Diff for "Cytoscape_3/Cy3TestPlan/misc"

Differences between revisions 1 and 4 (spanning 3 versions)

Editor Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import a network file (eg. galFiltered.sif)	CE1	Click and drag a new node from the Editor tab and drop into an empty space on the graph	A new node should appear number sequentially according to the number of times a new node has been added
	CE2	1. Click and drag a new directed edge and drop it on top of the new node created in the previous case 2. Click on an already existing node as the target for the interaction	A directed edge between the new node and the existing node should appear
	CE3	1. Select the new node and edge alone by dragging a box around them 2. Right-click on the node and then click Delete selected nodes and edges	The selected edge and node should be deleted and no longer appear on the graph

GraphMerge Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import two network files: (eg. galFiltered.sif and BINDyeast.sif) 3. Click on Plugins and select Advanced Network Merge 4. Select each network from the available networks box and then click the right arrow to move them to the selected networks box. 5. Click OK to merge the selected networks (Note: with large networks Cytoscape may not automatically create a graphical view, so click on the Edit menu with the network highlighted and click on Create View)	GM1	Before precondition step 5 select the Union operation	A new graph should be created displaying the merged networks (If this does not happen see preconditions Note)
	GM2	Before precondition step 5 select the Intersection operation	A new graph should be created displaying the common nodes from the two networks
	GM3	Before precondition step 5 select the Difference operation (order matters)	A new graph should be created displaying the parts of the first network that are not in the second network

LinkOut Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import a network file (eg. galFiltered.sif)	LO1	1. Right click on a node and select LinkOut from the right-click menu 2. Select Reactome → ReactomeID	The link should open the web page www.reactome.org
	LO2	1. Right click on a node and select LinkOut from the right-click menu 2. Select Entrez → Protein	The link should open the web page www.ncbi.nlm.nih.gov
	LO3	1. Right click on a node and select LinkOut from the right-click menu 2. Select iHOP → yeast	The link should open the web page www.ihop-net.org

PSI-MI Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import a network file (eg. Sample1.xml++)	P1		The graph produced should contain only 6 nodes and 8 edges

++File from: Kerrien S et al (2007) Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 5:44.

QuickFind Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import a network file (eg. galFiltered.sif)	QF1.1	Enter text into the search field on the Tool bar and press Enter	If the search term is found it should be highlighted and zoomed the view panel should zoom in
	QF1.2	With text in the search field click on the triangle tab at the end of the field	A list of similar terms to the text entered in the search field should appear
	QF1.3	Enter irrelevant text into the search field	The field should be highlighted red and the drop down menu should display the search term followed by 0 hits
	QF2.1	Select the Configure search options and then click cancel	The dialog box should disappear and settings should remain the same
	QF2.2	1. Select the Configure search options, then click on the Node or Edge radio buttons and change the Selected attribute and click Apply 2. Enter text appropriate for the new search parameters	The search configuration box should disappear and the drop down menu should contain the corresponding style of suggestions to the search parameters. The term entered should highlight the object in the graph

Table Import Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. File → Import network from Table (eg. SampleHumanNetwork.xlsx Note: This file can also be found in the testData directory.)	TI1	1.Before pressing Import, select the Show Text File Import Options (under the Advanced heading) 2. Ensure that the preview options are working by changing the radio button to Show First and then enter 5 entries 3. Press the refresh preview button	The preview box should reflect the changes made to the Preview Options and should now show only the first 5 entries in the file
	TI2	1. Repeat step 1 from TI1 2. Click on the Transfer first line as attribute names check box	The bolded cells at the top of each column that were labeled Column 1, Column 2 etc should now contain the contents of the 1st row of the table (eg. Gene, Interaction)
	TI3	1. In the Interaction Definition box select column 1 from the drop down menu for Source Interaction and select Column three from the menu for Target Interaction 2. Click Import taking note of the contents of the Default interaction field 3. Select the newly created network from the network tab and click the Edge Attribute Browser 4. Select an edge	Every edge selected should display the Default interaction type between the two nodes (eg. pp). Repeat steps 1-4, but change the Default interaction (eg. cc)
	TI4	1. Repeat step 1 from TI1 bit do not designate a file to upload yet 2. Click the Show all entries radio button under Preview Options 3. Select a file to upload	This should work normally, but if the known bug is still present a message appears: File is broken or empty!
	TI5	1. In the Interaction definition box select column 1 from the drop down menu for Source Interaction 2. Repeat step 1 from TI1	A graph containing only the genes listed in the Source Interaction column should appear (with no edges)

SBML Reader Core Plugin Test Cases

Preconditions	Test Case ID	Instructions	Expected Results	Date Executed	Pass/Fail
1. Start Cytoscape 2. Import a network file (eg.EcoliSBML.sbml)	SR1		A network should appear in the viewing panel and the results panel should contain a visual legend of the features in the graph

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+== Editor Test Cases ==



|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||

||<|3> 1. Start Cytoscape <<BR>>2. Import a network file (eg. galFiltered.sif) ||CE1||Click and drag a new node from the Editor tab and drop into an empty space on the graph||A new node should appear number sequentially according to the number of times a new node has been added|| || ||

||CE2||1. Click and drag a new directed edge and drop it on top of the new node created in the previous case <<BR>>2. Click on an already existing node as the target for the interaction||A directed edge between the new node and the existing node should appear|| || ||

||CE3||1. Select the new node and edge alone by dragging a box around them <<BR>>2. Right-click on the node and then click Delete selected nodes and edges||The selected edge and node should be deleted and no longer appear on the graph|| || ||
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-== ManualLayout Core Plugin Test Cases ==

|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||

|| 1. Start Cytoscape <<BR>>2. Import a network file (eg. galFiltered.sif)||ML1||Select a node on the graph and drag it to a new position and then drop it||The node selected should be highlighted and the user should be able to move it around, the edges connected moving with it|| || ||
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+== QuickFind Core Plugin Test Cases ==





|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||

||<|5> 1. Start Cytoscape <<BR>>2. Import a network file (eg. galFiltered.sif)||QF1.1||Enter text into the search field on the Tool bar and press Enter||If the search term is found it should be highlighted and zoomed the view panel should zoom in|| || ||

||QF1.2||With text in the search field click on the triangle tab at the end of the field||A list of similar terms to the text entered in the search field should appear|| || ||

||QF1.3||Enter irrelevant text into the search field||The field should be highlighted red and the drop down menu should display the search term followed by 0 hits|| || ||

||QF2.1||Select the Configure search options and then click cancel||The dialog box should disappear and settings should remain the same|| || ||

||QF2.2||1. Select the Configure search options, then click on the Node or Edge radio buttons and change the Selected attribute and click Apply <<BR>>2. Enter text appropriate for the new search parameters||The search configuration box should disappear and the drop down menu should contain the corresponding style of suggestions to the search parameters. The term entered should highlight the object in the graph|| || ||







== Table Import Core Plugin Test Cases ==

|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||

||<|5> 1. Start Cytoscape <<BR>>2. File → Import network from Table (eg. [[attachment:SampleHumanNetwork.xlsx]] Note: This file can also be found in the ''testData'' directory.)||TI1||1.Before pressing Import, select the Show Text File Import Options (under the Advanced heading) <<BR>>2. Ensure that the preview options are working by changing the radio button to Show First and then enter 5 entries <<BR>>3. Press the refresh preview button||The preview box should reflect the changes made to the Preview Options and should now show only the first 5 entries in the file|| || ||

||TI2||1. Repeat step 1 from TI1 <<BR>>2. Click on the Transfer first line as attribute names check box||The bolded cells at the top of each column that were labeled Column 1, Column 2 etc should now contain the contents of the 1st row of the table (eg. Gene, Interaction)|| || ||

||TI3||1. In the Interaction Definition box select column 1 from the drop down menu for Source Interaction and select Column three from the menu for Target Interaction <<BR>>2. Click Import taking note of the contents of the Default interaction field <<BR>>3. Select the newly created network from the network tab and click the Edge Attribute Browser <<BR>>4. Select an edge||Every edge selected should display the Default interaction type between the two nodes (eg. pp). Repeat steps 1-4, but change the Default interaction (eg. cc)|| || ||

||TI4||1. Repeat step 1 from TI1 bit do not designate a file to upload yet <<BR>>2. Click the Show all entries radio button under Preview Options <<BR>>3. Select a file to upload||This should work normally, but if the known bug is still present a message appears: File is broken or empty!|| || ||

||TI5||1. In the Interaction definition box select column 1 from the drop down menu for Source Interaction <<BR>>2. Repeat step 1 from TI1||A graph containing only the genes listed in the Source Interaction column should appear (with no edges)|| || ||



== SBML Reader Core Plugin Test Cases ==





|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||||

||1. Start Cytoscape <<BR>>2. Import a network file (eg.[[attachment:EcoliSBML.sbml]])||SR1|| ||A network should appear in the viewing panel and the results panel should contain a visual legend of the features in the graph|| || ||