file_fetching_workflow
Created: 2008-07-14 17:09:56
Last updated: 2008-07-14 17:25:15
This workflow demonstrates interaction with an instance of an omixed server (omixed.org) hosting a very simple model and containing some sequence files. The server is available for public access so you should be able to try this out.
Notes:
With the versions of Taverna and Axis2 I am using, I had to massage the WSDL emitted by Axis2 in order to keep Taverna happy. This involved removing the sections relating to SOAP12.
The workflow first connects to the server and obtains a session token which is fed to all other processors.
An XML splitter is needed on the front of each call to omixed.
File downloading is done via the rest API, which involves constructing a URL and fetching it with the 'get a web page' widget.
The workflow does not currently log off at the end, which is a bit naughty.
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Workflow Components
Processors (18)
| Name |
Type |
Description |
| connect |
arbitrarywsdl |
|
| connectionParams |
local |
|
| connectionResult |
local |
|
| getItemTypes |
arbitrarywsdl |
|
| getItemTypesParams |
local |
|
| getItemTypesResult |
local |
|
| getItems |
arbitrarywsdl |
|
| getItemsParams |
local |
|
| seq1_Sequence |
stringconstant |
|
| getDomainName |
arbitrarywsdl |
|
| getDomainNameParameters |
local |
|
| partialItemIDForSequence |
local |
|
| getDomainNameResult |
local |
|
| extractFileIdentifiers |
local |
|
| fetchSequenceFiles |
local |
|
| makeFileURL1 |
local |
|
| makeFileURL2 |
local |
|
| makeFileURL3 |
local |
|
Outputs (3)
| Name |
Description |
| itemTypes |
|
| allSequenceItems |
|
| allSequenceFiles |
|
Links (22)
| Source |
Sink |
| connect:parameters |
connectionResult:input |
| connectionParams:output |
connect:parameters |
| connectionResult:return |
getDomainNameParameters:sessionID |
| connectionResult:return |
getItemTypesParams:sessionID |
| connectionResult:return |
getItemsParams:sessionID |
| connectionResult:return |
makeFileURL1:string2 |
| extractFileIdentifiers:nodelist |
makeFileURL3:string2 |
| fetchSequenceFiles:contents |
allSequenceFiles |
| getDomainName:parameters |
getDomainNameResult:input |
| getDomainNameParameters:output |
getDomainName:parameters |
| getDomainNameResult:return |
partialItemIDForSequence:string1 |
| getItemTypes:parameters |
getItemTypesResult:input |
| getItemTypesParams:output |
getItemTypes:parameters |
| getItems:parameters |
extractFileIdentifiers:xml-text |
| getItemsParams:output |
getItems:parameters |
| makeFileURL1:output |
makeFileURL2:string1 |
| makeFileURL2:output |
makeFileURL3:string1 |
| makeFileURL3:output |
fetchSequenceFiles:url |
| getItemTypesResult:return |
itemTypes |
| getItems:parameters |
allSequenceItems |
| partialItemIDForSequence:output |
getItemsParams:partialItemID |
| seq1_Sequence:value |
partialItemIDForSequence:string2 |
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