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Reference manager

This currently only understands:

  • Singleton values
    • Strings
    • Byte arrays
  • Lists of singletons/lists/error documents
    • Lists have a specific depth so cannot have list that contains a list and a string
  • Error documents

The singleton values can be either in-memory, in a database, a local file, a remote file or at a URL. The list and error documents are either in-memory or in a database. Unless explicitly stated, it should be assumed that services consume/produce values that are in-memory or in a database.

There is no way of identifying that a string or byte array contains structured data.

Workflow inputs and outputs

The workflow inputs take

  • Singleton values
    • Strings
    • Byte arrays
  • Lists of singletons/lists/error documents
    • Lists have a specific depth so cannot have list that contains a list and a string

Note that the strings can have a file encoding and be in a specific character set

The values can be specified explicitly, or as coming from a file or a URL

Can save the set of values in an XML format called Baclava

The workflow output types are derived from the workflow inputs and the workflow.
The actual values will be the same as for the reference manager

Example values

Example values can be specified for a workflow or service input or output port.

Example values can only be strings.

Service types

API Consumer

Passes around Java Virtual Machine objects.

No description of what is passed. No way to create or subset the object.


Just lists and singletons


Can output results as:

  • Multiple ports one per attribute
    • Needs dot product "downstream"
  • Formatted single string
    • HTML
    • Text
    • csv
    • tsv
    • xls


Uses inputs and outputs that are XML documents. Documents conform to an xsd based on an ontology

For example:

Have services for splitting and forming objects (constructors and parsers)

Pass the structured objects between Biomoby services

Note: No mechanism for displaying the Biomoby objects. They are just shown "verbatim" as above.

Dataflow (nested workflows)

Input and output is same as for workflow

Tool service

Passes around either normal reference objects or references to local or remote files. The file encoding and the character set can be specified.

Local worker

Same as beanshell


Takes in singletons and outputs singletons.

The singleton strings are often XML or JSON documents of specific format.

Note: No ability to create input documents

Note: Output XML documents can be subsetted using XPath


Inputs can be:

  • Singleton
    • Logical
    • Numeric
    • Integer
    • String
  • Vector
    • Logical
    • Numeric
    • Integer
    • String
  • Text file (actually string that is uploaded)
  • R-expression - a structured object

Outputs can be the same plus

  • PNG

The text file v PNG choice is really just deciding on textual or binary data


The inputs and outputs are

  • strings
  • byte arrays
  • lists of (lists of...) strings
  • list of byte array

Soaplab, and probably Soaplab2, can include more information about the data. This is ignored by Taverna.

Spreadsheet import

Input is

  • Reference to a file or URL that contains either
    • csv
    • Excel spreadsheet
    • ODF spreadsheet

The service configuration allows the selection of rows within specific columns.

The output is

  • List of values, one list per column - or
  • Single csv file

Text constant

Output is a string.

Note there are no mechanisms for creating constant values of other types

Note there are no mechanisms for specifying the format of the text

  • None