README.md - incubator-taverna-common-activities - Git at Google

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 # Apache Taverna Common Activities

 Common Activities to be invoked as part of
 [Apache Taverna](https://taverna.incubator.apache.org/) workflows.

 Note that this module relies on other
 [Apache Taverna modules](https://taverna.incubator.apache.org/code) for
 the actual workflow execution.


 ## License

 * (c) 2007-2014 University of Manchester
 * (c) 2014-2016 Apache Software Foundation

 This product includes software developed at The
 [Apache Software Foundation](http://www.apache.org/).

 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file
 [LICENSE](LICENSE) for details.

 The file [NOTICE](NOTICE) contains any additional attributions and
 details about embedded third-party libraries and source code.


 # Contribute

 Please subscribe to and contact the
 [dev@taverna](https://taverna.incubator.apache.org/community/lists#dev mailing list)
 mailing list for any questions, suggestions and discussions about
 Apache Taverna.

 Bugs and planned features are tracked in the Jira
 [Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326811)
 under the `TAVERNA` component _Taverna Common Activities._ Feel free
 to add an issue!

 To suggest changes to this source code, feel free to raise a
 [GitHub pull request](https://github.com/apache/incubator-taverna-common-activities/pulls).
 Any contributions received are assumed to be covered by the [Apache License
 2.0](https://www.apache.org/licenses/LICENSE-2.0). We might ask you
 to sign a [Contributor License Agreement](https://www.apache.org/licenses/#clas)
 before accepting a larger contribution.

 ## Disclaimer

 Apache Taverna is an effort undergoing incubation at the
 [Apache Software Foundation (ASF)](http://www.apache.org/),
 sponsored by the [Apache Incubator PMC](http://incubator.apache.org/).

 [Incubation](http://incubator.apache.org/incubation/Process_Description.html)
 is required of all newly accepted projects until a further review
 indicates that the infrastructure, communications, and decision-making process
 have stabilized in a manner consistent with other successful ASF projects.

 While incubation status is not necessarily a reflection of the completeness
 or stability of the code, it does indicate that the project has yet to be
 fully endorsed by the ASF.


 ## Prerequisites

 * Java 1.8 or newer (tested with OpenJDK 1.8)
 * [Apache Maven](https://maven.apache.org/download.html) 3.2.5 or newer (older
   versions probably also work)

 This code relies on other
 [Apache Taverna modules](https://taverna.incubator.apache.org/download/code/),
 which Maven shuold automatically
 download from
 [Apache's Maven repository](https://taverna.incubator.apache.org/download/maven/);
 however you might want to compile these yourself in the below order:

 * [taverna-language](https://taverna.incubator.apache.org/download/language/)
 * [taverna-osgi](https://taverna.incubator.apache.org/download/osgi/)
 * [taverna-engine](https://taverna.incubator.apache.org/download/engine/)

 Please see the `<properties>` of this [pom.xml](pom.xml) to find the
 correct versions to build.


 # Building

 To build, use

     mvn clean install

 This will build each module and run their tests.


 ## Building on Windows

 If you are building on Windows, ensure you unpack this source code
 to a folder with a [short path name](http://stackoverflow.com/questions/1880321/why-does-the-260-character-path-length-limit-exist-in-windows)
 lenght, e.g. `C:\src` - as
 Windows has a [limitation on the total path length](https://msdn.microsoft.com/en-us/library/aa365247%28VS.85%29.aspx#maxpath)
 which might otherwise
 prevent this code from building successfully.


 ## Skipping tests

 To skip the tests (these can be time-consuming), use:

     mvn clean install -DskipTests


 If you are modifying this source code independent of the
 Apache Taverna project, you may not want to run the
 [Rat Maven plugin](https://creadur.apache.org/rat/apache-rat-plugin/)
 that enforces Apache headers in every source file - to disable it, try:

     mvn clean install -Drat.skip=true

 # Modules

 Each module implement a particular type of
 Taverna [Activity](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html).

 * [taverna-beanshell-activity](taverna-beanshell-activity/): Apache Taverna Beanshell Activity,
   runs [Beanshell](https://github.com/beanshell/beanshell/) scripts.
 * [taverna-external-tool-activity](taverna-external-tool-activity/): Apache Taverna External Tool Activity,
   run command line locally or over SSH
 * [taverna-interaction-activity](taverna-interaction-activity/): Apache Taverna Interaction Activity,
   ask questions to the user through a browser
 * [taverna-rest-activity](taverna-rest-activity/): Apache Taverna REST Activity,
   invoke [RESTful](https://en.wikipedia.org/wiki/Representational_state_transfer) HTTP(S) web services based on a URI template.
 * [taverna-spreadsheet-import-activity](taverna-spreadsheet-import-activity/): Apache Taverna Spreadsheet Import Activity,
   imports from CSV, Excel and OpenOffice.
 * [taverna-wsdl-activity](taverna-wsdl-activity/): Apache Taverna WSDL Activity,
   invoke [WSDL](https://en.wikipedia.org/wiki/Web_Services_Description_Language)-described SOAP services.
 * [taverna-wsdl-generic](taverna-wsdl-generic/): Apache Taverna WSDL-generic Library,
   library for parsing WSDL and calling SOAP services
 * [taverna-xpath-activity](taverna-xpath-activity/): Apache Taverna XPath Activity,
   select XML fragments using [XPath](https://www.w3.org/TR/xpath/) expressions


 # Export restrictions

 This distribution includes cryptographic software.
 The country in which you currently reside may have restrictions
 on the import, possession, use, and/or re-export to another country,
 of encryption software. BEFORE using any encryption software,
 please check your country's laws, regulations and policies
 concerning the import, possession, or use, and re-export of
 encryption software, to see if this is permitted.
 See <http://www.wassenaar.org/> for more information.

 The U.S. Government Department of Commerce, Bureau of Industry and Security (BIS),
 has classified this software as Export Commodity Control Number (ECCN) 5D002.C.1,
 which includes information security software using or performing
 cryptographic functions with asymmetric algorithms.
 The form and manner of this Apache Software Foundation distribution makes
 it eligible for export under the License Exception
 ENC Technology Software Unrestricted (TSU) exception
 (see the BIS Export Administration Regulations, Section 740.13)
 for both object code and source code.

 The following provides more details on the included cryptographic software:

 * [taverna-rest-activity](taverna-rest-activity)
   depends on
   [Apache HttpComponents](https://hc.apache.org/) Client,
   and can be configured to initiate
   `https://` connections.
 * [taverna-wsdl-generic](taverna-wsdl-generic)
   and [taverna-wsdl-activity](taverna-wsdl-activity) use
   [Java Secure Socket Extension](https://docs.oracle.com/javase/8/docs/technotes/guides/security/jsse/JSSERefGuide.html)
   (JSSE) and depend on
   [Apache WSS4J](https://ws.apache.org/wss4j/),
   [Apache XML Security for Java](https://santuario.apache.org/javaindex.html)
   for accessing secure SOAP Web Services.
 * Apache Taverna Common Activities depends on the
   [Apache Taverna Engine](http://taverna.incubator.apache.org/download/engine/)
   Credential Manager API for
   management of username/password and client/server SSL certificates.
 * [taverna-interaction-activity](taverna-interaction-activity) depends on
   [Jetty](http://www.eclipse.org/jetty/),
   which includes UnixCrypt.java for one way cryptography, and can be
   configured for SSL encryption using
   [Java Secure Socket Extension](https://docs.oracle.com/javase/8/docs/technotes/guides/security/jsse/JSSERefGuide.html).
	<!--
	Licensed to the Apache Software Foundation (ASF) under one or more
	contributor license agreements. See the NOTICE file distributed with
	this work for additional information regarding copyright ownership.
	The ASF licenses this file to You under the Apache License, Version 2.0
	(the "License"); you may not use this file except in compliance with
	the License. You may obtain a copy of the License at

	http://www.apache.org/licenses/LICENSE-2.0

	Unless required by applicable law or agreed to in writing, software
	distributed under the License is distributed on an "AS IS" BASIS,
	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	See the License for the specific language governing permissions and
	limitations under the License.
	-->

	# Apache Taverna Common Activities

	Common Activities to be invoked as part of
	[Apache Taverna](https://taverna.incubator.apache.org/) workflows.

	Note that this module relies on other
	[Apache Taverna modules](https://taverna.incubator.apache.org/code) for
	the actual workflow execution.


	## License

	* (c) 2007-2014 University of Manchester
	* (c) 2014-2016 Apache Software Foundation

	This product includes software developed at The
	[Apache Software Foundation](http://www.apache.org/).

	Licensed under the
	[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file
	[LICENSE](LICENSE) for details.

	The file [NOTICE](NOTICE) contains any additional attributions and
	details about embedded third-party libraries and source code.


	# Contribute

	Please subscribe to and contact the
	[dev@taverna](https://taverna.incubator.apache.org/community/lists#dev mailing list)
	mailing list for any questions, suggestions and discussions about
	Apache Taverna.

	Bugs and planned features are tracked in the Jira
	[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326811)
	under the `TAVERNA` component _Taverna Common Activities._ Feel free
	to add an issue!

	To suggest changes to this source code, feel free to raise a
	[GitHub pull request](https://github.com/apache/incubator-taverna-common-activities/pulls).
	Any contributions received are assumed to be covered by the [Apache License
	2.0](https://www.apache.org/licenses/LICENSE-2.0). We might ask you
	to sign a [Contributor License Agreement](https://www.apache.org/licenses/#clas)
	before accepting a larger contribution.

	## Disclaimer

	Apache Taverna is an effort undergoing incubation at the
	[Apache Software Foundation (ASF)](http://www.apache.org/),
	sponsored by the [Apache Incubator PMC](http://incubator.apache.org/).

	[Incubation](http://incubator.apache.org/incubation/Process_Description.html)
	is required of all newly accepted projects until a further review
	indicates that the infrastructure, communications, and decision-making process
	have stabilized in a manner consistent with other successful ASF projects.

	While incubation status is not necessarily a reflection of the completeness
	or stability of the code, it does indicate that the project has yet to be
	fully endorsed by the ASF.



	## Prerequisites

	* Java 1.8 or newer (tested with OpenJDK 1.8)
	* [Apache Maven](https://maven.apache.org/download.html) 3.2.5 or newer (older
	versions probably also work)

	This code relies on other
	[Apache Taverna modules](https://taverna.incubator.apache.org/download/code/),
	which Maven shuold automatically
	download from
	[Apache's Maven repository](https://taverna.incubator.apache.org/download/maven/);
	however you might want to compile these yourself in the below order:

	* [taverna-language](https://taverna.incubator.apache.org/download/language/)
	* [taverna-osgi](https://taverna.incubator.apache.org/download/osgi/)
	* [taverna-engine](https://taverna.incubator.apache.org/download/engine/)

	Please see the `<properties>` of this [pom.xml](pom.xml) to find the
	correct versions to build.


	# Building

	To build, use

	mvn clean install

	This will build each module and run their tests.


	## Building on Windows

	If you are building on Windows, ensure you unpack this source code
	to a folder with a [short path name](http://stackoverflow.com/questions/1880321/why-does-the-260-character-path-length-limit-exist-in-windows)
	lenght, e.g. `C:\src` - as
	Windows has a [limitation on the total path length](https://msdn.microsoft.com/en-us/library/aa365247%28VS.85%29.aspx#maxpath)
	which might otherwise
	prevent this code from building successfully.


	## Skipping tests

	To skip the tests (these can be time-consuming), use:

	mvn clean install -DskipTests


	If you are modifying this source code independent of the
	Apache Taverna project, you may not want to run the
	[Rat Maven plugin](https://creadur.apache.org/rat/apache-rat-plugin/)
	that enforces Apache headers in every source file - to disable it, try:

	mvn clean install -Drat.skip=true

	# Modules

	Each module implement a particular type of
	Taverna [Activity](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html).

	* [taverna-beanshell-activity](taverna-beanshell-activity/): Apache Taverna Beanshell Activity,
	runs [Beanshell](https://github.com/beanshell/beanshell/) scripts.
	* [taverna-external-tool-activity](taverna-external-tool-activity/): Apache Taverna External Tool Activity,
	run command line locally or over SSH
	* [taverna-interaction-activity](taverna-interaction-activity/): Apache Taverna Interaction Activity,
	ask questions to the user through a browser
	* [taverna-rest-activity](taverna-rest-activity/): Apache Taverna REST Activity,
	invoke [RESTful](https://en.wikipedia.org/wiki/Representational_state_transfer) HTTP(S) web services based on a URI template.
	* [taverna-spreadsheet-import-activity](taverna-spreadsheet-import-activity/): Apache Taverna Spreadsheet Import Activity,
	imports from CSV, Excel and OpenOffice.
	* [taverna-wsdl-activity](taverna-wsdl-activity/): Apache Taverna WSDL Activity,
	invoke [WSDL](https://en.wikipedia.org/wiki/Web_Services_Description_Language)-described SOAP services.
	* [taverna-wsdl-generic](taverna-wsdl-generic/): Apache Taverna WSDL-generic Library,
	library for parsing WSDL and calling SOAP services
	* [taverna-xpath-activity](taverna-xpath-activity/): Apache Taverna XPath Activity,
	select XML fragments using [XPath](https://www.w3.org/TR/xpath/) expressions


	# Export restrictions

	This distribution includes cryptographic software.
	The country in which you currently reside may have restrictions
	on the import, possession, use, and/or re-export to another country,
	of encryption software. BEFORE using any encryption software,
	please check your country's laws, regulations and policies
	concerning the import, possession, or use, and re-export of
	encryption software, to see if this is permitted.
	See <http://www.wassenaar.org/> for more information.

	The U.S. Government Department of Commerce, Bureau of Industry and Security (BIS),
	has classified this software as Export Commodity Control Number (ECCN) 5D002.C.1,
	which includes information security software using or performing
	cryptographic functions with asymmetric algorithms.
	The form and manner of this Apache Software Foundation distribution makes
	it eligible for export under the License Exception
	ENC Technology Software Unrestricted (TSU) exception
	(see the BIS Export Administration Regulations, Section 740.13)
	for both object code and source code.

	The following provides more details on the included cryptographic software:

	* [taverna-rest-activity](taverna-rest-activity)
	depends on
	[Apache HttpComponents](https://hc.apache.org/) Client,
	and can be configured to initiate
	`https://` connections.
	* [taverna-wsdl-generic](taverna-wsdl-generic)
	and [taverna-wsdl-activity](taverna-wsdl-activity) use
	[Java Secure Socket Extension](https://docs.oracle.com/javase/8/docs/technotes/guides/security/jsse/JSSERefGuide.html)
	(JSSE) and depend on
	[Apache WSS4J](https://ws.apache.org/wss4j/),
	[Apache XML Security for Java](https://santuario.apache.org/javaindex.html)
	for accessing secure SOAP Web Services.
	* Apache Taverna Common Activities depends on the
	[Apache Taverna Engine](http://taverna.incubator.apache.org/download/engine/)
	Credential Manager API for
	management of username/password and client/server SSL certificates.
	* [taverna-interaction-activity](taverna-interaction-activity) depends on
	[Jetty](http://www.eclipse.org/jetty/),
	which includes UnixCrypt.java for one way cryptography, and can be
	configured for SSL encryption using
	[Java Secure Socket Extension](https://docs.oracle.com/javase/8/docs/technotes/guides/security/jsse/JSSERefGuide.html).