
-			File passwordFile = new File(cmDir, "password.txt");
-			BufferedReader buffReader = null;
-			try {
-				buffReader = new BufferedReader(new FileReader(passwordFile));
-				password = buffReader.readLine();
-			} catch (IOException ioe) {
-				// For some reason the error of the exception thrown
-				// does not get printed from the Launcher so print it here as
-				// well as it gives more clue as to what is going wrong.
-				logger.error("There was an error reading the Credential Manager password from "
-						+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
-				throw new CommandLineMasterPasswordException(
-						"There was an error reading the Credential Manager password from "
-								+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
-			} finally {
-				try {
-					buffReader.close();
-				} catch (Exception ioe1) {
-					// Ignore
-				}
-			}
-		}
-		return password;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
deleted file mode 100644
index 368527d..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
+++ /dev/null
@@ -1,437 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.data.InputsHandler;
-import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.security.credentialmanager.CMException;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
-import org.apache.log4j.PatternLayout;
-import org.apache.log4j.PropertyConfigurator;
-import org.apache.log4j.RollingFileAppender;
-import org.purl.wf4ever.robundle.Bundle;
-
-import uk.org.taverna.configuration.database.DatabaseConfiguration;
-import uk.org.taverna.configuration.database.DatabaseManager;
-import uk.org.taverna.databundle.DataBundles;
-import uk.org.taverna.platform.execution.api.ExecutionEnvironment;
-import uk.org.taverna.platform.execution.api.InvalidExecutionIdException;
-import uk.org.taverna.platform.execution.api.InvalidWorkflowException;
-import uk.org.taverna.platform.report.State;
-import uk.org.taverna.platform.report.WorkflowReport;
-import uk.org.taverna.platform.run.api.InvalidRunIdException;
-import uk.org.taverna.platform.run.api.RunProfile;
-import uk.org.taverna.platform.run.api.RunProfileException;
-import uk.org.taverna.platform.run.api.RunService;
-import uk.org.taverna.platform.run.api.RunStateException;
-import uk.org.taverna.scufl2.api.common.NamedSet;
-import uk.org.taverna.scufl2.api.container.WorkflowBundle;
-import uk.org.taverna.scufl2.api.core.Workflow;
-import uk.org.taverna.scufl2.api.io.ReaderException;
-import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
-import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
-import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
-import uk.org.taverna.scufl2.validation.ValidationException;
-import uk.org.taverna.scufl2.validation.correctness.CorrectnessValidator;
-import uk.org.taverna.scufl2.validation.correctness.ReportCorrectnessValidationListener;
-import uk.org.taverna.scufl2.validation.structural.ReportStructuralValidationListener;
-import uk.org.taverna.scufl2.validation.structural.StructuralValidator;
-
-/**
- * A utility class that wraps the process of executing a workflow, allowing workflows to be easily
- * executed independently of the GUI.
- *
- * @author Stuart Owen
- * @author Alex Nenadic
- */
-public class CommandLineTool {
-	private static boolean BOOTSTRAP_LOGGING = false;
-	private static Logger logger = Logger.getLogger(CommandLineTool.class);
-
-	private RunService runService;
-	private CredentialManager credentialManager;
-	private CommandLineOptions commandLineOptions;
-	private WorkflowBundle workflowBundle;
-	private WorkflowBundleIO workflowBundleIO;
-	private DatabaseConfiguration databaseConfiguration;
-	private DatabaseManager databaseManager;
-
-	public void run() {
-		try {
-			if (BOOTSTRAP_LOGGING)
-				initialiseLogging();
-			int result = setupAndExecute();
-			System.exit(result);
-		} catch (InvalidOptionException | IOException | ReadInputException
-				| InvalidRunIdException | RunStateException
-				| InvalidExecutionIdException | OpenDataflowException
-				| RunProfileException e) {
-			error(e.getMessage());
-		} catch (CMException e) {
-			error("There was an error initializing Taverna's SSLSocketFactory from Credential Manager. "
-					+ e.getMessage());
-		} catch (ReaderException e) {
-			error("There was an error reading the workflow: " + e.getMessage());
-		} catch (ValidationException e) {
-			error("There was an error validating the workflow: " + e.getMessage());
-		} catch (InvalidWorkflowException e) {
-			error("There was an error validating the workflow: " + e.getMessage());
-		} catch (DatabaseConfigurationException e) {
-			error("There was an error configuring the database: " + e.getMessage());
-		}
-		System.exit(1);
-	}
-
-	private void initialiseLogging() {
-		LogManager.resetConfiguration();
-
-		if (System.getProperty("log4j.configuration") == null) {
-			try {
-				PropertyConfigurator.configure(CommandLineTool.class.getClassLoader()
-						.getResource("cl-log4j.properties").toURI().toURL());
-			} catch (MalformedURLException e) {
-				logger.error("There was a serious error reading the default logging configuration",
-						e);
-			} catch (URISyntaxException e) {
-				logger.error("There was a serious error reading the default logging configuration",
-						e);
-			}
-
-		} else {
-			PropertyConfigurator.configure(System.getProperty("log4j.configuration"));
-		}
-
-		if (commandLineOptions.hasLogFile()) {
-			RollingFileAppender appender;
-			try {
-
-				PatternLayout layout = new PatternLayout("%-5p %d{ISO8601} (%c:%L) - %m%n");
-				appender = new RollingFileAppender(layout, commandLineOptions.getLogFile());
-				appender.setMaxFileSize("1MB");
-				appender.setEncoding("UTF-8");
-				appender.setMaxBackupIndex(4);
-				// Let root logger decide level
-				appender.setThreshold(Level.ALL);
-				LogManager.getRootLogger().addAppender(appender);
-			} catch (IOException e) {
-				System.err.println("Could not log to " + commandLineOptions.getLogFile());
-			}
-		}
-	}
-
-	public int setupAndExecute() throws InputMismatchException, InvalidOptionException,
-			CMException, OpenDataflowException, ReaderException, IOException, ValidationException,
-			ReadInputException, InvalidWorkflowException, RunProfileException,
-			InvalidRunIdException, RunStateException, InvalidExecutionIdException, DatabaseConfigurationException {
-
-		if (!commandLineOptions.askedForHelp()) {
-			 setupDatabase(commandLineOptions);
-
-			if (commandLineOptions.getWorkflow() != null) {
-				
-				/* Set context class loader to us, 
-				 * so that things such as JSON-LD caching of
-				 * robundle works.
-				 */
-				
-				Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
-				
-				
-				/*
-				 * Initialise Credential Manager and SSL stuff quite early as
-				 * parsing and validating the workflow may require it
-				 */
-				String credentialManagerDirPath = commandLineOptions.getCredentialManagerDir();
-
-				/*
-				 * If credentialManagerDirPath is null, the Credential Manager
-				 * will be initialized from the default location in
-				 * <TAVERNA_HOME>/security somewhere inside user's home
-				 * directory. This should not be used when running command line
-				 * tool on a server and the Credential Manager dir path should
-				 * always be passed in as we do not want to store the security
-				 * files in user's home directory on the server (we do not even
-				 * know which user the command line tool will be running as).
-				 */
-				if (credentialManagerDirPath != null) {
-					credentialManager.setConfigurationDirectoryPath(new File(
-							credentialManagerDirPath));
-				}
-
-				// Initialise the SSL stuff - set the SSLSocketFactory
-				// to use Taverna's Keystore and Truststore.
-				credentialManager.initializeSSL();
-
-				URL workflowURL = readWorkflowURL(commandLineOptions.getWorkflow());
-
-				workflowBundle = workflowBundleIO.readBundle(workflowURL, null);
-
-				logger.debug("Read the wf bundle");
-
-				validateWorkflowBundle(workflowBundle);
-				logger.debug("Validated the wf bundle");
-
-
-				Set<ExecutionEnvironment> executionEnvironments = runService
-						.getExecutionEnvironments();
-
-				ExecutionEnvironment executionEnvironment = null;
-
-				/*
-				 * Find the right execution environment, e.g. local execution
-				 * with the correct reference service based on command line
-				 * options
-				 */
-				while (executionEnvironments.iterator().hasNext()) {
-					// TODO Choose the right one
-					// take the fist one for now
-					executionEnvironment = executionEnvironments.iterator().next();
-					break;
-				}
-
-				logger.debug("Got the execution environment");
-
-				InputsHandler inputsHandler = new InputsHandler();
-				Map<String, InputWorkflowPort> portMap = new HashMap<String, InputWorkflowPort>();
-
-				Workflow workflow = workflowBundle.getMainWorkflow();
-
-				for (InputWorkflowPort port : workflow.getInputPorts()) {
-					portMap.put(port.getName(), port);
-				}
-				inputsHandler.checkProvidedInputs(portMap, commandLineOptions);
-				logger.debug("Checked inputs");
-
-				Bundle inputs = inputsHandler.registerInputs(portMap, commandLineOptions, null);
-				logger.debug("Registered inputs");
-
-				RunProfile runProfile = new RunProfile(executionEnvironment, workflowBundle, inputs);
-
-				String runId = runService.createRun(runProfile);
-
-				runService.start(runId);
-				logger.debug("Started wf run");
-
-				WorkflowReport report = runService.getWorkflowReport(runId);
-
-				while (!workflowFinished(report)) {
-					try {
-						Thread.sleep(500);
-					} catch (InterruptedException e) {
-						System.err.println("Interrupted while waiting for workflow to finish");
-						return 1;
-					}
-				}
-
-				NamedSet<OutputWorkflowPort> workflowOutputPorts = workflow.getOutputPorts();
-				if (!workflowOutputPorts.isEmpty()) {
-					File outputDir = null;
-
-					if (commandLineOptions.saveResultsToDirectory()) {
-						outputDir = determineOutputDir(commandLineOptions, workflowBundle.getName());
-						outputDir.mkdirs();
-					}
-
-					Path outputs = DataBundles.getOutputs(runService.getDataBundle(runId));
-
-					if (outputDir != null) {
-						SaveResultsHandler saveResultsHandler = new SaveResultsHandler(outputDir);
-
-						for (OutputWorkflowPort outputWorkflowPort : workflowOutputPorts) {
-							String workflowOutputPortName = outputWorkflowPort.getName();
-							Path output = DataBundles.getPort(outputs, workflowOutputPortName);
-							if (!DataBundles.isMissing(output)) {
-								saveResultsHandler.saveResultsForPort(workflowOutputPortName, output);
-							}
-						}
-					}
-				}
-				if (commandLineOptions.saveResultsToBundle() != null) {
-					Path bundlePath = Paths.get(commandLineOptions.saveResultsToBundle());
-					DataBundles.closeAndSaveBundle(runService.getDataBundle(runId), bundlePath);
-					System.out.println("Workflow Run Bundle saved to: " + bundlePath.toAbsolutePath());
-				} else {
-					System.out.println("Workflow Run Bundle: " + runService.getDataBundle(runId).getSource());
-					// For debugging we'll leave it in /tmp for now
-					runService.getDataBundle(runId).setDeleteOnClose(false);
-					DataBundles.closeBundle(runService.getDataBundle(runId));
-				}
-
-				if (report.getState().equals(State.FAILED)) {
-					System.out.println("Workflow failed - see report below.");
-					System.out.println(report);
-				} else if (report.getState().equals(State.COMPLETED)) {
-					System.out.println("Workflow completed.");
-				}
-
-			}
-		} else {
-			commandLineOptions.displayHelp();
-		}
-
-		// wait until user hits CTRL-C before exiting
-		if (commandLineOptions.getStartDatabaseOnly()) {
-			// FIXME: need to do this more gracefully.
-			while (true) {
-				try {
-					Thread.sleep(500);
-				} catch (InterruptedException e) {
-					return 0;
-				}
-			}
-		}
-
-		return 0;
-	}
-
-	private boolean workflowFinished(WorkflowReport report) {
-		State state = report.getState();
-		if (state == State.CANCELLED || state == State.COMPLETED || state == State.FAILED) {
-			return true;
-		}
-		return false;
-	}
-
-	protected void validateWorkflowBundle(WorkflowBundle workflowBundle) throws ValidationException {
-		CorrectnessValidator cv = new CorrectnessValidator();
-		ReportCorrectnessValidationListener rcvl = new ReportCorrectnessValidationListener();
-		cv.checkCorrectness(workflowBundle, true, rcvl);
-		if (rcvl.detectedProblems()) {
-			throw rcvl.getException();
-		}
-
-		StructuralValidator sv = new StructuralValidator();
-		ReportStructuralValidationListener rsvl = new ReportStructuralValidationListener();
-		sv.checkStructure(workflowBundle, rsvl);
-		if (rsvl.detectedProblems()) {
-			throw rcvl.getException();
-		}
-	}
-
-	private void setupDatabase(CommandLineOptions options)
-			throws DatabaseConfigurationException {
-		DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
-				options, databaseConfiguration, databaseManager);
-		dbHandler.configureDatabase();
-		try {
-			if (!options.isInMemory())
-				dbHandler.testDatabaseConnection();
-		} catch (NamingException e) {
-			throw new DatabaseConfigurationException(
-					"There was an error trying to setup the database datasource: "
-							+ e.getMessage(), e);
-		} catch (SQLException e) {
-			if (options.isClientServer())
-				throw new DatabaseConfigurationException(
-						"There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
-						e);
-			if (options.isEmbedded())
-				throw new DatabaseConfigurationException(
-						"There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
-						e);
-		}
-	}
-
-	private File determineOutputDir(CommandLineOptions options, String dataflowName) {
-		File result = new File(dataflowName + "_output");
-		int x = 1;
-		while (result.exists()) {
-			result = new File(dataflowName + "_output_" + x);
-			x++;
-		}
-		System.out.println("Outputs will be saved to the directory: "
-				+ result.getAbsolutePath());
-		return result;
-	}
-
-	protected void error(String msg) {
-		System.err.println(msg);
-	}
-
-	private URL readWorkflowURL(String workflowOption) throws OpenDataflowException {
-		try {
-			return new URL(new URL("file:"), workflowOption);
-		} catch (MalformedURLException e) {
-			throw new OpenDataflowException("The was an error processing the URL to the workflow: "
-					+ e.getMessage(), e);
-		}
-	}
-
-	public void setCommandLineOptions(CommandLineOptions commandLineOptions){
-		this.commandLineOptions = commandLineOptions;
-	}
-
-	public void setRunService(RunService runService) {
-		this.runService = runService;
-	}
-
-	public void setCredentialManager(CredentialManager credentialManager) {
-		this.credentialManager = credentialManager;
-	}
-
-	public void setWorkflowBundleIO(WorkflowBundleIO workflowBundleIO) {
-		this.workflowBundleIO = workflowBundleIO;
-	}
-
-	/**
-	 * Sets the databaseConfiguration.
-	 *
-	 * @param databaseConfiguration the new value of databaseConfiguration
-	 */
-	public void setDatabaseConfiguration(DatabaseConfiguration databaseConfiguration) {
-		this.databaseConfiguration = databaseConfiguration;
-	}
-
-	/**
-	 * Sets the databaseManager.
-	 *
-	 * @param databaseManager the new value of databaseManager
-	 */
-	public void setDatabaseManager(DatabaseManager databaseManager) {
-		this.databaseManager = databaseManager;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
deleted file mode 100644
index 46b6c92..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.Properties;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.configuration.database.DatabaseConfiguration;
-import uk.org.taverna.configuration.database.DatabaseManager;
-
-/**
- * Handles the initialisation and configuration of the data source according to
- * the command line arguments, or a properties file.
- * This also handles starting a network based instance of a Derby server, if requested.
- *
- * @author Stuart Owen
- *
- */
-public class DatabaseConfigurationHandler {
-
-	private static Logger logger = Logger.getLogger(DatabaseConfigurationHandler.class);
-	private final CommandLineOptions options;
-	private final DatabaseConfiguration dbConfig;
-	private final DatabaseManager databaseManager;
-
-	public DatabaseConfigurationHandler(CommandLineOptions options, DatabaseConfiguration databaseConfiguration, DatabaseManager databaseManager) {
-		this.options = options;
-		this.dbConfig = databaseConfiguration;
-		this.databaseManager = databaseManager;
-		databaseConfiguration.disableAutoSave();
-	}
-
-	public void configureDatabase() throws DatabaseConfigurationException {
-		overrideDefaults();
-		useOptions();
-		if (dbConfig.getStartInternalDerbyServer()) {
-			databaseManager.startDerbyNetworkServer();
-			System.out.println("Started Derby Server on Port: "
-					+ dbConfig.getCurrentPort());
-		}
-	}
-
-	public DatabaseConfiguration getDBConfig() {
-		return dbConfig;
-	}
-
-	private void importConfigurationFromStream(InputStream inStr)
-			throws IOException {
-		Properties p = new Properties();
-		p.load(inStr);
-		for (Object key : p.keySet()) {
-			dbConfig.setProperty((String)key, p.getProperty((String)key).trim());
-		}
-	}
-
-	protected void overrideDefaults() throws DatabaseConfigurationException {
-
-		InputStream inStr = DatabaseConfigurationHandler.class.getClassLoader().getResourceAsStream("database-defaults.properties");
-		try {
-			importConfigurationFromStream(inStr);
-		} catch (IOException e) {
-			throw new DatabaseConfigurationException("There was an error reading the default database configuration settings: "+e.getMessage(),e);
-		}
-	}
-
-	protected void readConfigirationFromFile(String filename) throws IOException {
-		FileInputStream fileInputStream = new FileInputStream(filename);
-		importConfigurationFromStream(fileInputStream);
-		fileInputStream.close();
-	}
-
-	public void testDatabaseConnection()
-			throws DatabaseConfigurationException, NamingException, SQLException {
-		//try and get a connection
-		Connection con = null;
-		try {
-			con = databaseManager.getConnection();
-		} finally {
-			if (con!=null)
-				try {
-					con.close();
-				} catch (SQLException e) {
-					logger.warn("There was an SQL error whilst closing the test connection: "+e.getMessage(),e);
-				}
-		}
-	}
-
-	public void useOptions() throws DatabaseConfigurationException {
-
-		if (options.hasOption("port")) {
-			dbConfig.setPort(options.getDatabasePort());
-		}
-
-		if (options.hasOption("startdb")) {
-			dbConfig.setStartInternalDerbyServer(true);
-		}
-
-		if (options.hasOption("inmemory")) {
-			dbConfig.setInMemory(true);
-		}
-
-		if (options.hasOption("embedded")) {
-			dbConfig.setInMemory(false);
-			dbConfig.setDriverClassName("org.apache.derby.jdbc.EmbeddedDriver");
-		}
-
-		if (options.isProvenanceEnabled()) {
-			dbConfig.setProvenanceEnabled(true);
-		}
-
-		if (options.hasOption("clientserver")) {
-			dbConfig.setInMemory(false);
-			dbConfig.setDriverClassName("org.apache.derby.jdbc.ClientDriver");
-			dbConfig.setJDBCUri("jdbc:derby://localhost:" + dbConfig.getPort() + "/t2-database;create=true;upgrade=true");
-		}
-
-		if (options.hasOption("dbproperties")) {
-			try {
-				readConfigirationFromFile(options.getDatabaseProperties());
-			} catch (IOException e) {
-				throw new DatabaseConfigurationException("There was an error reading the database configuration options at "+options.getDatabaseProperties()+" : "+e.getMessage(),e);
-			}
-		}
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
deleted file mode 100644
index 44faea5..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.List;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import uk.org.taverna.databundle.DataBundles;
-import uk.org.taverna.databundle.ErrorDocument;
-
-/**
- * Handles ErrorValues and transforming them into String representations
- * that can be stored as a file, or within a Baclava document.
- *
- * @author Stuart Owen
- * @author David Withers
- */
-public class ErrorValueHandler {
-
-	/**
-	 * Creates a string representation of the ErrorValue.
-	 * @throws IOException
-	 */
-	public static String buildErrorValueString(ErrorDocument errorValue) throws IOException {
-
-		String errDocumentString = errorValue.getMessage() + "\n";
-
-		String exceptionMessage = errorValue.getMessage();
-		if (exceptionMessage != null && !exceptionMessage.equals("")) {
-			DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
-					exceptionMessage);
-			errDocumentString += exceptionMessageNode + "\n";
-			errDocumentString += errorValue.getTrace();
-		}
-
-		List<Path> errorReferences = errorValue.getCausedBy();
-		if (!errorReferences.isEmpty()) {
-			errDocumentString += "Set of cause errors to follow." + "\n";
-		}
-		int errorCounter = 1;
-		for (Path cause : errorReferences) {
-			if (DataBundles.isError(cause)) {
-			errDocumentString += "ErrorValue " + (errorCounter++) + "\n";
-			errDocumentString += buildErrorValueString(DataBundles.getError(cause)) + "\n";
-			}
-		}
-
-		return errDocumentString;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
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diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
deleted file mode 100644
index bcaa7fb..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
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@@ -1,280 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.StandardOpenOption;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.invocation.InvocationContext;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.jdom.JDOMException;
-import org.purl.wf4ever.robundle.Bundle;
-
-import uk.org.taverna.databundle.DataBundles;
-import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
-
-/**
- * Handles the reading, or processing, or input values according to arguments provided to the
- * commandline.
- * The may be either as direct values, from a file, or from a Baclava document.
- * Also handles registering the input values with the Data Service, ready to initiate
- * the workflow run.
- *
- * @author Stuart Owen
- */
-public class InputsHandler {
-
-	private static Logger logger = Logger.getLogger(InputsHandler.class);
-
-	public void checkProvidedInputs(Map<String, InputWorkflowPort> portMap,
-			CommandLineOptions options) throws InputMismatchException {
-		// we dont check for the document
-                Set<String> providedInputNames = new HashSet<String>();
-                for (int i = 0; i < options.getInputFiles().length; i += 2) {
-                        // If it already contains a value for the input port, e.g
-                        // two inputs are provided for the same port
-                        if (providedInputNames.contains(options.getInputFiles()[i])) {
-                                throw new InputMismatchException(
-                                        "Two input values were provided for the same input port "
-                                        + options.getInputFiles()[i] + ".", null, null);
-                        }
-                        providedInputNames.add(options.getInputFiles()[i]);
-                }
-
-                for (int i = 0; i < options.getInputValues().length; i += 2) {
-                        // If it already contains a value for the input port, e.g
-                        // two inputs are provided for the same port
-                        if (providedInputNames.contains(options.getInputValues()[i])) {
-                                throw new InputMismatchException(
-                                        "Two input values were provided for the same input port "
-                                        + options.getInputValues()[i] + ".", null, null);
-                        }
-                        providedInputNames.add(options.getInputValues()[i]);
-                }
-
-                if (portMap.size() * 2 != (options.getInputFiles().length + options.getInputValues().length)) {
-                        throw new InputMismatchException(
-                                    "The number of inputs provided does not match the number of input ports.",
-						portMap.keySet(), providedInputNames);
-                }
-
-                for (String portName : portMap.keySet()) {
-                        if (!providedInputNames.contains(portName)) {
-                                throw new InputMismatchException(
-                                        "The provided inputs does not contain an input for the port '"
-                                        + portName + "'", portMap.keySet(), providedInputNames);
-			}
-		}
-	}
-
-	public Bundle registerInputs(Map<String, InputWorkflowPort> portMap,
-			CommandLineOptions options, InvocationContext context) throws InvalidOptionException,
-			ReadInputException, IOException {
-		Bundle inputDataBundle;
-		inputDataBundle = DataBundles.createBundle();
-		inputDataBundle.setDeleteOnClose(false);
-		System.out.println("Bundle: " + inputDataBundle.getSource());
-		
-		Path inputs = DataBundles.getInputs(inputDataBundle);
-
-		URL url;
-		try {
-			url = new URL("file:");
-		} catch (MalformedURLException e1) {
-			// Should never happen, but just in case:
-			throw new ReadInputException(
-					"The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",
-					e1);
-		}
-
-		if (options.hasInputFiles()) {
-			regesterInputsFromFiles(portMap, options, inputs, url);
-		}
-
-		if (options.hasInputValues()) {
-			registerInputsFromValues(portMap, options, inputs);
-
-		}
-
-		return inputDataBundle;
-	}
-
-	private void registerInputsFromValues(Map<String, InputWorkflowPort> portMap,
-			CommandLineOptions options, Path inputs) throws InvalidOptionException {
-		String[] inputParams = options.getInputValues();
-		for (int i = 0; i < inputParams.length; i = i + 2) {
-			String inputName = inputParams[i];
-			try {
-				String inputValue = inputParams[i + 1];
-				InputWorkflowPort port = portMap.get(inputName);
-
-				if (port == null) {
-					throw new InvalidOptionException("Cannot find an input port named '"
-							+ inputName + "'");
-				}
-
-				Path portPath = DataBundles.getPort(inputs, inputName);
-				if (options.hasDelimiterFor(inputName)) {
-					String delimiter = options.inputDelimiter(inputName);
-					Object value = checkForDepthMismatch(1, port.getDepth(), inputName,
-							inputValue.split(delimiter));
-					setValue(portPath, value);
-				} else {
-					Object value = checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
-					setValue(portPath, value);
-				}
-
-			} catch (IndexOutOfBoundsException e) {
-				throw new InvalidOptionException("Missing input value for input " + inputName);
-			} catch (IOException e) {
-				throw new InvalidOptionException("Error creating value for input " + inputName);
-			}
-		}
-	}
-
-	private void regesterInputsFromFiles(Map<String, InputWorkflowPort> portMap,
-			CommandLineOptions options, Path inputs, URL url) throws InvalidOptionException {
-		String[] inputParams = options.getInputFiles();
-		for (int i = 0; i < inputParams.length; i = i + 2) {
-			String inputName = inputParams[i];
-			try {
-				URL inputURL = new URL(url, inputParams[i + 1]);
-				InputWorkflowPort port = portMap.get(inputName);
-
-				if (port == null) {
-					throw new InvalidOptionException("Cannot find an input port named '"
-							+ inputName + "'");
-				}
-
-				Path portPath = DataBundles.getPort(inputs, inputName);
-				if (options.hasDelimiterFor(inputName)) {
-					String delimiter = options.inputDelimiter(inputName);
-					Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);
-					value = checkForDepthMismatch(1, port.getDepth(), inputName, value);
-					setValue(portPath, value);
-				} else {
-					Object value = IOUtils.toByteArray(inputURL.openStream());
-					value = checkForDepthMismatch(0, port.getDepth(), inputName, value);
-					setValue(portPath, value);
-				}
-			} catch (IndexOutOfBoundsException e) {
-				throw new InvalidOptionException("Missing input filename for input " + inputName);
-			} catch (IOException e) {
-				throw new InvalidOptionException("Could not read input " + inputName + ": "
-						+ e.getMessage());
-			}
-		}
-	}
-
-	private void setValue(Path port, Object userInput) throws IOException {
-		if (userInput instanceof File) {
-			DataBundles.setReference(port, ((File) userInput).toURI());
-		} else if (userInput instanceof URL) {
-			try {
-				DataBundles.setReference(port, ((URL) userInput).toURI());
-			} catch (URISyntaxException e) {
-				logger.warn(String.format("Error converting %1$s to URI", userInput), e);
-			}
-		} else if (userInput instanceof String) {
-			DataBundles.setStringValue(port, (String) userInput);
-		} else if (userInput instanceof byte[]) {
-			Files.write(port, (byte[]) userInput, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE);
-		} else if (userInput instanceof List<?>) {
-			DataBundles.createList(port);
-			List<?> list = (List<?>) userInput;
-			for (Object object : list) {
-				setValue(DataBundles.newListItem(port), object);
-			}
-		} else {
-			logger.warn("Unknown input type : " + userInput.getClass().getName());
-		}
-	}
-
-	private Object checkForDepthMismatch(int inputDepth, int portDepth, String inputName,
-			Object inputValue) throws InvalidOptionException {
-		if (inputDepth != portDepth) {
-			if (inputDepth < portDepth) {
-				logger.warn("Wrapping input for '" + inputName + "' from a depth of " + inputDepth
-						+ " to the required depth of " + portDepth);
-				while (inputDepth < portDepth) {
-					List<Object> l = new ArrayList<Object>();
-					l.add(inputValue);
-					inputValue = l;
-					inputDepth++;
-				}
-			} else {
-				String msg = "There is a mismatch between depth of the list for the input port '"
-						+ inputName + "' and the data presented. The input port requires a "
-						+ depthToString(portDepth) + " and the data presented is a "
-						+ depthToString(inputDepth);
-				throw new InvalidOptionException(msg);
-			}
-		}
-
-		return inputValue;
-	}
-
-	private String depthToString(int depth) {
-		switch (depth) {
-		case 0:
-			return "single item";
-		case 1:
-			return "list";
-		case 2:
-			return "list of lists";
-		default:
-			return "list of depth " + depth;
-		}
-	}
-
-	private int getObjectDepth(Object o) {
-		int result = 0;
-		if (o instanceof Iterable) {
-			result++;
-			Iterator i = ((Iterable) o).iterator();
-
-			if (i.hasNext()) {
-				Object child = i.next();
-				result = result + getObjectDepth(child);
-			}
-		}
-		return result;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
deleted file mode 100644
index 1df05c2..0000000
--- a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
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@@ -1,87 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.List;
-import java.util.Map;
-
-import uk.org.taverna.databundle.DataBundles;
-
-/**
- * Handles all recording of results as they are received by the {@link CommandLineResultListener} or
- * when the workflow enactment has completed.
- * This includes saving as a Baclava Document, or storing individual results.
- *
- * @author Stuart Owen
- * @see BaclavaHandler
- * @see CommandLineResultListener
- */
-public class SaveResultsHandler {
-
-	private final File outputDirectory;
-
-	public SaveResultsHandler(File rootOutputDir) {
-		this.outputDirectory = rootOutputDir;
-	}
-
-	/**
-	 * Given the Data on an output port, saves the data on a disk in the
-	 * output directory.
-	 *
-	 * @param portName
-	 * @param data
-	 * @throws IOException
-	 */
-	public void saveResultsForPort(String portName, Path data) throws IOException {
-		if (DataBundles.isList(data)) {
-			Path outputPath = outputDirectory.toPath().resolve(portName);
-			Files.createDirectories(outputPath);
-			saveList(DataBundles.getList(data), outputPath);
-		} else if (DataBundles.isError(data)) {
-			Files.copy(data, outputDirectory.toPath().resolve(portName + ".error"));
-		} else {
-			Files.copy(data, outputDirectory.toPath().resolve(portName));
-		}
-	}
-
-	private void saveList(List<Path> list, Path destination) throws IOException {
-		int index = 1;
-		for (Path data : list) {
-			if (data != null) {
-				if (DataBundles.isList(data)) {
-					Path outputPath = destination.resolve(String.valueOf(index));
-					Files.createDirectories(outputPath);
-					saveList(DataBundles.getList(data), outputPath);
-				} else if (DataBundles.isError(data)) {
-					Files.copy(data, destination.resolve(String.valueOf(index) + ".error"));
-				} else {
-					Files.copy(data, destination.resolve(String.valueOf(index)));
-				}
-			}
-			index++;
-		}
-	}
-
-}