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tl;dr: The Taverna code base is no longer maintained and is provided here for archival purposes.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 project Apache Taverna (incubating) (see web archive and podling status).

In 2020 the Taverna community voted 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While the code base is no longer actively maintained, Pull Requests are welcome to the GitHub organization taverna, which may infrequently be considered by remaining volunteer caretakers.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/

Taverna Engine

Workflow engine for Taverna.

The engine executes a Taverna workflow, defined using Taverna Language.

Note that the engine does not include the activity implementations that actually perform work (e.g. calling a REST service). To use the engine, use the Taverna Command Line or Taverna Server.

All Taverna Engine modules are also valid OSGi bundles, providing OSGi Spring services.

License

• (c) 2007-2014 University of Manchester
• (c) 2014-2018 Apache Software Foundation

This product includes software developed at The Apache Software Foundation.

Licensed under the Apache License 2.0, see the LICENSE file for details.

The NOTICE file contains any additional attributions as well as details about embedded third-party libraries and source code.

Contribute

Any contributions received are assumed to be covered by the Apache License 2.0.

Prerequisites

• Java 1.8 or newer (tested with OpenJDK 1.8)
• Apache Maven 3.2.5 or newer (older versions probably also work)

This code relies on other Taverna modules, which Maven shuold automatically download from Apache's Maven repository; however you might want to compile these yourself in the below order:

• taverna-language
• taverna-osgi

Please see the <properties> of this 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 lenght, e.g. C:\src - as Windows has a limitation on the total path length 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 that enforces Apache headers in every source file - to disable it, try:

mvn clean install -Drat.skip=true

Modules

The Taverna Engine modules are generally split into -api and -impl. The -api modules contain Java interfaces, abstract classes, and minimal dependencies while -impl modules contain the corresponding implementation(s).

Thus, the taverna-common-activities should only need to depend on the -api modules, while the -impl are added by the packaging of the taverna-commandline-product.

• taverna-capability-api Taverna Platform Capability API
• taverna-capability-impl Taverna Platform Capability impl
• taverna-credential-manager-api Taverna Credential Manager API
• taverna-credential-manager-impl Taverna Credential Manager impl
• taverna-database-configuration-api Taverna Database Configuration API
• taverna-database-configuration-impl Taverna Database Configuration impl
• taverna-execution-api Taverna Platform Execution Service API
• taverna-execution-impl Taverna Platform Execution Service impl
• taverna-execution-local Taverna Platform Local Execution Service
• taverna-reference-api Taverna Reference Manager API
• taverna-reference-impl Taverna Reference Manager impl
• taverna-reference-types Taverna Engine Reference Types
• taverna-report-api Taverna Platform Report Service
• taverna-run-api Taverna Platform Run Service API
• taverna-run-impl Taverna Platform Run Service impl
• taverna-services-api Taverna Services API
• taverna-services-impl Taverna Platform Services impl
• taverna-workflowmodel-api Taverna Workflow Model API
• taverna-workflowmodel-impl Taverna Workflow Model impl
• taverna-workflowmodel-extensions Taverna Workflow Model Extension Points

These modules include utilities used by the above, or for test purposes:

• taverna-observer Taverna Observer pattern
• taverna-activity-test-utils Taverna Activity test utils
• taverna-reference-testhelpers Taverna Reference Test Helpers

These modules include structural workflow activities:

• taverna-dataflow-activity Taverna Dataflow Activity
• taverna-stringconstant-activity Taverna StringConstant Activity

See the separate release of taverna-common-activities for activities that invoke Beanshell, WSDL, REST and command line tool services.

These modules are experimental:

• taverna-execution-remote Taverna Platform Remote Execution Service
• taverna-execution-hadoop Taverna Hadoop Workflow Execution Service

These modules are not yet fully updated to Taverna 3 (contributions welcome!):

• taverna-activity-archetype Taverna Activity archetype
• taverna-prov Taverna PROV support ()
• taverna-provenanceconnector Taverna Provenance Connector
• taverna-prov-owl-bindings Taverna PROV OWL bindings

See the taverna-engine JavaDoc for more details.

Which module does what?

This section shows how different Taverna Engine module are involved when running a Taverna workflow, e.g. from the Taverna Command Line.

There are two layers of Taverna Engine:

• Taverna Platform provides an outer API for creating and managing workflow runs, potentially remotely.
• Taverna Core (aka workflowmodel, formerly t2.core) is the orchestrating part of the Taverna Engine. Its Activity is implemented by multiple plugins depending on the activity type.

Preparations

• Load a SCUFL2 WorkflowBundle from a .wfbundle or .t2flow file using WorkflowBundleIO from Taverna Language.

• (Optional) Choose a Workflow to bind workflows (usually the main workflow).
• (Optional) Choose a Profile to bind workflow implementations. (There is normally only one profile.)

• Create or load a Bundle with the expected inputs of the main workflow using DataBundles from Taverna Language.

Running a workflow

• You must be running within OSGi to support multiple Taverna activities and their dependencies, e.g. by using the OsgiLauncher from Taverna OSGi. See the TavernaStarter example for details.
• (Optional) Populate service credentials (username/password) to be used by the workflow into the CredentialManager from taverna-credential-manager-api.
• Use the RunService from the taverna-run-api (discovered as a Spring service).
• Use runService.getExecutionEnvironments() to find an executer for your workflow bundle or profile.
  • The RunService selects an appropriate ExecutionService service (taverna-execution-api), checking the Profile against the installed activity types from common-activities and plugins; discovered by the taverna-capability-api.
  • In the Taverna Command Line there is typically only one match, a LocalExecutionEnvironment, representing the LocalExecutionService from taverna-execution-local.
  • The experimental module taverna-execution-remote aims to execute a workflow on a remote Taverna Server - e.g. for running workflows remotely from Taverna Workbench.
  • The prototype module taverna-execution-hadoop is an attempt to execute compatible Taverna workflows as an Apache Hadoop map-reduce workflow. (This code needs to be updated for newer Hadoop releases.) For details, see the SCAPE report on feasibility of parallelising preservation processes.
• Create an execution job, and provide the ExecutionEnvironment, the WorkflowBundle, its Workflow, Profile and data Bundle with inputs. A workflow run id String is returned for subsequent calls.
  • Typically this creates a LocalExecution instance (taverna-execution-local), which converts the abstract SCUFL2 Workflow to an executable Dataflow (taverna-workflowmodel-api) which has corresponding Processors and Activity implementations from the installed plugins.
  • A WorkflowInstanceFacade is prepared - the engine's top-level representation of a workflow run.
  • A LocalExecutionManager is added as a bridge between the Taverna Core engine and the Platform.
• Start the run using runService.start().
  • Input values from the data Bundle are converted to be registered with a ReferenceService (taverna-reference-api) - as Taverna workflows pass T2References.
  • Values are represented as either a InlineStringReference or InlineByteArrayReference, or could be external HttpReferences or FileReferences (taverna-reference-types). These types are recognized by the Activity implementations, allowing pass-by-reference where supported, with conversion to strings and bytes if needed.
  • Lists, values and references are stored in memory.
  • This was previously backed by Hibernate stored in Apache Derby - this code was removed due to license incompatibility.
  • TODO: Add a different ReferenceSetDao implementation that is backed directly by the platform's Bundle (effectively file-based).
• Monitor the state of the run or get the WorkflowReport for detailed progress (taverna-report-api), such as the number of jobs completed for a given Processor.
• Once the workflow is COMPLETED (and even while it is RUNNING), you can retrieve the bundle containing the output values and intermediate values.
  • To relate intermediate values, you will need to inspect either the WorkflowReport, ProcessorReport or ActivityReports to get the invocations, which provide the inputs and outputs as Paths within the bundle.

Spring services

The OSGi services should be discoverable as Spring services, e.g., by adding the following code to your META-INF/spring/update-context-osgi.xml:

  <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">

  <reference id="executionService" interface="org.apache.taverna.platform.execution.api.ExecutionService"/>
  <reference id="runService" interface="org.apache.taverna.platform.run.api.RunService"/>
  <reference id="credentialManager" interface="org.apache.taverna.security.credentialmanager.CredentialManager" />
  <reference id="databaseConfiguration" interface="org.apache.taverna.configuration.database.DatabaseConfiguration" />
  <reference id="databaseManager" interface="org.apache.taverna.configuration.database.DatabaseManager" />

  </beans:beans>

You might want to combine these with the Taverna OSGi services.

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-credential-manager-impl manages an encrypted keystore for username/passwords and client/server SSL certificates. It is designed to be used with Java Secure Socket Extension (JSSE), Java Cryptography Extension (JCE), and depends on the BouncyCastle bcprov encryption library. The JCE Unlimited Strength Jurisdiction Policy may need to be installed separately to use keystore passwords with 7 or more characters.
• Taverna Engine depends on Taverna Language, Taverna OSGi and Apache Jena, which depend on Apache HttpComponents Client, which can initiate encrypted https:// connections using Java Secure Socket Extension (JSSE).
• taverna-database-configuration-impl and taverna-reference-impl depend on Apache Derby, which uses the Java Cryptography Extension (JCE) API.