Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.0.1 Minor Release
-
Labels:
-
Story Points:2
-
Sprint:Fall 2017
Description
While testing IGBF-1092 I noticed that the Save As... feature is not useable at all on Windows. This is because the filename gets appended with additional text causing the file name to be invalid. This is also happening on Mac, but on Mac the filename is not invalid, but the extra text still gets appended.
For example, if you try to save a graph file as a bedgraph named "test.bedgraph", IGB will actually save the file as "test.bedgraph.*.bedgraph".
To reproduce:
1) Select Arabidopsis thaliana genome - go to start screen and click the Arabidopsis image
2) Choose Data Access > RNA-Seq > Loraine Lab > Mixed Cold > SM > Graph
3) Select a graph, zoom in on a region
4) Click Load Data to load some data
5) Right-click or CNTRL-click track label and select Save As...
6) Save a file with the name "test.bedgraph"
Observe: On Mac = the file actually gets saved as test.bedgraph..bedgraph
On Windows = the file will not be saved at all and there is an exception in the console.
Attachments
Issue Links
- relates to
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
-
IGBF-1090 Implement saving of all chromosomes when exporting as bedgraph
-
- Closed
-
Activity
Edited pull request to remove changes from IGBF-1090. This pull request now only contains the two changes specific to this issue.
This branch has been merged, so I am moving to 'needs testing'
After testing this issue it seems that files are being properly saved as .bedgraph or .gr files on Windows and Mac. However, I noticed on Windows that the file extension (bedgraph or gr) is listed twice in the Save As File Type drop-down menu, which seems a little weird. For example, it says "Graph (bedgraph) (bedgraph)" (see attached screenshot). I wonder if I should create a new issue to track this issue or if I should move this issue back to the To-Do column so the issue can be fixed before this story is closed. Jennifer, please let me know your thoughts on this when you are able.
Re-assign it to Jenny and move it to To-Do.
The image attached here points out that the file type is listed twice in the pulldown menu.
This may be related to the file extensions that are being saved. The pull down menu option is only an issue in windows. We've added screen shots from linux and mac.
So this is a two-fold issue.
- the pull down
- the file names for saved files
On Ashwini's Win8 laptop there were no duplicate file names in the drop down.
Moving to 'Needs 1st level review' so that someone with a Windows machine can look into this issue.
First level review done.
I reviewed this issue on my Windows 10 machine. I cannot see duplicate file names in the drop down. Refer the screenshot attached.
Issue looks fixed to me and is good to go for second level review.
I tested this on my mac, everything looks good. Files save with appropriate endings. There is no duplication of the file extension in the save-window pull down menu.
I also tested this on my Windows 7 laptop.
In IGB live (9.0.0 from bioviz.org) I cannot save a file at all. After I enter a file name and hit enter, I get an error message saying "Problem saving file".
In the pull down, there is no duplication of the file type in the live version.
In branch 1128, I can save a file and it saves with the appropriate name, but the file type in the pull down is duplicated.
I also checked out main master and went to a commit before 1128 was merged in. There, there was no duplication of the filename. That trait is introduced when 1128 gets merged in. It seems odd that we are doing first level review of a branch that has already been merged into main master. 
I don't know what version of Windows Mason uses for testing. It sounds like the issue appears in Windows 7, but not in Windows 8 (Ashwini's laptop) or Windows 10 (Deepti's laptop). And it does not appear in macOS 10.12.5 (my laptop) or linux (Jenn's laptop).
Which fork and which branch is this? Please add link.
I got it from fork:
bitbucket.org/jdaly8/integrated-genome-browser
branch name:
IGBF-1128
But I don't see that now on BitBucket.
I think we should move this issue to "Needs testing" because:
-**These changes have already been merged into lorainelab/integrated-genome-browser/master.**
-The main improvement (Files CAN BE saved and they save with the correct file extension) has been tested on several machines.
Downside:
There is a side-effect that the pull down menu shows the file extension twice. This side-effect only appears on some Windows computers. We can make a new issue for correcting this with appropriate priority. This new issue should be related to IGBF-1128. And whoever works on it needs to have easy access to a Windows 7 machine.
Since there is a side-affect that still needs to be addressed, and jumping from 1st level review to Needs Testing is unusual, I'm assigning this to Ann to make that judgement call.
Go ahead and move it to "Needs Testing" and re-assign to Mason
I tested this story today and it seems that the state is the same as my testing done on April 17, 2017; files are being properly saved as .bedgraph or .gr files on Windows and Mac, but on Windows the file extension is being duplicated in the file chooser's drop-down menu for file type. I looked at the live version (IGB 9.0.0) to see if this was occurring there and it is, meaning that the duplication of the file extension is not a result of any code change while fixing this issue, IGBF-1128. Since this is the case, and since everything is working as expected, I am closing this issue and creating IGBF-1162 to track the duplicate file extensions issue.
Edited abstractExportFileAction and UniFileFilter to resolve issue. Moving to 'needs testing'.