1. 15 Oct, 2018 1 commit
  2. 11 Jul, 2018 1 commit
  3. 26 Jun, 2018 2 commits
  4. 21 Mar, 2018 7 commits
    • Ryan Herbert's avatar
    • Ryan Herbert's avatar
      major refactor to use sample_set_id everywhere. · cc96b572
      Ryan Herbert authored
      There were some places where the patient/run/generic id was used (such
      as for permissions) but we want to migrate to full-on sample_set
      management, so we can display the sample_set id to users.
      cc96b572
    • Ryan Herbert's avatar
      sample set models removed unused get_add_route · fe5ffdfa
      Ryan Herbert authored
      sample sets now share a single add/edit route.
      fe5ffdfa
    • Ryan Herbert's avatar
      generic set add/edit form · cfd9d6ed
      Ryan Herbert authored
      moves the new patient/form and patient/submit routes to the sample_set
      controller and removes any add/edit routes from all set controllers.
      The same goes for the templates.
      
      Also allows the inclusion of different types of sets in a single form.
      
      For this, the sample_set/form.html template includes patials for each
      set type.
      
      See #2878
      
      One form to rule them all, one form the find them, one form to bring
      them all, and in the template bind them.
      cfd9d6ed
    • Ryan Herbert's avatar
      sample set models dict compatibility · 69bac869
      Ryan Herbert authored
      web2py Row objects are compatible with dot notation and getitem
      notation, so dot notation is preferable in that case. However, we want
      to be able to use dicts built from our json forms, so we need to use
      getitem notation everywhere.
      69bac869
    • Ryan Herbert's avatar
      refactor id strings and id extraction · 32fd3aca
      Ryan Herbert authored
      For adding files to sample_sets. Alters the existing id strings by
      removing dates.
      I wanted to clean things up a little and alter the way id_strings are
      created/decoded before making them a little more flexible in order to
      produce more aesthetically pleasing id_strings.
      32fd3aca
    • Ryan Herbert's avatar
      split add utils display_names · a5b87796
      Ryan Herbert authored
      this is a refactor of anon_names. We want to use anon_names elsewhere
      but without the id when the user is admin. display_names replaces
      anon_names and behaves as anon_names did before.
      a5b87796
  5. 08 Mar, 2018 1 commit
  6. 23 Feb, 2018 1 commit
  7. 22 Feb, 2018 2 commits
    • Ryan Herbert's avatar
      new stats view and results_file export · 509649f8
      Ryan Herbert authored
      adds a simple sample_set_list that the user can select in order to
      export all results_files for a given config that are associated to the
      selected sample_sets.
      The files are stored in a zip file along with a json file containing
      some metadata.
      509649f8
    • Ryan Herbert's avatar
      refactor set models filter method · 04a8695e
      Ryan Herbert authored
      We want to build a modular search string so we can have a reduced list
      of columns.
      04a8695e
  8. 18 Nov, 2017 1 commit
  9. 05 Oct, 2017 8 commits
  10. 14 Jun, 2017 1 commit
    • Ryan Herbert's avatar
      models/* add get_id_string method · c4fa34e8
      Ryan Herbert authored
      These methods are designed to generate the strings that are used in the
      add and edit file controllers. Since the code was duplicated, this
      should help clean the code base a little
      c4fa34e8
  11. 16 May, 2017 4 commits
  12. 02 Apr, 2017 1 commit
    • Mikaël Salson's avatar
      SampleSet.py: Function to get the sample name · f144ac81
      Mikaël Salson authored
      We would probably benefit from a class offering such functions.
      The class would have a constructor relying only on the sample set ID
      and would not need anything else.
      
      The SampleSet class doesn't behaves in this fashion as this would not
      be efficent enough (for the patient list for instance, see #2295).
      However in some cases we would need a more flexible way of accessing
      a sample set, even it is slower.
      f144ac81
  13. 23 Mar, 2017 2 commits
  14. 22 Mar, 2017 1 commit
  15. 17 Mar, 2017 1 commit
    • Ryan Herbert's avatar
      SampleSet.py manage missing attribute correctly · fcf8d7e7
      Ryan Herbert authored
      Two methods were managing missing attributes incorrectly. Therefore when
      using the helper classes without having loaded some of the information
      such as the sequence_count would raise an AttributeError exception.
      fcf8d7e7
  16. 16 Mar, 2017 2 commits
  17. 13 Jan, 2017 1 commit
  18. 07 Dec, 2016 1 commit
  19. 01 Dec, 2016 2 commits