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  1. Bug Repository
  2. BUG-274 Loading local .CHP file throws error on Windows
  3. BUG-275

CHP legacy format file don't show up in table

          Details

          • Type: Sub-task
          • Status: Closed (View Workflow)
          • Priority: Minor
          • Resolution: Fixed
          • Labels:
            None

            Description

            If chp file throws error that it is in legacy format, the it won't show up in table.

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                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
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                  hiralv Hiral Vora (Inactive) created issue -
                  david David Norris (Inactive) made changes -
                  Field Original Value New Value
                  Assignee David Norris [ david ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited

                  Works fine. Use the attached file to test the legacy CHP type.

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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited Works fine. Use the attached file to test the legacy CHP type.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment ArabidopsisATH1-121502.CHP.gz [ 10585 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 6.7 [ 10040 ] Bug Repository [ 10030 ]
                  Key IGBB-262 BUG-275
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited

                  Show up in data management table on 7.0.0 (11884) Mac.

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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited Show up in data management table on 7.0.0 (11884) Mac.
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Assignee Fuquan Wang [ fwang4 ] Alyssa Gulledge [ alyssa ]
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-622 [ BUG-622 ]
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                  richard Richard Linchangco (Inactive) added a comment -

                  V.13526, Mac, Java 1.06.0_37

                  When uploading CHP legacy file, through 'File' > 'Open file…' or by simply dragging the file into the main viewer, window appears displaying 'ERROR: CHP file is in legacy format, cannot be loaded'

                  A track for the data DOES appears in the viewer as well as the 'Data Management Table'. Is this what this bug checks for?

                  Java console shows:

                  Parsing CHP file: /var/folders/_k/y1wr6vjs6rd4pqpznf1rc7h80000gn/T/ArabidopsisATH1-121502.CHP.gz8281635960027639029.tmp
                  CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@159dab43
                  Alg name: ExpressionStat
                  Alg version: 5.0
                  Assay type: 0
                  Chip type: ATH1-121501
                  Rows: 712, Columns: 712
                  Parent .cel file: ArabidopsisATH1-121502.CEL
                  Program ID: GeneChipAnalysis.GEBaseCall.1
                  number of probesets: 22810
                  Stopped loading, parsing Legacy CHP data only partially implemented!

                  -------------------------------------------------------
                  ERROR: CHP file is in legacy format, cannot be loaded
                  -------------------------------------------------------

                  Show
                  richard Richard Linchangco (Inactive) added a comment - V.13526, Mac, Java 1.06.0_37 When uploading CHP legacy file, through 'File' > 'Open file…' or by simply dragging the file into the main viewer, window appears displaying 'ERROR: CHP file is in legacy format, cannot be loaded' A track for the data DOES appears in the viewer as well as the 'Data Management Table'. Is this what this bug checks for? Java console shows: Parsing CHP file: /var/folders/_k/y1wr6vjs6rd4pqpznf1rc7h80000gn/T/ArabidopsisATH1-121502.CHP.gz8281635960027639029.tmp CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@159dab43 Alg name: ExpressionStat Alg version: 5.0 Assay type: 0 Chip type: ATH1-121501 Rows: 712, Columns: 712 Parent .cel file: ArabidopsisATH1-121502.CEL Program ID: GeneChipAnalysis.GEBaseCall.1 number of probesets: 22810 Stopped loading, parsing Legacy CHP data only partially implemented! ------------------------------------------------------- ERROR: CHP file is in legacy format, cannot be loaded -------------------------------------------------------
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Hiral - you know how Fuquan? or you put in the option that if you load a file with an error in it, IGB will offer to remove it for you? This is one of those cases, and in fact all 'legacy formats' that IGB cannot open should have IGB offer to remove this for you.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Hiral - you know how Fuquan? or you put in the option that if you load a file with an error in it, IGB will offer to remove it for you? This is one of those cases, and in fact all 'legacy formats' that IGB cannot open should have IGB offer to remove this for you.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r13619-13621.

                  It would do the following and cannot it be fixed at this moment.
                  1) This would get logged on console as error.
                  2) It would show two popups i.e. one to show message about legacy format and another to give an option to remove the file.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r13619-13621. It would do the following and cannot it be fixed at this moment. 1) This would get logged on console as error. 2) It would show two popups i.e. one to show message about legacy format and another to give an option to remove the file.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  This is an acceptable resolution

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                  alyssa Alyssa Gulledge (Inactive) added a comment - This is an acceptable resolution
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

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                    • Assignee:
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                      Reporter:
                      hiralv Hiral Vora (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: