Update of Slicer issue tracker

jcfr · June 2, 2017, 9:17pm

Hi Everyone,

Now that @freephile migrated the issue tracker to its new home:

(still available from http://na-mic.org/Bug and http://www.na-mic.org/Bug to ensure existing links work)

We are planning to upgrade the version of the tracker:

You can get a feel for the interface here: My View - MantisBT
You will find below a preview of the Slicer interface below.
It will be a different user interface but we think that the new UI will improve the overall experience.
The update also includes a lot of security fixes that are long overdue. See Change Log - MantisBT

Note In the future, we may also transition to using solely the GitHub issue tracker and project features but that will be discussed later.

ihnorton · June 3, 2017, 6:33pm

Thanks for this work. to moving to GitHub (or GitLab). It may be worth considering whether any more effort should be put in Mantis at all – except possibly to migrate content to GitHub (there are some scripts available which could be modified). Leaving the tracker frozen like the old Kitware trackers would also be fine. There is relatively minimal recent activity on the current tracker because of the reliability and email issues, lack of OAuth, etc., though the history is useful to keep.

lassoan · June 3, 2017, 6:55pm

Fully agree with moving issue tracking to GitHub.

GitHub’s issue tracker is still very basic, but it should be good enough to manage Slicer issues. When source code hosting will transition to GitHub then we’ll have to use GitHub’s issue tracker anyway (for managing pull requests, etc), so it would be simpler if we don’t need to manage two trackers. It’ll be also great to have integration with source code repository and not requiring separate account.

I think the simplest would be to prevent adding new issues to Mantis, but we should be able to update/close issues. When we closed or migrated all issues, we can make the repository read-only.

fedorov · June 4, 2017, 2:22am

All for moving to GitHub for issue tracking!

Would be nice, but should not be a stopper, to time this with migration of the source code to git.

jcfr · June 6, 2017, 9:00pm

To follow up, the Slicer issue tracker has been updated.

https://issues.slicer.org

Make sure to CTRL-F5 next time you visit the site.

jcfr · June 8, 2017, 4:04am

While experimenting with the source integration plugin on Mantis, I re-triggered the import of the “correct” repository (Slicer/Slicer instead of jcfr/Slicer) and this took down the instance.

Waiting my mistake is addressed , the tracker is unavailable.

Cc: @freephile

freephile · June 8, 2017, 4:48am

Actually, the tracker is available. The source integration plugin has a nasty feature whereby it blocks (queues) all requests by the same client behind the long-running “import” – making it appear that the server is hung. Meanwhile, any other client can access the tracker and the load is miniscule.

@jcfr kill the import and/or use incognito mode and/or another browser. I can assure you that the server is fine.

jamesobutler · October 29, 2018, 7:26pm

Bumping this thread since there’s already been some good conversation on this topic.

I have found it pretty difficult to use the search within the Mantis Tracker to find relevant results. It’s hard to quickly find if there is already an issue for a bug that I observe.

ITK recently moved from their issue tracker (JIRA) to GitHub issues. See this post on their forum. Here is another post they had about using GitHub labels. For the most part I think Github Issues, Labels, and Milestones could replace a lot of primary functionality in the issue tracker. There isn’t default assigning of issues, but maybe some github apps could supplement any missing features.

jamesobutler · October 29, 2018, 8:05pm

Also Github has issue templates which could encourage detailed steps to reproduce, platform, expected behavior, etc. which would be similar to the header fields on the Mantis Tracker. ITK is also using github issue templates to encourage users to provide details about bugs/features/etc. See ITK Issue Template.

lassoan · November 12, 2018, 7:51pm

Since mantis stores issues in a structured way (not just somewhat encouraging structure by offering a template), I find it much more efficient to locate issues in Mantis compared to GitHub.

However, I agree that probably GitHub’s issue tracker would be sufficient for Slicer, and definitely more accessible to users and developers, because most people are already familiar with GitHub, they don’t need to register yet another account, and the issue tracker integrates well with other GitHub features.

I think we should just first release Slicer-4.10.1, then move Slicer’s official repository to GitHub (still SVN is the official repository) and then switch to GitHub’s issue tracker.

@jcfr

phcerdan · August 20, 2019, 12:37pm

Any ETA on enabling issues in github? Even if not official yet, would be nice to report bugs/issues there.

lassoan · August 20, 2019, 1:05pm

It would be nice to switch to github repository and issue tracker at the same time, to be able to leverage all the benefits of integration between github tools. However, there is no strict dependency, so we could start using github’s issue tracker for new issues any time.

@jcfr what is the planned date for switching to git?

jcfr · August 20, 2019, 1:16pm

This is the next major Slicer task on my list, we should expect the transition to happen in the next few weeks.

lassoan · August 21, 2019, 3:41pm

@phcerdan would this timeline work for you? Can you submit issues to issues.slicer.org?

rprueckl · September 6, 2019, 8:39am

Yesterday, I tried to register to the bug tracking system without success, I didn’t get back an email that probably should have contained my password. Following the advice of @lassoan, I will post some issues I encountered in this thread.

rprueckl · September 6, 2019, 8:43am

Bug report
Summary: Rulers that should be hidden are always visible after loading a scene
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

open slicer (standard layout)
create a ruler somewhere
hide it by clicking on the eye of the ruler in the Annotations module UI
save the scene as mrb
close scene (via file menu)
load the mrb
ruler is now visible in slice viewers, however the eye in the Annotations module UI is closed

rprueckl · September 6, 2019, 8:51am

Bug report
Summary: Missing repeated question for saving scene when ending slicer
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

open slicer (standard layout)
create a ruler somewhere (or make any other edit)
click File --> Exit
the confirmation dialog appears --> click ‘Cancel exit’
click File --> Exit
program ends without any further question to save the scene

This code causes the immediate exit:

github.com

Slicer/Slicer/blob/45cf7d262fc07078fa94ece66520b0ac58f321d7/Base/QTApp/qSlicerMainWindow.cxx#L1104-L1111


// This is necessary because of a Qt bug on MacOS.
// (https://bugreports.qt.io/browse/QTBUG-43344).
// This flag prevents a second close event to be handled.
if (d->IsClosing)
  {
  return;
  }
d->IsClosing = true;

(And another one in this post as I cannot post more than three consecutive posts):

Bug report
Summary: Broken marker placement cursor in non-standard layouts
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

open slicer (standard layout)
switch to another layout (e.g. Compare --> 2 viewers)
click on the tool button to create a fiducial
move cursor over the slice views
the cursor does not change to the markup insertion cursor

this is caused by this code:

github.com

Slicer/Slicer/blob/45cf7d262fc07078fa94ece66520b0ac58f321d7/Base/QTGUI/qSlicerMouseModeToolBar.cxx#L538-L570


// Updated all mapped 3D viewers
for (int i=0; i < layoutManager->threeDViewCount(); ++i)
  {
  qMRMLThreeDView* threeDView = layoutManager->threeDWidget(i)->threeDView();
  if (!threeDView->mrmlViewNode()->IsMappedInLayout())
    {
    return;
    }
  // Update cursor only if view interaction node corresponds to the one associated with the mouse toolbar
  if (threeDView->mrmlViewNode()->GetInteractionNode() != this->interactionNode())
    {
    continue;
    }
  threeDView->setViewCursor(cursor);
  threeDView->setDefaultViewCursor(cursor);
  }


// Updated all mapped slicer viewers
foreach(const QString& viewerName, layoutManager->sliceViewNames())
  {

This file has been truncated. show original

–> lines 544 and 561 should say continue;

pieper · September 6, 2019, 12:15pm

Hi -

I checked and your account exists on issues.slicer.org under the email you used. I had it send a password reset link so let’s see if that works.

Anyway thanks for the reports. One question: have you tried the nightly builds? The markups have gotten a lot of improvements.

rprueckl · September 6, 2019, 12:20pm

I tried the issue with the ruler not being visible after loading a scene also with the nighlty build from 2019-08-29. It was the same there. Regarding the other two issues, the cited source code is unchanged to version 4.10.2 and I debugged those issues, so I assume they are still relevant.

So far no email received.
Please remove my email address from your previous post - thanks!

pieper · September 6, 2019, 12:47pm

Sorry about that!

Not sure what’s up with that - I got the email that said your account was created. (I guess you checked your spam folder ).

Anyway looks like you’ve found some good fixes. The best way forward might be to put them in the form of a github pull request so people can easily test and comment.

Regarding the rulers they have always been a bit finicky and that’s why people have been moving functionality over to markups.

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Update of Slicer issue tracker

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