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  1. 06 Dec, 2018 1 commit
  2. 12 Nov, 2018 1 commit
  3. 07 Nov, 2018 1 commit
  4. 06 Nov, 2018 1 commit
  5. 26 Oct, 2018 1 commit
  6. 25 Oct, 2018 4 commits
  7. 24 Oct, 2018 6 commits
  8. 18 Oct, 2018 2 commits
  9. 17 Oct, 2018 1 commit
  10. 16 Oct, 2018 1 commit
  11. 15 Oct, 2018 3 commits
    • Wojtek Bazant's avatar
      Fix bug: use return instead of next · 4ab71f7e
      Wojtek Bazant authored
      return goes back one frame up the stack
      next goes back to the closest frame on the stack that supports the
      operation (that is close enough in RefSeqGPFFParser alone)
      It works unless I subclass create_xrefs, and then my Hive workers die:
      Lost control. Check your Runnable for loose 'next' statements that are
      not part of a loop       WORKER_ERROR
    • Wojtek Bazant's avatar
      C. elegans specific parsing of RefSeq_dna file · 7d6346f7
      Wojtek Bazant authored
      - New xref: to a WormBase CDS feature
      - Modify WormbaseCElegansRefSeqGPFFParser to serve both kinds of files
      - extract a utility method from RefSeqGPFFParser
      - xref_config.ini stanza for wormbase_cds
      - tests for new functionality
    • Wojtek Bazant's avatar
      C. elegans references use WormBase mapping to INSDC protein ids · d66449b6
      Wojtek Bazant authored
      - maintain naming convention: WormBase specific stuff says Wormbase at the front
      - rewrite WormBaseDirectParser
      - WormBaseDirectParser populates protein_ids
      - superclass method to make dependent protein_ids as parent
      - tap into UniProtParser
        + also skip EMBL scaffold ids (we can't reliably assign them)
      - tap into RefSeqGPFFParser
        + extract a method
      - tests for new stuff
        + add %args to parametrise test_parser
      Benefits for RefSeqGPFFParser:
      RefSeq proteins have coordinates as part of their identity, so we
      can't reliably sequence match them, we will also pick up all paralogs.
      This change fixes this spurious mapping.
      Benefits for UniProtParser:
      Not the above: UniProt entries are not tied to coordinates so all
      paralogs map to the same entry. We can handle versioning and updates
      a bit better: if WormBase updates an entry and a protein id changes but
      UniProt doesn't reflect this yet, with the change we will still pick up
      the UniProt entry although we can't sequence match any more.
  12. 01 Oct, 2018 4 commits
  13. 26 Sep, 2018 7 commits
  14. 25 Sep, 2018 1 commit
    • Marek Szuba's avatar distinguish between submitter and assignee · 98f8ba25
      Marek Szuba authored
      Useful under the circumstance when the person running the script is not
      in fact the RelCo for the next release, as it has already been the case
      before. Saves one having to manually reassign all the newly created
      tickets to the actual RelCo. Conversely, if it is the same person just
      omit the new argument and the RelCo user name will be used to connect to
      Note that the function validating user names is only applied to RelCo
      ones. This is intentional, JIRA itself will complain if the submitter is
      not authorised to create ENSCORESW tickets.
  15. 24 Sep, 2018 5 commits
  16. 11 Sep, 2018 1 commit