W3 Provenance WG ontology export for Taverna
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README.md

Taverna PROV support

Build Status

This is a plugin for the Taverna Workbench and Taverna Command Line which allows export of the provenance of a workflow run according to the W3C PROV-O standard.

Source code and license

This plugin is distributed under the GNU Lesser General Public License 2.1 (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-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. 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 from myExperiment (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.

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, 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.

This source includes an example bundle and unzipped bundle as a folder. This data bundle has been saved after running a simple hello world workflow.

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 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 export of the workflow run provenance (including nested workflows) in RDF Turtle format.

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           <http://ns.taverna.org.uk/2011/run/385c794c-ba11-4007-a5b5-502ba8d14263/> ;

See the provenance graph for a complete example. The provenance uses the vocabularies PROV-O, wfprov and tavernaprov.

Intermediate values

Intermediate values are stored in the intermediates/ folder and referenced from workflowrun.prov.ttl

Intermediate value from the example provenance:

<http://ns.taverna.org.uk/2011/data/385c794c-ba11-4007-a5b5-502ba8d14263/ref/d588f6ab-122e-4788-ab12-8b6b66a67354>
        tavernaprov:content          <intermediates/d5/d588f6ab-122e-4788-ab12-8b6b66a67354.txt> ;
        wfprov:describedByParameter  <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/processor/Concatenate_two_strings/in/string1> ;
        wfprov:describedByParameter  <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/processor/hello/out/value> ;
        wfprov:wasOutputFrom         <http://ns.taverna.org.uk/2011/run/385c794c-ba11-4007-a5b5-502ba8d14263/process/bbaedc02-896f-491e-88bc-8dd350fcc73b/> .

Here we see that the bundle file intermediates/d5/d588f6ab-122e-4788-ab12-8b6b66a67354.txt contains the output from the "hello" processor, which was also the input to the "Concatenate_two_strings" processor. Details about processor, ports and parameters can be found in the workflow definition.

Example listing:

c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>ls intermediates/d5
d588f6ab-122e-4788-ab12-8b6b66a67354.txt

c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>cat intermediates/d5/d58*
Hello,

Note that "small" textual values are also included as cnt:chars in the graph, while the referenced intermediate file within the workflow bundle is always present.

<intermediates/d5/d588f6ab-122e-4788-ab12-8b6b66a67354.txt>
        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 format. This is the format which will be used by The file workflow.wfbundle contains the executed workflow in Taverna 3.

You can use the 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 according to the wfdesc ontology.

c:\Users\stain\workspace\taverna-prov\example\helloanyone.bundle>cat .ro/annotations/workflow.wfdesc.ttl | head -n 20
@base <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
@prefix roterms: <http://purl.org/wf4ever/roterms#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix comp: <http://purl.org/DP/components#> .
@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
@prefix biocat: <http://biocatalogue.org/attribute/> .
@prefix : <#> .

<processor/Concatenate_two_strings/> a wfdesc:Process , wfdesc:Description , owl:Thing , wf4ever:BeanshellScript ;
        rdfs:label "Concatenate_two_strings" ;
        wfdesc:hasInput <processor/Concatenate_two_strings/in/string1> , <processor/Concatenate_two_strings/in/string2> ;
        wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> ;
        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 
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="unspecified"><dataflow id="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>

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 from test.sparql:

PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#> 
PREFIX wfprov: <http://purl.org/wf4ever/wfprov#> 
PREFIX tavernaprov: <http://ns.taverna.org.uk/2012/tavernaprov/>
PREFIX cnt:  <http://www.w3.org/2011/content#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX wf4ever: <http://purl.org/wf4ever/wf4ever#> 


SELECT DISTINCT ?paramName ?name ?value ?ended ?script
WHERE {
    ?greeting tavernaprov:content <outputs/greeting.txt> .
    ?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, 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 within the workflow definition.

We then look at the ?inputs 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 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 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 (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=<file:///home/stain/src/taverna-prov/example/helloanyone.bundle/inputs/name.txt>, value="fred"^^<http://www.w3.org/2001/XMLSchema#string>, ended="2014-05-28T11:49:43.711+01:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>, script="output = string1 + string2;"]
result: [, paramName="string1", name=<file:///home/stain/src/taverna-prov/example/helloanyone.bundle/intermediates/3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt>, value="Hello, "^^<http://www.w3.org/2001/XMLSchema#string>, ended="2014-05-28T11:49:43.711+01:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>, 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)

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. 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 <parent> section of pom.xml to match the Taverna release, e.g. <version>2.4.0</version>.

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 (run Taverna once to create the file) to include this section right before the final </plugins:plugins>. 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.

     <plugin>
        <provider>org.purl.wf4ever</provider>
        <identifier>org.purl.wf4ever.provtaverna.prov-taverna-plugin</identifier>
        <version>2.0.0-SNAPSHOT</version>
        <name>Taverna PROV plugin</name>
        <description/>
        <enabled>true</enabled>
        <repositories>
            <repository>file:///home/johndoe/.m2/repository/</repository>
            <repository>http://www.mygrid.org.uk/maven/repository/</repository>
            <repository>http://uk.maven.org/maven2/</repository>
            <repository>http://repo.aduna-software.org/maven2/releases/</repository>
            <repository>http://repo.aduna-software.org/maven2/snapshots/</repository>
            <repository>http://repo.aduna-software.org/maven2/ext/</repository>
            <repository>http://repository.aduna-software.org/maven2/</repository>
            <repository>http://repository.aduna-software.org/maven2-snapshots/</repository>
            <repository>http://people.apache.org/repo/m2-snapshot-repository/</repository>
            <repository>http://nexus.codehaus.org/snapshots/</repository>
            <repository>http://repository.jboss.org/maven2/</repository>
        </repositories>
        <profile>
            <dependency>
                <groupId>org.purl.wf4ever.provtaverna</groupId>
                <artifactId>prov-taverna-ui</artifactId>
                <version>2.0.0-SNAPSHOT</version>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.8.2</version>
            </dependency>
        </profile>
        <compatibility>
            <application>
                <version>2.5.0</version>
            </application>
        </compatibility>
    </plugin>
  1. Modify the line:

        <repository>file:///home/johndoe/.m2/repository/</repository>

    to match your $HOME/.m2/repository. On Windows this path should look like:

        <repository>file:///C:/Users/johndoe/.m2/repository/</repository>    
  2. Take care that the <version> of the <plugin> and prov-taverna-ui matches the <version> 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 <application><version> 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 if Taverna has downloaded the SNAPSHOT versions from the myGrid repository instead (for instance because you used the wrong <repository> path or did not update <version>).

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)