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资源说明：ARCHIVE - Moved to Apache Taverna
# Taverna PROV support
[](https://travis-ci.org/taverna/taverna-prov)
This is a plugin for the [Taverna](http://www.taverna.org.uk/) Workbench
and Taverna Command Line which allows export of the provenance of a
workflow run according to the [W3C PROV-O
standard](http://www.w3.org/TR/prov-o/).
## Source code and license
This plugin is distributed under the [GNU Lesser General Public License
2.1](http://www.gnu.org/licenses/lgpl-2.1.html) (LGPL). The source code
for this plugin is available at https://github.com/taverna/taverna-prov
## Installation for Taverna workbench
Installation of an released version of this plugin does not require
compilation, but uses Taverna's plugin mechanism.
You need:
* [Taverna Workbench 2.5](http://www.taverna.org.uk/download/workbench/2-5/)
* Java 1.7 (now comes included with Taverna)
* Internet connectivity
Taverna-PROV is included in Taverna 2.5 and later.
To install any updates to the Taverna-PROV plugin:
1. Start Taverna workbench
2. In the menu, click **Advanced** -> **Updates and plugins**
3. If Taverna does not say "An update is available" , click
**Find updates**
4. For **Taverna-PROV databundle**, click **Update** if shown.
5. Click **Close**
6. Exit and Restart Taverna workbench
## Usage in the Taverna Workbench
In order for PROV export to be possible from the Taverna Workbench,
click **Preferences** from the **File** or **Taverna** menu, then go to the
[Preferences for Data and Provenance](http://dev.mygrid.org.uk/wiki/display24/taverna/Data+and+provenance+preferences).
Ensure that **Provenance capture** is enabled (this is the default in 2.5).
If you would like Taverna to keep the provenance data between runs
of the workbench (in order to export at a later time), then you need to
also untick to *disable* **In memory storage**; note however that this may slow
down executions of some workflows.
Open and run a workflow to export provenance for. As a quick example,
try the very simple
[helloanyone.t2flow](http://www.myexperiment.org/workflows/2649/download/hello_anyone_895936.t2flow)
from [myExperiment](http://www.myexperiment.org/workflows/2649)
(included in the `example/` folder of this source code).
To save a Taverna-PROV databundle containing the workflow run
provenance:
1. Click **Results** perspective
2. Run a workflow, or select an existing run on the left
3. Click **Show workflow results** button (in case you are viewing intermediates)
4. Click **Save all values**
5. Ensure all ports are ticked
6. Click **Save Provenance bundle**
7. Browse and type the name of the bundle
8. Click **OK**
9. The provenance and results values is saved to the bundle with the
extension `.bundle.zip`
10. Provide the data bundle to a service that can understand it, such
as http://alpha2.myexperiment.org/ or http://sandbox.wf4ever-project.org/portal
11. You may also open the bundle in your operating system as it is
a ZIP file which contains workflow inputs, outputs, provenance and a
copy of the workflow.
### Usage on command line
The Taverna documentation has general information about [how to use the
Taverna Command line
tool](http://dev.mygrid.org.uk/wiki/display/taverna/Command+Line+Tool).
The Taverna-PROV command line does not support all the output options of
the regular Taverna command line, output has to be saved using
`-outputdir`. The databundle will be saved in a filename which
corresponds to the output directory, but with the extension
`.bundle.zip`.
To enable PROV export for the workflow run, add the parameter
`-provenance`, which requires the parameter `-embedded` or
`-clientserver`.
Note: `-embedded` allows only one concurrent execution at a time due to
database locking. To support multiple concurrent runs, start
`executeworkflow -startdb` separately to start the database server, and
use `executeworkflow -provenance -clientserver` for the workflow
executions.
Example:
```
stain@biggie-mint ~/src/taverna-prov/example $ executeworkflow -embedded -provbundle helloanyone.bundle.zip -inputvalue name fred helloanyone.t2flow
Provenance bundle zip will be saved to: /home/stain/src/taverna-prov/example/helloanyone.bundle.zip
stain@biggie-mint ~/src/taverna-prov/example $ mkdir helloanyone.bundle ; cd helloanyone.bundle
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle $ unzip ../helloanyone.bundle.zip
Archive: ../helloanyone.bundle.zip
extracting: mimetype
creating: inputs/
inflating: inputs/name.txt
creating: outputs/
inflating: outputs/greeting.txt
creating: intermediates/
creating: intermediates/3a/
inflating: intermediates/3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt
inflating: workflowrun.prov.ttl
inflating: workflow.wfbundle
creating: .ro/
creating: .ro/annotations/
inflating: .ro/annotations/workflow.wfdesc.ttl
inflating: .ro/annotations/a2f03983-8836-4c36-bfb2-d713d9a1928f.ttl
inflating: .ro/manifest.json
```
## Structure of exported provenance
The `.bundle.zip` file is a [RO bundle](https://w3id.org/bundle),
which species a structured ZIP file with a manifest
(`.ro/manifest.json`). You can explore the bundle by unzipping it or
browse it with a program like [7-Zip](http://7-zip.org/).
This source includes an [example
bundle](example/helloanyone.bundle.zip) and [unzipped
bundle](example/helloanyone.bundle/) as a folder. This data bundle
has been saved after running
a simple [hello world workflow](example/helloanyone.t2flow).
The remaining text of this section describes the content of the RO
bundle, as if it was unpacked to a folder. Note that many programming
frameworks include support for working with ZIP files, and so complete
unpacking might not be necessary for your application. For Java, the
[Data bundle API](https://github.com/taverna/databundle) gives a
programmating way to inspect and generate data bundles.
### Inputs and outputs
The folders `inputs/` and `outputs/` contain files and folders
corresponding to the input and output values of the executed
workflow. Ports with multiple values are stored as a folder with numbered
outputs, starting from `0`. Values representing errors have extension
`.err`, other values have an extension guessed by inspecting the value
structure, e.g. `.png`. External references have the extension `.url` -
these files can often be opened as "Internet shortcut" or similar,
depending on your operating system.
Example listing:
c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>ls
inputs intermediates mimetype outputs workflow.wfbundle workflowrun.prov.ttl
c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>ls outputs
greeting.txt
c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>cat outputs/greeting.txt
Hello, John Doe
### Workflow run provenance
The file `workflowrun.prov.ttl` contains the
[PROV-O](http://www.w3.org/TR/prov-o/) export of the workflow run
provenance (including nested workflows) in [RDF Turtle
format](http://www.w3.org/TR/turtle/).
This log details every intermediate processor invocation in the workflow
execution, and relates them to inputs, outputs and intermediate values.
Example listing:
c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>cat workflowrun.prov.ttl | head -n 40 | tail -n 8
<#taverna-prov-export>
rdf:type prov:Activity ;
prov:startedAtTime "2013-11-22T14:01:02.436Z"^^xsd:dateTime ;
prov:qualifiedCommunication _:b1 ;
prov:endedAtTime "2013-11-22T14:01:03.223Z"^^xsd:dateTime ;
rdfs:label "taverna-prov export of workflow run provenance"@en ;
prov:wasInformedBy
tavernaprov:content ;
wfprov:describedByParameter ;
wfprov:describedByParameter ;
wfprov:wasOutputFrom
rdf:type cnt:ContentAsText ;
cnt:characterEncoding "UTF-8"^^xsd:string ;
cnt:chars "Hello, "^^xsd:string ;
tavernaprov:byteCount "7"^^xsd:long ;
tavernaprov:sha512 "cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e"^^xsd:string ;
tavernaprov:sha1 "f52ab57fa51dfa714505294444463ae5a009ae34"^^xsd:string ;
rdf:type tavernaprov:Content .
### Workflow definition
The file `workflow.wfbundle` is a copy of the executed workflow in
[SCUFL2 workflow
bundle](http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle)
format. This is the format which will be used by
The file `workflow.wfbundle` contains the executed workflow in [Taverna
3](http://www.taverna.org.uk/developers/work-in-progress/taverna-3/).
You can use the [SCUFL2
API](http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API) to inspect the
workflow definition in detail, or unzip the workflow bundle to access the
complete workflow definition files as RDF/XML.
#### Workflow structure
Usually it is sufficient to inspect the simpler file
`.ro/annotations/workflow.wfdesc.ttl`, which contains the abstract structure
(but not all the implementation details) of the executed
workflow, in [RDF Turtle](http://www.w3.org/TR/turtle/)
according to the [wfdesc ontology](https://w3id.org/ro/#wfdesc).
c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>cat .ro/annotations/workflow.wfdesc.ttl | head -n 20
@base .
@prefix xsd: .
@prefix owl: .
@prefix prov: .
@prefix wfdesc: .
@prefix wf4ever: .
@prefix roterms: .
@prefix dc: .
@prefix dep: .
@prefix biocat: , ;
wfdesc:hasOutput ;
wf4ever:script "output = string1 + string2;" .
#### Original t2flow
If the workflow was executed in Taverna 2 (which is the case when using this plugin),
then the unzipped `workflow.wfbundle` will contain a copy of the original `.t2flow` within
its `history` folder:
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle $ mkdir workflow ; cd workflow ; unzip ../workflow.wfbundle
Archive: ../workflow.wfbundle
extracting: mimetype
creating: META-INF/
inflating: META-INF/manifest.xml
creating: annotation/
inflating: annotation/705d1f32-ea94-4a5b-b8fb-1cc1a5023427.ttl
inflating: annotation/0f1641bd-49ef-41bd-9e4b-e20cc2bf37bb.ttl
inflating: annotation/d007623d-cd94-4888-a583-e8d97953a159.ttl
inflating: annotation/e9eb11fa-fc63-4ddc-92ca-ec6921af1667.ttl
inflating: annotation/c5e91716-2f9f-4e7c-a692-8f58dba265e3.ttl
creating: history/
inflating: history/01348671-5aaa-4cc2-84cc-477329b70b0d.t2flow
creating: workflow/
inflating: workflow/Hello_Anyone.rdf
creating: profile/
creating: profile/unspecified/
creating: profile/unspecified/configuration/
inflating: profile/unspecified/configuration/Concatenate_two_strings.json
inflating: profile/unspecified/configuration/Concatenate_two_strings-proc.json
inflating: profile/unspecified/configuration/hello.json
inflating: profile/unspecified/configuration/hello-proc.json
inflating: profile/unspecified.rdf
inflating: workflowBundle.rdf
inflating: META-INF/container.xml
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle/workflow $ head history/01348671-5aaa-4cc2-84cc-477329b70b0d.t2flow
Hello_Anyone name 0 0
The UUID in the t2flow filename (`01348671-5aaa-4cc2-84cc-477329b70b0d` above)
should match the executed wfbundle URI as seen in the provenance
http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/
_Not yet implemented: a specific link to the `history/*.t2flow` file within the wfbundle._
## Querying provenance
Example [SPARQL query](http://www.w3.org/TR/sparql11-query/) from [test.sparql](example/test.sparql):
```sparql
PREFIX prov:
PREFIX wfdesc:
PREFIX wfprov:
PREFIX tavernaprov:
PREFIX rdfs:
PREFIX wf4ever:
SELECT DISTINCT ?paramName ?name ?value ?ended ?script
WHERE {
?greeting tavernaprov:content .
?greeting prov:wasGeneratedBy ?concatenate .
?concatenate prov:endedAtTime ?ended ;
wfprov:wasPartOfWorkflowRun ?run ;
wfprov:describedByProcess ?plan .
?concatenate wfprov:usedInput ?input .
?input tavernaprov:content ?name .
OPTIONAL { ?name cnt:chars ?value } .
OPTIONAL { ?plan wf4ever:script ?script } .
?input wfprov:describedByParameter ?param .
?plan wfdesc:hasInput ?param .
OPTIONAL { ?param rdfs:label ?paramName } .
}
```
This query will be starting with the data `?greeting` which content is
represented by the existing output file
[outputs/greeting.txt](example/helloanyone.bundle/outputs/greeting.txt), and
the remaining query tries to find which input or upstream values it has
effectively been derived from.
To do this, we find the `?concatenate` process run that generated
the greeting, and ask when it `?ended`. We also look up its `?plan`,
which should match the [process
identifier](example/helloanyone.bundle/.ro/annotations/workflow.wfdesc.ttl#L16)
within the workflow definition.
We then look at the `?input`s used by the `?concatenate` process run (this
should give two matches as the "Concatenate string" processor takes two
arguments). We look up their `?content` (a file witin this bundle), in addition
to its textual `?value` (optionally, as this is only included in the graph for
small non-binary content).
Now we do a lookup of the
[`?script`](example/helloanyone.bundle/.ro/annotations/workflow.wfdesc.ttl#L20)
behind the defined `?plan` - this is optional because not all processors have
scripts (it might be a web service).
This information is extracted from the
[.ro/annotations/workflow.wfdesc.ttl](example/helloanyone.bundle/.ro/annotations/workflow.wfdesc.)
file which must also be parsed before querying.
Lastly we look up the pararameters which describes `?input`, filtered by
the ones bound to the processor `?plan` (thus avoiding the workflow inputs
"name"), and include their `?paramName` - each result should therefore show the
input port name and value.
Query using [rdfproc](http://librdf.org/utils/rdfproc.html) (`apt-get install redland-utils`):
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle $ rdfproc test parse workflowrun.prov.ttl turtle
rdfproc: Parsing URI file:///home/stain/src/taverna-prov/example/helloanyone.bundle/workflowrun.prov.ttl with turtle parser
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle $ rdfproc test parse .ro/annotations/workflow.wfdesc.ttl turtle
rdfproc: Parsing URI file:///home/stain/src/taverna-prov/example/helloanyone.bundle/.ro/annotations/workflow.wfdesc.ttl with turtle parser
stain@biggie-mint ~/src/taverna-prov/example/helloanyone.bundle $ rdfproc test2 query sparql - "$(cat ../test.sparql)"
rdfproc: Warning - URI file:///home/stain/src/taverna-prov/example/helloanyone.bundle/:1: Variable run was bound but is unused in the query
rdfproc: Query returned bindings results:
result: [, paramName="string2", name=, value="fred"^^, ended="2014-05-28T11:49:43.711+01:00"^^, script="output = string1 + string2;"]
result: [, paramName="string1", name=, value="Hello, "^^, ended="2014-05-28T11:49:43.711+01:00"^^, script="output = string1 + string2;"]
rdfproc: Query returned 2 results
This shows that the `string2` input port was bound to value `"fred"` (content of `inputs/name.txt`) in the process run that generated `outputs/greeting.txt`. Next, `string` was bound to `"Hello, "` (content of `intermediates/3a/3a82..62b.txt`). The executed script was `output = string1 + string2`.
## Building
Note - you do not normally need to build from source code; unless you
are modifying the source code, the "Taverna Prov" plugin included
in Taverna's default plugins is the preferred way of using Taverna-PROV.
You need:
* Java JDK 1.7 or newer (tested with OpenJDK 1.7.0\_03)
* Note: Do not use the OpenJDK 1.6 (default in Ubuntu), as this is
buggy with GUI and File operations, both used by the Taverna Workbench.
* Maven 2.2 or newer (Tested with [Maven 3.0.4](http://maven.apache.org/download.html))
To compile, run `mvn clean install`
On first run this will download various open-source third-party
libraries from Maven repositories, including required modules of Taverna 2.4.
These JARs, and the compiled JARs from this source code, are
installed into `$HOME/.m2/repository/` [by
default](http://maven.apache.org/settings.html#Quick_Overview).
Depending on your network connection, this first run might take about 5
minutes to complete.
Example compilation:
stain@vmint:~/src/taverna-prov$ mvn clean install
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] Taverna PROV
[INFO] Taverna PROV W3 Provenance ontology Elmo bindings
[INFO] Taverna PROV export
[INFO] Taverna PROV activity UI bindings
[INFO] Taverna PROV plugin
[INFO] PROV Taverna command line
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Taverna PROV 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
(..)
Downloading: http://www.mygrid.org.uk/maven/repository/net/sf/taverna/t2/taverna-workbench/workbench-dev/2.5.0/workbench-dev-2.5.0.pom
Downloaded: http://www.mygrid.org.uk/maven/repository/net/sf/taverna/t2/taverna-workbench/workbench-dev/2.5.0/workbench-dev-2.5.0.pom (3 KB at 5.4 KB/sec)
(..)
[INFO] Installing /home/stain/src/taverna-prov/prov-taverna-cmdline/target/prov-taverna-cmdline-2.0.0-SNAPSHOT-tests.jar to /home/stain/.m2/repository/org/purl/wf4ever/provtaverna/prov-taverna-cmdline/2.0.0-SNAPSHOT/prov-taverna-cmdline-2.0.0-SNAPSHOT-tests.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Taverna PROV ...................................... SUCCESS [4.109s]
[INFO] Taverna PROV W3 Provenance ontology Elmo bindings . SUCCESS [1.55.270s]
[INFO] Taverna PROV export ............................... SUCCESS [45.873s]
[INFO] Taverna PROV activity UI bindings ................. SUCCESS [1.56.572s]
[INFO] Taverna PROV plugin ............................... SUCCESS [15.028s]
[INFO] PROV Taverna command line ......................... SUCCESS [1:12.093s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5:54.000s
[INFO] Finished at: Wed Jul 18 12:08:13 BST 2012
[INFO] Final Memory: 72M/274M
[INFO] ------------------------------------------------------------------------
Note that to work with Taverna 2's plugin system, the build is specific
for a particular Taverna version (but works for any edition). To build this
plugin for a different version of Taverna, modify the `` section of
`pom.xml` to match the Taverna release, e.g. `2.4.0 `.
In order for Taverna to find your install of the plugin rather than
download from the official plugin site, you will need to manually edit
`plugins/plugins.xml` of the [Taverna home
directory](http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory)
(run Taverna once to create the file) to include this section right
before the final ``. The
Note that you will get two copies of the "Save provenance" button, one for the
official version included from `workbench-plugin`, and one for the one you built.
```xml
org.purl.wf4ever
org.purl.wf4ever.provtaverna.prov-taverna-plugin
2.0.0-SNAPSHOT
Taverna PROV plugin
true
file:///home/johndoe/.m2/repository/
http://www.mygrid.org.uk/maven/repository/
http://uk.maven.org/maven2/
http://repo.aduna-software.org/maven2/releases/
http://repo.aduna-software.org/maven2/snapshots/
http://repo.aduna-software.org/maven2/ext/
http://repository.aduna-software.org/maven2/
http://repository.aduna-software.org/maven2-snapshots/
http://people.apache.org/repo/m2-snapshot-repository/
http://nexus.codehaus.org/snapshots/
http://repository.jboss.org/maven2/
org.purl.wf4ever.provtaverna
prov-taverna-ui
2.0.0-SNAPSHOT
junit
junit
4.8.2
2.5.0
```
1. Modify the line:
```xml
file:///home/johndoe/.m2/repository/
```
to match your $HOME/.m2/repository. On Windows this path should look like:
```xml
file:///C:/Users/johndoe/.m2/repository/
```
2. Take care that the `` of the `` and `prov-taverna-ui` matches
the `` specified in the `pom.xml` of this source code (typically `1.x-SNAPSHOT`).
3. If you are building for a different Taverna, check that the ``
matches the Taverna version (compare with the existing plugins)
4. Start Taverna Workbench.
You only need to do this plugin installation once - if you later
recompile the source code without changing the version numbers, next
start of Taverna will use the newer JARs from `mvn clean install` as
Taverna will prefer accessing `$HOME/.m2/repository`. You might however need to delete
the `repository/org/purl/wf4ever` folder of the
[Taverna home directory](http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory)
if Taverna has downloaded the SNAPSHOT versions from the myGrid repository
instead (for instance because you used the wrong `` path or
did not update ``).
To make the plugin installation system-side (ie. multiple UNIX users or
to make a customized Taverna distribution), copy `plugins/`
and `repository` with overwrite onto the Taverna installation directory.
(See _Installation for Taverna Command Line_ above)
本源码包内暂不包含可直接显示的源代码文件，请下载源码包。
