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  1. Jalview
  2. JAL-3692

Update ENA endpoint for EMBL/CDS sequence retrieval

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.11.1.0
    • Fix Version/s: 2.11.1.1
    • Component/s: data retrieval services
    • Labels:
      None
    • Sprint:
      2.11.1.1 Release

      Description

      The endpoint we currently use for fetching EMBL[CDS] is being retired on 5th August.
      https://www.ebi.ac.uk/about/news/service-news/retirement-old-ena-browser-5th-august-2020
      The path is hard coded in EBIFetchClient.buildUrl().

        Attachments

        1. ENAFeatureTable_10_9.html
          179 kB
        2. ENASequenceUserManaul_143.txt
          54 kB
        3. X53828.xml.txt
          5 kB
        4. X53828.1.embl.txt
          5 kB

          Issue Links

          related with

          Task - A task that needs to be done. JAL-3722 Comprehensive testing of ENA and GenBank flatfile

          • Critical - Crashes, loss of data, severe memory leak.
          • Open

          Task - A task that needs to be done. JAL-2138 Remove EMBLCDS as a database source

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

          New Feature - A new feature of the product, which has yet to be developed. JAL-1260 Import genbank file

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: