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Posted to commits@taverna.apache.org by st...@apache.org on 2020/03/12 16:26:19 UTC
[incubator-taverna-engine] branch master updated: Taverna retired
from Apache Incubator
This is an automated email from the ASF dual-hosted git repository.
stain pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/incubator-taverna-engine.git
The following commit(s) were added to refs/heads/master by this push:
new 5b180d5 Taverna retired from Apache Incubator
5b180d5 is described below
commit 5b180d5b0e54a9a235346141299ab50b7a1ad5ec
Author: Stian Soiland-Reyes <st...@apache.org>
AuthorDate: Thu Mar 12 17:25:31 2020 +0100
Taverna retired from Apache Incubator
---
DISCLAIMER | 12 +--
NOTICE | 3 +-
README.md | 251 +++++++++++++++++++++++++++++++++----------------------------
3 files changed, 138 insertions(+), 128 deletions(-)
diff --git a/DISCLAIMER b/DISCLAIMER
index 3e3a5ce..aa10f6e 100644
--- a/DISCLAIMER
+++ b/DISCLAIMER
@@ -1,10 +1,2 @@
-Apache Taverna is an effort undergoing incubation at the Apache Software
-Foundation (ASF), sponsored by the Apache Incubator PMC.
-
-Incubation 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.
+Taverna is no longer maintained and this code base
+is provided for archive purposes only.
diff --git a/NOTICE b/NOTICE
index f9c2689..5e1fbdd 100644
--- a/NOTICE
+++ b/NOTICE
@@ -1,5 +1,6 @@
+This product is based on:
Apache Taverna Engine
-Copyright 2014-2018 The Apache Software Foundation
+Copyright 2014-2020 The Apache Software Foundation
This product includes software developed at
The Apache Software Foundation (http://www.apache.org/).
diff --git a/README.md b/README.md
index 4ec6109..a3c078f 100644
--- a/README.md
+++ b/README.md
@@ -14,20 +14,66 @@
See the License for the specific language governing permissions and
limitations under the License.
-->
-# Apache Taverna Engine
+
+
+## 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 tl;dr: The Taverna code base is **no longer maintained**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 <http://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
-[Apache Taverna](http://taverna.incubator.apache.org/) (incubating).
+[Taverna](https://web.archive.org/web/*/https://taverna.incubator.apache.org/).
The engine executes a Taverna workflow, defined using
-[Apache Taverna Language](https://taverna.incubator.apache.org/download/language/).
+[Taverna Language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/).
Note that the engine does not include the
[activity implementations](https://github.com/apache/incubator-taverna-common-activities/)
that actually perform work (e.g. calling a REST service). To
use the engine, use the
-[Apache Taverna Command Line](https://github.com/apache/incubator-taverna-commandline/)
-or [Apache Taverna Server](https://github.com/apache/incubator-taverna-server/).
+[Taverna Command Line](https://github.com/apache/incubator-taverna-commandline/)
+or [Taverna Server](https://github.com/apache/incubator-taverna-server/).
All Taverna Engine modules are also valid [OSGi](http://www.osgi.org/) bundles,
providing OSGi [Spring services](#spring-services).
@@ -50,38 +96,9 @@ 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
-Apache Taverna.
-
-Bugs and planned features are tracked in the Jira
-[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326810)
-under the `TAVERNA` component _Taverna Engine_. 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-engine/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.
+2.0](https://www.apache.org/licenses/LICENSE-2.0).
-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.
@@ -92,14 +109,14 @@ fully endorsed by the ASF.
versions probably also work)
This code relies on other
-[Apache Taverna modules](https://taverna.incubator.apache.org/download/code/),
+[Taverna modules](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/code/),
which Maven shuold automatically
download from
-[Apache's Maven repository](https://taverna.incubator.apache.org/download/maven/);
+[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 below order:
-* [taverna-language](https://taverna.incubator.apache.org/download/language/)
-* [taverna-osgi](https://taverna.incubator.apache.org/download/osgi/)
+* [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/)
Please see the `<properties>` of this [pom.xml](pom.xml) to find the
correct versions to build.
@@ -131,7 +148,7 @@ To skip the tests (these can be time-consuming), use:
If you are modifying this source code independent of the
-Apache Taverna project, you may not want to run 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:
@@ -149,37 +166,37 @@ should only need to depend on the `-api` modules, while the `-impl` are added by
packaging of the
[taverna-commandline-product](https://github.com/apache/incubator-taverna-commandline/tree/master/taverna-commandline-product).
-* [taverna-capability-api](taverna-capability-api/) Apache Taverna Platform Capability API
-* [taverna-capability-impl](taverna-capability-impl/) Apache Taverna Platform Capability impl
-* [taverna-credential-manager-api](taverna-credential-manager-api/) Apache Taverna Credential Manager API
-* [taverna-credential-manager-impl](taverna-credential-manager-impl/) Apache Taverna Credential Manager impl
-* [taverna-database-configuration-api](taverna-database-configuration-api/) Apache Taverna Database Configuration API
-* [taverna-database-configuration-impl](taverna-database-configuration-impl/) Apache Taverna Database Configuration impl
-* [taverna-execution-api](taverna-execution-api/) Apache Taverna Platform Execution Service API
-* [taverna-execution-impl](taverna-execution-impl/) Apache Taverna Platform Execution Service impl
-* [taverna-execution-local](taverna-execution-local/) Apache Taverna Platform Local Execution Service
-* [taverna-reference-api](taverna-reference-api/) Apache Taverna Reference Manager API
-* [taverna-reference-impl](taverna-reference-impl/) Apache Taverna Reference Manager impl
-* [taverna-reference-types](taverna-reference-types/) Apache Taverna Engine Reference Types
-* [taverna-report-api](taverna-report-api/) Apache Taverna Platform Report Service
-* [taverna-run-api](taverna-run-api/) Apache Taverna Platform Run Service API
-* [taverna-run-impl](taverna-run-impl/) Apache Taverna Platform Run Service impl
-* [taverna-services-api](taverna-services-api/) Apache Taverna Services API
-* [taverna-services-impl](taverna-services-impl/) Apache Taverna Platform Services impl
-* [taverna-workflowmodel-api](taverna-workflowmodel-api/) Apache Taverna Workflow Model API
-* [taverna-workflowmodel-impl](taverna-workflowmodel-impl/) Apache Taverna Workflow Model impl
-* [taverna-workflowmodel-extensions](taverna-workflowmodel-extensions/) Apache Taverna Workflow Model Extension Points
+* [taverna-capability-api](taverna-capability-api/) Taverna Platform Capability API
+* [taverna-capability-impl](taverna-capability-impl/) Taverna Platform Capability impl
+* [taverna-credential-manager-api](taverna-credential-manager-api/) Taverna Credential Manager API
+* [taverna-credential-manager-impl](taverna-credential-manager-impl/) Taverna Credential Manager impl
+* [taverna-database-configuration-api](taverna-database-configuration-api/) Taverna Database Configuration API
+* [taverna-database-configuration-impl](taverna-database-configuration-impl/) Taverna Database Configuration impl
+* [taverna-execution-api](taverna-execution-api/) Taverna Platform Execution Service API
+* [taverna-execution-impl](taverna-execution-impl/) Taverna Platform Execution Service impl
+* [taverna-execution-local](taverna-execution-local/) Taverna Platform Local Execution Service
+* [taverna-reference-api](taverna-reference-api/) Taverna Reference Manager API
+* [taverna-reference-impl](taverna-reference-impl/) Taverna Reference Manager impl
+* [taverna-reference-types](taverna-reference-types/) Taverna Engine Reference Types
+* [taverna-report-api](taverna-report-api/) Taverna Platform Report Service
+* [taverna-run-api](taverna-run-api/) Taverna Platform Run Service API
+* [taverna-run-impl](taverna-run-impl/) Taverna Platform Run Service impl
+* [taverna-services-api](taverna-services-api/) Taverna Services API
+* [taverna-services-impl](taverna-services-impl/) Taverna Platform Services impl
+* [taverna-workflowmodel-api](taverna-workflowmodel-api/) Taverna Workflow Model API
+* [taverna-workflowmodel-impl](taverna-workflowmodel-impl/) Taverna Workflow Model impl
+* [taverna-workflowmodel-extensions](taverna-workflowmodel-extensions/) Taverna Workflow Model Extension Points
These modules include utilities used by the above, or for test purposes:
-* [taverna-observer](taverna-observer/) Apache Taverna Observer pattern
-* [taverna-activity-test-utils](taverna-activity-test-utils/) Apache Taverna Activity test utils
-* [taverna-reference-testhelpers](taverna-reference-testhelpers/) Apache Taverna Reference Test Helpers
+* [taverna-observer](taverna-observer/) Taverna Observer pattern
+* [taverna-activity-test-utils](taverna-activity-test-utils/) Taverna Activity test utils
+* [taverna-reference-testhelpers](taverna-reference-testhelpers/) Taverna Reference Test Helpers
These modules include structural workflow activities:
-* [taverna-dataflow-activity](taverna-dataflow-activity/) Apache Taverna Dataflow Activity
-* [taverna-stringconstant-activity](taverna-stringconstant-activity/) Apache Taverna StringConstant Activity
+* [taverna-dataflow-activity](taverna-dataflow-activity/) Taverna Dataflow Activity
+* [taverna-stringconstant-activity](taverna-stringconstant-activity/) Taverna StringConstant Activity
_See the separate release of
[taverna-common-activities](taverna.incubator.apache.org/download/common-activities/)
@@ -188,95 +205,95 @@ for activities that invoke Beanshell, WSDL, REST and command line tool services.
These modules are experimental:
-* [taverna-execution-remote](taverna-execution-remote/) Apache Taverna Platform Remote Execution Service
-* [taverna-execution-hadoop](taverna-execution-hadoop/) Apache Taverna Hadoop Workflow Execution Service
+* [taverna-execution-remote](taverna-execution-remote/) Taverna Platform Remote Execution Service
+* [taverna-execution-hadoop](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/) Apache Taverna Activity archetype
-* [taverna-prov](taverna-prov/) Apache Taverna PROV support ()
-* [taverna-provenanceconnector](taverna-provenanceconnector/) Apache Taverna Provenance Connector
-* [taverna-prov-owl-bindings](taverna-prov-owl-bindings/) Apache Taverna PROV OWL bindings
+* [taverna-activity-archetype](taverna-activity-archetype/) Taverna Activity archetype
+* [taverna-prov](taverna-prov/) Taverna PROV support ()
+* [taverna-provenanceconnector](taverna-provenanceconnector/) Taverna Provenance Connector
+* [taverna-prov-owl-bindings](taverna-prov-owl-bindings/) Taverna PROV OWL bindings
-See the [taverna-engine JavaDoc](http://taverna.incubator.apache.org/javadoc/taverna-engine/)
+See the [taverna-engine JavaDoc](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/)
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
-[Apache Taverna Command Line](https://github.com/apache/incubator-taverna-commandline/).
+[Taverna Command Line](https://github.com/apache/incubator-taverna-commandline/).
There are two layers of Taverna Engine:
-* Apache Taverna Platform provides an outer API for creating and managing workflow runs, potentially remotely.
-* Apache Taverna Core (aka `workflowmodel`, formerly `t2.core`) is the orchestrating part of the Taverna Engine. Its [Activity](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html) is implemented by multiple plugins depending on the activity type.
+* 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](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html) is implemented by multiple plugins depending on the activity type.
### Preparations
-* Load a SCUFL2 [WorkflowBundle](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html)
+* Load a SCUFL2 [WorkflowBundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html)
from a `.wfbundle` or `.t2flow` file
- using [WorkflowBundleIO](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/io/WorkflowBundleIO.html)
- from [Taverna Language](http://taverna.incubator.apache.org/download/language/).
- + (Optional) Choose a [Workflow](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getWorkflows--) to bind
+ using [WorkflowBundleIO](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/io/WorkflowBundleIO.html)
+ from [Taverna Language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/).
+ + (Optional) Choose a [Workflow](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getWorkflows--) to bind
workflows (usually the
- [main workflow](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getMainWorkflow--)).
- + (Optional) Choose a [Profile](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getProfiles--) to bind
+ [main workflow](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getMainWorkflow--)).
+ + (Optional) Choose a [Profile](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getProfiles--) to bind
workflow implementations. (There is normally only one profile.)
-* Create or load a [Bundle](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html)
- with the expected [inputs](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Workflow.html#getInputPorts--) of the
- [main workflow](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getMainWorkflow--) using
- [DataBundles](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/databundle/DataBundles.html)
-from [Taverna Language](http://taverna.incubator.apache.org/download/language/).
+* Create or load a [Bundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html)
+ with the expected [inputs](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Workflow.html#getInputPorts--) of the
+ [main workflow](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getMainWorkflow--) using
+ [DataBundles](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/databundle/DataBundles.html)
+from [Taverna Language](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/language/).
### Running a workflow
* You must be running within OSGi to support multiple Taverna activities
and their dependencies, e.g. by using the
- [OsgiLauncher](https://taverna.incubator.apache.org/javadoc/taverna-osgi/org/apache/taverna/osgilauncher/OsgiLauncher.html) from [Apache Taverna OSGi](http://taverna.incubator.apache.org/download/osgi/).
+ [OsgiLauncher](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-osgi/org/apache/taverna/osgilauncher/OsgiLauncher.html) from [Taverna OSGi](https://web.archive.org/web/*/https://taverna.incubator.apache.org/download/osgi/).
See the [TavernaStarter example](https://github.com/taverna-extras/taverna-starter/blob/master/src/main/java/org/apache/taverna/osgistarter/TavernaStarter.java)
for details.
* (Optional) Populate service credentials (username/password)
to be used by the workflow into the
- [CredentialManager](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/security/credentialmanager/CredentialManager.html) from
+ [CredentialManager](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/security/credentialmanager/CredentialManager.html) from
[taverna-credential-manager-api](taverna-credential-manager-api/).
-* Use the [RunService](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html) from the [taverna-run-api](taverna-run-api) (discovered as a [Spring service](#spring-services)).
-* Use [runService.getExecutionEnvironments()](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getExecutionEnvironments-org.apache.taverna.scufl2.api.container.WorkflowBundle-) to find an executer for your workflow bundle or profile.
+* Use the [RunService](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html) from the [taverna-run-api](taverna-run-api) (discovered as a [Spring service](#spring-services)).
+* Use [runService.getExecutionEnvironments()](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getExecutionEnvironments-org.apache.taverna.scufl2.api.container.WorkflowBundle-) to find an executer for your workflow bundle or profile.
+ The RunService selects an appropriate
- [ExecutionService](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionService.html)
- service ([taverna-execution-api](taverna-execution-api)), checking the [Profile](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getProfiles--) against the installed [activity types](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionEnvironment.html#getActivityTypes--) from [common-activities](https://github.com/apache/incubator-taverna-common-activit [...]
- + In the Taverna Command Line there is typically only one match, a [LocalExecutionEnvironment](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/impl/local/LocalExecutionEnvironment.html), representing the [LocalExecutionService](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/impl/local/LocalExecutionService.html) from [taverna-execution-local](taverna-execution-local).
+ [ExecutionService](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionService.html)
+ service ([taverna-execution-api](taverna-execution-api)), checking the [Profile](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/container/WorkflowBundle.html#getProfiles--) against the installed [activity types](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionEnvironment.html#getActivityTypes--) from [common-activities [...]
+ + In the Taverna Command Line there is typically only one match, a [LocalExecutionEnvironment](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/impl/local/LocalExecutionEnvironment.html), representing the [LocalExecutionService](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/impl/local/LocalExecutionService.html) from [taverna [...]
+ The experimental module [taverna-execution-remote](taverna-execution-remote) aims to execute a workflow on a remote [Taverna Server](http://github.com/apache/incubator-taverna-server/) - e.g. for running workflows remotely from Taverna Workbench.
+ The prototype module [taverna-execution-hadoop](taverna-execution-hadoop) is an attempt to execute compatible Taverna workflows as an [Apache Hadoop](http://hadoop.apache.org/) 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](http://scape-project.eu/wp-content/uploads/2013/04/SCAPE_D6.1_TUB_V1.2.pdf).
-* [Create an execution job](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionService.html#createExecution-org.apache.taverna.platform.execution.api.ExecutionEnvironment-org.apache.taverna.scufl2.api.container.WorkflowBundle-org.apache.taverna.scufl2.api.core.Workflow-org.apache.taverna.scufl2.api.profiles.Profile-org.apache.taverna.robundle.Bundle-), and provide the `ExecutionEnvironment`, the `WorkflowBundle`, its `Workflow`, [...]
+* [Create an execution job](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/execution/api/ExecutionService.html#createExecution-org.apache.taverna.platform.execution.api.ExecutionEnvironment-org.apache.taverna.scufl2.api.container.WorkflowBundle-org.apache.taverna.scufl2.api.core.Workflow-org.apache.taverna.scufl2.api.profiles.Profile-org.apache.taverna.robundle.Bundle-), and provide the `ExecutionEnvironment`, the `Wo [...]
+ Typically this creates a [LocalExecution](taverna-execution-local/src/main/java/org/apache/taverna/platform/execution/impl/local/LocalExecution.java#L105) instance ([taverna-execution-local](taverna-execution-local)), which converts the
- abstract SCUFL2 [Workflow](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Workflow.html) to an executable
- [Dataflow](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/Dataflow.html) ([taverna-workflowmodel-api](taverna-workflowmodel-api)) which has corresponding [Processor](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/Processor.html)s and
- [Activity](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html) implementations from the installed plugins.
- + A [WorkflowInstanceFacade](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/facade/WorkflowInstanceFacade.html) is prepared - the engine's top-level representation of a workflow run.
+ abstract SCUFL2 [Workflow](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Workflow.html) to an executable
+ [Dataflow](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/Dataflow.html) ([taverna-workflowmodel-api](taverna-workflowmodel-api)) which has corresponding [Processor](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/Processor.html)s and
+ [Activity](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/workflowmodel/processor/activity/Activity.html) implementations from the installed plugins.
+ + A [WorkflowInstanceFacade](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/facade/WorkflowInstanceFacade.html) is prepared - the engine's top-level representation of a workflow run.
+ A [LocalExecutionManager](https://github.com/apache/incubator-taverna-engine/blob/master/taverna-execution-local/src/main/java/org/apache/taverna/platform/execution/impl/local/LocalExecutionMonitor.java) is added as a bridge between the Taverna Core engine and the Platform.
-* Start the run using [runService.start()](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#start-java.lang.String-).
- * Input values from the data [Bundle](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html) are
+* Start the run using [runService.start()](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#start-java.lang.String-).
+ * Input values from the data [Bundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html) are
[converted](https://github.com/apache/incubator-taverna-engine/blob/master/taverna-execution-local/src/main/java/org/apache/taverna/platform/execution/impl/local/T2ReferenceConverter.java#L34) to be registered with a
-[ReferenceService](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/ReferenceService.html) ([taverna-reference-api](taverna-reference-api)) - as Taverna workflows pass [T2Reference](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/T2Reference.html)s.
- + Values are represented as either a [InlineStringReference](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/external/object/InlineStringReference.html) or [InlineByteArrayReference](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/external/object/InlineByteArrayReference.html), or could be external [HttpReference](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/ref [...]
+[ReferenceService](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/ReferenceService.html) ([taverna-reference-api](taverna-reference-api)) - as Taverna workflows pass [T2Reference](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/T2Reference.html)s.
+ + Values are represented as either a [InlineStringReference](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/external/object/InlineStringReference.html) or [InlineByteArrayReference](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/external/object/InlineByteArrayReference.html), or could be external [HttpReference](https://web.archive.or [...]
where supported, with conversion to strings and bytes if needed.
- + Lists, values and references are stored [in memory](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/InMemoryReferenceSetDao.html).
+ + Lists, values and references are stored [in memory](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/impl/InMemoryReferenceSetDao.html).
+ This was previously backed by [Hibernate](https://github.com/apache/incubator-taverna-engine/blob/old/core-pre-incubator-20141219/reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateReferenceSetDao.java) stored in [Apache Derby](http://db.apache.org/derby/) - this code was removed due to license incompatibility.
- + TODO: Add a different [ReferenceSetDao](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/ReferenceSetDao.html) implementation
- that is backed directly by the platform's [Bundle](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html)
+ + TODO: Add a different [ReferenceSetDao](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/reference/ReferenceSetDao.html) implementation
+ that is backed directly by the platform's [Bundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/robundle/Bundle.html)
(effectively file-based).
-* Monitor the [state of the run](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getState-java.lang.String-) or
-[get](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getWorkflowReport-java.lang.String-) the [WorkflowReport](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/WorkflowReport.html) for detailed progress ([taverna-report-api](taverna-report-api)), such as
-the [number of jobs completed](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ProcessorReport.html#getJobsCompleted--) for a given [Processor](https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Processor.html).
-* Once the workflow is [COMPLETED](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/State.html#COMPLETED) (and even while it is [RUNNING](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/State.html#RUNNING)), you can
-retrieve the [bundle](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getDataBundle-java.lang.String-) containing the output values and intermediate values.
+* Monitor the [state of the run](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getState-java.lang.String-) or
+[get](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getWorkflowReport-java.lang.String-) the [WorkflowReport](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/WorkflowReport.html) for detailed progress ([taverna-report-api](taverna-report-api)), such as
+the [number of jobs completed](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ProcessorReport.html#getJobsCompleted--) for a given [Processor](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Processor.html).
+* Once the workflow is [COMPLETED](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/State.html#COMPLETED) (and even while it is [RUNNING](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/State.html#RUNNING)), you can
+retrieve the [bundle](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/run/api/RunService.html#getDataBundle-java.lang.String-) containing the output values and intermediate values.
+ To relate intermediate values, you will need to inspect either the
- [WorkflowReport](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/WorkflowReport.html),
- [ProcessorReport](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ProcessorReport.html) or [ActivityReport](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ActivityReport.html)s
- to [get the invocations](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/StatusReport.html#getInvocations--), which provide the [inputs](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/Invocation.html#getInputs--)
- and [outputs](https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/Invocation.html#getOutputs--) as
+ [WorkflowReport](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/WorkflowReport.html),
+ [ProcessorReport](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ProcessorReport.html) or [ActivityReport](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/ActivityReport.html)s
+ to [get the invocations](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/StatusReport.html#getInvocations--), which provide the [inputs](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/Invocation.html#getInputs--)
+ and [outputs](https://web.archive.org/web/*/https://taverna.incubator.apache.org/javadoc/taverna-engine/org/apache/taverna/platform/report/Invocation.html#getOutputs--) as
[Path](http://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html)s within the bundle.
@@ -340,9 +357,9 @@ The following provides more details on the included cryptographic software:
[BouncyCastle](https://www.bouncycastle.org/) bcprov encryption library.
The [JCE Unlimited Strength Jurisdiction Policy](http://www.oracle.com/technetwork/java/javase/downloads/jce8-download-2133166.html)
may need to be installed separately to use keystore passwords with 7 or more characters.
-* Apache Taverna Engine depends on
- [Apache Taverna Language](http://taverna.incubator.apache.org/download/language/),
- [Apache Taverna OSGi](http://taverna.incubator.apache.org/download/osgi/) and
+* Taverna Engine depends on
+ [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/) and
[Apache Jena](http://jena.apache.org/), which depend on
[Apache HttpComponents](https://hc.apache.org/) Client, which can
initiate encrypted `https://` connections using