Cytoscape_3/Cy3TestPlan/file_menu

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Results

1. Start Cytoscape
2. Import a network file (e.g. galFiltered.sif)
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
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
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
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
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

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

1. Start Cytoscape
2. Import a network file (e.g. galFiltered.sif)
3. Click on File from the toolbar

FM9.1

1. Select Import → Network (multiple file types)…
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…
2. Select Gene Association File for Saccharomyces cerevisiae from the Annotation menu and leave the default setting for Ontology
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…
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…
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
3. Click EntrezGene ID check box on the list of available attributes and click Import
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…
2. Select EntrezGene ID-TOP for Attribute
3. Select all of the items in the Available Annotation Category
4. Click Import
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.

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (e.g. galFiltered.sif)
3. Click on File from the toolbar

FM10.1

1. Select Export → Network and attributes as XGMML…
2. Save as Test1.xgmml
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…
2. Save as Test2.gml
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…
2. Save as Test3.sif
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
1. Select Export → Node Attributes
2. Click the "Ensembl Family ID" check box from the list of attributes
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
2. Click the interaction check box from the list of attributes
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
2. Change the node color for the copied style
3. Select Export → Vizmap properties
4. Type Test4.props as the file name, choose the appropriate directory and click save
4. Exit Cytoscape and restart it
5. Import galFiltered.sif and Import → Vizmap Property File…
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…
2. Click Choose and type Yeast Network as the file name and click Save
3. Leave the Format as PDF and Click OK
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
2. Select .PNG from the format menu and click OK
3. Leave the bitmap settings as default and click OK
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

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
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
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
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
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
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
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
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
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
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
2. Set the limit to 20 and click search

cPath should generate a network containing the genes related to BKCa in R. norvegicus

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

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. File → Import network → File... (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

1. 7-5-12

1. Pass; bug with .xlsx already reported

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)

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
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)

1. 7-5-12

1. Pass

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!

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
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

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