crunch_scripts/pgp-survey-import

   1 #!/usr/bin/env python
   2
   3 import arvados
   4 import string
   5 import json
   6 import UserDict
   7 import sys
   8
   9 this_job = arvados.current_job()
  10 this_task = arvados.current_task()
  11 this_job_input = this_job['script_parameters']['input']
  12
  13 out = arvados.CollectionWriter()
  14 out.set_current_file_name("arvados_objects.json")
  15 out.write("[\n")
  16 separator = ""
  17
  18 traits = {}
  19 done_bytes = 0
  20 done_ratio = 0
  21 for input_file in arvados.CollectionReader(this_job_input).all_files():
  22     for line_number, line in enumerate(input_file.readlines()):
  23
  24         done_bytes += len(line)
  25         new_done_ratio = 1.0 * done_bytes / input_file.size()
  26         if line_number == 2 or new_done_ratio - done_ratio > 0.05:
  27             sys.stderr.write("progress: %d%% after %d lines\n" % (int(done_ratio * 100), line_number+1))
  28             done_ratio = new_done_ratio
  29
  30         words = string.split(string.strip(line), "\t")
  31         if line_number == 0:
  32             headings = words
  33             for t in arvados.api('v1').traits().list(
  34                 where={'name':words},
  35                 limit=1000
  36                 ).execute()['items']:
  37                 traits[t['name']] = t
  38             for i, trait_name in enumerate(words[3:], start=3):
  39                 # find or create trait
  40                 if trait_name not in traits:
  41                     traits_match = arvados.api('v1').traits().list(
  42                         where={'name':trait_name}
  43                         ).execute()['items']
  44                     if len(traits_match) > 0:
  45                         traits[trait_name] = traits_match[0]
  46                     else:
  47                         traits[trait_name] = arvados.api('v1').traits().create(
  48                             trait={'name':trait_name}).execute()
  49                 out.write(separator)
  50                 out.write(json.dumps(traits[trait_name]))
  51                 separator = ",\n"
  52         else:
  53             huID_links_match = arvados.api('v1').links().list(
  54                 where={'link_class':'identifier','name':words[0]}
  55                 ).execute()['items']
  56             if len(huID_links_match) > 0:
  57                 human_uuid = huID_links_match[0]['head_uuid']
  58             else:
  59                 human = arvados.api('v1').humans().create(
  60                     body={}
  61                     ).execute()
  62                 huID_link = arvados.api('v1').links().create(
  63                     body={
  64                         'link_class':'identifier',
  65                         'name':words[0],
  66                         'head_kind':'arvados#human',
  67                         'head_uuid':human['uuid']
  68                         }
  69                     ).execute()
  70                 human_uuid = human['uuid']
  71             human_trait = {}
  72             for t in arvados.api('v1').links().list(
  73                 limit=10000,
  74                 where={
  75                     'tail_uuid':human_uuid,
  76                     'tail_kind':'arvados#human',
  77                     'head_kind':'arvados#trait',
  78                     'link_class':'human_trait',
  79                     'name':'pgp-survey-response'
  80                     }
  81                 ).execute()['items']:
  82                 human_trait[t['head_uuid']] = t
  83             for i, trait_value in enumerate(words[3:], start=3):
  84                 trait_uuid = traits[headings[i]]['uuid']
  85                 if trait_uuid in human_trait:
  86                     trait_link = human_trait[trait_uuid]
  87                     if trait_link['properties']['value'] != trait_value:
  88                         # update database value to match survey response
  89                         trait_link['properties']['value'] = trait_value
  90                         arvados.api('v1').links().update(
  91                             uuid=trait_link['uuid'],
  92                             body={'properties':trait_link['properties']}
  93                             ).execute()
  94                     out.write(",\n")
  95                     out.write(json.dumps(trait_link))
  96                 elif trait_value == '':
  97                     # nothing in database, nothing in input
  98                     pass
  99                 else:
 100                     trait_link = {
 101                         'tail_uuid':human_uuid,
 102                         'tail_kind':'arvados#human',
 103                         'head_uuid':traits[headings[i]]['uuid'],
 104                         'head_kind':'arvados#trait',
 105                         'link_class':'human_trait',
 106                         'name':'pgp-survey-response',
 107                         'properties': { 'value': trait_value }
 108                         }
 109                     arvados.api('v1').links().create(
 110                         body=trait_link
 111                         ).execute()
 112                     out.write(",\n")
 113                     out.write(json.dumps(trait_link))
 114
 115 out.write("\n]\n")
 116 this_task.set_output(out.finish())