## page was renamed from Master Test Plan/UI Test Cases/File menu - main
Tested under conditions: 1 = Win7; 64 bits; 16 gig. Remarks have been added to redmine
||'''Preconditions'''||'''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Results'''||
||<|10> 1. Start Cytoscape <<BR>>2. Import a network file (e.g. galFiltered.sif) <<BR>>3. Click on File from the toolbar||
||FM1.1||Select New → Network → Empty Network||A new empty network canvas should appear called Network and it should appear in the list under the Networks tab in the control panel||1. 7-4-12 ||1. pass; remark: no sample data in cy3 yet ||
||FM1.2||1. Hold shift and click on 5 nodes near each other <<BR>>2. Select New → Network → From selected nodes, all edges||A new network canvas, with the selected nodes and all the edges that connect them, should be created and appear in the Network tab with appendix <subnetwork>||1. 7-4-12 ||1. pass ||
||FM1.3||1. Drag and select several nodes and edges <<BR>>2. Select New → Network → From selected nodes, selected edges||A new network canvas with only selected nodes and edges with their adjacent nodes should be created||1. 7-4-12 ||1. pass ||
||FM2||Select New → Session, click Yes when the caution box appears||A new session should be started with a clear canvas and no networks||1. 7-4-12 ||1. pass; remark; the caution box contains a checkbox with no meaning ||
||FM3||Select Open and choose the galFiltered.cys session file from the sampleData directory||A session file with the galFiltered.gml network imported should be displayed||1. 7-11-12 ||1. pass ||
||FM4||Click Save||Cytoscape should save your progress to the current session file (galFiltered.cys)||1. 7-11-12 ||1. pass ||
||FM5||1. Click Save As… and type “galFiltered1.cys” into the text field <<BR>>2. Click Save||Cytoscape should create a new .cys file with the name entered in the specified directory||1. 7-11-12 ||1. pass ||
||FM6||Select Print and choose the appropriate printer and desired settings and then click print||A print out of the currently selected network should be produced||1. 7-11-12 ||1. pass ||
||FM7||1. Select Quit and click Yes, save and quit <<BR>>2. Start Cytoscape and load the .cys file||The .cys should contain the latest version of the test session with all the changes saved before quitting||1. 7-11-12 ||1. pass ||

## page was renamed from Cytoscape_2.7/UI Test Cases/Import sub menu
== UI Test Cases for File Menu - Import sub menu ==
||'''Preconditions'''||'''Test Case ID'''||'''Instructions'''||'''Expected Results'''||||'''Date Executed'''||
||<|12> 1. Start Cytoscape <<BR>>2. Import a network file (e.g. galFiltered.sif) <<BR>>3. Click on File from the toolbar||
||FM9.1||1. Select Import → Network (multiple file types)… <<BR>>2. Choose the galFiltered.xgmml file from the sampelData directory and click Import||A new version of the galFiltered network should appear in a different window||1. 7-11-12 ||1. pass ||
||FM9.2||Import Network from Table (Text/MS Excel) is covered under the Table Import core plugin test cases|| || || ||
||FMFM9.3|| Select Import -> from public databases, enter a valid gene and select the organism. Select the gene from the list that is produced and hit 'Retrieve Interactions' button, click ok on the window that appears|| The network of genes related to the entered gene should appear||1. 7-11-12 ||1. pass; term import from public databases doesn't match dialog ||
||FM9.4||Importing node attributes is covered under the Node Attribute Browser core plugin test cases|| || || ||
||FM9.5||Importing Attributes from Table (Text/MS Excel) is covered under the Browser Core Plugins Test Cases|| || || ||
||FM9.6||Importing edge attributes is covered under the Edge Attribute Browser core plugin test cases|| || || ||
||FMFM9.7||1. Select Import → Ontology and Annotation… <<BR>>2. Select Gene Association File for Saccharomyces cerevisiae from the Annotation menu and leave the default setting for Ontology <<BR>>3. Select one of the galFiltered networks and click on Go common Name from the Node Attribute Browser Select Attributes menu||Cytoscape should show a large network under the Networks tab in the Control Panel (view not created due to size) and there should be new attributes available for selection in the Node Attribute Browser||1. 7-11-12 ||1. pass;Progress bar doesn't show progress in first stages (20 secs) ||
||FM9.8||Importing an Attribute Expression Matrix is covered under the Node Attribute Browser core plugin test cases|| || || ||
||FM9.9||1. Select Import → Vizmap Property File… <<BR>>2. Choose sampleStyles.props from the sampleData directory and click Open||All the nodes in the galFiltered network should be light gray with no border and each edge should be a black line labelled with the type of interaction that it represents||1. 7-11-12 ||1. fail; vizmap is not applied to network ||
||FM9.10||1. Select Import → Import Attributes from Biomart… <<BR>>2. Select ''ENSEMBL GENES xx (SANGER UK) – Saccharomyces cerevisiae genes (SGD1.01)'' (where xx is the latest version of ENSEMBL data set) from the Data Source menu and ''ENSEMBLE Gene ID'' from the Data Type menu <<BR>>3. Click ''!EntrezGene ID'' check box on the list of available attributes and click Import <<BR>>4. Select one of the galFiltered networks and click on the new attribute from the Node Attribute Browser Select Attributes menu||New attributes ''!EntrezGene ID'' and ''!EntrezGene ID-TOP'' should be available for selection under the Node Attribute Browser||1. 7-11-12 ||1. fail; no biomart attributes||
||FM9.11 ||1. Select Import → Import Attributes from NCBI Entrez Gene…  <<BR>>2. Select ''!EntrezGene ID-TOP'' for Attribute<<BR>>3. Select all of the items in the ''Available Annotation Category''<<BR>>4. Click Import <<BR>>5. Select one of the galFiltered networks and click on ''Pathway'' in the Node Attribute Browser Select Attributes menu||New attributes should be available for selection under the Node Attribute Browser and some of the nodes should have KEGG Pathway information.|| ||||



== UI Test Cases for File Menu - Export sub menu ==

||'''Preconditions'''||'''Test Case ID'''||'''Instructions'''||'''Expected Results'''||'''Date Executed'''||'''Pass/Fail'''||
||<|10> 1. Start Cytoscape <<BR>>2. Import a network file (e.g. galFiltered.sif) <<BR>>3. Click on File from the toolbar||FM10.1||1. Select Export → Network and attributes as XGMML… <<BR>>2. Save as Test1.xgmml <<BR>>3. Close Cytoscape and restart it, Select Import → Network (multiple file types)… and import Test1.xgmml||Test1 should be an exact copy of the network exported before restarting Cytoscape|| ||||
||FM10.2||1. Select Export → Network as GML… <<BR>>2. Save as Test2.gml <<BR>>3. Select Import → Network (multiple file types)… and import Test2.gml||Test2 should be a copy of the network exported but should have slightly different features (e.g. Background)|| || ||
||FM10.3||1. Select Export → Network as SIF File… <<BR>>2. Save as Test3.sif <<BR>>3. Select Import → Network (multiple file types)… and import Test3.sif||Test3 should be a copy of the network exported and should be exactly the same as galFiltered.sif|| || ||
||FM10.4||0. Load galFiltered.cys<<BR>>1. Select Export → Node Attributes <<BR>>2. Click the "Ensembl Family ID" check box from the list of attributes <<BR>>3. Click Choose Directory and Save, select the desired directory and click Choose||Verify that the attributes were saved by opening the attribute file in a text editor, the file should contain a list of the gene IDs from the network and their corresponding GO common names|| || ||
||FM10.5||1. Select Export → Edge Attributes <<BR>>2. Click the interaction check box from the list of attributes <<BR>>3. Click Choose Directory and Save, select the desired directory and click Choose||Verify that the attributes were saved by opening the attribute file in a text editor, the file should contain a list of the edge IDs from the network and their corresponding interactions|| || ||
||FM10.6||1. Create a copy of the current visual style and give it a new name<<BR>>2. Change the node color for the copied style<<BR>>3. Select Export → Vizmap properties <<BR>>4. Type Test4.props as the file name, choose the appropriate directory and click save <<BR>>4. Exit Cytoscape and restart it<<BR>>5. Import galFiltered.sif and Import → Vizmap Property File…<<BR>>6. Change the visual style to the imported style||The node colours should change to those of the visual style that was saved|| || ||
||FM10.7||1. Select Export → Network as Graphics… <<BR>>2. Click Choose and type Yeast Network as the file name and click Save <<BR>>3. Leave the Format as PDF and Click OK <<BR>>4. Open Yeast Network.pdf in a PDF reader||The PDF should contain a screen shot of the portion of the network visible in the canvas|| || ||
||FM10.8||1. Repeat steps 1 & 2 from FM10.7 <<BR>>2. Select .PNG from the format menu and click OK <<BR>>3. Leave the bitmap settings as default and click OK <<BR>>4. Open the Yeast Network.png in a picture viewer||The PNG should contain a screen shot of the portion of the network visible in the canvas|| || ||
||FM10.9||Export of PSI-MI 1.0 under construction|| || || ||
||FM10.10||Export of PSI-MI 2.5 under construction|| || || ||


== cPath 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|| || ||

== PSI-MI Test Cases ==

|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||
||1. Start Cytoscape <<BR>>2. Import a network file (eg. [[attachment: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.


== Table Import Test Cases ==
|| '''Preconditions'''|| '''Test Case ID'''||'''Instructions'''||'''Expected Results'''|| '''Date Executed'''||'''Pass/Fail'''||
||<|5> 1. Start Cytoscape <<BR>>2. File → Import network →  File... (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||1. 7-5-12 || 1. Pass; bug with .xlsx already reported ||
||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)||1. 7-5-12  ||1. Pass ||
||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)||1. 7-5-12 ||1. Pass ||
||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!||1. 7-5-12  ||1. Not testable; no file selection in dialog anymore||
||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||After showing a confirmation dialog graph containing only the genes listed in the Source Interaction column should appear (with no edges)||1. 7-5-12 ||1. Pass ||


== 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|| || ||