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  1. IGB
  2. IGBF-1414

Check that 2008 yeast genome synonyms are in species.txt and synonyms.txt

        Details

        • Story Points:
          0.25
        • Sprint:
          Fall 2018 Sprint 3

          Description

          • Find resource tab-delimited data files species.txt and synonyms.txt in the IGB code base
          • Check that they contain the following lines. If not, add them
          • Respect and preserve alphabetical order of entries in the file

          species.txt:
          Saccharomyces cerevisiae yeast S_cerevisiae sacCer

          synonyms.txt:
          S_cerevisiae_Jun_2008 sacCer2 SGD June 2008

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              relates to

              Task - A task that needs to be done. IGBF-1189 Add S. Cerevisiae June 2008 genome to IGB Quickload - User request

              • Major - Major loss of function.
              • Closed

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Link This issue relates to IGBF-1189 [ IGBF-1189 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                The entries present in synonyms.txt and species.txt are as follows:

                in species.txt :
                Saccharomyces cerevisiae Budding Yeast S_cerevisiae sacCer Saccharomyces_cerevisiae

                in synonyms.txt :
                S_cerevisiae_Jun_2008 sacCer2

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                stiwari8 Srishti Tiwari (Inactive) added a comment - The entries present in synonyms.txt and species.txt are as follows: in species.txt : Saccharomyces cerevisiae Budding Yeast S_cerevisiae sacCer Saccharomyces_cerevisiae in synonyms.txt : S_cerevisiae_Jun_2008 sacCer2
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] Needs 1st Level Review [ 10005 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ] Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Please add direct link to these files in BitBucket.

                For how to do this, see:

                example) https://bitbucket.org/user/repository/src/branch/path/file

                Show
                ann.loraine Ann Loraine added a comment - Please add direct link to these files in BitBucket. For how to do this, see: https://stackoverflow.com/questions/11692124/link-latest-file-on-bitbucket-git-repository example) https://bitbucket.org/user/repository/src/branch/path/file
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Hello Dr. Loraine,

                Please find below links of species.txt and synonyms.txt. Please note that these entries were already present.

                On line 131:
                https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/synonym-lookup/src/main/resources/species.txt

                On line 193:
                https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/synonym-lookup/src/main/resources/synonyms.txt

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Hello Dr. Loraine, Please find below links of species.txt and synonyms.txt. Please note that these entries were already present. On line 131: https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/synonym-lookup/src/main/resources/species.txt On line 193: https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/synonym-lookup/src/main/resources/synonyms.txt
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] Needs 1st Level Review [ 10005 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Needs 1st Level Review [ 10005 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18119 ] Fall 2019 Workflow Update [ 19946 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19946 ] Revised Fall 2019 Workflow Update [ 22067 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: