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  1. IGB
  2. IGBF-1515

Improve feedback when files can't be opened

    Details

    • 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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          Issue Links

            Activity

            aloraine Ann Loraine created issue -
            aloraine Ann Loraine made changes -
            Field Original Value New Value
            Link This issue relates to IGBF-517 [ IGBF-517 ]
            aloraine Ann Loraine made changes -
            Rank Ranked higher
            aloraine Ann Loraine made changes -
            Sprint Winter 2018 Sprint 3 [ 58 ] Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ]
            aloraine Ann Loraine made changes -
            Rank Ranked higher
            aloraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Assignee Riddhi Jagdish Patil [ rpatil14 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            nfreese Nowlan Freese made changes -
            Attachment GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14242 ]
            nfreese Nowlan Freese made changes -
            Attachment GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14242 ]
            nfreese Nowlan Freese made changes -
            Attachment GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14243 ]
            nfreese Nowlan Freese made changes -
            Attachment GSM1163096_H3K27ac_ESC_Rep_1_JW-H14c_SHORT.wig [ 14243 ]
            nfreese Nowlan Freese made changes -
            nfreese Nowlan Freese made changes -
            Attachment aligned.sorted.broken.sam [ 14245 ]
            Attachment aligned.sorted.sam [ 14246 ]
            Hide
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment - - 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

            Show
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment - - 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
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Assignee Riddhi Jagdish Patil [ rpatil14 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Attachment brokenBed.bed [ 14251 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Attachment Test_document_IGBF_1515.xlsx [ 14255 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Attachment Test_document_IGBF_1515.xlsx [ 14255 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Needs 1st Level Review [ 10005 ] Testing In Progress [ 10003 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Testing In Progress [ 10003 ] Reviewing [ 10301 ]
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            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"

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - 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"
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ] Riddhi Jagdish Patil [ rpatil14 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Reviewing [ 10301 ] Open [ 1 ]
            Hide
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment -

            Corrected spelling error in ErroHandler.java file.

            Show
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment - Corrected spelling error in ErroHandler.java file.
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Status Open [ 1 ] Needs 1st Level Review [ 10005 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Assignee Riddhi Jagdish Patil [ rpatil14 ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Status Ready for Pull Request [ 10304 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            I have checked the comment. It is now corrected.

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - I have checked the comment. It is now corrected.
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ] Riddhi Jagdish Patil [ rpatil14 ]
            Show
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment - Pull request submitted:- https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/666/igbf-1515-improve-feedback-when-files-cant/diff
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            rpatil14 Riddhi Jagdish Patil (Inactive) made changes -
            Assignee Riddhi Jagdish Patil [ rpatil14 ]
            aloraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            aloraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            aloraine Ann Loraine added a comment -

            Merged into master.

            Show
            aloraine Ann Loraine added a comment - Merged into master.
            aloraine Ann Loraine made changes -
            Status Reviewing Pull Request [ 10303 ] Needs Testing [ 10002 ]
            aloraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            Jill Jill Jenkins (Inactive) made changes -
            Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
            Hide
            karthik Karthik Raveendran added a comment -

            Testing Windows: Working correctly

            Show
            karthik Karthik Raveendran added a comment - Testing Windows: Working correctly
            Hide
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment -

            Windows testing successful

            Show
            rpatil14 Riddhi Jagdish Patil (Inactive) added a comment - Windows testing successful
            Hide
            Jill Jill Jenkins (Inactive) added a comment -

            MacOS testing successful.

            Show
            Jill Jill Jenkins (Inactive) added a comment - MacOS testing successful.
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            Linux testing successful.

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - Linux testing successful.
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Resolution Done [ 10000 ]
            Status Testing In Progress [ 10003 ] Closed [ 6 ]
            nfreese Nowlan Freese made changes -
            Assignee Riddhi Jagdish Patil [ rpatil14 ]
            aloraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 18231 ] Fall 2019 Workflow Update [ 20009 ]
            aloraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 20009 ] Revised Fall 2019 Workflow Update [ 22136 ]
            Show
            nfreese Nowlan Freese added a comment - 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
            Hide
            aloraine Ann Loraine added a comment -

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

            Show
            aloraine Ann Loraine added a comment - Merged but not yet deployed to "early releases" on Bioviz.

              People

              • Assignee:
                rpatil14 Riddhi Jagdish Patil (Inactive)
                Reporter:
                aloraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                6 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: