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SCUFL2 information web service
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README.md

scufl2-info

Build Status

Returns Linked Data information about a SCUFL2 resource.

The idea is that say

http://ns.taverna.org.uk/2010/workflowBundle/74674670-04d0-4832-9651-bfc3a2ec3a19/workflow/HelloWorld/processor/Hello/out/fred"

will redirect to this service to "guess" the partial workflow structure expressed in the URI - e.g. that we're talking about an output port fred in processor Hello in workflow HelloWorld in workflow bundle with uuid 746....a19.

Example

http://localhost:3000/workflowBundle/74674670-04d0-4832-9651-bfc3a2ec3a19/workflow/HelloWorld/processor/Hello%20there/out/fred

returns JSON-LD):

{
  "workflow": {
    "processor": {
      "inputProcessorPort": {
        "@id": "workflow/HelloWorld/processor/Hello/in/hello",
        "@type": "InputProcessorPort",
        "name": "hello"
      },
      "@id": "workflow/HelloWorld/processor/Hello/",
      "@type": "Processor",
      "name": "Hello"
    },
    "@id": "workflow/HelloWorld/",
    "@type": "Workflow",
    "name": "HelloWorld"
  },
  "@context": {
    "@base": "http://ns.taverna.org.uk/2010/workflowBundle/74674670-04d0-4832-9651-bfc3a2ec3a19/",
    "@vocab": "http://ns.taverna.org.uk/2010/scufl2#"
  },
  "@id": "http://ns.taverna.org.uk/2010/workflowBundle/74674670-04d0-4832-9651-bfc3a2ec3a19/",
  "@type": "WorkflowBundle"
}

Which is equivalent to the RDF triples:

@base <http://ns.taverna.org.uk/2010/workflowBundle/74674670-04d0-4832-9651-bfc3a2ec3a19/> .
<> <http://ns.taverna.org.uk/2010/scufl2#workflow> <workflow/HelloWorld/> .
<> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle> .
<workflow/HelloWorld/> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://ns.taverna.org.uk/2010/scufl2#Workflow> .
<workflow/HelloWorld/> <http://ns.taverna.org.uk/2010/scufl2#name> "HelloWorld" .
<workflow/HelloWorld/> <http://ns.taverna.org.uk/2010/scufl2#processor> <workflow/HelloWorld/processor/Hello/> .
<workflow/HelloWorld/processor/Hello/> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://ns.taverna.org.uk/2010/scufl2#Processor> .
<workflow/HelloWorld/processor/Hello/> <http://ns.taverna.org.uk/2010/scufl2#inputProcessorPort> <workflow/HelloWorld/processor/Hello/in/hello> .
<workflow/HelloWorld/processor/Hello/> <http://ns.taverna.org.uk/2010/scufl2#name> "Hello" .
<workflow/HelloWorld/processor/Hello/in/hello> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort> .
<workflow/HelloWorld/processor/Hello/in/hello> <http://ns.taverna.org.uk/2010/scufl2#name> "hello" .

This corresponds to what is defined inside the scufl2 workflow bundle.

TODO

  • control links, activities, profiles, configurations, dispatch layer
  • Other RDF formats: RDF/XML and Turtle
  • Search myExperiment by UUID to add rdfs:seeAlso
  • wfdesc

Prerequisites

You will need Leiningen 1.7.0 or above installed.

Running

To start a developer web server for the application, run:

lein ring server

To generate a WAR that can be installed into a servlet container like Apache Tomcat:

lein ring uberwar

Docker image

This service is also available as a Docker image stain/scufl2-info, exposing the ports 8080 (HTTP) and 8009 (AJP) through tomcat.

docker run -p 8080:8080 stain/scufl2-info

cgi-bin

If you are old-skool and unable to run a Servlet application server, it is possible to create a cgi-bin version, that although very slow (~ 4s response time), does not require any running processes or memory usage when the scufl2info service is not being accessed.

Build as:

lein ring uberjar

This produces a single jar in target/scufl2-info-0.4.1-SNAPSHOT-standalone.jar. You can test this as:

stain@biggie-utopic:~/src/scufl2-info$ PATH_INFO=/workflowBundle/2f0e94ef-b5c4-455d-aeab-1e9611f46b8b/ java -jar target/scufl2-info-0.4.1-SNAPSHOT-standalone.jar
Status: 200
Content-Type: application/json; charset=utf-8

{
  "@context" : {
    "@base" : "http://ns.taverna.org.uk/2010/workflowBundle/2f0e94ef-b5c4-455d-aeab-1e9611f46b8b/",
    "@vocab" : "http://ns.taverna.org.uk/2010/scufl2#"
  },
  "@id" : "http://ns.taverna.org.uk/2010/workflowBundle/2f0e94ef-b5c4-455d-aeab-1e9611f46b8b/",
  "@type" : "WorkflowBundle"
}

See RFC3875 for details about the cgi-bin environment variables.

Now simply create a scufl2info.cgi script to execute scufl2-info-0.4.1-SNAPSHOT-standalone.jar:

#!/bin/sh
## Small memory footprint!
java -Xmx32M -jar lib/scufl2-info-0.4.1-SNAPSHOT-standalone.jar 2>&1

Remember to make the script executable with

chmod 755 scufl2info.cgi

Configuring your web server to run cgi-bin is out of scope for this document.

You might want to pretend this is in a folder /scufl2info/ using this .htaccess:

RewriteEngine On
RewriteRule (.*) /cgi-bin/scufl2info.cgi/$1

Remember to add the final / as otherwise the relative links will be wrong.

License

Copyright © 2014-2015 University of Manchester

This software is licensed under the MIT license.

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