## page was renamed from Test Plan - 2.7/Core Plugins Test Cases/AL_Test Cases_2.7
== Automatic Layout Core Plugin Test Cases ==

||<|2> '''Preconditions'''||<|2> '''Test Case ID'''||<|2> '''Instructions'''||<|2> '''Expected Results'''||
||'''Date Executed'''||'''Pass/Fail'''||
||1. Start Cytoscape 2. Import a network file (eg. galFiltered.sif)||AL1|| ||The graph should take on one of the Cytoscape Automatic Layouts (in this case a grid)|| || ||



== cPath Core Plugin Test Cases ==

||'''Preconditions'''||'''Test Case ID'''||'''Instructions'''||'''Expected Results'''||'''Date Executed'''||'''Pass/Fail'''||
||<|11> 1. Start Cytoscape <<BR>>2. Click File → New → Network → Create network using cPath…||C1||1. Click the Help button||A window entitled Quick Reference Manual should appear describing the basics of using cPath searches|| || ||
||C2||Click the About button||A widow containing details on the cPath plugin should appear|| || ||
||C3||1. Select All Organisms and type “p53” into the search field <<BR>>2. Set the limit to 10 and click search||cPath should generate a network containing genes related to p53 for all organisms in the list|| || ||
||C4||1. Select C. elegans and type “rpl-12” into the search field <<BR>>2. Set the limit to 20 and click search||cPath should generate a network containing the genes related to rpl-12 in C. elegans|| || ||
||C5||1. Select D. melanogaster and type “DPP” into the search field <<BR>>2. Set the limit to 50 and click search||cPath should generate a network containing the genes related to DPP in D. melanogaster|| || ||
||C6||1. Select E. coli and type “LacI” into the search field <<BR>>2. Set the limit to 100 and click search||cPath should generate a network containing the genes related to LacI in E. coli|| || ||
||C7||1. Select H. Sapiens and type “CD4” into the search field <<BR>>2. Set the limit to 500 and click search||cPath should generate a network containing the genes related to CD4 in H. sapiens|| || ||
||C8||1. Select H. pylori 26695 and type “” into the search field  <<BR>>2. Set the limit to 1000 and click search||This appears to be broken at the moment since no search is returning any results|| || ||
||C9||1. Select M. musculus and type “CLCA” into the text field <<BR>>2. Set the limit to 5000 and click search||cPath should generate a network containing genes related to CLCA in M. musculus|| || ||
||C10||1. Select S. cerevisiae and type “STE7” into the search field <<BR>>2. Set the limit to 10 and click search||cPath should generate a network containing genes related to STE7 in S. cerevisiae|| || ||
||C11||1. Select R. norvegicus and type “BKCa” into the search field <<BR>>2. Set the limit to 20 and click search||cPath should generate a network containing the genes related to BKCa in R. norvegicus|| || ||


== CytoscapeEditor Core Plugin 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) <<BR>>3. Select the Editor tab from the Control Panel||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|| || ||


Test Cases/Old Filters_TestCases_2.7
== Old Filters Core Plugin Test Cases ==
|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||
||<|9> 1. Start Cytoscape <<BR>>2. Import a network file (eg. galFiltered.sif)  <<BR>>3. Click Create new (Integer) Attribute from the Node Attribute Browser and call it Numbers <<BR>>4.  Drag and select a group of nodes and click on the Attribute Batch Editor <<BR>>5. Choose Set from the Operation tab and Numbers from the Attribute menu and type “3” into the text field then click GO, repeat using “2” and “4” <<BR>>6. Click Select → Use Old Filters||OF1||1. Click Create new filter from the Manage Filters box and select Numeric Filter <<BR>>2. Leave the default settings in the Numeric Attribute Filter box but type “3” into the text field, click Apply selected filter||The nodes highlighted should contain “3” in the Numbers attribute column (since the default operation is “=”)|| ||  ||
||OF2||1. Change the operation to “<” from the menu in the Numeric Attribute Filter box and type “3” into the text field <<BR>>2. Click Apply selected filter||All the nodes with “2” in the Numbers attribute column (or any number less than 3) should be highlighted|| ||  ||
||OF3||1. Change the operation to “>” from the menu in the Numeric Attribute Filter box and type “3” into the text field <<BR>>2. Click Apply selected Filter||All the nodes with “4” in the Numbers attribute column (or any number greater than 3) should be highlighted|| ||  ||
||OF4||Click Remove selected filter with the Numbers>3 filter selected||The filter should no longer be listed in the Available Filters box|| ||  ||
||OF5||1. Click Create new filter from the Manage Filters box and select String Filter <<BR>>2. Select canonicalName from the text attribute menu in the String Pattern Filter box <<BR>>3. Type “?” into the text field and click Apply selected Filter||The node whose canonicalName value is “?” should be highlighted|| ||  ||
||OF6||1. Click Create new filter from the Manage Filters box and select Topology Filter <<BR>>2. Change the “Select nodes with at least” text field to “2” and click Apply selected filter||Only nodes that are the source or target of at least two edges should be highlighted|| ||  ||
||OF7||1. Click Create new filter from the Manage Filters box and select Boolean Meta-Filter <<BR>>2. Select the Topology and String filters and click the Negate check box <<BR>>3. Chose ALL, ONLY ONE or AT LEAST ONE from the “Select objects that pass” menu and click Apply selected filter in each case||With the ALL parameter every node apart from “?” should be highlighted, with the AT LEAST ONE parameter every node apart from “?” with at least two interactions should be highlighted and with the ONLY ONE parameter only nodes with one interaction should be highlighted|| ||  ||
||OF8||1. Click Create new filter from the Manage Filters box and select Edge Interaction <<BR>>2. Choose “source or target” from the “Select edges with a node” menu and the Topology Filter from the “which passes the filter” menu <<BR>>3. Click Apply selected filter||The edges that connect the nodes which pass the Topology filter should be highlighted (similar results for just target or source)|| ||  ||
||OF9||1. Click the Create new filter from the Manage Filters box and select String Filter <<BR>>2. Choose Edge from the “select graph objects of type” menu and interaction from the text attribute menu and type “pp” into the text field <<BR>>3. Click create new filter from the Manage Filters box and select Node Interactions <<BR>>4. Choose “source or target” from the “Select nodes that are” menu and the String Filter created in step 1 in the “at least one edge that passes the filter” menu <<BR>>5. Click Apply selected filter||The nodes that are connected by edges that represents pp interactions should be highlighted|| ||  ||


== Filters Core Plugin Test Cases ==
|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||
||<|14> 1. Start Cytoscape <<BR>>2. Import a network file (eg. galFiltered.sif) <<BR>>3. Click Create New Attribute in the Node Attribute Browser and select Integer from the menu <<BR>>4. Drag and select some nodes <<BR>>5. Select Attribute Batch Editor and choose Set from the operation tab <<BR>>6. Type an integer and click GO <<BR>>7. Repeat steps 5-7 for two other groups of nodes (with different integers) <<BR>>8. Click Select → Use Filters (F7) (Alternatively, click on the Filters tab in the Control Panel)||F1||1. Click on the Options button and select Create new filter… from the menu <<BR>>2. Call the new Filter Numbers <<BR>>3. In the Filter Definition section select node.Numbers from the menu <<BR>>4. Click Add, double click the range bar and set the Low and High Bound to 5, click Apply||All the nodes with “5” in their Numbers attribute column should be highlighted|| || ||
||F2||1. (Repeat steps 1-4 from F1) <<BR>>2. Click the Not check box next to the range bar (then click Apply)||All the nodes that do not have “5” in their Numbers attribute column should be highlighted|| || ||
||F3||1. (Repeat steps 1-4 from F1) <<BR>>2. Click the Advanced “+” symbol in the Filter Definition area and click on the Negation check box||All the nodes that do not have “5” in their Numbers attribute column should be highlighted|| || ||
||F4||1. (Repeat steps 1-4) <<BR>>2. Select node.Numbers from the Attribute/Filter menu again and click Add <<BR>>3. Set the Low and High bounds to 1 and click Apply (ensuring that AND appears between the two range bars)||There should be no selected nodes on the graph because the Numbers attribute only contains one integer|| || ||
||F5||1. (Repeat steps 1-3 from F4) <<BR>>2. Ensure that OR appears between the two range bars by selecting the OR radio button from the Filter Definition area||All the nodes that have either a 1 or a 5 in their Numbers attribute column should be highlighted|| || ||
||F6||1. (Repeat steps 1-4 from F1) <<BR>>2. Click the garbage can icon beside the range bar||The parameter should be deleted and no longer appear in the Filter Definition area|| || ||
||F7||1. Select edge.interaction from the Attribute/Filter menu and click Add <<BR>>2. Type “pp” into the text field and click Apply||All the edges in the graph that represent pp interactions should be highlighted|| || ||
||F8||1. Click the Options button and select Rename Filter <<BR>>2. Type “Filter 1” into the text field and click OK||The Current Filter menu should reflect the name change to “Filter 1”|| || ||
||F9||1. Click the Options button and select Create new topology filter <<BR>>2. Type “Topology” into the text field and click OK <<BR>>3. Under Toplogy Filter Definition type “1” into the first and second text fields and leave the menu on none for additional Filters to pass||All the nodes that have 1 neighbour within 1 edge interaction should be highlighted (eg. All the nodes in galFiltered.sif)|| || ||
||F10||Select Filter 1 from the Topology Filter Definition and click Apply||Only those nodes that pass Filter 1 as well as the Topology Filter should be highlighted|| || ||
||F11||1. Click the Options button and select Create new Node``Interaction Filter <<BR>>2. Type “Node” into the text field and press OK <<BR>>3. Leave the default settings in the Interaction Filter Definition area and click Apply||All the nodes that are either the source or the target of at least one edge that passes Filter 1 (eg. Is a pp interaction edge)|| || ||
||F12||1. Click the Options button and select Create new Edge``Interaction Filter <<BR>>2. Type “Edge” into the text field and press OK <<BR>>3. Select Node from the Filter menu in the Interaction Filter Definition area||All the edges whose source or target node pass the Node``Interaction filter Node should be highlighted|| || ||
||F13||1. Select Edge from the Current Filter menu <<BR>>2. Click the Options button and select Delete Filter, click YES when the Warning box appears||The Edge Filter should be deleted and should no longer appear in the Current Filter menu|| || ||
||F14||1. Select Filter 1 from the Current Filter menu <<BR>>2. Click on the Global check box under Advanced in the Filter Definition area <<BR>>3. Import another network file (eg. galFiltered.gml) <<BR>>4. Type “pp” into the text filed next to interaction in the Filter Definition area <<BR>>5. Click Apply||All of the edges that represent pp interactions in both graphs should be highlighted|| || ||