[IGBF-1515] Improve feedback when files can't be opened - JIRA UNCC

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Type: Story
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.0 Major Release
Labels:
- Intermediate

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.

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aligned.sorted.broken.sam
2 kB
07/Feb/19 11:13 AM
aligned.sorted.broken.sam_result.PNG
22 kB
07/Feb/19 5:18 PM
aligned.sorted.sam
2 kB
07/Feb/19 11:13 AM
brokenbed_result.PNG
20 kB
07/Feb/19 5:18 PM
brokenBed.bed
0.2 kB
07/Feb/19 5:21 PM
brokenWig-hasTwoFileTypes-actualExample_result.PNG
22 kB
07/Feb/19 5:18 PM
brokenWig-hasTwoFileTypes-actualExample.wig
3.38 MB
07/Feb/19 10:49 AM

Issue Links

relates to

IGBF-517 Add additional information about why a file is unable to load

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Riddhi Jagdish Patil (Inactive) added a comment - 07/Feb/19 5:06 PM - edited

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~~

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Riddhi Jagdish Patil (Inactive) added a comment - 07/Feb/19 5:06 PM - edited 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

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Riddhi Jagdish Patil (Inactive) added a comment - 14/Feb/19 5:11 PM

Windows testing successful

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Riddhi Jagdish Patil (Inactive) added a comment - 14/Feb/19 5:11 PM Windows testing successful

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Jill Jenkins (Inactive) added a comment - 14/Feb/19 5:11 PM

MacOS testing successful.

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Jill Jenkins (Inactive) added a comment - 14/Feb/19 5:11 PM MacOS testing successful.

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Sai Charan Reddy Vallapureddy added a comment - 14/Feb/19 6:01 PM

Linux testing successful.

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Sai Charan Reddy Vallapureddy added a comment - 14/Feb/19 6:01 PM Linux testing successful.

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Nowlan Freese added a comment - 25/Nov/19 9:53 AM

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

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Nowlan Freese added a comment - 25/Nov/19 9:53 AM 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

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Ann Loraine added a comment - 25/Nov/19 9:56 AM

Merged but not yet deployed to "early releases" on Bioviz.

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Ann Loraine added a comment - 25/Nov/19 9:56 AM Merged but not yet deployed to "early releases" on Bioviz.

Improve feedback when files can't be opened

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