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  1. 12 Feb, 2019 13 commits
  2. 15 Jan, 2019 4 commits
  3. 14 Jan, 2019 4 commits
  4. 13 Jan, 2019 1 commit
  5. 11 Jan, 2019 4 commits
    • Mark McDowall's avatar
      Removed legacy warn function · a1eb705d
      Mark McDowall authored
    • Mark McDowall's avatar
    • Marek Szuba's avatar
    • Marek Szuba's avatar
      dbConnection.t: do not use $dbh->ping() to check if disconnected from DB · b11de370
      Marek Szuba authored
      A bugfix implemented in DBD::mysql between 4.049 and 4.050 means that
      pinging a MySQL server now implicitly reestablishes the connection if
      down for whatever reason. Moreover, it is not clear from DBI
      documentation whether ping() is supposed to check if the connection to
      the database was open before calling it or not (it says "if the database
      server is still running and the connection to it is still working",
      which may well mean the _network_ connection between the client and the
      server rather than an open _database_ connection) and the behaviour of
      specific implementations varies. For instance:
       - DBD::Oracle: according to documentation it returns "either 0,
         indicating that the connection is no longer valid, or 1 indicating
         the connection is valid", under the bonnet it calls either OCIPing()
         (if available) or OCIServerVersion(). In light of the facts both of
         these methods take a service-context handle as an argument and that
         disconnect() calls OCIServerDetach(), which quite thoroughly releases
         resources allocated to the database client, it is likely ping() will
         return 0 if disconnected;
       - DBD::Pg: according to documentation it checks "if there is a
         working connection to an active database server", the code under
         the bonnet is non-trivial but the module's test suite indicates
         ping() is supposed to return 0 after disconnect();
       - DBD::SQLite: according to documentation it checks "if the
         database connection is active", under the bonnet seems to rely on
         the "Active" flag (see below);
       - finally, DBD::mysql - documentation simply says "this can be used to
         ping the server" and under the bonnet the module explicitly attempts
         to reconnect to the database, which only did not happen due to the
         aforementioned bug.
      In light of the above, we now check the "Active" attribute of the
      database handle to check if we are still connected. According to DBI
      documentation, "the exact meaning of active is somewhat vague at the
      moment. For a database handle it typically means that the handle is
      connected to a database ($dbh->disconnect sets Active off)"; the latter
      is indeed the case for all four DBD modules mentioned above.
      This fixes dbConnection.t test failures when running with
      Note that there are still some occurrences of ping() in the test file,
      however in the remaining cases it is called as a method of
      $dbc->db_handle rather than of $dbh. These should in theory be one and
      the same but just to be extra careful, we will take care of those
  6. 10 Jan, 2019 3 commits
  7. 04 Jan, 2019 2 commits
  8. 02 Jan, 2019 2 commits
    • Tiago Grego's avatar
      Yearly copyright update · a8c451eb
      Tiago Grego authored
    • Wojtek Bażant's avatar
      Document a feature: update() removes web_data · 90186c04
      Wojtek Bażant authored
      I call update() to populate analysis descriptions, from a script `ensembl_genomes/eg-pipelines/scripts/production_db/`. I found this when I was searching why `analysis_description.web_data` wasn't populated in WormBase ParaSite. Ensembl probably populates `analysis_description.web_data` differently, and has it working.
       As far as I see the code has been like that for a long time (2 years?), and there's some special behaviour and disclaimers about this field which I don't understand. I also don't really understand the consequences of making the column populated again. So I'm calling it a feature instead of a bug.
      @nerdstrike you might know what to do with it!
  9. 23 Dec, 2018 1 commit
  10. 19 Dec, 2018 6 commits