You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2016/02/03 01:23:58 UTC
[2/2] incubator-taverna-language git commit: Updated wfdesc README
Updated wfdesc README
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/cbe22180
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/cbe22180
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/cbe22180
Branch: refs/heads/master
Commit: cbe22180ee2893c2863339799319821dd9d34010
Parents: 2d91241
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Feb 3 00:23:51 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Feb 3 00:23:51 2016 +0000
----------------------------------------------------------------------
taverna-scufl2-wfdesc/README.md | 158 +++++++----------------------------
1 file changed, 30 insertions(+), 128 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cbe22180/taverna-scufl2-wfdesc/README.md
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/README.md b/taverna-scufl2-wfdesc/README.md
index 9de5c2b..a39f352 100644
--- a/taverna-scufl2-wfdesc/README.md
+++ b/taverna-scufl2-wfdesc/README.md
@@ -1,81 +1,20 @@
Convert SCUFL2 to wfdesc
========================
-[](https://travis-ci.org/wf4ever/scufl2-wfdesc)
-[](http://dx.doi.org/10.5281/zenodo.10650)
-
-
-
-This is an extension to [Scufl2](https://github.com/mygrid/scufl2/) which
+This is an extension to [Scufl2 API](../taverna-scufl2-api) which
provides the export capability to wfdesc ontology from the
-[Wf4Ever](http://www.wf4ever-project.org/) [2] RO
+[Wf4Ever](http://www.wf4ever-project.org/) [2] RO
[wfdesc ontology](https://w3id.org/ro#wfdesc).
This is exposed as a command line tool `scufl2-to-wfdesc`, but can also be
-accessed programmatically as a plugin for the
-[SCUFL2 API](http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API).
-
-
-Download
---------
-You can download the latest `scufl2-wfdesc-*-standalone.jar` (command line tool)
-from the myGrid Maven repository:
-
-* http://build.mygrid.org.uk/maven/repository/org/purl/wf4ever/scufl2-wfdesc/
-
-For instance, for version 0.3.7:
-
-* http://build.mygrid.org.uk/maven/repository/org/purl/wf4ever/scufl2-wfdesc/0.3.7/scufl2-wfdesc-0.3.7-standalone.jar
+accessed programmatically as a plugin for the
+[Scufl2 API](../taverna-scufl2-api).
-License
--------
-(c) 2011-2014 University of MAnchester
-
-scufl2-wfdesc is licensed under the [MIT license](http://opensource.org/licenses/MIT). See the file [LICENCE.txt](LICENCE.txt) for details
-
-[SCUFL2 API](https://github.com/myGrid/scufl2/) is licensed under the [LGPL 2.1 license](https://www.gnu.org/licenses/lgpl-2.1.html) which applies
-to the build binary.
-
Building
--------
-Requirements:
- * [Java JDK 7](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [OpenJDK 7](http://openjdk.java.net/install/
-) (higher versions not tested)
- * [Maven 3](http://maven.apache.org/download.html) or higher (for building)
-
-To build, simply use `mvn clean install`
-
-Example:
-
- : stain@ralph ~/src/wf4ever/scufl2-wfdesc;mvn clean install
- [INFO] Scanning for projects...
- [INFO]
- [INFO] ------------------------------------------------------------------------
- [INFO] Building SCUFL2 to wfdesc 0.1-SNAPSHOT
- [INFO] ------------------------------------------------------------------------
- [INFO]
- [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ scufl2-wfdesc ---
- [INFO]
- [INFO] --- maven-antrun-plugin:1.6:run (default) @ scufl2-wfdesc ---
- [INFO] Executing tasks
-
- main:
- [mkdir] Created dir: /home/stain/stuff/src/wf4ever/scufl2-wfdesc/target/generated-sources
- (..)
- [INFO] ------------------------------------------------------------------------
- [INFO] BUILD SUCCESS
- [INFO] ------------------------------------------------------------------------
- [INFO] Total time: 46.734s
- [INFO] Finished at: Wed Jan 04 15:22:58 WET 2012
- [INFO] Final Memory: 18M/129M
- [INFO] ------------------------------------------------------------------------
-
-
-Note that the first time you build, Maven will download several
-required dependencies from Maven repositories. Depending on your network
-connection this might take some time to complete.
+ mvn clean install
@@ -85,9 +24,9 @@ Command line tool
After building, the folder `target/scufl2-wfdesc` contains a
distribution of the command line tool `scufl2-to-wfdesc`, with launchers
generated for Unix and Windows. You may copy and distribute this folder for a standalone usage of the
-conversion tool.
+conversion tool.
-Alternatively, you can use the `target/scufl2-wfdesc-0.3.0-SNAPSHOT-standalone.jar` directly with
+Alternatively, you can use the `target/scufl2-wfdesc-0.3.0-SNAPSHOT-standalone.jar` directly with
`java -jar` - this JAR embeds all required libraries and hence can
be copied anywhere on your file system. This JAR is however not recommended for programmatic
use as it embeds third party libraries.
@@ -101,14 +40,15 @@ The argument `-h` or `--help` should give a minimal help.
Example:
- : stain@ralph ~/src/wf4ever/scufl2-wfdesc; target/scufl2-wfdesc/bin/scufl2-to-wfdesc src/test/resources/helloworld.t2flow
+ : stain@ralph ~/src/wf4ever/scufl2-wfdesc; target/scufl2-wfdesc/bin/scufl2-to-wfdesc src/test/resources/helloworld.t2flow
Converted src/test/resources/helloworld.t2flow to src/test/resources/helloworld.wfdesc.ttl
The output is a [RDF Turtle](http://www.w3.org/TR/turtle/) document containing statements about the workflow structure
according to the [RO ontology wfdesc](https://w3id.org/ro#wfdesc) ontology.
- : stain@ralph ~/src/wf4ever/scufl2-wfdesc; cat src/test/resources/helloworld.wfdesc.ttl
+ : stain@ralph ~/src/wf4ever/scufl2-wfdesc; cat src/test/resources/helloworld.wfdesc.ttl
+```turtle
@base <http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/workflow/Hello_World/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@@ -146,6 +86,7 @@ according to the [RO ontology wfdesc](https://w3id.org/ro#wfdesc) ontology.
<processor/hello/out/value> a wfdesc:Output , wfdesc:Description ;
rdfs:label "value" .
+```
@@ -159,9 +100,10 @@ Annotations in the workflow are also extracted for the workflow, processors and
* biocat:exampleData
Richer semantic annotations (e.g. on
- [Taverna Components](http://dev.mygrid.org.uk/wiki/display/taverna/Components)) are
+ [Taverna Components](http://dev.mygrid.org.uk/wiki/display/taverna/Components)) are
extracted verbatim, e.g.:
+```turtle
<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
comp:fits comp:MigrationAction ;
comp:migrates _:node18musbm56x1 .
@@ -169,67 +111,27 @@ extracted verbatim, e.g.:
_:node18musbm56x1 a comp:MigrationPath ;
comp:fromMimetype "image/tiff" ;
comp:toMimetype "image/tiff" .
+```
-See [`valid_component_imagemagickconvert.wfdesc.ttl`](src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl)
+See [`valid_component_imagemagickconvert.wfdesc.ttl`](src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl)
for the complete example.
-See the scufl2-wfdesc wiki for [common wfdesc queries](https://github.com/wf4ever/scufl2-wfdesc/wiki/Common-queries).
-
-
-Programmatic use
-----------------
-
-Add a Maven dependency to "scufl2-wfdesc":
-
- <dependency>
- <groupId>org.purl.wf4ever</groupId>
- <artifactId>scufl2-wfdesc</artifactId>
- <version>0.3.7</version>
- </dependency>
-
-See the pom.xml file of the latest git tag for the latest version.
-
-Stable builds are available from
-http://www.mygrid.org.uk/maven/repository/
--- to retrieve artifacts from the myGrid repository, also add
-to your POM:
-
- <repositories>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- </repositories>
-
-
Example:
- import org.apache.taverna.scufl2.api.container.WorkflowBundle;
- import org.apache.taverna.scufl2.api.io.ReaderException;
- import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
- import org.apache.taverna.scufl2.api.io.WriterException;
-
- ..
- File original = new File("helloworld.t2flow");
- File output = new File("helloworld.wfdesc.ttl");
- String original = null; // to guess filetype
- WorkflowBundle wfBundle = io.readBundle(original, null);
- io.writeBundle(wfBundle, output, "text/vnd.wf4ever.wfdesc+turtle");
-
-
-
-
-
-References
-----------
- * [SCUFL2 API](http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API)
- * [RO ontology wfdesc](https://w3id.org/ro#wfdesc)
- * [RDF Turtle](http://www.w3.org/TR/turtle/)
-
+```java
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+..
+File original = new File("helloworld.t2flow");
+File output = new File("helloworld.wfdesc.ttl");
+String original = null; // to guess filetype
+WorkflowBundle wfBundle = io.readBundle(original, null);
+io.writeBundle(wfBundle, output, "text/vnd.wf4ever.wfdesc+turtle");
+```
+
+# Common queries