This project is mirrored from https://github.com/Ensembl/ensembl.git. Pull mirroring updated .
  1. 20 Jun, 2019 1 commit
  2. 17 Jun, 2019 2 commits
  3. 14 Jun, 2019 2 commits
  4. 05 Jun, 2019 1 commit
  5. 29 May, 2019 1 commit
    • Marek Szuba's avatar
      ENSCORESW-3148: update Coveralls URIs in the README · 68b8f997
      Marek Szuba authored
      The Coveralls URI need to contain the branch name for the badge to work,
      moreover URIs for GitHub repositories are (now?) different. The URIs use
      now both are what Coveralls Web site suggests and have been demonstrated
      to work in case of ensembl-xref.
      68b8f997
  6. 24 May, 2019 1 commit
    • Marek Szuba's avatar
      Travis: Add mysql to the list of services · a6ae7f55
      Marek Szuba authored
      Ubuntu Xenial, which is now being rolled out as the default Linux distro
      for Travis builds following the end of life of Ubuntu Trusty, does not
      start services such as MySQL unless told to. We use the default distro
      in our builds so we are likely to be affected.
      a6ae7f55
  7. 08 May, 2019 2 commits
  8. 12 Apr, 2019 1 commit
  9. 11 Apr, 2019 2 commits
  10. 02 Apr, 2019 1 commit
  11. 21 Mar, 2019 2 commits
  12. 20 Mar, 2019 2 commits
  13. 19 Mar, 2019 10 commits
  14. 18 Mar, 2019 12 commits
    • Marek Szuba's avatar
      95953fbe
    • Marek Szuba's avatar
    • Marek Szuba's avatar
      Patch test databases for RNAPRoduct tests · 733760f8
      Marek Szuba authored
      Apply patch_96_97_{c,d,e}, insert the necessary data into
      homo_sapiens/core.
      733760f8
    • Marek Szuba's avatar
      Schema updates · af5a5c4e
      Marek Szuba authored
      Three separate patches here:
      
      1. Create Create tables for RNAProduct. Basically renamed copies of
      Translation tables "translation" and "translation_attrib" plus a
      new column rnaproduct_type_id, complete with a corresponding table
      rnaproduct_type, which is used to distinguish between RNA-product
      types;
      
      2. Add type RNAProduct to object_xref.ensembl_object_type. This is
      needed to support e.g. miRBase xrefs for microRNAs;
      
      3. Add type rnaproduct to stable_id_event.type. This is needed to
      support mature RNA products in stable-id mapping.
      af5a5c4e
    • Marek Szuba's avatar
      RNAPRoduct: exon support · 734bf270
      Marek Szuba authored
      734bf270
    • Marek Szuba's avatar
      RNAProductAdaptor: exon support in storing · 473b3f1c
      Marek Szuba authored
      473b3f1c
    • Marek Szuba's avatar
      RNAProductAdaptor: exon support in retrieval · 9c4944b5
      Marek Szuba authored
      9c4944b5
    • Marek Szuba's avatar
      rnaProduct.t: partial compliance with perlcritic level 2 · 4760a398
      Marek Szuba authored
      Quote noisy strings properly + avoid double-sigil dereferences.
      4760a398
    • Marek Szuba's avatar
      rnaproduct exon tests · 3a075243
      Marek Szuba authored
      3a075243
    • Marek Szuba's avatar
      Annual copyright update · 370b4bca
      Marek Szuba authored
      370b4bca
    • Marek Szuba's avatar
      de2d6f02
    • Marek Szuba's avatar
      RNAProduct: implement synchronise_attributes() · b1c97544
      Marek Szuba authored
      Properties of specific types of mature RNA products such as microRNAs
      are stored in the database as attributes (so that we needn't add
      type-specific columns to the rnaproduct table) but have shorthand
      accessors such as MicroRNA::arm() backed by cache member variables
      in the API (for convenience and speed). In order for this to work
      properly we have to push possible changes to the cache variables back
      to attributes before they are stored in the database - which is what
      this method does.
      
      The synchronisation code itself is generic and has been implemented
      in the superclass. Specialisation is handled by class-specific mappings
      between member names and respective Attribute codes, provided
      by RNAProductTypeMapper.
      
      Limitations:
       - at present there can only be either zero or one target attribute;
         having many attributes with the same code results in an exception
         because we do not know which one(s) to update. In the future we might
         have to extend the mapping syntax to support multiple attributes, for
         now however (i.e. for microRNA arms) we do not need it;
       - chances are things will break badly if we fetch a MicroRNA object
         from the database, change the arm and push it back. Right now this is
         not a problem because RNAProducts do not support database updates at
         all, then again should we want to support them we will have to check
         how AttributeAdaptor handles updates of existing objects (as well as
         the same for DBEntryAdaptor, as a matter of fact).
      b1c97544