Class: Aqueduct::Wrappers::I2b2

Inherits:
Object
  • Object
show all
Includes:
Aqueduct::Wrapper
Defined in:
lib/aqueduct/wrappers/i2b2.rb

Constant Summary collapse

DOMAIN = 
'i2b2demo'

Instance Method Summary collapse

Instance Method Details

#concept_tables(query_concept) ⇒ Object 



61
62
63
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 61

def concept_tables(query_concept)
  { result: [], error: '' }
end

#conditions(query_concepts) ⇒ Object 



65
66
67
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 65

def conditions(query_concepts)
  { conditions: "#{query_concepts.collect{|qc| qc.id}}", error: '' }
end

#connect ⇒ Object

TODO: Update i2b2 connect to make sure the server is up and running



110
111
112
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 110

def connect
  true
end

#count(query_concepts, conditions, tables, join_conditions, concept_to_count) ⇒ Object 



53
54
55
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 53

def count(query_concepts, conditions, tables, join_conditions, concept_to_count)
  get_total_count(query_concepts.find_all_by_id(eval(conditions)))
end

#external_concept_information(external_key = '') ⇒ Object 



21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 21

def external_concept_information(external_key = '')
  error = ''
  result = {}

  service_url = '/i2b2/rest/OntologyService/getTermInfo'

  xml = ::Builder::XmlMarkup.new
  xml.instruct! :xml, standalone: 'yes'
  xml.tag!("ns3:request", "xmlns:ns3" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
                          "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
                          "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/plugin/") do |req|
    req.message_header do |mhr|
      mhr << message_header(service_url, 'i2b2 Ontology', 1.6, 'i2b2 Hive',
                                         'Ontology Cell', 1.6, 'i2b2 Hive')
    end
    req.request_header do |rqh|
      rqh.result_waittime_ms 180000
    end
    req.message_body do |mgb|
      mgb.tag!('ns4:get_term_info', "blob" => "true", "type" => "core", "synonyms" => "true", "hiddens" => "true") do |gti|
        gti.tag!('self') do |sef|
          sef.text! external_key
        end
      end
    end
  end

  result_hash = process_concepts(send_message(xml.target!, service_url))
  result = result_hash[:result].first unless result_hash[:result].first.blank?
  { result: result, error: result_hash[:error] }
end

#external_concepts(folder = '', search_term = '') ⇒ Object 



17
18
19
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 17

def external_concepts(folder = '', search_term = '')
  search_term.blank? ? get_concepts(folder) : search_for_term(folder, search_term)
end

#query(sql_statement) ⇒ Object 



69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 69

def query(sql_statement)
  # result = [[['cname', 'cname2', 'cname3', 'cname4'],[1,2,3,4],[5,nil,7,8]],2]
  result = [[]]

  concept_list = []
  # TODO: Replace this with query_concepts (pass in query concepts initially?)

  query_concepts = QueryConcept.find_all_by_id(eval(sql_statement))


  result_hash = get_all_covariates(query_concepts)

  result = result_hash[:result]
  error = result_hash[:error]

  # THIS WORKS! (For limited ors and non complex things)
  # query_concepts.each_with_index do |query_concept, index|
  #   concept_list << { key: query_concept.external_key, right_operator: query_concept.right_operator, negated: query_concept.negated }
  # end
  #
  # conditions = query_definition(concept_list)
  #
  # patient_data = run_query_get_patient_data(conditions)
  #
  # if patient_data.first and patient_data.first[1]
  #   all_concepts = patient_data.first[1].keys
  #   result[0] = ['patient_id'] + all_concepts
  # end
  #
  # patient_data.each_pair do |patient_id, value_hash|
  #   row_data = [patient_id]
  #   all_concepts.each do |concept|
  #     row_data << value_hash[concept][:value]
  #   end
  #   result << row_data
  # end

  [result, result.size]
end

#use_sql? ⇒ Boolean

Returns:

  • (Boolean) 


57
58
59
 
# File 'lib/aqueduct/wrappers/i2b2.rb', line 57

def use_sql?
  false
end