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  1. Jalview
  2. JAL-2246

Create suite of "Network" tests that verify fetched data is in an expected format

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    • Type: Task
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
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      Description

      Write tests that fetch a (hopefully stable) entry from a remote database and verify that Jalview can process it.
      These would be annotated (groups="Network") as distinct from our standalone "Functional" tests.
      The intention is to give early warning when remote services change behaviour.

      As for example lately (but not limited to):
      - format of ENA XML changed - Castor binding failed - unable to fetch EMBL sequence data
      - Ensembl gff changed from "transcript" to "mRNA" for transcript feature type in gene features

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2482 Error in the latest SIFTS Update - some residues' RESNUM are assigned "null" string

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2485 Exception while querying Uniprot via the REST API

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2254 Fetch DBRefs from EMBL gives Illegal Text data found as child of: ROOT

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

          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

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Created:
                Updated: