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    • 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
    • Marek Szuba's avatar
      MicroRNA: having multiple mirna_arms in the DB is now fatal · 8b4b7967
      Marek Szuba authored
      On the one hand there seems to be no good reason for a MicroRNA object
      having multiple arm attributes, on the other hand simply taking the
      first one in the event of it happening may not even return the same
      value every time (it depends on a lot of factors, from the
      implementation details of AttributeAdaptor up to and including the
      underlying database system). There was a warning but who reads those
      anyway. Just throw an exception instead, if someone decides to allow
      such a case they can always catch it.
      8b4b7967
    • Marek Szuba's avatar