Reminders:

• Test using a User account rather than an Admin or Sysops account (e.g., TestUser : h4ppyt3st1ng).

• Check which systems have already been tested on and log your information  below.

• Enter bug into the bug tracker:  http://www.bigcat.unimaas.nl/tracprojects/pathvisio/

Web Interface Testing

General

Test	Procedure	Expected behavior
Searching for pathways	On the main WikiPathways page, type in a key word in the Google search box. Click the enter key or the "Search" button to search.	Search results will appear on a separate page. Note: search always brings you to the main site, so make sure you navigate back to the test site

Browsing pathways

Procedure	Expected behavior
On the main WikiPathways page, click the "Browse" thumbnail or click the "Browse" link in the left side panel.	The browse page will appear.
At the top of the page, select a species to browse in the drop-down menu and further limit the selection to a pathway category in the "Categories" drop-down. The page should refresh as soon as you selected a category or species.	All pathways for the relevant species and category will be listed.
Click any of the pathway links.	The relevant pathway page will open.

Pathway page

Test	Procedure	Expected behavior
Adding Description	Click the "Edit" button to the right of the Description section and type in a description in the "Description" field. Click the "Close the editor" button to submit or the stop button to exit.	When the pathway page reloads, the description will be visible in the Description section. "Modified description" will be added to history.
Adding Categories	Click the "Edit" button to the right of the Categories section and select which categories to add to the pathway in the check boxes. Click the "Close the editor" button to submit or the stop button to exit.	When the pathway page reloads, the description will be visible in the Description section. "Modified categories" will be added to history.
Reverting to a previous version	In the History section of the pathway page, click the "View All" link. Click the "revert" link for the version you want to revert to.	The pathway page will revert to the selected version.
Watch/unwatch a pathway	At the top of the pathway page, click the "watch" or "unwatch" tab.	A page will appear informing you that the pathway is being placed on or removed from your watch list.
Viewing the difference between versions of a pathway	In the History section of the pathway page, click the "View All" link. In the list that appears, select two versions using the radio buttons and then click "Compare selected versions".	The visual difference tool will open with the two selected pathways showing. Any differences between the two versions will be highlighted.
Viewing data nodes	In the Pathway Info section at the bottom of the pathway page, click on the link to view all data nodes.	The list of data nodes for the pathway will be displayed as a list, with information on name, type, backpage header and Entrez Gene ID.
Delete pathway	Log with an account that has administrator rights. Click the 'delete' tab on the pathway page. Specify a reason for deletion and click 'delete'.	The pathway page should now show a message stating that the pathway has been deleted and a table containing the history. The pathway should also disappear from the browse page and batch download
Undelete pathway	To undelete a pathway, visit the page of the deleted pathway and view the history table and click revert on the revision before deletion.	The pathway should be restored and reappear in the browse pages and batch download.

Curation tags

Add curation tag	In the curation tags section, add the 'New tag' button	A form with a selection box and text field should appear
Add curation tag	Select a tag, specify tag text and click the 'Apply' button	The tag you selected should appear in the tag list
Remove curation tag	In the top-right corner of a tag, click the 'Remove' button	The tag will be removed
Edit curation tag	In the top-right corner of a tag, click the 'Edit' button	The edit form will appear
Edit curation tag	Change the tag text in the edit form and click the 'Apply' button	The tag will be updated

Editor Testing

Toolbar

Test	Procedure	Expected behavior
Export pathway	Click on the “Export pathway” button.	File browser appears where user can choose file name, choose location for export and file format for export. The File Format drop-down list should include gpml, pdf, png, svg and MAPP.
Export to gpml	Select gpml as the file type in the File browser	A gpml-formatted file is saved to the selected location.
Export to pdf	Select pdf as the file type in the File browser	A pdf-formatted file is saved to the selected location.
Export to png	Select png as the file type in the File browser	A png-formatted file is saved to the selected location.
Export to svg	Select svg as the file type in the File browser	An svg-formatted file is saved to the selected location.
Export to MAPP	Select MAPP as the file type in the File browser	On Windows operating systems, a MAPP-formatted file to the selected location. On all other operating systems, nothing will happen.
Copy selected pathway objects to clipboard	Select a set of objects on the pathway by clicking and dragging a rectangle around the objects, then click the "Copy selected pathway objects to clipboard" button.	Any selected objects will be copied to the clipboard.
Paste pathway objects from clipboard	Click the “Paste pathway objects from clipboard” button.	Any elements on the clipboard will be copied to the pathway, slightly offset to their original location.
Undo last action	Click the “Undo” button.	Last action will be undone. Multiple clicks will undo additional actions.
Zoom drop-down	Click the Zoom drop-down menu and select a zoom factor. Alternatively, type a zoom factor directly in the drop-down box and click Enter.	Pathway will be zoomed to selected zoom factor. The “Fit to window” option will zoom the pathway to make it fit completely within the editor bounds.
Switch to full-screen mode	Click the “Switch to full-screen mode” button.	The editor appears as a separate window.
Manually resize window	Mouseover bottom-right corner of applet window to find achnor point, then click and drag to resize	PV applet should resize keeping pathway and property sections in reasonable proportion
Draw new GeneProduct	Click the “Draw new GeneProduct?” button and then click anywhere on the pathway to place the gene product. Double-click on the gene product and enter a symbol or identifier for the gene product in the DataNode? properties window, select a database to search and then click to lookup either the identifier or symbol.	A new gene product linked to the selected ID will appear on the pathway in the selected location.
Draw new Metabolite	Click the “Draw new Metabolite” button and then click anywhere on the pathway to place the metabolite. Double-click on the metabolite and enter a symbol or identifier for the metabolite in the DataNode properties window, select a database to search and then click to lookup either the identifier or symbol.	A new metabolite linked to the selected ID will appear on the pathway in the selected location.
Draw new label	Click the “Draw new label” button and then click anywhere on the pathway. In the Properties panel, enter the text for the label in the Text field and click Enter.	A new label will appear on the pathway in the selected location with the selected text displayed.
New line drop-down	In the “New line” drop-down menu, select a line type. Click anywhere on the pathway to place it.	A new line will appear with its starting point in the selected location.
Draw new rectangle	Click the “Draw new rectangle” button and then click anywhere on the pathway. In the Properties panel, change the shape of the rectangle in the Shape Type drop-down. Also change the entries for Color, Fill Color and Line Style to customize the rectangle.	A new rectangle with the selected shape will appear on the pathway in the selected location. The Color, Fill Color and Line Style will correspond with selections in the Properties panel.
Draw new oval	Click the “Draw new oval” button and then click anywhere on the pathway. In the Properties panel, change the Color and Line Style.	A new oval with the selected Color and Line Style will appear on the pathway in the selected location.
Draw new arc	Click the “Draw new arc” button and then click anywhere on the pathway. In the Properties panel, change the Color and Line Style.	A new arc with the selected Color and Line Style will appear on the pathway in the selected location.
Draw new brace	Click the “Draw new brace” button and then click anywhere on the pathway. In the Properties panel, change the Color and Line Style.	A new brace with the selected Color and Line Style will appear on the pathway in the selected location.
Draw new T-bar	Click the “New TBar” button and then click anywhere on the pathway.	A new T-bar will appear with its starting point in the selected location.
New receptor/ligand drop-down	In the “Receptor/Ligand” drop-down menu, select either a receptor or ligand. Click anywhere on the pathway to place it.	A new receptor or ligand line will appear with its starting point in the selected location.
Draw new interaction	Click the “Draw new interaction” button and then click anywhere on the pathway to place it. Double-click on either of the gene products and enter a symbol or identifier in the DataNode properties window, select a database to search and then click to lookup either the identifier or symbol. Repeat with the other Gene Product.	A new interaction consisting of two gene products linked by a line will appear.
Draw new reaction	Click the “Draw new reaction” button and then click anywhere on the pathway to place it. Double-click on either of the reaction components and enter a symbol or identifier in the DataNode properties window, select a database to search and then click to lookup either the identifier or symbol. Repeat with the other components.	A new reaction between a substrate and product, with a catalyst will appear.
Align horizontal centers	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Align horizontal centers” button.	Selected objects will be moved horizontally so that their horizontal centers align with the horizontal center of the top-most selected object.
Align vertical centers	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Align vertical centers” button.	Selected objects will be moved vertically so that their vertical centers align with the vertical center of the left-most selected object.
Set common width	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Set common width” button.	Selected objects will be resized so that their width is the same as the width of the widest selected object.
Set common height	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Set common height” button.	Selected objects will be resized so that their height is the same as the height of the tallest selected object.
Stack vertical center	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Stack vertical center” button.	Selected objects will be moved so that the vertical centers of the objects align with the vertical center of the top-most selected object and so that the edges are stacked vertically.
Stack horizontal center	Select a set of objects on the pathway by clicking and dragging a rectangle around them. Then click the “Stack horizontal center” button.	Selected objects will be moved so that the horizontal centers of objects align with the horizontal center of the left-most selected object and so that the edges are stacked horizontally.
Save pathway and close editor	Click on the “Close the editor” button and agree to save the changes. In the message that appears, describe the changes you made.	The pathway will be saved to WikiPathways?.org and the editor will be closed. A message will appear during saving and once the page reloads the pathway page will be displayed with the newly made changes visible.
Discard pathway and close editor	Click on the “Close the editor” button and select not to save the pathway in the message that appears.	Once the page reloads the pathway page will be displayed as it was prior to edits.

Drawing area

Test	Procedure	Expected behavior
Moving objects by click and drag	Select one or more objects. Click in the middle of the selection or object and drag to move the object.	Object(s) will be moved according to user selection
Moving objects by arrow keys	Select one or more objects. Click the left, right, up or down arrow key to move objects. Hold down the Shift key and click the left, right, up or down arrow keys to move objects with a larger increment.	Object(s) will be moved in the direction of the arrow key pressed. If the Shift key is held down, objects will be moved with a larger increment.
Deleting objects	Select one or more objects. Right click on the selection and click “Delete” to the object(s)	The objects will be permanently deleted
Resize/Change direction of lines/T-bars	Click on a line or T-bar to select it. Resize and change the direction of the line/T-bar by clicking and dragging any of the endpoints when the line is selected.	Line/T-bar will be resized and the direction changed according to the new position of the endpoints.
Create sticky edges	Select a line object. Drag one of the line endpoints near the object to which you want to attach it. 12 Link targets should appear. When the link target has a green outline, release the line.	The line is now attached to the object. If the object is moved, the linked line follows.
Add comments to objects	Select any object and then click on Comments field of the Properties panel. Click the “Add comment” button and enter your comment in the specified field. Click OK to save	The comment will be visible in the Properties panel, under Comments.
View datanode backpage	Select a datanode object, then click the Backpage tab in the side panel.	Information from the database relevant to the selected gene will be displayed in the side panel.
Add Literature reference to an object or pathway	Right-click on an object or anywhere on the pathway. Select “Literature>Add literature reference”. In the Literature reference properties window, enter a Pubmed ID and click “Query PubMed?”. Click Ok to continue.	If the Pubmed ID is valid, the remaining fields in the Literature reference properties window will be filled in. If the literature reference is added to the pathway, it will be listed under Bibliography after the pathway is saved.
Edit Literature reference to an object or pathway	Right-click on an object or anywhere on the pathway. Select “Literature>Edit literature reference”. In the DataNode properties window Literature tab, click Edit and edit the citation in the Literature reference properties window. Alternatively, click Remove to remove the citation, or Add to add another citation.	If Edit or Add is selected, the Literature reference properties window will appear. If Remove is selected, the citation is deleted. If the literature reference refers to the pathway, any changes will be reflected under Bibliography after the pathway is saved.
Select all objects	Right-click anywhere on the pathway and select “Select>Select all”.	All pathway objects are selected.
Select all DataNode objects	Right-click anywhere on the pathway and select “Select>Select all DataNode objects”.	All data node objects are selected.
Change drawing order of objects	Create two objects of the same type (e.g. two shapes) and set a fill color for each object. Right-click on the top object, and click "Order->Send to back". Right click the same object again, and click "Order->Bring to front"	By clicking "Send to back", the object should be drawn below all other objects of the same type. By clicking "Bring to front" the object should be drawn on top of all other objects of the same type

Workflow Testing

Drawing a new pathway

Procedure	Expected behavior
On the main page, click on the "Create" link in the left side panel, or the "Create" thumbnail in the center of the page.	The "Create new pathway" page will open.
Enter a new for the pathway and select a species from the Species drop-down menu. Click "Create pathway " to continue.	A blank pathway page should open.

Edit an existing pathway

Procedure	Expected behavior
On the pathway page of interest, click the "Edit pathway" button under the pathway.	A window may appear asking you to confirm if you trust the publisher of the application. An embedded pathway editor will then appear on the pathway page.
In the editor, make your changes to the pathway. When you are finished, click the "Close the editor" button on the toolbar ("Save pathway and close editor").	The pathway page will be updated based on your changes.

Uploading a locally stored gpml pathway

Procedure	Expected behavior
On the main page, click on the "Create" link in the left side panel, or the "Create" thumbnail in the center of the page.	The "Create new pathway" page will open.
Enter a name for the pathway and select a species from the Species drop-down menu. Click "Create pathway " to continue.	A blank pathway page with the embedded editor active should open.
Click on the import button and select a local GPML file	The GPML should be imported and editable
Make any additional changes and the click the "Close the editor" button on the toolbar ("Save pathway and close editor").	The pathway page will be updated to show the pathway from the gpml file.

Using anchored lines

Procedure	Expected behavior
Select a line object. Create an anchor point by either of the following methods: 1. Click on line and the Ctrl/Command+R. 2. Right-click on the line and select "Add anchor".	An anchor point will appear in the middle of the line.
Select the anchor point and drag it to move it along the line.	The anchor point will be moved to a new location on the line
Select the start or end of a different line. Drag the selected point over the anchor point. When the anchor point is highlighted as a target, let go of the selection.	The line end/start will be linked to the anchor point and will move with it.

Copying between PathVisio and WikiPathways

Procedure	Expected behavior
On the main page, click on the "Create" link in the left side panel, or the "Create" thumbnail in the center of the page.	The "Create new pathway" page will open.
Enter a new for the pathway and select a species from the Species drop-down menu. Click "Create pathway " to continue.	A blank pathway page with the embedded editor active should open.
Launch PathVisio (www.PathVisio.org) and open the locally stored gpml file under File>Open. Select all pathway objects (Ctrl+A) and copy them (Ctlr+C).	All pathway objects should be highlighted when selected
In the WikiPathways embedded editor, click "Paste pathway elements from clipboard".	The entire pathway should be pasted into the editor.
Make any additional changes and the click the "Close the editor" button on the toolbar ("Save pathway and close editor").	The pathway page will be updated to show the pathway from the gpml file.

Copying between WikiPathways and Cytoscape

Procedure	Expected behavior
Install the Cytoscape gpml reader.
Launch Cytoscape and open a blank network.
Browse to the relevant pathway page at WikiPathways? and click the "Edit pathway" button.	The editor applet will open with the relevant pathway.
Copy all pathway objects.	Pathway will be copied to the clipboard.
In the Cytoscape empty network, paste the selection by clicking Ctrl+V.	The pathway from WikiPathways will appear as a Cytoscape network.

Adding pathways to the Pathway wishlist

Procedure	Expected behavior
On the main WikiPathways page, click the "Wish List" link on the left side panel, or click the "Suggest" thumbnail.	The Wish List page will open.
Click the "Add new wishlist item" link at the top left of the page.	Fields for specifying name and description of the new pathway will appear.
Enter a name in the "Name of pathway" field and a description in the "Description" field. Click Add when finished.	Your entry will appear in the wish list.

Misc

Test	Procedure	Expected behavior
Opening a WikiPathways pathway in Cytoscape	Make sure the gpml reader plugin is installed in Cytoscape. On the pathway page of interest, click on the "Download" button below the pathway and select "Open in Cytoscape".	A window will open asking you to confirm the opening of the Cytoscape application. Cytoscape will open with the pathway displayed.
Download individual pathway	On the pathway page of interest, click on the "Download" button below the pathway. In the "Download for" drop-down, select either PathVisio, Gene list, Eu.Gene, png image or Acrobat format.	A separate download window will appear with an option to save or to open a zipped archive of files.
Download pathways in batch	On the main page of WikiPathways?.org, click "Download" in the left side panel. On the Download page, choose any species and format and click on the corresponding link to download.	A separate download window will appear with an option to save or to open a zipped archive of files.

Test Results

If you're done testing, please add your info to this table:

Name	date / milestone	Software versions	issues found
Martijn	Feb 18, 2008, for milestone 1	OS: Linux / Ubuntu 7.10 Browser: Firefox 2.0.0.12 Java plugin: Sun java 5	mantis bugs 341 to 345
Alex	2/18/08: milestone 1	Intel Mac 10.5 Leopard; Firefox 3 (beta); J2SE 5	Bugs 351-362, added notes to 341, 343
Alex	3/9/08: milestone 2	WinXP (Parallels VM); IE7; Java SE 6	Bugs 384-396
Kristina	3/11/08: milestone 2	Intel Mac; Firefox 2.0.0.5	Issues 402-412
Martijn	Mar 16, 2008: milestone 2	WinXP (Virtualbox); IE6; Java SE 6	Bugs 416-417
Kristina	Apr 16, 2008	Intel Mac; Firefox 2.0.0.5	Bugs 454-459 and 484
Thomas	May 13, 2008	WinXP (Parallels VM); IE7; Java SE 6	Bugs 502 - 508
Kristina	June 13, 2008	Intel Mac; Firefox 2.0.0.5	Bugs 566-567
Thomas	June 23	WinXP (VirtualBox); IE7; Java SE 6	Bugs 583-585
Thomas	Oct 7	WinXP (VirtualBox); IE7; Java SE 6	Bugs 651,652
Martijn	Oct 8	Linux / Ubuntu 8.04; FF 3.0; Java SE 6	Bugs 609, 653, 654
Kristina	Nov 10, 2008	Intel Mac; Firefox 2.0.0.5	Bugs 693-695 and addition to bug 685
Thomas	Nov 11, 2008	Ubuntu 8.10; Firefox 3.03	Bugs 682-685
Alex	Dec 10, 2008	Intel Mac 10.5; Firefox 3.04; Java 1.5.0_16	bugs 737-740
Martijn + Charlie	Feb 19, 2009	Biobuntu 5; Firefox	bugs 832-839
Adem	Mar 25, 2009	Ubuntu; Firefox	-
Martijn	Mar 25, 2009	Ubuntu 8.10; Firefox 3.07, Java6-plugin	Bugs 857-860
Kristina	Mar 25, 2009 / M12	Mac OSX 10.5.5; Firefox 3.0.7	Bugs 861-866
Thomas	Mar 26, 2009	Ubuntu 8.10; Firefox 3.07, Sun Java 6	Bug #868
Alex	Mar 26, 2009	Mac OS X 10.5.6; Opera 9.27, Java 1.5.0_16
Jonas Hummel	May 20, 2009	Windows XP; Google Chrome 1.0.154.65	Bug #901
Jonas Hummel	May 20, 2009	Windows XP; Safari	Bug #902, #904
Pieter Giesbertz	May 20, 2009	Windows XP; IE6	Bug #903
Kristina	May 21, 2009	WIndows XP, IE 6	Bugs #909-913
Kristina	September 9, 2009	Mac OSX, FF	Bugs 990-991
Martijn	October 12, 2009	Ubuntu 9.04, FF	Bug #1010
Kristina	February 3, 2010	Mac OSX, FF	Bugs 1110-1112

Please pick different software versions each time you go through the test setup. Here are some suggestions:

Browsers:

• Firefox 2

• Firefox 3 (beta)

• IE6

• IE7

• Safari

• Opera

• ...

Operating Systems:

• Intel Mac 10.5 Leopard

• Intel Mac 10.4 Tiger

• Linux Ubuntu 7.10 Gutsy (32 bit)

• Linux Ubuntu 7.10 Gutsy (64 bit)

• Windows XP

• Windows Vista

• ...

Java:

• Sun Java 5

• Sun Java 6

• ...