Changes to the Vernalis Plugin for KNIME 3.0

We list below the detailed changes made to the Vernalis plugin in readiness for KNIME 3.0 (versions 1.6.0 of our plugin onwards):

GENERAL

  • All nodes are now parallelised wherever possible
  • All plugins manifests were updated to bind KNIME component versions into range [3.0.0, 4.0.0)
  • All plugin.xml's had deprecated nodes re-added, and the deprecation flag set
  • All plugin.xml's had disused expert-mode property of node extensions removed

Main Vernalis Plugin

Fingerprint properties Node

  • Parallelised execution
  • Fingerprint type names no longer end 'Cell', so are SparseBitVector, DenseBitVector, SparseByteVector, DenseByteVector
  • Test case updated to reflect this change
  • BUG:    Although the node could process ByteVectors, the column selector doesnt let it select them

FASTA Sequence Node

  • Updated all counters for rows and subrows to longs

EuroPMC Node

  • Updated hit, page and row counters to longs (flow variables for hit counter may therefore behave strangely)

List Dirs node

  • Updated file and added row counters to longs

Load local PDB file node

  • Parallelised
  • Converted to use PDBCellFactory

Save local PDB file Node

  • Parallelised
  • Converted to use BooleanCellFactory for result cell

PDB Downloader (Manipulator)

  • Parallelised
  • Converted to use PDBCellFactory

PDB Downloader (Source)

  • Updated row and PDB ID counters to longs (NB this is probably irrelevant as they are processed via arrays!)

Load Text files

  • Parallelised

Save Text files

  • Parallelised
  • Add logging explanation for save failures where easily possible
  • Return value now uses BooleanCellFactory

Random Number Generator

  • Original Version deprecated due to change in settings model type
  • Maximum number of rows changed to a Long (and Settings Model changed to SettingsModelLongBounded), and artificial 10,000 row cap removed
  • Row counters changed to longs
  • Generator methods changed to not work via intermediate collections but add directly, and thus to allow cancelling during number generation as well as table writing, and old methods deprecated
  • New Test Case created for new version

PDB To Sequence

  • Updated to handle long tables

PDB Properties

  • Parallelised

PDB Connector / PDB Connector (XML Query)

  • Updated to allow long tables at both outputs

 

MMPs Plugin

  • Modified canonicalisation during fragmentation to resolve duplicate leaves canonically (results in possible changes to canonicalisation)
  • Converted to SmilesCellFactory

 

Flow Control Plugin

  • All PortType constructors replaced with PortTypeRegistry.getInstance().getPortType() constructors

All nodes

  • Now all use #size() in place of #getRowCount()
  • Iteration counters now all long (flow variables for iteration counters may therefore behave strangely)

 

Performance Monitoring Plugin

Loop End Nodes

  • Iteration counter now long (flow variables for iteration counters may therefore behave strangely)
  • Iteration column in timing table now LongCell (previously IntCell)

    
Loop Start Nodes

  • Iteration counter now long (flow variables for iteration counters may therefore behave strangely)
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