Workbench

User Guide

Description of Available Views

In the following the KNIME workbench and its features are described in more detail.

When KNIME is initially opened it starts with the following arrangement of views :

KNIME Workbench overview

Workflow Projects

All KNIME workflows are displayed in the Workflow Projects view. The status of the workflow is indicated by an icon showing whether the workflow is closed, idle, executing or if execution is complete.

Favorite Nodes

The Favorite Nodes view displays your favorite, most frequently used and last used nodes. A node is added to your favorites by dragging it from the node repository into the personal favorite nodes category. Whenever a node is dragged onto the workflow editor, the last used and most frequently used categories are updated.

The favorite nodes view comes with the following actions in the menu bar of the view:

collapse all icon Collapses all expanded categories
expand all icon Expands all categories
clear history icon Clears the last used and most frequently used categories
remove favorite node icon Removes the selected node from your favorites

 

The number of nodes in the most frequently and last used categories is per default restricted to ten nodes. This number can be adjusted in preferences. Select "File/Preferences.."/KNIME/KNIME GUI to set different values for the maximum size of frequently used nodes and maximum number of last used nodes.

Node Repository

The node repository contains all KNIME nodes ordered in categories. A category can contain another category, for example, the Read category is a subcategory of the IO category.

Nodes are added from the repository to the workflow editor by dragging them to the workflow editor.

Selecting a category displays all contained nodes in the node description view; selecting a node displays the help for this node.

If you know the name of a node you can enter parts of the name into the search box of the node repository. As you type, all nodes are filtered immediately to those that contain the entered text in their names:

entering a search term in the node repository

Outline

The outline view provides an overview over the whole workflow even if only a small part is visible in the workflow editor (marked in gray in the outline view). The outline view can also be used for navigation: the gray rectangle can be moved with the mouse, which causes the editor to scroll so that the visible part matches the gray rectangle.

outline view

Console

The console view prints out error and warning messages in order to give you a clue of what is going on under the hood. The same information (with a DEBUG detail level is written to a log file, which is located at {workspace}/.metadata/knime/knime.log).

If you want to change the level of detail (either of the log file or of the console view) go to
File/Preferences.../KNIME for the level of detail of the log file or to
File/Preferences.../KNIME/KNIME GUI for the level of detail of the console view.

You can choose between:

DEBUG
Debug messages mainly used for development. It is not recommended to use this for the console view since it slows down KNIME.
INFO
Logs information messages. Not really important but also not completely useless!
WARNING
If a node fails in configure a warning message is also issued. Warning messages are not fatal; usually the workflow can continue to be executed but they denote that something worth to knowing about has taken place. Default and recommended level for the console view.
ERROR
Only issued when something fatal has happened, i.e. the workflow can no longer be executed.

Node Description

The node description displays information about the selected node (or the nodes contained in a selected category). In particular, it explains the dialog options, the available views, the expected input data and resulting output data.

Under Linux there are some issues with this view, since it needs the system's web browser. KNIME/Eclipse tries to find a Mozilla-based browser automatically, if the environment variable MOZILLA_FIVE_HOME is not set. The knime.sh should note which browser it is using in this case. You can try to explicitly set MOZILLA_FIVE_HOME to the firefox directory and if this doesn't help you can also try passing "-Dorg.eclipse.swt.browser.XULRunnerPath=..." to knime.sh. There is a known problem with Firefox 3 (and xulrunner >= 1.9) for which there is no workaround other than using an older version. This may also cause you some trouble.

See also the linked Eclipse bug report

In order to provide a full text search, the node descriptions are also integrated in the Eclipse help. Select Help/Help Contents from the menu in order to open the Eclipse built-in help. There is a KNIME category, which has a Node Descriptions submenu. In the search field you can perform a full text search across all the node descriptions. If, for example, you type "cluster", all node descriptions containing the word cluster are displayed:

screenshot of help application

Preferences

The preferences are opened with File/Preferences... The KNIME-related preferences are separated into three categories:

KNIME

preferences of KNIME which also apply to KNIME if started in batch mode

  • Log file Log Level
    Level of detail for the log file. Default value is DEBUG, which means that information for developers is also logged. Sending this log file to us if you encounter any unexpected behavior may give us a hint at what caused the problem.

  • Maximum working threads for all nodes:
    The KNIME workflow manager tries to optimize the execution time of all nodes, for example, by distributing separate branches of the workflow to several threads. It boils down to running nodes in parallel wherever possible. And here you can enter how many threads should be used for parallelization. By default it is twice the number of CPU's. This has proven to be a good amount.

  • Directory for temporary files
    KNIME needs to store some temporary files (data of executed but not yet saved workflows) somewhere. This is where you can specify the location.

KNIME GUI:

preferences related to the graphical user interface of KNIME.

  • Console View Log Level
    Level of detail for the log messages displayed in the console view. Usually WARNING is enough. DEBUG slows down performance and is mostly useful for development.

  • Confirm Node Reset
    Check or uncheck whether you want a confirmation dialog to pop up when you reset an already executed node. If you checked the "Do not ask again" checkbox in this type of dialog, go to preferences to make them reappear.

    screenshot of confirmation dialog

  • Confirm Node/Connection Deletion
    Same as above but for confirmation of deleting nodes and/or connections.

  • Confirm reconnection of already connected nodes
    As of KNIME 2.0 it is possible to drag a connection to an already connected port. The connection is replaced if the node is configured, but if it is executed (and thus will be reset by replacing the connection) a confirmation dialog appears. This confirmation dialog can also be turned on or off via this preference.

  • Maximum size for most frequently used nodes
    The amount of nodes maintained by the most frequently used nodes category of the Favorite Nodes view.

  • Maximum size of last used nodes
    The amount of nodes maintained by the last used nodes category of the Favorite Nodes view.

Master Key

KNIME does not store any passwords (e.g. for databases) in plain tests but encrypts them using a master key.

Workflow Editor

The workflow editor is used to assemble workflows, configure and execute nodes, inspect the results and explore your data. This section describes the interactions possible within the editor.

Node Options

Configure

When a node is dragged to the workflow editor or is connected, it usually shows the red status light indicating that it needs to be configured, i.e. the dialog has to be opened. This can be done by either double-clicking the node or by right-clicking the node to open the context menu. The first entry of the context menu is "Configure", which opens the dialog. If the node is selected you can also choose the related button from the toolbar above the editor. The button looks like the icon next to the context menu entry.

Execute

In the next step, you probably want to execute the node, i.e. you want the node to actually perform its task on the data. To achieve this right-click the node in order to open the context menu and select "Execute". You can also choose the related button from the toolbar. The button looks like the icon next to the context menu entry.

It is not necessary to execute every single node: if you execute the last node of connected but not yet executed nodes, all predecessor nodes will be executed before the last node is executed.

Execute All

In the toolbar above the editor there is also a button to execute all not yet executed nodes on the workflow.

This also works if a node in the flow is lit with the red status light due to missing information in the predecessor node. When the predecessor node is executed and the node with the red status light can apply its settings it is executed as well as its successors.

The underlying workflow manager also tries to execute branches of the workflow in parallel.

Execute and Open View

The node context menu also contains the "Execute and open view" option. This executes the node and immediately opens the view. If a node has more than one views only the first view is opened.

Open View

A node can have no, one or several views. Each view appears as an entry in the node's context menu. Select it in order to open the related view. A view that is opened before the node has been executed, is updated as soon as the node is executed. You can open the view of a node several times, e.g. if you want to compare different columns in a scatter plot. A view is automatically reset if the node is reset.

Open Out-port View

If a node does not have a view but you are interested in the result of the node's operation on the data, you can inspect the data. It is available at the node's out-port. At the bottom of the context menu there is an entry for each outport of the node. Each one opens the referring out-port view. Note, that the out-port view does not support any interaction or hiliting. If you want to hilite data or see hilited data you have to connect the out-port to the Interactive Table node.

Reset

You can reset a node by choosing the reset option from the context menu. The node returns from the executed state (green status light) to configured state (yellow status light). If the node is selected you can also choose the related button from the toolbar above the editor. The button looks like the icon next to context menu entry.

Cancel

If a node is currently executing you can cancel the execution by selecting the "Cancel" option from the context menu or the related button (same icon as in the context menu) from the toolbar.

Cancel All

The toolbar also contains a "Cancel All" button, which cancels the execution of all running nodes.

Enter Custom Node Name

When a node is dragged to the workflow it has a name such as "Node 1" or similar by default below the status light. You can change this name to better describe what the node is actually doing, e.g. "filter values > 10". This can be done by selecting the node and then clicking on the name: the name becomes editable. Press "Return" to apply your changes.

Enter Custom Node Description

In the context menu you will also find the "Node name and description" option. Selecting this opens a dialog to enter a new name for the node. In addition you can enter a more detailed description or notes about the node. This action is also available via a button in the toolbar.

Connections

You can connect two nodes by dragging the mouse from the out-port of one node to the in-port of another node. Loops are not permitted.

If a node is already connected you can replace the existing connection by dragging a new connection onto it. If the node is already connected you will be asked to confirm the resulting reset of the target node.

You can also drag the end of an existing connection to a new in-port (either of the same node or to a different node).

Import/Export of workflows

Import of Workflows

You can import a workflow either from a different workspace or from a zip file, e.g. if the workflow was exported from KNIME. The import wizard is either opened from the menu "File/Import KNIME workflow..." or by opening the context menu in the workflow projects view and selecting "Import KNIME workflow...".

import wizard

Select the root directory if you want to import workflows from another workspace. Select the archive file option if you want to browse to the zipped workflow. Select the workflows you want to import. If a workflow with the same name already exists in your current workspace you can rename the imported one on the next page of the wizard. By clicking OK the project is imported to your workspace. If you unchecked the "Copy projects into workspace", changes to that workflow will also apply to the workflow in the source location.

Export of Workflows

The export workflow action is also available via the menu (File/Export KNIME workflow...") or via the context menu of the workflow projects view. Both open the export workflow wizard. Select the workflow you want to export. If you right-clicked a workflow to open the export wizard this workflow is pre-selected. In the second field browse to the target location or enter the path leading to the export location.

export wizard

The option to exclude data from being exported is activated by default. If checked, only the structure of the workflow is exported, which will result in a configured but non-executed workflow if it is re-imported. If you explicitly share the data (for example if the other person does not have access to a database) you can uncheck this option.