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  1. Jalview
  2. JAL-2656

More robust recognition of GZipped files - for local files and data retrieved via URL

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.1.1, 2.11.2.0
    • Component/s: None
    • Labels:
      None
    • Sprint:
      2.11.1.1 Release

      Description

      Jalview can read gzipped streams - either from local file, URL or otherwise, but it needs to recognize the stream first.

      The URL Gzip stream recognition looks for a .gz suffix on the URL - this is fragile, and doesn't work with - for example, Rfam's Gzipped Stockholm file URLs:
      http://rfam.xfam.org/family/RF00014/alignment/stockholm?gzip=1&download=1
      These download as a .gz file (the browser recognizes this somehow) but Jalview throws a 'File format not recognized' error.

        Attachments

          Issue Links

          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3698 Data fetched via URL could be named according to Content-Disposition header

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3615 xfam accession fetcher should employ .gz download endpoints

          • Major - Major loss of function.
          • Closed
          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-3744 Cannot read Gzip file in JalviewJS

          • Blocker - Blocks development and/or testing work, production could not run.
          • Being tested
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-3699 Loading a gzipped file and saving it leaves the new file uncompressed

          • Major - Major loss of function.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-2425 Pfam seed and full alignment retrieval does not have alignment metadata

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

            Activity

              People

              Assignee:
              soares Ben Soares
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: