Wf-RO transformation service

Version 9 by Stian Soiland-Reyes
on may 11, 2012 15:48.

<< Changes from 8 to 9

compared with

Version 10 by Stian Soiland-Reyes
on may 11, 2012 16:09.

Changes from 10 to 11 >>

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...

Input:
# t2flow workflow
# RO identifier
# ROSRS URI
# OAuth access token

Output:
# HTTP Status code: 200 OK or other

Service algorithm:
# Extract the RO ID from the t2flow.
# For each workflow in t2flow:
## Extract the UUID
## Generate a wfdesc description from t2flow (RDF graph)
## Generate a roevo description from UUID chain from t2flow (RDF graph)
# Check if  RO exists in ROSRS:
## if yes, update identifier = RO ID and remove annotations of the workflow made by this service
## if no, create a new one (with identifier = RO ID)
# For each workflow in t2flow:
## Upload the workflow
## Upload wfdesc and roevo descriptions as 2 annotations of the workflow
# Return 200 OK

Questions and answers:

# {color:#993300}Question 1: A t2flow can have many workflows (right?), each with a UUID. Do we assign each UUID to a resource (wf dcterms:identifier uuid), and assign no id to the RO itself?{color}## {color:#993300}Yes, but one-and-only-one of them will be the 'main' workflow - and its UUID is used for making the WorkflowBundle URI{color}
# {color:#993300}Question 2: WorkflowBundle#getMainWorkflow#getWorkflowIdentifier returns a URI - how is it related to the UUID, why should we use UUID not this URI?{color}## {color:#993300}It's constructed from the t2flow UUID. However there will be both the workflow bundle ID and the workflow ID - both URIs have the same UUID from the main workflow, but different prefix. We should use the WorkflowBundle URI (that's WorkflowBundle.getGlobalBaseURI()) as the identifier for the RO, and the individual workflow's identifier for the wfdesc (the Workflow.getWorkflowIdentfier).{color}
# {color:#993300}Question 3: Is there a javadoc for the scufl2 API? I see that the WorkflowBundleIO can save to file, but I'll need something else.{color}
## {color:#993300}Easiest in Eclipse is to click F3 to get the source code - otherwise see{color} [http://mygrid.github.com/scufl2/api/0.9/|http://mygrid.github.com/scufl2/api/0.9/]

The authorization algorithm is rather weak - an access token is shared between the caller and the service. A better solution would be one of the following:
* The caller sends a single-use authorization code, which is exchanged by the service for an access token. Safer but requires constant reauthorization, especially difficult for offline clients such as ro-manager
* The service is considered trusted and has its own access token - currently not supported by RODL (actually I'm not sure that this one is better)

h2. API draft

Considerations:
* The translator might behave differently for different formats, like Galaxy, SCUFL2 .wfbundle, WINGS - (arguably this could come from the Content-Type of the resource, but that might only works for single-resource workflows!)
* The given ro might or might not exist. RODL API should support PUT to create.
* Translation might take some time, so a status is returned
* Cache headers tell us

h3. POST a conversion

...

{code}
POST http://example.net/translate/jobs HTTP/1.1
Authorization: OAuth realm="Wf4Ever",
oauth_consumer_key="dpf43f3p2l4k3l03",
oauth_token="nnch734d00sl2jdk",
oauth_signature_method="HMAC-SHA1",
oauth_timestamp="137131202",
oauth_nonce="chapoH",
oauth_signature="MdpQcU8iPSUjWoN%2FUDMsK2sui9I%3D"
Content-Type: multipart/form-data

resource: http://www.example.com/workflow.t2flow
format: http://taverna.sf.net/2008/xml/t2flow
ro: http://www.example.org/rodl/ROs/someRO/

201 Created
Location: http://example.net/translate/jobs/fefe-fefefef-fefefefefefe
{code}

or..

{code}
POST http://example.net/translate/jobs HTTP/1.1
Authorization: OAuth realm="Wf4Ever",
oauth_consumer_key="dpf43f3p2l4k3l03",
oauth_token="nnch734d00sl2jdk",
oauth_signature_method="HMAC-SHA1",
oauth_timestamp="137131202",
oauth_nonce="chapoH",
oauth_signature="MdpQcU8iPSUjWoN%2FUDMsK2sui9I%3D"
Content-Type: application/json

{
"resource": "http://www.example.com/workflow.t2flow"
"format": "http://taverna.sf.net/2008/xml/t2flow"
"ro": "http://www.example.org/rodl/ROs/someRO/"
}

201 Created
Location: http://example.net/translate/jobs/fefe-fefefef-fefefefefefe
{code}

h3. Check status

{code}
GET http://example.net/translate/jobs/fefe-fefefef-fefefefefefe HTTP/1.1
Accept: application/json
Authorization: OAuth realm="Wf4Ever", ...

200 OK
Content-Type: application/json
Last-Modified: Sat, 29 Oct 2010 19:43:31 GMT
ETag: "152"

{
"resource": "http://www.example.com/workflow.t2flow"
"format": "http://taverna.sf.net/2008/xml/t2flow"
"ro": "http://www.example.org/rodl/ROs/someRO/"
"status": "running"
}
{code}

{code}
GET http://example.net/translate/jobs/fefe-fefefef-fefefefefefe HTTP/1.1
Accept: application/json
If-Modified-Since: Sat, 29 Oct 2010 19:43:31 GMT
If-None-Match: "152"
Authorization: OAuth realm="Wf4Ever", ...

304 Not Modified
Last-Modified: Sat, 29 Oct 2010 19:43:31 GMT
ETag: "152"
{code}

{code}
GET http://example.net/translate/jobs/fefe-fefefef-fefefefefefe HTTP/1.1
Accept: application/json
If-Modified-Since: Sat, 29 Oct 2010 19:43:31 GMT
If-None-Match: "152"
Authorization: OAuth realm="Wf4Ever", ...

200 OK
Content-Type: application/json

Last-Modified: Sat, 29 Oct 2010 20:54:41 GMT
ETag: "155"

Expires: Sat, 6 Nov 2010 20:54:41 GMT

{

...

204 No content
{code}

h3. Retrieving cancelled job

{code}
GET http://example.net/translate/jobs/fefe-fefefef-fefefefefefe HTTP/1.1
Authorization: OAuth realm="Wf4Ever", ...

410 Gone
{code}

h3. Retrieving expired job

{code}
GET http://example.net/translate/jobs/fefe-fefefef-fefefefefefe HTTP/1.1
Authorization: OAuth realm="Wf4Ever", ...

404 Not found
{code}