1. 20 Feb, 2018 1 commit
  2. 09 Feb, 2018 1 commit
  3. 17 Nov, 2017 1 commit
  4. 05 Oct, 2017 2 commits
  5. 23 May, 2017 2 commits
    • Ryan Herbert's avatar
      task.py schedule_fuse only if needed · a3b9b6cb
      Ryan Herbert authored
      a3b9b6cb
    • Ryan Herbert's avatar
      file.py, task.py refactor schedule_fuse · 66a6f8ae
      Ryan Herbert authored
      The previous implementation of schedule fuse would only refuse a single
      sample_set and a single config. The goal of the function being to refuse
      all fused_files associated with a removed sequence_file, this was
      obviously not adequate.
      The function now takes a list of sample_set ids and a list of config ids
      in order to detect at one sequence file per sample_set and per config
      and refuse these results.
      66a6f8ae
  6. 19 May, 2017 1 commit
    • Ryan Herbert's avatar
      task.py add schedule_fuse · 822105da
      Ryan Herbert authored
      We now want to be able to schedule a fuse task in order to refuse a
      sample_set from which a sequence_file has been deleted.
      822105da
  7. 10 May, 2017 2 commits
  8. 17 Feb, 2017 1 commit
    • Ryan Herbert's avatar
      task.py fix mixcr deleted files issue · d6f7e591
      Ryan Herbert authored
      as mentioned in #2185 MiXCR runs would display deleted in the
      filenames/info field although the files did in fact exist.
      This was due to the wrong value being stored in the original_names field
      and therefore no match could be made with the sequence_file database
      entries.
      d6f7e591
  9. 24 Jan, 2017 1 commit
    • Mikaël Salson's avatar
      task.py: Get updated database version · ef909825
      Mikaël Salson authored
      This commit fixes the issue of having STOPPED jobs stuck in that state.
      I have assumptions on why the commit fixes the issue but no certainty.
      
      When entering the `schedule_run` controller, web2py loads the database
      in its current state. If someone then clicks on  to run the sample
      that is currently being preprocessed, the task will be put in STOPPED
      state to wait for the preprocess to finish.
      Once the preprocess is finished, we query the DB to know which
      tasks have been stopped. But as the DB has been loaded at the start
      of the controller, it is not up-to-date anymore and doesn't
      get all the STOPPED jobs. Doing a db.commit() just before
      querying the STOPPED jobs could refresh the loaded DB.
      
      Fix #2053.
      ef909825
  10. 12 Jan, 2017 1 commit
    • RyanHerb's avatar
      task.py add defs variable FUSE_SERVER · b3a20800
      RyanHerb authored
      the fuse server was referenced as localhost in the code. However, for
      the separation of reposibilities to work correctly in the docker
      installation it was necessary to add a variable in order to be able to
      reference the correct container for running custom fuse jobs
      b3a20800
  11. 14 Dec, 2016 2 commits
    • RyanHerb's avatar
      task.py fix some pre_process changes · f56f3c64
      RyanHerb authored
      In d67262 the DIR_PEAR variable was applied incorrectly.
      Instead, we now pass the pear directory to the pear.py script
      
      closes #2051
      f56f3c64
    • RyanHerb's avatar
      task.py defs.py.sample DIR_PEAR · d6726287
      RyanHerb authored
      Currently PEAR must be installed in a specific directory in order to be
      executed during pre-processes.
      Therefore adding a DIR_PEAR to the defs.py file will allow users to
      reference existing PEAR installations without the need for adding
      symbolic links to the vidjil installation.
      d6726287
  12. 03 Nov, 2016 1 commit
    • HERBERT Ryan's avatar
      task.py progressively delete fused_files · c23928ca
      HERBERT Ryan authored
      Fused_files were previously preserved from previous runs. However the
      decision has been made to no longer preserve these files as they do not
      serve the expected purpose.
      c23928ca
  13. 27 Oct, 2016 2 commits
  14. 21 Oct, 2016 1 commit
  15. 18 Oct, 2016 1 commit
    • Mikaël Salson's avatar
      models/task.py: Remove temporary fused file · 9c2f883a
      Mikaël Salson authored
      In case of success we can remove the file in the temporary directory as it is
      stored elsewhere through Web2py mechanism. Storing it twice was space
      consuming.
      
      We modifie the log message correspondingly so that it can display the real
      stored file.
      9c2f883a
  16. 07 Oct, 2016 1 commit
  17. 29 Sep, 2016 1 commit
    • Mikaël Salson's avatar
      models/task.py: run_copy takes name of the original filename · cf31f66a
      Mikaël Salson authored
      run_copy copied the sequence file into the result file. But the filename used was the internal Web2py filename (which is quite long).
      And it was reencoded for the results_file which lead to a very long filename which was likely to exceed the limit of the
      filename length.
      Now we take the original filename for the data file, which will lead to a much shorter encoded filename
      cf31f66a
  18. 23 Sep, 2016 1 commit
    • HERBERT Ryan's avatar
      task.py separate germline folder · 223c9a49
      HERBERT Ryan authored
      With the new vidjil packaging, the vidjil executable may not be situated
      in the vidjil directory. Therefore it has become necessary to add a
      separate DIR_GERMLINE variable to task.py which needs to be added to
      defs.py
      223c9a49
  19. 22 Sep, 2016 1 commit
  20. 19 Jul, 2016 1 commit
  21. 13 Jul, 2016 1 commit
  22. 08 Jul, 2016 1 commit
    • HERBERT Ryan's avatar
      default.py results_file.py task.py fix unfused runs · 2a954227
      HERBERT Ryan authored
      This commit resolves an issue where running a sequence file would not
      trigger the fuse on other sample sets.
      To achieve this fix, schedule run no longer depends on sample sets and
      database calls to fuse are done on each run_fuse
      2a954227
  23. 18 Jun, 2016 2 commits
  24. 14 May, 2016 2 commits
  25. 27 Apr, 2016 1 commit
  26. 22 Apr, 2016 2 commits
  27. 21 Apr, 2016 5 commits
  28. 18 Apr, 2016 1 commit