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  11. 12 Dec, 2007 1 commit
  12. 11 Dec, 2007 1 commit
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  16. 25 Oct, 2007 2 commits
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  19. 24 Sep, 2007 1 commit
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  22. 02 Jul, 2007 1 commit
  23. 18 Jun, 2007 2 commits
  24. 15 Jun, 2007 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Change to the load_all() method: · 2285d12f
      Andreas Kusalananda Kähäri authored
          Allow aliases to also be specified in the 'default' section, but
          require that there must also be a 'species' setting in the same
          section.  Aliases will never be installed if there is no 'speices'
          setting in the current section.  The 'species' section may be
          inherited from the 'default' section.
      
          Example:
      
          [default]
          host    = db.example.com
          user    = anonymous
          species = Human
          alias   = H_Sapiens
          alias   = Homo_Sapiens
          alias   = Me
      
          [my_core_db]
          group   = core
          dbname  = homo_sapiens_core_45_36g
      
          [my_estgene_db]
          group   = estgene
          dbname  = homo_sapiens_estgene_29_35b
      2285d12f
  25. 14 Jun, 2007 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Allow the registry to load ini-files with load_all(). · 96c9ac3a
      Andreas Kusalananda Kähäri authored
      The Registry will try to load the specified file (specified by argument
      to the method load_all(), in the envrionment variable ENSEMBL_REGISTRY,
      or the file '~/.ensembl_init', as before) as an ini-file.  If this fails
      due to the file having the wrong format, the code reverts to the old
      behaviour of using require() on the same file.
      
      This is an example of a simple ini-file.  There is no check to see
      that e.g. 'dbname' is actually present or to avoid calling the adaptor
      initialization routines with unnecessary parameters (we trust the user
      to get this right).  The correct adaptor is chosen by peeking at the
      'group' setting.
      
      
      ; Simple Ensembl config file example
      
      ; The 'default' section is special and its settings will be implicit for
      ; all other sections in this file but may be overridden by individual           ; sections.  There should be no 'alias' settings in the 'default'
      ; section.
      
      [default]
      user    = anonymous
      host    = ensembldb.ensembl.org
      group   = Core
      
      [the_human_db]
      species = Human
      dbname  = homo_sapiens_core_45_36g
      alias   = mary
      alias   = john
      
      [the_mouse_db]
      species = Mouse
      dbname  = mus_musculus_core_45_36f
      alias   = minnie
      alias   = mickey
      
      ; Configuration ends here
      96c9ac3a
  26. 30 May, 2007 1 commit
  27. 29 May, 2007 1 commit
  28. 26 Apr, 2007 1 commit
  29. 20 Apr, 2007 2 commits
  30. 17 Apr, 2007 1 commit
  31. 06 Mar, 2007 1 commit