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Posted to commits@taverna.apache.org by st...@apache.org on 2018/06/29 08:58:34 UTC
[1/3] incubator-taverna-plugin-component git commit: Taverna
Component documentation
Repository: incubator-taverna-plugin-component
Updated Branches:
refs/heads/master 00c2f0686 -> 72ec68298
Taverna Component documentation
Moved from
https://github.com/apache/incubator-taverna-site/tree/8aea1aea1f859cf7ce0ce72f31f168f94e0672b5/content/documentation/components
https://github.com/apache/incubator-taverna-site/tree/8aea1aea1f859cf7ce0ce72f31f168f94e0672b5/content/img
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/commit/0f0b3b69
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/tree/0f0b3b69
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/diff/0f0b3b69
Branch: refs/heads/master
Commit: 0f0b3b69892b281ac6c5cc485812b0c6220af99e
Parents: 00c2f06
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 09:56:59 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 09:56:59 2018 +0100
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doc/component-validator.md | 30 ++++++
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diff --git a/doc/component-profile-editor.md b/doc/component-profile-editor.md
new file mode 100644
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--- /dev/null
+++ b/doc/component-profile-editor.md
@@ -0,0 +1,26 @@
+Title: Component profile editor
+Notice: 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.
+
+The Taverna Component Profile Editor is a simple tool for editing and creating profiles for
+ [Taverna Components[(/documentation/components).
+Component profiles define the required and supported interface of components;
+ they are not intended to be easily edited by normal users.
+The editor guides an expert user as they define a profile,
+ showing features that they may use and providing assistance for defining semantic annotation requirements.
+
+<div align="center"><img src="img/component-profile-editor.png" alt="Component Profile Editor" width="600" /></div>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/0f0b3b69/doc/component-validator.md
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diff --git a/doc/component-validator.md b/doc/component-validator.md
new file mode 100644
index 0000000..145e8d0
--- /dev/null
+++ b/doc/component-validator.md
@@ -0,0 +1,30 @@
+Title: Component validator
+Notice: 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.
+
+The Taverna Component Validator is a tool and library for checking whether a
+ [Taverna Component](/documentation/components) satisfies the component profile defined by the family of which it is a member.
+It applies a number of checks to the component such that when they are all satisfied,
+ the component can be considered to be a high-quality member of the component family,
+ and provides human-readable descriptions of the conditions that are checked and whether they were satisfied or not.
+
+
+
+We currently have the validator deployed on
+ [myExperiment.org](http://www.myexperiment.org) as an integrated feature of the metadata displayed about components.
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/0f0b3b69/doc/img/ComponentValidityDetails.png
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/0f0b3b69/doc/index.md
----------------------------------------------------------------------
diff --git a/doc/index.md b/doc/index.md
new file mode 100644
index 0000000..2f647bc
--- /dev/null
+++ b/doc/index.md
@@ -0,0 +1,161 @@
+Title: Workflow Components
+Notice: 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.
+
+[TOC]
+
+## Overview
+Taverna Workflow Components are a system for creating shareable, reusable,
+ encapsulated sub-workflows that perform clearly defined tasks while abstracting
+ the details of how those tasks are performed.
+They are an integrated feature of Taverna since Workbench 2.5.0 and Server 2.5.4.
+
+Taverna's system of service components was developed as part of the BioVeL and SCAPE projects. They consist of tools for the creation, management and use of workflow components,
+ along with a repository for the storage and sharing of those components.
+Workflow components within a given component family will work together cleanly,
+ for example, by adhering to a tidy type system and being well described.
+
+## Requirements
+
+A set of minimal functional requirements for service component management has been developed. These requirements are
+ based upon previous component-related work carried out as part of the e-Lico project as well as an examination of the needs of BioVeL and SCAPE.
+
+The requirements include:
+
+ - The ability to create components
+ - The specification of the characteristics that are necessary for a set of components to
+ ‘play’ together – called a ‘component profile’
+ - Creating a component so it complies with a given profile
+ - Checking that a component complies with a given profile
+ - Publishing a component
+ - Discovering a component
+ - Including a component in a workflow
+ - Executing the component within a workflow run
+
+<img class="aligncenter" title="The Model of Components" src="img/registry.png" alt=""
+ width="433" height="251" />
+
+## Workflows
+### Example workflow with components
+
+This is an example workflow that includes components, with internal ports hidden for simplicity:
+
+<img class="alignnone" title="Componentized Workflow" src="img/component_b_1.png" alt=""
+ width="679" height="294" />
+
+Without components, using the same view, it would instead look like this:
+
+[<img class="aligncenter" title="Un-componentized Workflow" src="img/component_c.png" alt="" width="245" height="526" />](http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/component_c.png)
+
+### Including a component in a workflow
+
+A component can be added into a Taverna workflow in the same way as an ordinary service:
+ by dragging it from the service panel of the workbench into the workflow design view.
+ *Although it may be realized internally as a workflow,
+ a user sees it as a ‘black box’ and cannot (normally) edit the component’s workflow.*
+
+<img class="aligncenter" src="img/arch3.png" alt="" width="500" height="401" />
+
+It is intended that there will be consistency checks to ensure components are only plugged
+ together in a sensible manner, and for the discovery of (and connection to) suitable components
+ based upon existing workflow structure.
+
+### Executing a component in a workflow run
+
+When a component is invoked during a workflow run, the underlying workflow is called with the
+ corresponding data.
+The results of the workflow are used as the output data for the component invocation.
+*The user sees the component invocation as a ‘black box’ and cannot see details of
+ what happens inside.*
+
+>If you publish a workflow containing a component, you *must* make sure the
+ component is publicly readable in a globally-accessible component registry;
+ myExperiment is such a suitable registry.
+
+## Components
+### Component creation
+
+It was decided that the majority of the information necessary for a component will be specified
+ as a Taverna workflow.
+This allows complex internal component functionality and removes the need for extensive new
+ software to design components.
+
+<img class="aligncenter" src="img/arch1.png" alt="" width="340" height="433" />
+
+### Component profile
+
+A specification of the format for the component profile has been agreed.
+The format is in XML and an XML schema (xsd) has been created.
+An example [component profile](http://www.myexperiment.org/files/905/versions/1/download/Characterisation%20Component.xml)
+ is available.
+Components that share a profile will be collected together into component families.
+A [component profile editor](/documentation/components/component-profile-editor)
+ is being developed.
+
+<p style="text-align: center;">
+<img class="aligncenter" src="img/arch2.png" alt="" width="359" height="412" />
+</p>
+
+The SCAPE project has an
+ [extended discussion of component profiles](https://github.com/openpreserve/scape-component-profiles)
+ available.
+
+### Component creation against a profile
+
+In order to conform to a component profile, it can be necessary to make semantic annotations
+ parts of the corresponding workflow.
+For example, the annotation of the type of format in which data is output by a port or
+ a service with the task it performs.
+
+The component profile specifies the ontologies that will be used for the components within the
+ family, the correspondence between object classes within a workflow
+ (input port, service etc.) and the concepts within the ontologies.
+
+### Checking a component against a profile
+
+Although the components will be modified using a chosen profile,
+ it is unlikely that the components can be assured as being ‘correct by construction’.
+For this reason, a separate
+ [component validator](/documentation/components/component-validator)
+ is being implemented.
+The component validator is included within
+ [myExperiment](http://www.myexperiment.org).
+
+### Publishing a component
+
+Since components are realized as ‘extensions’ to Taverna workflows,
+ it was decided that rather than using a separate component repository,
+ the extensive capabilities of myExperiment would be used.
+Thus a component is currently published and shared on myExperiment as (a pack containing)
+ a workflow.
+The components themselves are items within a pack corresponding to the component family.
+
+To facilitate the development of components, a workflow can also be saved to the user’s local
+ machine.
+
+When a user publishes a component either to myExperiment or to their local file system,
+ their service panel is updated to reflect the new component.
+
+### Discovering a component
+
+Since component families are realized as packs on myExperiment
+ (or by analogous structures in the user’s file system),
+ we use the existing Taverna code to talk to the myExperiment REST interface to give users
+ access to families of components.
+Users can then see the discovered families of components via the Taverna Workbench service
+ panel, and the components within those families.
+A component can then be added to a workflow.
[2/3] incubator-taverna-plugin-component git commit: clarify w3c
license
Posted by st...@apache.org.
clarify w3c license
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/commit/f6746021
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/tree/f6746021
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/diff/f6746021
Branch: refs/heads/master
Commit: f6746021b303938c743e4fbea9a7d8cdc624f059
Parents: 0f0b3b6
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 09:57:43 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 09:57:43 2018 +0100
----------------------------------------------------------------------
LICENSE | 32 ++++++++++++++++++++++++++++++++
NOTICE | 8 --------
2 files changed, 32 insertions(+), 8 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/f6746021/LICENSE
----------------------------------------------------------------------
diff --git a/LICENSE b/LICENSE
index d645695..7c19697 100644
--- a/LICENSE
+++ b/LICENSE
@@ -200,3 +200,35 @@
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.
+
+------------------------------------------------------
+./taverna-component-repository-api/src/main/catalog/xml.xsd
+./taverna-component-activity/src/main/catalog/xml.xsd
+
+xml.xsd
+Extensible Markup Language (XML) 1.0 (Fifth Edition)
+W3C Recommendation 26 November 2008
+http://www.w3.org/2001/xml.xsd
+http://www.w3.org/TR/xml/
+
+Copyright (c) 2015 W3C(R) (MIT, ERCIM, Keio, Beihang). This software or
+document includes material copied from or derived from:
+
+W3C liability, trademark and document use rules apply.
+http://www.w3.org/Consortium/Legal/2015/doc-license
+
+------------------------------------------------------
+./taverna-component-repository-api/src/main/catalog/XMLSchema.xsd
+./taverna-component-activity/src/main/catalog/XMLSchema.xsd
+
+XMLSchema.xsd
+
+XML Schema Part 1: Structures Second Edition
+W3C Recommendation 28 October 2004
+http://www.w3.org/TR/2004/REC-xmlschema-1-20041028/
+https://www.w3.org/2001/XMLSchema.xsd
+
+
+Copyright © 2004 W3C® (MIT, ERCIM, Keio), All Rights Reserved.
+W3C liability, trademark and document use rules apply.
+http://www.w3.org/Consortium/Legal/2015/doc-license
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/f6746021/NOTICE
----------------------------------------------------------------------
diff --git a/NOTICE b/NOTICE
index 23e78b1..35c354c 100644
--- a/NOTICE
+++ b/NOTICE
@@ -9,11 +9,3 @@ Portions of this software were originally based on the following:
These have been licensed to the Apache Software Foundation under a software grant.
---------------------------------------------------------
-
-TODO: These XSD files are from W3C - which license?
-
-./taverna-component-repository-api/src/main/catalog/xml.xsd
-./taverna-component-repository-api/src/main/catalog/XMLSchema.xsd
-./taverna-component-activity/src/main/catalog/xml.xsd
-./taverna-component-activity/src/main/catalog/XMLSchema.xsd
-
[3/3] incubator-taverna-plugin-component git commit: Remove Apache
branding, retired to taverna-extras
Posted by st...@apache.org.
Remove Apache branding, retired to taverna-extras
See
https://lists.apache.org/thread.html/547b87fa93601d42ef77a778f80bf59fe9a300fffd7d3a6bcb7a7d81@%3Cdev.taverna.apache.org%3E
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/commit/72ec6829
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/tree/72ec6829
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/diff/72ec6829
Branch: refs/heads/master
Commit: 72ec68298e35557b0e8017af153e26ddf91727cc
Parents: f674602
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 09:57:55 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 09:57:55 2018 +0100
----------------------------------------------------------------------
DISCLAIMER | 10 ----------
README.md | 61 ++++++++++++++++++---------------------------------------
2 files changed, 19 insertions(+), 52 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/72ec6829/DISCLAIMER
----------------------------------------------------------------------
diff --git a/DISCLAIMER b/DISCLAIMER
deleted file mode 100644
index 3e3a5ce..0000000
--- a/DISCLAIMER
+++ /dev/null
@@ -1,10 +0,0 @@
-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.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/72ec6829/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
index ff278af..bbee7db 100644
--- a/README.md
+++ b/README.md
@@ -15,24 +15,34 @@
limitations under the License.
-->
-# Apache Taverna Component Plugin
+# Component Plugin for Apache Taverna
Plugins for
[Apache Taverna](http://taverna.incubator.apache.org/) for
-supporting bioinformatics-specific services.
+supporting components.
-Note this module relies on other
+[Taverna Workflow Components](doc/index.md) are a system for creating shareable,
+reusable, encapsulated sub-workflows that perform clearly defined tasks while
+abstracting the details of how those tasks are performed.
+
+
+This plugin is **no longer maintained** by the Apache Taverna project, but
+has been made available to [taverna-extras](https://github.com/taverna-extras/)
+for archival purposes, open for third-party contributions.
+
+This module relies on official
[Apache Taverna modules](http://taverna.incubator.apache.org/code) for
the actual workflow execution.
+
## License
(c) 2013-2014 University of Manchester
(c) 2014-2018 Apache Software Foundation
-This product includes software developed at The
+This product includes software developed at the
[Apache Software Foundation](http://www.apache.org/).
Licensed under the
@@ -43,40 +53,14 @@ The file [NOTICE](NOTICE) contain 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
-for any questions, suggestions and discussions about
-Apache Taverna.
-
-Bugs and feature plannings are tracked in the Jira
-[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326817)
-under the `TAVERNA` component _Taverna Plugin Component._ 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-plugin-component/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.
+# Contribute
-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.
+This plugin is **not actively maintained**, but feel free to raise a
+[GitHub pull request](https://github.com/taverna-extras/taverna-plugin-component/pulls).
+Any contributions received are assumed to be covered by the
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).
## Prerequisites
@@ -111,10 +95,3 @@ To skip the tests (these can be timeconsuming), 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