RFC Name : …

Editor(s): …

Date: …

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Automatic error detecting and reporting has become common practice in desktop and web-based applications. The bugs found in the field may be types that wouldn't ever be caught during testing. With an automatic bug report system, filing a bug report is just a click on a button in a dialog. Many more bug-reports from various kinds of users become possible, including non-technical users and those who can't be bothered to login to a bug tracker and file a detailed report.

Cytoscape should consider a similar automatic bug reporting system, which could potentially increase feedback from Cytoscape users and provide developers useful information needed to fix the bugs. This RFC describes how we might build an automatic bug reporter for Cytoscape.

Use Cases

1. GUI mode

Scenario: A user is using Cytoscape and suddenly Cytoscape runs into a problem. An exception is caught and the exception is classified as a bug. A dialog box pops up and asks user if he/she wants to report the error to Cytoscape. If user says “Yes”, information about the bug will be sent to Cytoscape bug tracker.

2. Headless mode

3. Do not report any bug

In the case that a user decides not to report any error, the user has the option to set the property value “automaticErrorReport” (true, by default) to false and Cytoscape will remember the decision.

Collecting data from Cytoscape user

When Cytoscape crashes or exception thrown, the following information from user should be collected and submitted directly to Cytoscape bug tracker, Mantis

The category of bug report in Mantis may be infered from the specific exception type. We encourage users to give a description of what they did before Cytoscape ran into the problem. This will be very helpful for developers to reproduce the bug. User email address is optional. Many users may not give us their email address at all. However, in cases where the same bug is reported multiple times, and developer has questions about it, it could be useful to contact user if he/she did provide an email address

Format of bug report and identification of duplicated bugs

The subject (summary) of bug report should have the format something like this:

ExceptionType:ClassName:Method:LineNumber:OS:OSVersion This string is used to determine if a bug has already been reported.

If a bug has already been reported (with the same subject), the report should be appended to the existing one, rather than opened as a new one.

Mantis bug Data structure:


OS version: XP/???

Product build: Cytoscape 3.0


Additional Information: User’s comment, User’s e-mail contact, if any

Steps to reproduce:Command history

Attached file: If session file is attached, it will be added as an attached file.

Notes:If duplicated bug, add a note only,including OS, OS_Version, User’s e-mail,User’s comment, Time stamp

Automatic bug reporter could be part of CyLogger

Since Cytoscape 2.6.1, Cytoscape has its own Logger, CyLogger, which catches all kinds of error messages and present them to the users or developers. CyLogger may be extended to include the automatic error reporter.

The primary job of the reporter is to report RuntimeException, such as NullPointerException, ArrayOutOfBoundException, etc. The sources of the exception may be identified through different types of exception, for example, CyModelException, CyViewException, CyIOException, CyVSException. In turn, the type of CyException can be used to categorize the bug report. In this way, we don’t need to set ErrorCode for each report.


The implementation of the automatic bug reporter includes two parts, client side (Cytosape) and server side (Mantis). The client would be responsible for data collecting and submission and the server for data processing. If a task can be done in either client or server side, we prefer to put it on server side. This is important for easy maintenance in the future.

Cytoscape (client side)

Two Java classes in cytoscape.logger package are needed for automatic bug reporter.

  1. BugReport.java: Java bean class, to hold bug data

  2. BugReportUtil.java: This class is responsible for the bug data validation and submission.

Mantis (Server side)

  1. Virtual person: Automatic bug reporter should have its own user name “Automatic bug reporter” in Mantis -- a virtual person, instead of a real developer.
  2. Mantis PHP script (bug_report_auto.php): the new Mantis PHP script will be triggered by “BugReportUtil.SubmitBugReport(URL, BugReport)” of Cylogger. This PHP script will (1) check the summary (subject line of the bug report) of the Bug report (2) if this is a new bug, create a new Bug in Mantis, if this is a duplicated bug, append the new report to existing one.

Web page about fixed-bugs

We may need a web page to list bugs-fixed (CyBugsFixed.php) at Cytoscape web site. On the page, fixed bugs for each Cytoscape versions would be listed, so that users could search for the bugs they care about and get advice/suggestions on possible work-arounds. Currently users can search for particular bugs in Cytoscape bug tracker, Mantis. But this is mainly for developers, not for ordinary users.

Integrating Mantis and Subversion

Mantis can be integrated with Subversion, so that if a developer fixes a bug and checks in the change into Subversion, the change can be immediately reflected in Mantis. There is a step-by-step instruction on how to setup the post-commit script in Subversion to make this happen, here.

Link to other related RFCs


List any issues, conflict, or dependencies raised by this proposal



Peng-Liang Wang




Peng-Liang Wang


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Peng-Liang Wang


Peng-Liang Wang

AutomaticBugReporter (last edited 2009-02-12 01:03:36 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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