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The Cytoscape Test Plan

The purpose of this document is to describe testing procedures to ensure that new releases of Cytoscape do not break existing functionality. The release is broken down into two general sections: Coverage Testing and Workflow Testing.

Coverage Testing

This section describes tests for Cytoscape that must be run by hand.

Tool Bar

Open Session File

Procedure

1. Start Cytoscape.
2. Click the "Open Session File" icon on the Toolbar.
3. Open a session file.

Expected Results

1. The "Open a Session File" dialog should appear.
2. The network contained in the session file should be visible in Cytoscape.

Save Current Session As

Procedure

1. Start Cytoscape.
2. Click the "Save Current Session As" icon on the Toolbar.

Expected Results

1. A "Saving Cytoscape Session" status window should appear.

Zoom out / Zoom in

Procedure

1. Start Cytoscape.
2. Load a network.
3. Click the "Zoom Out" icon on the Toolbar.
4. Click the "Zoom In" icon on the Toolbar.

Expected Results

1. Clicking "Zoom Out" should result in the view of the network being more zoomed out and less detailed.
2. Clicking "Zoom In" should result in the view of the network being more zoomed in and more detailed.

Zoom to display all of current network

Procedure

1. Start Cytoscape.
2. Load a network.
3. Click the "Zoom to display all of current network" icon on the Toolbar.

Expected Results

1. The view of the network should zoom in or out to fit the entire network in the main window at the highest possible zoom factor.

Help

Procedure

1. Start Cytoscape.
2. Click the "Help" icon on the Toolbar.

Expected Results

1. The Cytoscape Users Manual should open.

Open VizMapper

Procedure

1. Start Cytoscape.

2. Click the "Open VizMapper" icon on the Toolbar.

Expected Results

1. The VizMapper interface should open in Control Panel.

Use Filters

Procedure

1. Start Cytoscape.
2. Click the "Use Filters" icon on the Toolbar.

Expected Results

1. The Filters interface should open in Control Panel.

Search

Procedure

1. Start Cytoscape.
2. Load a network.
3. Type a search term in the "Search" field in the Toolbar. For example, search for the ID of one of the nodes in the network.

Expected Results

1. If you searched for a node that is in the currently loaded network, the node will become highlighted.

File MenuMike File -> New through File -> Save As

File -> New -> Session

Procedure

1. Start Cytoscape.

2. Click File -> New -> Session

3. Load a network.

4. Click File -> New -> Session

5. Click yes.
6. Repeat, Click no.

Expected Results

1. Nothing should happen because no networks have been loaded, there is no session yet.
2. You should be prompted with a dialog that reminds you that your current session will be lost.
3. If you click yes, you should get a new session with no networks in the network manager.
4. When you click no, you should see your existing session without any changes.

File -> New -> Network -> Empty Network

Procedure

1. Start Cytoscape.

2. Click File -> New -> Network -> Empty Network

Expected Results

1. An empty network and view should be created. The Control Panel should be changed to the Editor Tab.

File -> New -> Network -> Construct network using cPath...

Procedure

1. Start Cytoscape.

2. Click File -> New -> Network -> Construct network using cPath...

3. Type the example "p53" into the cPath dialog.
4. Change the species drop-down menu to "Homo Sapiens"
5. Click Help then close the Help dialog.
6. Click About the close the About dialog.
7. Click Search.
8. Click the "X" in the dialog frame to close the cPath dialog.

Expected Results

1. The cPath dialog should appear.
2. Another dialog should be displayed with text describing the features of the cPath dialog.
3. Another dialog should be displayed with text describing the authors of the software.
4. A network should be loaded with more than one node.
5. The dialog should close.

File -> New -> Network -> Clone current network

Procedure

1. Start Cytoscape.
2. Load a network.
3. Lay the network out in something other than a grid.
4. Change the visual style to something other than default.

5. Click File -> New -> Network -> Clone current network.

Expected Results

1. You should see a new network with the same name as the previous network, but with the word " Copy" appended to it. This view should have the exact same node layout and visual style as the original network.

File -> New -> Network -> From selected nodes, all edges

Procedure

1. Start Cytoscape.
2. Load Network.
3. Make sure that NO nodes or edges are selected (i.e. click on the view somewhere other than on a node or edge).

4. Click File -> New -> Network -> From selected nodes, all edges.

5. Select some nodes and edges in the view.

6. Click File -> New -> Network -> From selected nodes, all edges.

Expected Results

1. You shouldn't be able to click this option because it should be grayed out. This is because no nodes or edges are currently selected.
2. A new network and view should be created. The nodes should have the same layout as the parent network.

File -> New -> Network -> From selected nodes, selected edges

Procedure

1. Start Cytoscape.
2. Load Network.
3. Make sure that NO nodes or edges are selected (i.e. click on the view somewhere other than on a node or edge).

4. Click File -> New -> Network -> From selected nodes, selected edges.

5. Click Select -> Mouse Drag Selects -> Nodes Only.

6. Select some nodes in the view.

7. Click File -> New -> Network -> From selected nodes, selected edges.

Expected Results

1. You shouldn't be able to click this option because it should be grayed out. This is because no nodes or edges are currently selected.
2. A new network and view should be created. This network should only include the selected nodes and no edges. This network will be laid out in the default grid layout.

Edit Menu

View Menu

Piet

Select Menu

Piet

Layout Menu

Plugins Menu

Plugins -> Manage Plugins -> Install

Procedure

1. Start Cytoscape

2. Click Plugins -> Manage Plugins.

3. In the Manage Plugins window, expand the "Currently Installed" folder by double-clicking the folder icon, then expand the Core folder by clicking on the arrow symbol next to it.
4. Select any of the plugins listed by clicking on it.
5. Expand the "Available for Install" folder.
6. Select any plugin that is not already installed. Click the Install button.

Expected Results

1. The Manage Plugins window should open with folder "Currently Installed" and "Available for Install" in the left panel. The first time Manage Plugins is selected in an instance of Cytoscape, a connection status window should open before the Manage Plugins window appears.
2. Under "Currently Installed" and "Available for Install" there should be subfolders listing individual plugins.
3. When clicking on a plugin, information about the plugin should appear in the right panel.
4. During plugin installation, you should get an installation progress window. When installation is complete, a message in red is displayed under the left panel stating that the installation is complete.
5. The newly installed plugin should be visible under "Currently Installed" folder.

Plugins -> Manage Plugins -> Change Download Site

Procedure

1. In the Plugin Manager window, click the "Change Download Site" button.

2. In the drop-down menu, change the download site to Test and then click the Ok button.
3. In the Manage Plugin main window, click the "Change Download Site" button again.
4. In the Plugin Download Sites window, click the "Add Site" button.
5. Click the "Add" button.
6. Type in a name and a URL (any) and click OK.
7. Click OK to exit the Bookmark Manager. Click OK in the Plugin Download Sites window to get back to the Plugin Manager main window. Click the Close button to exit the Plugin Manager and close Cytoscape.

Expected Results

1. A Plugin Download Sites window will appear with a drop-down menu for selecting download site.
2. A progress bar should appear. When the download site has been switched, you should see a different folder structure under Available for Install.
3. When selecting the Add Site button in the Plugin Download Sites window, a Bookmark manager window will appear.
4. When clicking Add in the Bookmark manager, an Add new bookmark window will appear.
5. After adding a new site, the new download site will appear in the list of Bookmarks.

Plugins -> Update Plugins

Procedure

1. Start Cytoscape

2. Click Plugins -> Update Plugins

Expected Results

1. A progress window will appear informing you of the status of updates. If no updates are available for installed plugins, a message will appear telling you that no updates where available.

Plugins -> Merge networks

Procedure

1. Start Cytoscape
2. Load two or more networks.

3. Click Plugins -> Merge networks.

4. To select networks, click on the network and then click the right arrow. Select two or more networks from the list.
5. Select an operation in the Operation drop-down menu.
6. Click OK to merge the networks.

Expected Results

1. A Merge Networks dialog should appear with the loaded networks listed under Available Networks.
2. A new network view will open with the results of the merge.

Help Menu

Control Panel - Network

Control Panel - VizMapper

Control Panel - Editor

There are multiple tests for the Cytoscape Editor:

Control Panel - Editor -> add a simple interaction

Procedure

1. Click File -> New -> Network -> Empty Network to bring up a new network and the editor palette.

2. click on a node in the editor Palette and drag/drop it onto the network view to form node0.

3. repeat step 2 to add a second node to the network view (node1).

4. click on an edge in the editor palette, drag/drop it onto onto node0.

5. move the mouse to drag the rubberband line from node0 to node1.

6. release mouse when over node1.

Expected Results

1. You should see a network of two nodes, node0 and node1, connected by a single edge.

Control Panel - Editor -> keyboard accelerators

Procedure

1. Click File -> New -> Network -> Empty Network to bring up a new network and the editor palette.

2. control-click on an empty space on the canvas to add a node to the network view.
3. repeat step 2 to add a second node to the network view

4. control click on one of the two added nodes to begin an edge. This will be source node.

5. move the mouse to drag the rubberband line from source node to the other node (target node).

6. release mouse when over target node.

Expected Results

1. You should see a network of two nodes, source node and target node, connected by a single edge.

Control Panel - Editor -> connect selected nodes

Procedure

1. Click File -> New -> Network -> Empty Network to bring up a new network and the editor palette.

2. control-click on an empty space on the canvas to add a node to the network view.

3. repeat step 2 several times to add other nodes to the network view '

4. select all the nodes by clicking on an empty space on the canvas, then dragging a rubberband rectangle around all the nodes (or use Control-A keyboard accelerator)

5. select Edit -> Connect Selected Nodes menu item.

Expected Results

1. You should see a clique, i.e. there is an edge connecting every pair of nodes

Control Panel - Filters

Data Panel - Node, Edge, and Attribute Browser

Workflow Testing

The goal of this section is to verify that the various [:Workflows:workflows] described for Cytoscape do actually work. In addition to the workflows described, we will also verify that each [:Presentations:tutorial] also works. The output of these tests will be different than simply a checklist. The goal is to capture the steps in the workflow in a screencapture movie. The movie should capture the screen as a user follows each step in the workflow or tutorial. Audio commentary is preferred since this allows to both see and hear the steps being followed.