GravesDisease NetBeans Development Requirements

Summariesed from GDScenarioReqsWP6Annotations^? to pull out what needs to be built in terms of NetBeans:

MIR general

• NetBeans MIR filesystem/view, showing a User's WorkContext^? hierarhy, DataThings^?, WorkflowInstances^? and associated inputs and outputs.
• New Project template, and appropriate NetBeans New Wizard support.
• Import Data Wizard, including source data selection and assignment of concept and MIME type, placing data into MIR (via MIR filesystem) as a new DataThing^?.
  • Option: support for pasting a file into the MIR filesystem.
  • Option: Classify Data Wizard, to classify these file(s).

Personalisation

MIR

• • Option: separate MIR filesystem and view, with different view organisation options.

Workflows

Workflow Discovery

• Find and Run Workflow Wizard, part a: Find Workflow. Including checking of current selection concept types, interaction with SemanticFindService^?, WorkflowDefinition^? listing, visualisation, and selection.
  • Also requires semantic annotation of WorkflowDefinitions and indexing of WorkflowDefinitions in the MIR by the SemanticFindService^?.

Workflow execution

• Find and Run Workflow Wizard, part b: Run Workflow. Including viewing and changing of default parameters (simple version), choice of 'foreach input', and starting.
• Workflow monitor TopComponent^?, showing status of current and recent WorkflowInstances^?.
• Option: Workflow summary top component, showing tabular summary of multiple selected WorkflowInstances^? and their inputs and outputs.
• Option: workflow summary generator, outputting the above to (say) an HTML document placed in the current WorkContext^?.

Provenance and metadata

• Option: Annotation/metadata add/view TopComponent^?
• Check XML support for viewing provenance XML document.
  • Option: XSL prettification of provenance XML
  • Option: custom DataLoader^?/Object/Node support for viewing provenance XML.

Notification

• NetBeans Notification service filesystem, showing subscriptions and notifications, with support for maintenance, garbage collection, ordering.
  • Option: Notification ticker tape TopComponent^??
  • Option: link from selected notifications to corresponding entities in the Explorer?
  • Requires notifications from the MIR, e.g. from DataThing^? added to WorkContext^? of interest.
• Action on a WorkContext^? to request (subscribe to) notifications of changes to it, i.e. additions of DataThings^? (new data or outputs) and WFInstances (new workflow runs)

Bio-informatics specific support

Record IDs

• Support for loading and explorer display of files of type text/x-record-ids, i.e. RecordIDsDataLoader^?, RecordIDsDataObject^?, RecordIDsNode^?, RecordsIDs^?, RecordIDsChildren^?, RecordIDNode^? and RecordID^?.
• Support for viewing of RecordIDNode^? and RecordIDsNode^?, i.e. RecordIDListPanel^?, and corresponding View and RecordIDCookie^? support in those nodes.
• Action available on RecordIDNode^? to fetch corresponding record from external CGI or WebService^?, and import as a DataThing^? of type text/x-sequence-record or text/plain (text/xml etc) as appropriate. Supporting Option configuration for this.

Sequence Records

• Support for loading and explorer display of files of type text/x-sequence-record, i.e. SequenceFileDataLoader^?, SequenceFileDataObject^?, SequenceFileNode^?, SequenceSet^?, SequenceFileChildren^?, SequenceNode^? and Sequence (the last from BioJava^??!).
• Support for viewing of SequenceNode^?, i.e. SequenceViewPanel^? (based on BioJava^? sequence rendering classes?!), and corresponding View and SequenceCookie^? support in those nodes.

Sequence structure

• Support for PDB as an external viewer for files of the appropriate MIME type.

Information extraction

• Link to pesto!?

Branding and packaging

• myGrid splash screen, window title, etc.
• Custom distribution, e.g. without Java development support

Other issues

Plus, of course:

• Seed data
• WorkflowDefinitions
• Semantic annotations of WorkflowDefinitions
• Services used by workflows, and their annotations

-- ChrisGreenhalgh - 25 Apr 2003