App Manager Test Plan

1. Initial install of core apps (empty CytoscapeConfiguration) Start Cytoscape with empty CytoscapeConfiguration directory Open App Manager Verify that all core apps installed properly Restart Cytoscape and verify again

2. Update core app Start Cytoscape with available core app updates (use test App Store) Open App Manager and check for updates Install available updates Verify that updates installed correctly Restart Cytoscape and verify again

3. Uninstall core app update Start Cytoscape with installed core app updates Open App Manager Uninstall update Verify that update uninstalled correctly and old version restored Restart Cytoscape and verify again

4. Install bundle app by App Manager Start Cytoscape Open App Manager Install an app Verify that it installed OK Restart Cytoscape and verify again

5. Update bundle app Start Cytoscape with available app updates Open App Manager and check for updates Install available updates Verify that updates installed correctly Restart Cytoscape and verify again

6. Uninstall bundle app Start Cytoscape with installed app Open App Manager Uninstall app Verify that app uninstalled correctly Restart Cytoscape and verify again

7. Install bundle app by copy Start Cytoscape Copy an app to the installed directory Verify that it installed OK Restart Cytoscape and verify again

8. Uninstall bundle app by delete Start Cytoscape Delete an app from the installed directory Verify that app uninstalled correctly Restart Cytoscape and verify again

9. Install bundle app via App Store Start Cytoscape Open App Store in browser Install an app from the App Store page Verify that the app installed correctly Restart Cytoscape and verify again

10. Disable App in App Manager Start Cytoscape Open App Manager Disable an app Verify that the app disabled correctly Restart Cytoscape and verify again

11. Enable App in App Manager Start Cytoscape Open App Manager Enable an app Verify that the app re-enabled correctly Restart Cytoscape and verify again

12. Install simple app Start Cytoscape Open App Manager Install a simple app Verify that it installed OK Restart Cytoscape and verify again

13. Update simple app Start Cytoscape with available simple app updates Open App Manager and check for updates Install available updates Verify that updates installed correctly Restart Cytoscape and verify again

14. Disable Simple App Start Cytoscape Open App Manager Disable simple app Verify that the simple app disabled correctly Restart Cytoscape and verify again

15. Enable Simple app Start Cytoscape Open App Manager Enable simple app Verify that the app re-enabled correctly Restart Cytoscape and verify again

16. Uninstall Simple app Start Cytoscape Open App Manager Uninstall simple app Verify that the app uninstalled correctly Restart Cytoscape and verify again

17. Install multiple versions Start Cytoscape Install an older version of an app using Install from File Install a newer version of an app using Install from File Verify that only newer version is installed Reinstall the older version using Install from File Verify that only older version is installed Restart Cytoscape and verify again

18. Copy older and then newer version Start Cytoscape Copy an older version of an app to the installed directory Copy a newer version of the same app to the installed directory Verify that only newer version is installed Restart Cytoscape and verify again

19. Copy newer and then older version Start Cytoscape Copy an newer version of an app to the installed directory Copy a older version of the same app to the installed directory Verify that newer version is still installed (and not older) Restart Cytoscape and verify again

20. Upgrade app from App Store Start Cytoscape Go to App Store and bring up page for already-installed app with updates available Click “Upgrade” Verify that it installed OK Restart Cytoscape and verify again

21. Rebuild based on symbolic link Start Cytoscape with app symbolicly-linked from target directory Verify app installed correctly Rebuild app with no changes Verify app still installed Rebuild app with version number change Verify app updated correctly.

22. Incompatible bundle app Start Cytoscape Install bundle app with incompatible update available in test App Store (i.e. one that depends on a newer Cytoscape - edit manifest to achieve this) Try to install update via Update Manager Try to install update with Install from File Try to copy update (app should not load in any of the previous cases) Restart Cytoscape and verify that old compatible app loaded/new incompatible app not loaded

23. Incompatible simple app Start Cytoscape Install simple app with incompatible update available with Install from File (i.e. one that depends on a newer Cytoscape - edit manifest to achieve this) Try to copy update (app should not load in any of the previous cases) Restart Cytoscape and verify that old compatible app loaded/new incompatible app not loaded

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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