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  1. Jalview
  2. JAL-1855

Update to latest version of ENA fetch service

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.0
    • Fix Version/s: 2.10.0
    • Component/s: data retrieval services
    • Labels:
      None

      Description

      From EBI support desk, 24/03/2015:
      As far as XML records from ENA go, we'd definitely recommend looking at the ENA service and making sure in your examples you're using an up to database and entry format that they support - they are more
      likely to make sure such requests are handled in a timely fashion.

      You can find examples at http://www.ebi.ac.uk/ena/browse/data-retrieval-rest
      which as you see, are now using emblxml-1.2 which if using dbfetch should be retieved via:

      http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_coding&id=aah29712&format=emblxml1.2&style=default

      (please also note emblcds is out of date - it's now ena_coding)

        Attachments

          Issue Links

          depends on

          Task - A task that needs to be done. JAL-2114 Parse GenBank/ENA location specifiers

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2113 Update EMBL fetch to parse version 1.2 of EMBLXML

          • Major - Major loss of function.
          • Closed
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-1919 import of 3D structure data from flat file and EMBL-PDBe via PDBx/mmCIF

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2027 EMBL parsing of CDS does not respect 'complement()' operator

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2748 Uniprot dbfetch returning errors

          • Major - Major loss of function.
          • Closed

          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

          Task - A task that needs to be done. JAL-2628 Review new Uniprot Proteins REST API

          • Major - Major loss of function.
          • In Progress

          Task - A task that needs to be done. JAL-2245 (unannounced) changes to ENA 1.2 XML format

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2113 Update EMBL fetch to parse version 1.2 of EMBLXML

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1856 Better error handling if DBRefFetcher fails

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

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: