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Test results for build 456 on OS X

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Notes

biomartandembossmouserat_365285.t2flow

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Runs with errors but same result as 2.4

demonstration_of_configurable_iteration_667929.t2flow

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ebi_interproscan_newservices_900329.t2flow

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Error output - ok on 2.4

example_for_external_tools_with_zip_and_unzip_208995.t2flow

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External tool not done yet

example_of_conditional_invocation_850670.t2flow

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example_of_explicit_looping_253706.t2flow

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example_workflow_for_rest_and_xpath_activities_483512.t2flow

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XPath error

fetch_pdb_flatfile_from_rcsb_server_440785.t2flow

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No jmol renderer

fetch_today_s_xkcd_comic_186869.t2flow

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gbseq_test_310396.t2flow

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hello_anyone_730275.t2flow

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hello_world_398701.t2flow

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multiple_choice_quiz_42858.t2flow

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Looks like a looping error

numerically_adding_two_values._557465.t2flow

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External tool not done yet

pipelined_list_iteration_261838.t2flow

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render_gene_via_biogps_164294.t2flow

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secure_rest_service_call_example_323172.t2flow

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secure_web_service_call_example_304465.t2flow

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Error message - doesn't add certificate

simple_python_example_285475.t2flow

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External tool not done yet

spreadsheet_import_example_166335.t2flow

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unix_tool_service_using_string_replacement_16330.t2flow

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External tool not done yet

Dispatch stack issues

The current behaviour when creating a new processor in Taverna 3 is that no dispatch stack is created. When the workflow is compiled to a local execution a default dispatch stack is added to processors that have no dispatch stack defined. The default dispatch stack is defined in the DefaultDispatchStackEdit.

This is problematic in the workbench when displaying the contextual views or configuration dialogs for dispatch layers because there are no dispatch layers (or configurations) to show.

I think the solutions are:

  1. Add a default dispatch stack when creating the processor in SCUFL2
  2. Display default dispatch layer configurations for in dialogs and add a dispatch stack to the processor if the user changes a dispatch layer configuration property and clicks OK.
    1. What would happen if the user doesn't change a configuration property in the dialog and clicks OK (i.e. specifies the default)?
    2. Where is the default dispatch stack defined?
  3. Create a 'dummy' default dispatch stack to display in the workbench and add it to the processor if the user edits a dispatch layer configuration property. Similar issues to 2.
  4. Remove the dispatch stack ...
  5. Donal and Stian's suggestion: Dispatch stack remains in the engine, but disappears from SCUFL2. SCUFL2 however has a Processor configuration with subkeys like "retry", "looping" etc. When running, the Platform will configure the corresponding layers in the default dispatch stack - for convenience we can give each layer such a name. If a configuration lists a subkey like "conditional" but the engine does not find anything about it in the dispatch stack, it is a workflow from a future Taverna or using a plugin, and he should bail out. Example of normal config:
    If the default values are fine (it has not been configured), then it is not listed. So for maxJobs 1, the key "parallelize" above can be dropped without implying that there is no parallelize layer. The default dispatch stack is not changeable beyond its configuration.
  6. As above, but third-party layers can be added by including in their sub-configuration the properties "type" to match with the plugin (as it happens today) and "after"/"before" to indicate position, e.g. for a theoretical conditional execution layer with the configuration property "condition":

The type and position are not normally needed (or possibly not even supported) for the default layers. which would remain like above.

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