silebat / fsk-lab Goto Github PK

de.bund.bfr.knime.fsklab.rakip.nodes

• WriterNodeFactory.kt
• WriterNodeModel.kt
• Writer.png
• WriterNodeFactory.kt

Replace duplicated class de.bund.bfr.knime.fsklab.nodes.RScript with de.bund.bfr.knime.RScript

• Replace with empty species (don't throw NPE)
• Check matrix detail

Include missing dependencies in the DRM branch.

• ez-vcard deps
• JRis

The models should be validated with custom parameter values in metadata

The models are currently validated with the parameter values from the parameter script while the parameter values in the metadata are not validated.

Replace free text field in metadata table in the FSK Editor with a JComboBox with the two options: R and Matlab.

Create basic website with:

• Description of included nodes
• Installation instructions using update site
• Example workflows

Implement an "FSK to R" node that extracts the R workspace out of an FSK Port Object.

• NoInternalsModel
• StatelessModel

Replace settings to external R environment with the R environment provided by the R binary plugin. The KNIME BfR preferences page should be deleted as well.

• Parameter script must be optional. Ignored if missing.
• Add tooltip on parameter script DialogComponentFileChooser. E.g.

Script with the parameter values of the model.

Add icons in the extension node list in the README file like in PMM-Lab

Remove the class de.bund.bfr.knime.fsklab.nodes.URIS. The URIS should be provided by fskml and no the tool using fskml.

• de.bund.bfr.knime.fsklab.nodes.URIS (impl)
• de.bund.bfr.knime.nodes.URISTest (unit test)

After adding a Creator the item in the table has text {0}{1}{2} instead of given name_family name_contact.

• Visualization script must be optional. Ignored when missing.
• Add tooltip on visualization script DialogComponentFileChooser. E.g.

Script with a number of commands in a scripting language to create plots or charts using the results generated in a simulation.

Add basic settings to FSK Runner like in the R View Node.

• Image width (short)
• Image height (short)
• Image resolution (string)
• Background colour (string)
• Text point size (byte)

• FSK Creator
• FSKX Reader
• FSKX Writer
• FSK Runner
• FSK Editor
• FSK Metadata Editor

• Replace missing species with empty string (do not throw NPE)
• Check species detail too

org.knime.core.node.rakip

• FskPortObject.kt
• FskPortObjectSpec.kt

New references are not added. NPE in EditReferencePanel#get().

Transpose table for metadata.

It would be more convenient to have one row per metadata field than one single row with all the metadata (current table).

Create a Wiki page for each of the nodes

• FSK Creator
• FSKX Writer
• FSKX Reader
• FSK Runner
• FSK Metadata Editor
• FSK to R
• FSK to metadata
• FSK Editor
• FSK Editor JS

The dialog of the FSK creator node is fairly simple and could be defined in FskCreatorNodeFactory#createNodeDialogPane. The class is unnecessary.

See: FskxReaderNodeFactory and FskxWriterNodeFactory

• CreatorNodeFactory.kt
• CreatorNodeModel.kt
• Creator.png
• CreatorNodeFactory.xml

Document XLSX file with metadata for the wiki page of the FSK Creator. It is not described anywhere else.

Remove the ouput KNIME table port in the reader. It should be replaced with a "Extract FSK metadata" node.

Add required factory classes to support old FSK nodes from PmmLab.
Must include deprecated="true" in plugin.xml.

• Fsk2RNodeFactory.java
• fsk2r.png
• Fsk2RNodeFactory.xml

• Model script must be mandatory. Throw InvalidSettingsException when misssing.
• Add tooltip on Model script DialogComponentFileChooser. E.g.

Script that calculates the values of the model.

Include splash extension with icons and tooltip

The FSK feature has the description from the internal BfR Nodes:

<description url="http://www.example.com/description"> Internal BfR Nodes. </description>

Replace "Select libs" widget with automatic parse and download of libraries

• ReaderNodeFactory.java
• ReaderNodeModel.java
• Reader.png
• ReaderNodeFactory.xml

• XLSX spreadsheet must be optional. Ignored if
• Add tooltip on the spreadsheet DialogComponentFileChooser. E.g.

XLSX file with model metadata

New behaviour with optional input port.

• When the input port is provided modify the input model.
• When the input port is not provided create an empty model (empty scripts and metadata) and let the user modify it. (Create brand new model)

Implement "Extract FSK metadata" node. May reuse FskMetaDataTuple.

Functions of interest in RController:

• installRServe
• installLib
• installMiniCRAN

{0}{1}{2}

See #22

• Modify with PortObjectHolder so that it works in server
• Use jQueryUI tabbed component

• Mark parameters script as optional
• Mark visualization script as optional
• Mark spreadsheet as optional
• Remove description of libraries

Remove R ports in FSK nodes, currently runner and reader. These R ports should be obtained with the "FSK to R" node.

1. Indicate mandatory & optional fields. -> Mark mandatory fields with an asterisk.
   • Model, param and visualization scripts are mandatory
   • XLSX file is mandatory
2. Explain better the options in the dialogue
   • Longer & more meaningful descriptions in the XML description file
   • "Select spreadsheet" option is too cryptic <- (What could be done about it?)
   • param and visualization scripts are indicated as optional <- Change it!!
   • Model metadata has not info about being mandatory or ooptional <- Mark it as mandatory
   • "Set of libraries used". No info about being mandatory or optional. <- Mark it as optional.
   • Explain better the options in the dialog -> Use tooltips in DialogComponentFileChooser.
3. "Select libs" widget is so poorly designed <- To be removed and replaced with automatic detection of used libraries in scripts

Not working. Only paths working are local paths.

The spinners for publication page and publication issue take negative ints. Only positive ints should be allowed.