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)
