Details
-
Type:
Story
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.1.0 Major Release
-
Labels:
-
Story Points:2
-
Sprint:Winter 2018 Sprint 3, Spring 2019 Sprint 1
Description
Typical users need to open and load data from a variety of file formats. Often, files users try to open have problems that prevent IGB from reading them. Currently, users have a hard time understanding and debugging their files because IGB's error messages upon failure to open or load are confusing or inconsistent.
Let's implement error-handling code that is consistent across all files types and which provides the user with good information about what when wrong when IGB tries to open a file where the format does not fit the expectation.
Attachments
Issue Links
- relates to
-
IGBF-517 Add additional information about why a file is unable to load
-
- Closed
-
Activity
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Riddhi Jagdish Patil [ rpatil14 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Attachment | GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14242 ] |
| Attachment | GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14242 ] |
| Attachment | GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14243 ] |
| Attachment | GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14243 ] |
| Attachment | brokenWig-hasTwoFileTypes-actualExample.wig [ 14244 ] |
| Attachment | aligned.sorted.broken.sam [ 14245 ] | |
| Attachment | aligned.sorted.sam [ 14246 ] |
| Attachment | aligned.sorted.broken.sam_result.PNG [ 14248 ] | |
| Attachment | brokenbed_result.PNG [ 14249 ] | |
| Attachment | brokenWig-hasTwoFileTypes-actualExample_result.PNG [ 14250 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Riddhi Jagdish Patil [ rpatil14 ] |
| Attachment | brokenBed.bed [ 14251 ] |
| Attachment | Test_document_IGBF_1515.xlsx [ 14255 ] |
| Attachment | Test_document_IGBF_1515.xlsx [ 14255 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Needs 1st Level Review [ 10005 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Reviewing [ 10301 ] |
I have tested with three attached files. I have checked the code and everything is working as expected.
Please change the comment in following file and line.
File : core/genometry/src/main/java/com/affymetrix/genometry/util/ErrorHandler.java
Line : 130
Change text from "Add a link to hel page in case of error while loading a file" to "Add a link to help page in case of error while loading a file"
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Riddhi Jagdish Patil [ rpatil14 ] |
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
Corrected spelling error in ErroHandler.java file.
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Riddhi Jagdish Patil [ rpatil14 ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
I have checked the comment. It is now corrected.
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Riddhi Jagdish Patil [ rpatil14 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Riddhi Jagdish Patil [ rpatil14 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
Merged into master.
| Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Testing Windows: Working correctly
Windows testing successful
MacOS testing successful.
Linux testing successful.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Riddhi Jagdish Patil [ rpatil14 ] |
| Workflow | Loraine Lab Workflow [ 18231 ] | Fall 2019 Workflow Update [ 20009 ] |
| Workflow | Fall 2019 Workflow Update [ 20009 ] | Revised Fall 2019 Workflow Update [ 22136 ] |
I made a few changes to the error formatting: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/757/igbf-1515-2-additional-formatting-of-file/diff
Merged but not yet deployed to "early releases" on Bioviz.
Issue:- To provide more informative error message when a file cannot be opened in IGB
Solution:-
Provide meaningful message by fetching the root cause from the stack trace and provide a link to IGB help page
Files changed:-
core/genometry/src/main/java/com/affymetrix/genometry/util/ErrorHandler.java
core/igb/src/main/java/com/affymetrix/igb/view/load/GeneralLoadUtils.java
plugins/bam/src/main/java/org/lorainelab/igb/bam/SAM.java
Testing steps:-
(Error files used for testing are attached to the ticket)
Drag and drop a broken file into IGB get the informative message.
Test results:-
Please check the attached test results
Code changes:-
https://bitbucket.org/rpatil14/riddhifork-igb/branch/IGBF-1515#diff
Note:-
The error message displayed while loading a bed file does not have Arial font and is not in sync with the rest of the application. This issue is fixed with ticket
IGBF-1518