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| |
| # Taverna Command-line Tool |
| |
| ## Taverna Project Retired |
| |
| > tl;dr: The Taverna code base is **no longer maintained** |
| > and is provided here for archival purposes. |
| |
| From 2014 till 2020 this code base was maintained by the |
| [Apache Incubator](https://incubator.apache.org/) project _Apache Taverna (incubating)_ |
| (see [web archive](https://web.archive.org/web/20200312133332/https://taverna.incubator.apache.org/) |
| and [podling status](https://incubator.apache.org/projects/taverna.html)). |
| |
| In 2020 the Taverna community |
| [voted](https://lists.apache.org/thread.html/r559e0dd047103414fbf48a6ce1bac2e17e67504c546300f2751c067c%40%3Cdev.taverna.apache.org%3E) |
| to **retire** Taverna as a project and withdraw the code base from the Apache Software Foundation. |
| |
| This code base remains available under the Apache License 2.0 |
| (see _License_ below), but is now simply called |
| _Taverna_ rather than ~~Apache Taverna (incubating)~~. |
| |
| While the code base is no longer actively maintained, |
| Pull Requests are welcome to the |
| [GitHub organization taverna](http://github.com/taverna/), |
| which may infrequently be considered by remaining |
| volunteer caretakers. |
| |
| |
| ### Previous releases |
| |
| Releases 2015-2018 during incubation at Apache Software Foundation |
| are available from the ASF Download Archive <https://archive.apache.org/dist/incubator/taverna/> |
| |
| Releases 2014 from the University of Manchester are on BitBucket <https://bitbucket.org/taverna/> |
| |
| Releases 2009-2013 from myGrid are on LaunchPad <https://launchpad.net/taverna/> |
| |
| Releases 2003-2009 are on SourceForge <https://sourceforge.net/projects/taverna/files/taverna/> |
| |
| Binary JARs for Taverna are available from |
| Maven Central <https://repo.maven.apache.org/maven2/org/apache/taverna/> |
| or the myGrid Maven repository <https://repository.mygrid.org.uk/> |
| |
| |
| |
| ## About Taverna Command-line Tool |
| |
| Taverna Command-line Tool provides a shell command |
| for executing |
| [Taverna](https://web.archive.org/web/*/https://taverna.incubator.apache.org/) workflows, |
| defined using either the [Taverna Language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/) |
| API in the |
| [SCUFL2](https://web.archive.org/web/*/https://taverna.incubator.apache.org/documentation/scufl2/) |
| `.wfbundle` format, or in the `.t2flow` format from |
| [Taverna Workbench 2.5](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/workbench/). |
| |
| Workflow inputs can be provided as parameters or files, |
| while outputs can be saved either to a folder or a |
| [Research Object bundle](https://w3id.org/bundle) |
| including detailed provenance, which can be inspected |
| using Taverna Language's |
| [DataBundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/databundle/DataBundles.html) |
| support. |
| |
| In addition to the |
| [Taverna Common Activities](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/common-activities/), |
| the Command-line supports plugins using |
| [Taverna OSGi services](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/osgi/). |
| |
| |
| Note that, except for command-line handling, this |
| module relies on other |
| [Taverna components](https://web.archive.org/web/*/https://taverna.incubator.apache.org/code) for the actual workflow execution. |
| |
| |
| ## License |
| |
| * (c) 2007-2014 University of Manchester |
| * (c) 2014-2020 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](http://taverna.incubator.apache.org/community/lists#dev) mailing list |
| mailing list for any questions, suggestions and discussions about |
| Taverna. |
| |
| Bugs and planned features are tracked in the Jira |
| [issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326812) |
| under the `TAVERNA` component _Taverna Command-line Tool._ Feel free |
| to [add an issue](https://web.archive.org/web/*/https://taverna.incubator.apache.org/community/issue-tracker)! |
| |
| To suggest changes to this source code, feel free to raise a |
| [GitHub pull request](https://github.com/apache/incubator-taverna-commandline/pulls). |
| --> |
| |
| Taverna Command-line Tool product relies on |
| [other Taverna components](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/code/) |
| which have their own source code repositories. |
| |
| Any contributions received are assumed to be covered by the |
| [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0). |
| |
| |
| ## 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 |
| [Taverna modules](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/code/), |
| which Maven should download |
| automatically from |
| [Apache's Maven repository](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/maven/); |
| however you might want to compile these yourself in the order below: |
| |
| * [taverna-language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/) |
| * [taverna-osgi](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/osgi/) |
| * [taverna-engine](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/engine/) |
| * [taverna-common-activities](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/common-activities/) |
| |
| 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 its tests. |
| |
| Note that this repository relies on |
| other [Taverna modules](https://web.archive.org/web/*/https://taverna.incubator.apache.org/code) |
| which will be downloaded from Maven repositories if they are not |
| already present in the equivalent of your `~/.m2/repository` in the |
| correct version. |
| |
| ## 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 |
| 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 |
| |
| |
| ## SNAPSHOT dependencies |
| |
| If you are building a non-released version of this repository, |
| (e.g. the `pom.xml` declares a `-SNAPSHOT` version), then Maven might |
| download unreleased |
| [snapshot builds](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/code/#snapshot-builds) |
| for other `-SNAPSHOT` Taverna dependencies. |
| |
| |
| If you are developing one of the |
| [Taverna modules](https://web.archive.org/web/*/http://taverna.incubator.apache.org/download/code) |
| and want to test it with the |
| Taverna Command-line Tool, make sure you build it |
| locally first with `mvn clean install` to avoid downloading it from |
| the snapshot repository. |
| |
| Then check that the the `<properties>` section of the `pom.xml` |
| matches the `<version>` of the module you are developing. |
| See also `taverna-commandline-product/pom.xml` |
| to hard-code versions of other dependencies. |
| |
| The default SNAPSHOT update policy for `mvn` is _daily_ - |
| you can modify this behaviour with |
| `--update-snapshots` or `--no-snapshot-updates` |
| |
| |
| ## Binary distribution |
| |
| To build a binary distribution ZIP file that |
| includes third-party dependencies as JAR files, |
| build with the `-Prelease` option, which would make |
| `taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-release.zip` |
| or equivalent. |
| |
| After building, see the file `target/maven-shared-archive-resources/META-INF/DEPENDENCIES` for |
| details of the licenses of the third-party dependencies. All dependencies should |
| be [compatible with Apache License 2.0](http://www.apache.org/legal/resolved.html). |
| |
| |
| # Running |
| |
| After [building](#building), see the `taverna-commandline-product/target` |
| directory. Inside you should find a folder like |
| `apache-taverna-commandline-3.1.0-incubating/` |
| which contains the built Taverna Command-line Tool product. |
| |
| If you prefer a ZIP file, then instead build with |
| the Maven `-Prelease` option. You can then unzip at a location of |
| your choice. |
| |
| If you are running on Windows you may need to |
| put Taverna Command-line Tool in a folder high in the |
| disk hierarchy (e.g. `C:\Taverna`), this helps |
| avoid problems with Windows path-length restrictions. |
| |
| |
| Running `executeworkflow.sh` (or `executeworkflow.bat`) without arguments |
| will show the help: |
| |
| ``` |
| $ ./executeworkflow.sh |
| usage: executeworkflow [options] [workflow] |
| -bundle <bundle> Save outputs to a new Workflow |
| Run Bundle (zip). |
| -clientserver Connect as a client to a derby |
| server instance. |
| -cmdir <directory path> Absolute path to a directory |
| where Credential Manager's files |
| (keystore and truststore) are |
| located. |
| ... |
| ``` |
| |
| The folder `examples` contains a Hello World type example workflow in |
| [SCUFL2 format](http://taverna.incubator.apache.org/documentation/scufl2/). |
| |
| ``` |
| $ ./executeworkflow.sh examples/helloworld.wfbundle |
| Outputs will be saved to the directory: /home/johndoe/apache-taverna-commandline-3.1.0/Hello_World_output |
| Workflow completed. |
| |
| $ cat Hello_World_output/greeting ; echo |
| Hello, World! |
| ``` |
| |
| On Windows: |
| |
| ``` |
| C:\home\apache-taverna-commandline-3.1.0>executeworkflow.bat examples\helloworld.wfbundle |
| Outputs will be saved to the directory: C:\home\apache-taverna-commandline-3.1.0\Hello_World_output |
| Workflow completed. |
| |
| C:\home\apache-taverna-commandline-3.1.0>type Hello_World_output\greeting |
| Hello, World! |
| ``` |
| |
| # 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 Command-line Tool depends on and interacts with the |
| [Taverna Engine](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/engine/), |
| credential manager. |
| * After building, the [taverna-commandline-product](taverna-commandline-product) |
| archive `lib` folder includes |
| [BouncyCastle](https://www.bouncycastle.org/) bcprov encryption library, |
| [Apache HttpComponents](https://hc.apache.org/) Core and Client, |
| [Apache Derby](http://db.apache.org/derby/), |
| [Jetty](http://www.eclipse.org/jetty/), |
| [Apache WSS4J](https://ws.apache.org/wss4j/), |
| [Apache XML Security for Java](https://santuario.apache.org/javaindex.html), |
| [Open SAML Java](https://shibboleth.net/products/opensaml-java.html), |
| [Taverna Language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/), |
| [Taverna OSGi](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/osgi/), |
| [Taverna Engine](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/engine/), |
| and |
| [Taverna Common Activities](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/common-activities/). |
