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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:42:14 UTC
[7/8] incubator-taverna-commandline git commit: temporarily empty
repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
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diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
deleted file mode 100644
index e7ae701..0000000
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context-osgi.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
-
- <service ref="commandLineMasterPasswordProvider" interface="net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider" />
-
- <reference id="commandLineOptions" interface="net.sf.taverna.t2.commandline.options.CommandLineOptions"/>
- <reference id="runService" interface="uk.org.taverna.platform.run.api.RunService"/>
- <reference id="credentialManager" interface="net.sf.taverna.t2.security.credentialmanager.CredentialManager" />
- <reference id="databaseConfiguration" interface="uk.org.taverna.configuration.database.DatabaseConfiguration" />
- <reference id="databaseManager" interface="uk.org.taverna.configuration.database.DatabaseManager" />
-
- <reference id="workflowBundleIO" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleIO" />
- <reference id="t2flowWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(mediaType=application/vnd.taverna.t2flow+xml)"/>
- <reference id="rdfXMLWorkflowBundleReader" interface="uk.org.taverna.scufl2.api.io.WorkflowBundleReader" filter="(org.springframework.osgi.bean.name=rdfXMLReader)"/>
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
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diff --git a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml b/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
deleted file mode 100644
index 52c0f29..0000000
--- a/taverna-commandline-common/src/main/resources/META-INF/spring/taverna-commandline-common-context.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="commandLineTool" class="net.sf.taverna.t2.commandline.CommandLineTool" init-method="run">
- <property name="commandLineOptions" ref="commandLineOptions" />
- <property name="runService" ref="runService" />
- <property name="credentialManager" ref="credentialManager" />
- <property name="workflowBundleIO" ref="workflowBundleIO" />
- <property name="databaseConfiguration" ref="databaseConfiguration" />
- <property name="databaseManager" ref="databaseManager" />
- </bean>
-
- <bean id="commandLineMasterPasswordProvider"
- class="net.sf.taverna.t2.commandline.CommandLineMasterPasswordProvider">
- <constructor-arg name="commandLineOptions"
- ref="commandLineOptions" />
- </bean>
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/resources/database-defaults.properties
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diff --git a/taverna-commandline-common/src/main/resources/database-defaults.properties b/taverna-commandline-common/src/main/resources/database-defaults.properties
deleted file mode 100644
index 1080856..0000000
--- a/taverna-commandline-common/src/main/resources/database-defaults.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-pool_max_active = 50
-pool_min_idle = 50
-pool_max_idle = 10
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/main/resources/help.txt
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diff --git a/taverna-commandline-common/src/main/resources/help.txt b/taverna-commandline-common/src/main/resources/help.txt
deleted file mode 100644
index fb082cc..0000000
--- a/taverna-commandline-common/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then a new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option. The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of your workflow inputs is a list, you can create a list
-input by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to
-put the delimiter character in quotes as it may be interpreted by the shell
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option. However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth. Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the properties file, for which the following
-example contains the default settings:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
-
--cmdir option lets you specify an absolute path to a directory where
-Credential Manager's files (keystore and truststore - containing user's
-credentials and trusted certificates for accessing secure services) are stored.
-If not specified and the workflow requires access to these files, Taverna will
-try to find them in the default location in <TAVERNA_HOME>/security somewhere
-inside user's home directory (depending on the platform).
-
--cmpassword option can be used to tell Taverna to expect the password for the
-Credential Manager on standard input. If the password is not piped in, Taverna
-will prompt you for it in the terminal and block until it is entered. Do not
-enter your password in the command line! If -cmpassword option is not specified
-and -cmdir option is used, Taverna will try to find the password in a special
-file password.txt in the directory specified with -cmdir option.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
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diff --git a/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java b/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
deleted file mode 100644
index 4c00e3a..0000000
--- a/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-//import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-
-import org.junit.Ignore;
-import org.junit.Test;
-
-public class TestDatabaseConfigurationHandler {
-
-// @Test
-// public void testDefaults() throws Exception {
-// CommandLineOptions opts = new CommandLineOptions(new String[]{"myworkflow.t2flow"});
-// DatabaseConfigurationHandler handler = new DatabaseConfigurationHandler(opts);
-// handler.configureDatabase();
-// assertEquals("org.apache.derby.jdbc.EmbeddedDriver", DataManagementConfiguration.getInstance().getDriverClassName());
-// assertEquals(false, DataManagementConfiguration.getInstance().getStartInternalDerbyServer());
-// }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-launcher/pom.xml
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diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
deleted file mode 100644
index 42208e3..0000000
--- a/taverna-commandline-launcher/pom.xml
+++ /dev/null
@@ -1,83 +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>
- <artifactId>taverna-commandline-launcher</artifactId>
- <name>Apache Taverna Commandline Launcher</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jar-plugin</artifactId>
- <version>2.4</version>
- <configuration>
- <archive>
- <manifest>
- <addClasspath>true</addClasspath>
- <mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
- <classpathLayoutType>custom</classpathLayoutType>
- <customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
- </manifest>
- </archive>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-commandline-api</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>osgi-launcher</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.cli</artifactId>
- <version>${commons.cli.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
- <dependency>
- <groupId>org.eclipse</groupId>
- <artifactId>org.eclipse.osgi</artifactId>
- <version>${osgi.equinox.version}</version>
- </dependency>
- <!-- TODO: replace equinox with:
- <dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.apache.felix.main</artifactId>
- <version>4.4.1</version>
- </dependency>
- -->
-
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
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diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
deleted file mode 100644
index b702e03..0000000
--- a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
+++ /dev/null
@@ -1,445 +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 uk.org.taverna.commandline;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.GnuParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Handles the processing of command line arguments for enacting a workflow.
- * This class encapsulates all command line options, and exposes them through higher-level
- * accessors. Upon creation it checks the validity of the command line options and raises an
- * {@link InvalidOptionException} if they are invalid.
- *
- * @author Stuart Owen
- * @author David Withers
- */
-public class CommandLineOptionsImpl implements CommandLineOptions {
-
- private static final String OUTPUTDIR = "outputdir";
- private static final String BUNDLE = "bundle";
- private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
- private Options options;
- private CommandLine commandLine;
-
- public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
- this.options = intitialiseOptions();
- this.commandLine = processArgs(args);
- checkForInvalid();
- }
-
- @Override
- public boolean askedForHelp() {
- return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
- }
-
- @Override
- public boolean isProvenanceEnabled() {
- return hasOption("provenance");
- }
-
- protected void checkForInvalid() throws InvalidOptionException {
- if (askedForHelp()) return;
- if (isProvenanceEnabled()
- && !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if (isProvenanceEnabled() && hasOption("inmemory"))
- throw new InvalidOptionException(
- "You should be running with a database to use provenance");
- if ((hasOption("inputfile") || hasOption("inputvalue"))
- && hasOption("inputdoc"))
- throw new InvalidOptionException(
- "You can't provide both -input and -inputdoc arguments");
-
- if (hasOption("inputdelimiter") && hasOption("inputdoc"))
- throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
-
- if (getArgs().length == 0
- && !(hasOption("help") || hasOption("startdb")))
- throw new InvalidOptionException("You must specify a workflow");
-
- if (hasOption("inmemory") && hasOption("embedded"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("inmemory") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- if (hasOption("embedded") && hasOption("clientserver"))
- throw new InvalidOptionException(
- "The options -embedded, -clientserver and -inmemory cannot be used together");
- }
-
- @Override
- public void displayHelp() {
- boolean full = false;
- if (hasOption("help")) full=true;
- displayHelp(full);
- }
-
- @Override
- public void displayHelp(boolean showFullText) {
-
- HelpFormatter formatter = new HelpFormatter();
- try {
- formatter
- .printHelp("executeworkflow [options] [workflow]", options);
- if (showFullText) {
- InputStream helpStream = CommandLineOptionsImpl.class
- .getClassLoader().getResourceAsStream("help.txt");
- String helpText = IOUtils.toString(helpStream);
- System.out.println(helpText);
- }
-
- } catch (IOException e) {
- logger.error("Failed to load the help document", e);
- System.out.println("Failed to load the help document");
- //System.exit(-1);
- }
- }
-
- @Override
- public String[] getArgs() {
- return commandLine.getArgs();
- }
-
- /**
- *
- * @return the port that the database should run on
- */
- @Override
- public String getDatabasePort() {
- return getOptionValue("port");
- }
-
- /**
- *
- * @return a path to a properties file that contains database configuration
- * settings
- */
- @Override
- public String getDatabaseProperties() {
- return getOptionValue("dbproperties");
- }
-
- /**
- * 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.
- */
- @Override
- public String[] getInputFiles() {
- if (hasInputFiles()) {
- return getOptionValues("inputfile");
- } else {
- return new String[] {};
- }
- }
-
- @Override
- public String[] getInputValues() {
- if (hasInputValues()) {
- return getOptionValues("inputvalue");
- } else {
- return new String[] {};
- }
- }
-
- @Override
- public String getLogFile() {
- return getOptionValue("logfile");
- }
-
- public Option [] getOptions() {
- return commandLine.getOptions();
- }
-
- private String getOptionValue(String opt) {
- return commandLine.getOptionValue(opt);
- }
-
- private String[] getOptionValues(String arg0) {
- return commandLine.getOptionValues(arg0);
- }
-
- /**
- *
- * @return the directory to write the results to
- */
- @Override
- public String getOutputDirectory() {
- return getOptionValue(OUTPUTDIR);
- }
-
- @Override
- public boolean getStartDatabase() {
- return hasOption("startdb");
- }
-
- /**
- * @return the directory with Credential Manager's files
- */
- @Override
- public String getCredentialManagerDir() {
- return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
- }
-
- @Override
- public boolean getStartDatabaseOnly() throws InvalidOptionException {
- return (getStartDatabase() && (getWorkflow() == null));
- }
-
- @Override
- public String getWorkflow() throws InvalidOptionException {
- if (getArgs().length == 0) {
- return null;
- } else if (getArgs().length != 1) {
- throw new InvalidOptionException(
- "You should only specify one workflow file");
- } else {
- return getArgs()[0];
- }
- }
-
- @Override
- public boolean hasDelimiterFor(String inputName) {
- boolean result = false;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=true;
- break;
- }
- }
- }
- return result;
- }
-
- @Override
- public boolean hasInputFiles() {
- return hasOption("inputfile");
- }
-
- @Override
- public boolean hasInputValues() {
- return hasOption("inputvalue");
- }
-
- @Override
- public boolean hasLogFile() {
- return hasOption("logfile");
- }
-
- @Override
- public boolean hasOption(String option) {
- return commandLine.hasOption(option);
- }
-
- @Override
- public String inputDelimiter(String inputName) {
- String result = null;
- if (hasOption("inputdelimiter")) {
- String [] values = getOptionValues("inputdelimiter");
- for (int i=0;i<values.length;i+=2) {
- if (values[i].equals(inputName))
- {
- result=values[i+1];
- break;
- }
- }
- }
- return result;
- }
-
- @SuppressWarnings("static-access")
- private Options intitialiseOptions() {
- Option helpOption = new Option("help", "Display comprehensive help information.");
-
- Option outputOption = OptionBuilder
- .withArgName("directory")
- .hasArg()
- .withDescription(
- "Save outputs as files in directory, default "
- + "is to make a new directory workflowName_output.")
- .create(OUTPUTDIR);
-
- Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
- .withDescription("Save outputs to a new Workflow Run Bundle (zip).")
- .create(BUNDLE);
-
- Option logFileOption = OptionBuilder
- .withArgName("filename")
- .hasArg()
- .withDescription(
- "The logfile to which more verbose logging will be written to.")
- .create("logfile");
-
- Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
- .withDescription("Load inputs from a Baclava document.").create(
- "inputdoc");
-
- Option inputFileOption = OptionBuilder
- .withArgName("inputname filename").hasArgs(2)
- .withValueSeparator(' ').withDescription(
- "Load the named input from file or URL.").create(
- "inputfile");
-
- Option inputValueOption = OptionBuilder.withArgName("inputname value")
- .hasArgs(2).withValueSeparator(' ').withDescription(
- "Directly use the value for the named input.").create(
- "inputvalue");
-
- Option inputDelimiterOption = OptionBuilder
- .withArgName("inputname delimiter")
- .hasArgs(2)
- .withValueSeparator(' ')
- .withDescription(
- "Cause an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list.")
- .create("inputdelimiter");
-
- Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
- .withDescription(
- "Load a properties file to configure the database.")
- .create("dbproperties");
-
- Option port = OptionBuilder
- .withArgName("portnumber")
- .hasArg()
- .withDescription(
- "The port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
- .create("port");
-
- Option embedded = new Option("embedded",
- "Connect to an embedded Derby database. This can prevent mulitple invocations.");
- Option clientserver = new Option("clientserver",
- "Connect as a client to a derby server instance.");
- Option inMemOption = new Option(
- "inmemory",
- "Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
- Option startDB = new Option("startdb",
- "Automatically start an internal Derby database server.");
- Option provenance = new Option("provenance",
- "Generate provenance information and store it in the database.");
-
-
- Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
- hasArg().withDescription(
- "Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
- .create(CREDENTIAL_MANAGER_DIR_OPTION);
- Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
-
- Options options = new Options();
- options.addOption(helpOption);
- options.addOption(inputFileOption);
- options.addOption(inputValueOption);
- options.addOption(inputDelimiterOption);
- options.addOption(inputdocOption);
- options.addOption(outputOption);
- options.addOption(bundleOption);
- options.addOption(inMemOption);
- options.addOption(embedded);
- options.addOption(clientserver);
- options.addOption(dbProperties);
- options.addOption(port);
- options.addOption(startDB);
- options.addOption(provenance);
- options.addOption(logFileOption);
- options.addOption(credentialManagerDirectory);
- options.addOption(credentialManagerPassword);
-
- return options;
- }
-
- @Override
- public boolean isClientServer() {
- return hasOption("clientserver");
- }
-
- @Override
- public boolean isEmbedded() {
- return hasOption("embedded");
- }
-
- @Override
- public boolean isInMemory() {
- return hasOption("inmemory");
- }
-
- private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
- CommandLineParser parser = new GnuParser();
- CommandLine line = null;
- try {
- // parse the command line arguments
- line = parser.parse(options, args);
- } catch (ParseException exp) {
- // oops, something went wrong
-// System.err.println("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
-// System.exit(1);
- throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
- }
- return line;
- }
-
- /**
- * Save the results to a directory if -outputdir has been explicitly defined,
- * or if -outputdoc has not been defined.
- *
- * @return boolean
- */
- @Override
- public boolean saveResultsToDirectory() {
- return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
- }
-
- @Override
- public String saveResultsToBundle() {
- if (! hasSaveResultsToBundle()) {
- return null;
- }
- return getOptionValue(BUNDLE);
- }
-
- @Override
- public boolean hasSaveResultsToBundle() {
- return hasOption(BUNDLE);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
deleted file mode 100644
index 426ab98..0000000
--- a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
+++ /dev/null
@@ -1,143 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 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 uk.org.taverna.commandline;
-
-import java.io.File;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.osgi.framework.BundleContext;
-import org.osgi.framework.BundleException;
-
-import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
-import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
-import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
-import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
-import uk.org.taverna.osgi.OsgiLauncher;
-
-/**
- * Main entry point for starting the Taverna Command Line Tool.
- *
- * @author David Withers
- */
-public class TavernaCommandLine {
-
- private static final String COMMANDLINE_BUNDLE_NAME = "org.apache.taverna.commandline.taverna-commandline-common";
-
- private static File commandlineBundle = null;
-
- private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
-
- private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
-
- /**
- * Starts the Taverna Command Line Tool.
- *
- * @param args
- * Taverna Command Line arguments
- */
- public static void main(final String[] args) {
- try {
- CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
- if (commandLineOptions.askedForHelp()) {
- commandLineOptions.displayHelp();
- } else {
- log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
- log4jConfiguration.prepareLog4J();
- setDerbyPaths();
- OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
- setFrameworkConfiguration(osgilauncher);
- osgilauncher.start();
- BundleContext context = osgilauncher.getContext();
- context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
- commandLineOptions, null);
- osgilauncher.startServices(true);
- if (commandlineBundle == null) {
- System.err.println("Can't locate command line bundle " + COMMANDLINE_BUNDLE_NAME);
- System.exit(1);
- }
- osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
- }
- } catch (ArgumentsParsingException e) {
- System.out.println(e.getMessage());
- } catch (InvalidOptionException e) {
- System.out.println(e.getMessage());
- } catch (BundleException e) {
- System.out.println(e.getMessage());
- }
- }
-
- /**
- * Sets the OSGi Framework configuration.
- *
- * @param osgilauncher
- */
- private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
- ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
- List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
- .getFrameworkConfiguration();
- if (!frameworkConfigurations.isEmpty()) {
- Map<String, String> configurationMap = new HashMap<String, String>();
- for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
- configurationMap.put(frameworkConfiguration.getName(),
- frameworkConfiguration.getValue());
- }
- osgilauncher.setFrameworkConfiguration(configurationMap);
- }
- }
-
- private static List<URI> getBundleURIs() {
- List<URI> bundleURIs = new ArrayList<URI>();
- ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
- File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
- if (applicationProfile != null) {
- for (BundleInfo bundle : applicationProfile.getBundle()) {
- File bundleFile = new File(libDir, bundle.getFileName());
- if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
- commandlineBundle = bundleFile;
- } else {
- bundleURIs.add(bundleFile.toURI());
- }
- }
- }
- return bundleURIs;
- }
-
- private static File getAppDirectory() {
- return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
- }
-
- private static void setDerbyPaths() {
- System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
- File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
- System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-launcher/src/main/resources/help.txt
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/resources/help.txt b/taverna-commandline-launcher/src/main/resources/help.txt
deleted file mode 100644
index fb082cc..0000000
--- a/taverna-commandline-launcher/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then a new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option. The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of your workflow inputs is a list, you can create a list
-input by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to
-put the delimiter character in quotes as it may be interpreted by the shell
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option. However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth. Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the properties file, for which the following
-example contains the default settings:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
-
--cmdir option lets you specify an absolute path to a directory where
-Credential Manager's files (keystore and truststore - containing user's
-credentials and trusted certificates for accessing secure services) are stored.
-If not specified and the workflow requires access to these files, Taverna will
-try to find them in the default location in <TAVERNA_HOME>/security somewhere
-inside user's home directory (depending on the platform).
-
--cmpassword option can be used to tell Taverna to expect the password for the
-Credential Manager on standard input. If the password is not piped in, Taverna
-will prompt you for it in the terminal and block until it is entered. Do not
-enter your password in the command line! If -cmpassword option is not specified
-and -cmdir option is used, Taverna will try to find the password in a special
-file password.txt in the directory specified with -cmdir option.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
deleted file mode 100644
index 3e1d0f4..0000000
--- a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,267 +0,0 @@
-package uk.org.taverna.commandline;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.junit.Test;
-
-public class TestCommandLineOptionsHandler {
-
- @Test
- public void testWorkflowName() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(
- new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", handler.getWorkflow());
- }
-
- @Test
- public void shouldShowHelp() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-help" });
- assertTrue(options.askedForHelp());
- options = new CommandLineOptionsImpl(
- new String[] {});
- assertTrue(options.askedForHelp());
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.askedForHelp());
- }
-
- @Test
- public void getWorkflow() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-help" });
- assertNull(options.getWorkflow());
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertEquals("myworkflow.t2flow", options.getWorkflow());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputFileAndInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void cannotProvideInputValueAndInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
- "-inputdoc", "myworkflow.t2flow" });
- }
-
- @Test
- public void canProvideInputValueAndFileTogether() throws Exception {
- //should not be an error
- new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
- "-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
- }
-
- @Test
- public void getInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertEquals(2, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
-
- options = new CommandLineOptionsImpl(new String[] { "-inputfile", "fred",
- "fred.txt", "-inputfile", "fred2", "fred2.txt",
- "myworkflow.t2flow" });
- assertEquals(4, options.getInputFiles().length);
- assertEquals("fred", options.getInputFiles()[0]);
- assertEquals("fred.txt", options.getInputFiles()[1]);
- assertEquals("fred2", options.getInputFiles()[2]);
- assertEquals("fred2.txt", options.getInputFiles()[3]);
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputFiles());
- assertEquals(0, options.getInputFiles().length);
-
- }
-
- @Test
- public void hasInputValue() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertTrue(options.hasInputValues());
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputValues());
- }
-
- @Test
- public void getInputValues() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue", "fred", "abc", "myworkflow.t2flow" });
- assertEquals(2, options.getInputValues().length);
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertNotNull(options.getInputValues());
- assertEquals(0,options.getInputValues().length);
- }
-
- @Test
- public void hasInputs() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
- assertTrue(options.hasInputFiles());
-
- options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
- assertFalse(options.hasInputFiles());
- }
-
- @Test
- public void noWorkflowNameButStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptionsImpl(
- new String[] { "-startdb" });
- assertTrue(options.getStartDatabase());
- assertTrue(options.getStartDatabaseOnly());
- }
-
- @Test
- public void workflowNameAndStartDB() throws Exception {
- // should not throw an error
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-startdb", "myworkflow.t2flow" });
- assertTrue(options.getStartDatabase());
- assertFalse(options.getStartDatabaseOnly());
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-provenance",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void provenanceButNoDatabase2() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void provenanceDatabase() throws Exception {
- // should be no errors
- new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
- "myworkflow.t2flow" });
- new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
- "myworkflow.t2flow" });
- new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
- "dbproperties.properties", "myworkflow.t2flow" });
- }
-
- @Test
- public void testHasInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
- assertTrue(options.hasDelimiterFor("in1"));
- assertTrue(options.hasDelimiterFor("in2"));
- assertFalse(options.hasDelimiterFor("in3"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInputDelimiterInvalidWithInputDoc() throws Exception {
- new CommandLineOptionsImpl(new String[] {
- "-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
- }
-
-
- @Test
- public void testInputDelimiter() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
- assertEquals(",",options.inputDelimiter("in1"));
- assertEquals("!",options.inputDelimiter("in2"));
- assertNull(options.inputDelimiter("in3"));
- }
-
- @Test
- public void testInMemory() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-inmemory", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("inmemory"));
- }
-
- @Test
- public void testEmbedded() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-embedded", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("embedded"));
- }
-
- @Test
- public void testClientServer() throws Exception {
- CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
- "-clientserver", "myworkflow.t2flow" });
- assertTrue(handler.hasOption("clientserver"));
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndClientServer() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidEmbeddedAndMemory() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test(expected = InvalidOptionException.class)
- public void testInvalidClientServerAndInMemory() throws Exception {
- new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
- "myworkflow.t2flow" });
- }
-
- @Test
- public void isInMemory() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-inmemory", "myworkflow.t2flow" });
-
- assertTrue(options.isInMemory());
- assertFalse(options.isClientServer());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void isClientServer() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-clientserver", "myworkflow.t2flow" });
-
- assertTrue(options.isClientServer());
- assertFalse(options.isInMemory());
- assertFalse(options.isEmbedded());
- }
-
- @Test
- public void hasLogFile() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-logfile","/tmp/logging", "myworkflow.t2flow" });
-
- assertTrue(options.hasLogFile());
- assertEquals("/tmp/logging", options.getLogFile());
- }
-
- @Test(expected = InvalidOptionException.class)
- @SuppressWarnings("unused")
- public void hasLogFileNotValidWithoutWorkflow() throws Exception{
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-logfile","/tmp/logging"});
- }
-
- @Test
- public void isEmbedded() throws Exception {
- CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
- "-embedded", "myworkflow.t2flow" });
-
- assertTrue(options.isEmbedded());
- assertFalse(options.isInMemory());
- assertFalse(options.isClientServer());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/pom.xml b/taverna-commandline-product/pom.xml
deleted file mode 100644
index 38bcb42..0000000
--- a/taverna-commandline-product/pom.xml
+++ /dev/null
@@ -1,529 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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-command-line-product</artifactId>
- <name>Apache Taverna Commandline Product</name>
- <packaging>taverna-application</packaging>
- <profiles>
- <profile>
- <id>developer</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- <properties>
- <assembly.descriptor>src/main/assembly/developer-assembly.xml</assembly.descriptor>
- <!-- See http://updates.taverna.org.uk/ -->
- <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
- <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
- </properties>
- </profile>
- <profile>
- <id>nightly</id>
- <properties>
- <assembly.descriptor>src/main/assembly/nightly-assembly.xml</assembly.descriptor>
- <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
- <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
- </properties>
- </profile>
- <profile>
- <id>release</id>
- <properties>
- <assembly.descriptor>src/main/assembly/release-assembly.xml</assembly.descriptor>
- <profile.updateSite>https://taverna.incubator.apache.org/updates/commandline/</profile.updateSite>
- <profile.pluginSite>https://taverna.incubator.apache.org/plugins/commandline/</profile.pluginSite>
- </properties>
- </profile>
- </profiles>
- <build>
- <finalName>apache-taverna-commandline-${project.version}</finalName>
- <plugins>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <version>2.4</version>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <descriptors>
- <descriptor>${assembly.descriptor}</descriptor>
- </descriptors>
- <archiverConfig>
- <directoryMode>493</directoryMode> <!-- 493(dec) = 755(oct) -->
- <defaultDirectoryMode>493</defaultDirectoryMode>
- </archiverConfig>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>buildnumber-maven-plugin</artifactId>
- <version>1.0-beta-3</version>
- <executions>
- <execution>
- <id>buildnumber-validate</id>
- <phase>validate</phase>
- <goals>
- <goal>create</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <format>{0,date,yyyyMMdd}T{0,date,HHmm}</format>
- <items>
- <item>timestamp</item>
- </items>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-maven-plugin</artifactId>
- <version>${taverna.osgi.version}</version>
- <extensions>true</extensions>
- <configuration>
- <buildNumber>${buildNumber}</buildNumber>
- <updateSite>${profile.updateSite}</updateSite>
- <pluginSite>${profile.pluginSite}</pluginSite>
- <frameworkConfigurations>
- <frameworkConfiguration>
- <name>org.osgi.framework.bootdelegation</name>
- <value>sun.*,com.sun.*,java.*,javax.*,org.xml.*,org.w3c.*,apple.*,com.apple.*,org.omg.*,org.ietf.jgss.*,org.jcp.xml.dsig.internal.*</value>
- </frameworkConfiguration>
- <frameworkConfiguration>
- <name>org.osgi.framework.system.packages.extra</name>
- <value>com.sun.org.apache.xml.internal.utils,com.sun.source.util,com.sun.source.tree,org.apache.log4j;version=${log4j.version},net.sf.taverna.t2.commandline.options;version=${project.parent.version}</value>
- </frameworkConfiguration>
- <frameworkConfiguration>
- <name>org.osgi.framework.storage.clean</name>
- <value>onFirstInit</value>
- </frameworkConfiguration>
- </frameworkConfigurations>
- </configuration>
- </plugin>
- </plugins>
- <pluginManagement>
- <plugins>
- <!--This plugin's configuration is used to store Eclipse m2e settings
- only. It has no influence on the Maven build itself. -->
- <plugin>
- <groupId>org.eclipse.m2e</groupId>
- <artifactId>lifecycle-mapping</artifactId>
- <version>1.0.0</version>
- <configuration>
- <lifecycleMappingMetadata>
- <pluginExecutions>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-maven-plugin</artifactId>
- <versionRange>[0.3.1-SNAPSHOT,)</versionRange>
- <goals>
- <goal>profile-generate</goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute>
- <runOnIncremental>false</runOnIncremental>
- </execute>
- </action>
- </pluginExecution>
- </pluginExecutions>
- </lifecycleMappingMetadata>
- </configuration>
- </plugin>
- </plugins>
- </pluginManagement>
- </build>
-
- <dependencies>
-
- <!-- Explicit org.osgi.* with <scope>provided as these are also provided
- by the felix osgi package. Avoids: Caused by: java.lang.SecurityException:
- class "org.osgi.framework.hooks.bundle.CollisionHook"'s signer information
- does not match signer information of other classes in the same package -->
-
- <dependency>
- <groupId>org.osgi</groupId>
- <artifactId>org.osgi.core</artifactId>
- <version>${osgi.core.version}</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
- <groupId>org.osgi</groupId>
- <artifactId>org.osgi.compendium</artifactId>
- <version>${osgi.core.version}</version>
- <scope>provided</scope>
- </dependency>
-
- <!-- Invalid manifest header Import-Package: "com.sun.jdmk.comm;resolution:="optional"" : Cannot import a package more than once "com.sun.jdmk.comm"-->
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- <scope>provided</scope>
- </dependency>
-
- <!-- Spring DM -->
- <dependency>
- <groupId>net.sourceforge.cglib</groupId>
- <artifactId>com.springsource.net.sf.cglib</artifactId>
- <version>${cglib.version}</version>
- </dependency>
- <dependency>
- <groupId>org.springframework.osgi</groupId>
- <artifactId>spring-osgi-annotation</artifactId>
- <version>${spring.dm.version}</version>
- </dependency>
- <dependency>
- <groupId>org.springframework.osgi</groupId>
- <artifactId>spring-osgi-extender</artifactId>
- <version>${spring.dm.version}</version>
- </dependency>
- <!-- Spring -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>org.springframework.context</artifactId>
- <version>${spring.version}</version>
- </dependency>
-
- <!-- Java Extension Implementations -->
- <!-- Appears unrequired dependency>
- <groupId>javax.xml.bind</groupId>
- <artifactId>com.springsource.javax.xml.bind</artifactId>
- <version>2.2.0</version>
- </dependency-->
- <dependency>
- <groupId>javax.activation</groupId>
- <artifactId>com.springsource.javax.activation</artifactId>
- <version>${activation.version}</version>
- </dependency>
- <!-- The bundle "com.springsource.bsh_2.0.0.b4 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.servlet; version="[2.5.0,3.0.0)" -->
- <dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>com.springsource.javax.servlet</artifactId>
- <version>2.5.0</version>
- </dependency>
- <!-- The bundle "com.springsource.org.apache.axis_1.4.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.jms; version="[1.1.0,2.0.0)" -->
- <dependency>
- <groupId>javax.jms</groupId>
- <artifactId>com.springsource.javax.jms</artifactId>
- <version>1.1.0</version>
- </dependency>
- <!-- The bundle "com.springsource.javax.xml.rpc_1.1.0 " could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.soap; version="[1.3.0,2.0.0)" -->
- <dependency>
- <groupId>javax.xml.soap</groupId>
- <artifactId>com.springsource.javax.xml.soap</artifactId>
- <version>1.3.0</version>
- </dependency>
- <!-- The bundle "com.springsource.com.thoughtworks.xstream_1.4.1" could not be resolved. Reason: Missing Constraint: Import-Package: javax.xml.stream; version="[1.0.1,2.0.0)" -->
- <dependency>
- <groupId>javax.xml.stream</groupId>
- <artifactId>com.springsource.javax.xml.stream</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>com.springsource.javax.mail</artifactId>
- <version>${mail.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>${commons.codec.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-configuration</groupId>
- <artifactId>commons-configuration</artifactId>
- <version>1.10</version>
- </dependency>
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>2.2.11</version>
- </dependency>
-
-
- <!-- OSGi Enterprise Services -->
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>xml-parser-service</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>xml-transformer-service</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <!-- The bundle "uk.org.taverna.commons.taverna-plugin-impl_0.1.0.SNAPSHOT" could not be resolved. Reason: Missing Constraint: Import-Package: org.osgi.service.event; version="[1.3.0,2.0.0)" -->
- <dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.apache.felix.eventadmin</artifactId>
- <version>1.3.2</version>
- </dependency>
- <!-- Appears unrequired dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.apache.felix.configadmin</artifactId>
- <version>1.6.0</version>
- </dependency-->
-
- <!-- Taverna Activities -->
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-dataflow-activity</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-stringconstant-activity</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
-
- <!-- Taverna Common Activities -->
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-beanshell-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-external-tool-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- <!-- VERY broken :(
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-interaction-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- -->
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-rest-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-spreadsheet-import-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-wsdl-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-xpath-activity</artifactId>
- <version>${taverna.commonactivities.version}</version>
- </dependency>
-
-
- <!-- Taverna Commandline -->
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-commandline-common</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-commandline-launcher</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
-
- <!-- Taverna Platform -->
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-capability-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-run-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-execution-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-execution-local</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-database-configuration-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-services-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
-
- <!-- Taverna OSGi -->
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-configuration-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-app-configuration-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-download-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-plugin-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-update-impl</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
-
- <!-- Scufl2 -->
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-rdfxml</artifactId>
- <version>${taverna.language.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-t2flow</artifactId>
- <version>${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>
-
- <!-- Data bundle -->
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-databundle</artifactId>
- <version>${taverna.language.version}</version>
- </dependency>
- <!-- HTTP client needed by Data Bundle -->
- <!-- Appears unrequired dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpclient-osgi</artifactId>
- <version>4.2.5</version>
- </dependency-->
- <!-- Appears unrequired dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpcore-osgi</artifactId>
- <version>4.2.5</version>
- </dependency-->
- <!-- Jena bundle needed by jsonld-java-jena -->
- <!-- See https://github.com/stain/jena/tree/jena-bundle/jena-bundle -->
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-osgi</artifactId>
- <version>2.12.2-SNAPSHOT</version>
- </dependency>
- <!-- slf4j implementation -->
- <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: org.slf4j; version="[1.7.0,2.0.0)"-->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- <version>${slf4j.version}</version>
- </dependency>
-
- <!-- Appears unrequired: -->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>${slf4j.version}</version>
- </dependency>
-
- <!-- Taverna Security -->
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-credential-manager-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
-
- <!-- Taverna Workflow Engine -->
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-workflowmodel-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-workflowmodel-core-extensions</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-reference-impl</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-reference-types</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
-
- <!-- Taverna Provenance -->
- <!--dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>provenance-derby</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>provenance-mysql</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency-->
- <!-- The bundle "org.purl.wf4ever.robundle_0.3.1 " could not be resolved. Reason: Missing Constraint: Import-Package: com.fasterxml.jackson.annotation; version="[2.3.0,3.0.0)"-->
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- <version>2.3.0</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
- <version>2.3.0</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>2.3.0</version>
- </dependency>
-
- <dependency>
- <groupId>nu.validator.htmlparser</groupId>
- <artifactId>htmlparser</artifactId>
- <version>${htmlparser.version}</version>
- </dependency>
-
-
-
- </dependencies>
-
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/assembly/dependencies-component.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/dependencies-component.xml b/taverna-commandline-product/src/main/assembly/dependencies-component.xml
deleted file mode 100644
index 0e8640e..0000000
--- a/taverna-commandline-product/src/main/assembly/dependencies-component.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<component
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/component/1.1.2 http://maven.apache.org/xsd/component-1.1.2.xsd">
-
- <fileSets>
- <fileSet>
- <directory>src/main/etc</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- <filtered>true</filtered>
- </fileSet>
- <fileSet>
- <directory>${project.build.directory}/taverna-tmp</directory>
- <fileMode>0755</fileMode>
- <outputDirectory></outputDirectory>
- </fileSet>
- </fileSets>
-
-</component>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/assembly/developer-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/developer-assembly.xml b/taverna-commandline-product/src/main/assembly/developer-assembly.xml
deleted file mode 100644
index ae2a7c3..0000000
--- a/taverna-commandline-product/src/main/assembly/developer-assembly.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>dev</id>
- <formats>
- <format>dir</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/nightly-assembly.xml b/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
deleted file mode 100644
index f82e793..0000000
--- a/taverna-commandline-product/src/main/assembly/nightly-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>nightly</id>
- <baseDirectory>taverna-command-line-${project.version}-${buildNumber}-nightly</baseDirectory>
- <formats>
- <!-- <format>dir</format> -->
- <format>zip</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/assembly/release-assembly.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/assembly/release-assembly.xml b/taverna-commandline-product/src/main/assembly/release-assembly.xml
deleted file mode 100644
index 61da752..0000000
--- a/taverna-commandline-product/src/main/assembly/release-assembly.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<assembly
- xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
- <id>release</id>
- <baseDirectory>taverna-command-line-${project.version}</baseDirectory>
- <formats>
- <!-- <format>dir</format> -->
- <format>zip</format>
- </formats>
- <componentDescriptors>
- <componentDescriptor>dependencies-component.xml</componentDescriptor>
- </componentDescriptors>
-</assembly>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/etc/conf/log4j.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/log4j.properties b/taverna-commandline-product/src/main/etc/conf/log4j.properties
deleted file mode 100644
index 5014f2b..0000000
--- a/taverna-commandline-product/src/main/etc/conf/log4j.properties
+++ /dev/null
@@ -1,14 +0,0 @@
-# By default, WARN (our external libraries)
-log4j.rootLogger=INFO, CONSOLE
-
-# Get rid of some xml sec warnings
-log4j.logger.org.apache.ws.security=ERROR
-log4j.logger.org.apache.commons.httpclient=ERROR
-
-# Default output to console is restrictive
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
-
-# Output WARN and above to console -
-log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/etc/conf/logging.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/logging.properties b/taverna-commandline-product/src/main/etc/conf/logging.properties
deleted file mode 100644
index b03a43f..0000000
--- a/taverna-commandline-product/src/main/etc/conf/logging.properties
+++ /dev/null
@@ -1,10 +0,0 @@
-handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
-
-.level = ALL
-
-java.util.logging.ConsoleHandler.level = WARNING
-java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-
-java.util.logging.FileHandler.level = ALL
-java.util.logging.FileHandler.count = 5
-java.util.logging.FileHandler.limit = 1048576
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/conf/taverna.app.properties b/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
deleted file mode 100644
index 91522d4..0000000
--- a/taverna-commandline-product/src/main/etc/conf/taverna.app.properties
+++ /dev/null
@@ -1,2 +0,0 @@
-taverna.app.name=taverna-cl-3.0.0
-taverna.app.title=Taverna Command Line 3.0.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/etc/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.bat b/taverna-commandline-product/src/main/etc/executeworkflow.bat
deleted file mode 100644
index 2e18831..0000000
--- a/taverna-commandline-product/src/main/etc/executeworkflow.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-@ECHO OFF
-
-REM Taverna startup script
-
-REM distribution directory
-set TAVERNA_HOME=%~dp0
-
-
-REM 1 GB memory, 400 MB for classes
-set ARGS=-Xmx1g -XX:MaxPermSize=400m
-
-REM Taverna system properties
-set ARGS=%ARGS% "-Dlog4j.configuration=file:///%TAVERNA_HOME%conf/log4j.properties"
-set ARGS=%ARGS% "-Djava.util.logging.config.file=%TAVERNA_HOME%conf/logging.properties"
-set ARGS=%ARGS% "-Dtaverna.app.startup=%TAVERNA_HOME%."
-
-java %ARGS% -jar "%TAVERNA_HOME%lib\/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-product/src/main/etc/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/taverna-commandline-product/src/main/etc/executeworkflow.sh b/taverna-commandline-product/src/main/etc/executeworkflow.sh
deleted file mode 100644
index 5ef0916..0000000
--- a/taverna-commandline-product/src/main/etc/executeworkflow.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/sh
-
-set -e
-
-## resolve links - $0 may be a symlink
-prog="$0"
-
-real_path() {
- readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
-}
-
-realprog=`real_path "$prog"`
-taverna_home=`dirname "$realprog"`
-javabin=java
-if test -x "$JAVA_HOME/bin/java"; then
- javabin="$JAVA_HOME/bin/java"
-fi
-
-# 1 GB memory, 400 MB for classes
-exec "$javabin" -Xmx1g -XX:MaxPermSize=400m \
- "-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
- "-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
- "-Dtaverna.app.startup=$taverna_home" \
- -jar "$taverna_home/lib/org.apache.taverna.commandline/taverna-commandline-launcher-3.1.0.incubating-SNAPSHOT.jar" \
- ${1+"$@"}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/d57ed128/taverna-commandline-tests/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-tests/pom.xml b/taverna-commandline-tests/pom.xml
deleted file mode 100644
index e28c4a0..0000000
--- a/taverna-commandline-tests/pom.xml
+++ /dev/null
@@ -1,71 +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>
- <artifactId>taverna-command-line-tests</artifactId>
- <name>Apache Taverna Commandline Tests</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.12</version>
- <configuration>
- <systemPropertyVariables>
- <buildDirectory>${project.build.directory}</buildDirectory>
- </systemPropertyVariables>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-t2flow</artifactId>
- <version>${taverna.language.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-rdfxml</artifactId>
- <version>${taverna.language.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.8.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>2.2</version>
- <scope>test</scope>
- </dependency>
- <!-- Optional for scufl2-xdfxml -->
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>2.2.4-1</version>
- <scope>test</scope>
- </dependency>
- <!-- Required by scufl2-xdfxml, see SCUFL2-122 -->
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>1.1.0</version>
- <scope>test</scope>
- </dependency>
- <!-- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>jdom</artifactId>
- <version>1.1.2</version>
- <scope>test</scope>
- </dependency> -->
- </dependencies>
-</project>