== ProMoT Browser ==

=== Expectation (functional tests) ===
 * load: all models from kb should load
 * import SBML: all biomodels should load (events are not imported, needs better error handling in functional tests)
 * export SBML: model should be valid and match expected simulation results (which tool for tests, workflow/scripting needed)
 * import CNA (signaling): all example models from CNA should be imported and be identical (as close as possible) after export/round trip
 * export CNA (signaling): exported models should be ok for CNA (how to test?)
 * export diana: model should be simulatable, simulation result should be identical to expected result within given threshold 
 * save: versions (include library, library separate (model only), with dependencies): compare file as text with expectation, test whole kb/examples?

=== Tests for browser in JUnit tests ===

 1. round trip tested [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/cna/CNAImporterTest.java] for cna-model (sigtoynet-test) in test-suite   [source:/Promot/trunk/promot/kb/testsuite/CNA/sigtoynet-test/]
 2. round trip tested, see 5. test-model for export of modular models would be nice although no problems for export are known yet, right now only tested for diana (no scripts for DIVA yet)
 3. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdAddSubclassTest.java] 
 4. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdDeleteTest.java] 
 5. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/PromotTest.java] 
 6. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdCopyClassTest.java] 
 7. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdSelectTest.java]
 8. junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdChangeAbstractTest.java]
    junit test [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdChangeModelTest.java]
 9. optional junit test for parametrization from diana [source:/Promot/trunk/promot/src/gui/org/mpg/dcts/promot/DianaDataReader/DianaDataReaderTest.java] [[BR]][[BR]]

=== Tests ===

 10. Success if library isPresent (included in file so file changes might break the test), model class present as PromotTreeNode, load egf model ([source:/Promot/trunk/promot/kb/SignalTransd/EGF-model/LOAD-EGF-MODEL.mdl]); test contents of model/PromotTreeNode? [[BR]]
 11. Same as 1. with different library (logical library) and model (toy-model)
 12. Tested with import + simulation of all biomodels.org models, TODO: test for correctness of simulation results; layout should work without exceptions
 13. Save a model into mdl (selected, all), compare generated files to expected; depends on selection test (13), test round trip of load+save of example 
 14. Export egf-model to SBML, compare generated file with expected output (file content + simulation results), TODO: export should work (be tested) for all models in kb, which tool for simulation (scriptable required)? comparison of simulation results after SBML round trip
 15. Export egf-model to Diana/Diva [[BR]] Compare generated file with expected output (file content + simulation results), TODO: export should work (be tested) for all models in kb
 16. Run script [[BR]] Test with default inputs for synthetic biology scripts
 17. Change property [[BR]] in Browser tree select module, mouse right-click for context menu, choose Change Property --> Icon (Abstract, Model)
 18. Simulate model [[BR]] Load hafke model ([source:/Promot/trunk/promot/kb/hafke/obertopp/LOAD.mdl]), select hafke-process (module --> device --> process) in Browser, open simulation dialog from menu (Tools --> Simulate Model), check for diana app (see status in output log), edit the generation directory to '~/opertopp', click on 'Advanced...' in the solver options pane (new window with several options should appear), close options dialog, click on 'Simulate Model' button (simulation result should appear after a while, several text in output log), click on 'Edit Script' button (text editor should appear with python script), edit the script (e.g. set Tend to 60.0), save, simulate again (tend should be 60.0 now), click on 'reset' button (files in directories 'model', 'script' and 'results' should be removed, status in output log, 'Edit Script' button should be disabled). 

===  Visual Inspection for ===
 19. Start Visual Editor for a class
 20. Start Visual Explorer for a class
 21. !ViewMathematicalModel (display of instance)
 22. Exit with Dialog for modified in Editor + Browser (change properties, load, import) 
 23. Search class (+class for slot in class) dialog, model type is not important, so test with egf_model, [[br]]
      search egf_model (substring, class + slot; class) should return egf_model (class), egf_model_noint (class) [[br]]
      search proti (whole word, class + slot; slot) should return egf_model:proti (slot) [[br]]
      clear should remove displayed results;
 24. Comparison of models [[BR]] Load two different glycolysis models, e.g. [source:/Promot/trunk/promot/kb/testsuite/mdl/hynne.mdl] and [source:/Promot/trunk/promot/kb/testsuite/mdl/teusink.mdl]. Select the model classes (direct sub-classes of sbml-model) in browser and click compare models. Visual explorer should open, models should be displayed in common container. Edges connecting corresponding elements should be visible. Other example models for comparison (elements with same type +annotation or type + name) can be load with [source:/Promot/trunk/promot/kb/testsuite/mdl/egf+insulin.mdl]. [[BR]]
 25. Export documentation as HTML [[BR]] Open model, select model, export HTML (File --> Export --> Export HTML), use default options, click on 'Generate HTML' button, check results in a web browser. 

=== Open for testing ===
option handling save, restore?
test undo/redo in browser, include in tests for functionality if applicable

=== Known problems, missing tests ===
 * model of PromotTree under async updates 
   - array index out of bounds, 
   - display problems with null nodes in selection/displayed (update to slow, might be same problem as index out of bounds)
   - recovery from exception (refresh, seems to not restore content completely)
 * menu construction
   - only finished after PaletteWindow constructed at least once or JFileChooser dialog finished (open/import, directory select in export)
   - text for menu entries larger than pop-down menu (only vista so far, not happening after build (release version), cross-platform problem?)
 * export model to Matlab