Class: HQMF::ValueSet::Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/hqmf-parser/value_sets/value_set_parser.rb

Constant Summary collapse

GROUP_CODE_SET = 
"GROUPING"
ORGANIZATION_TITLE = 
"Value Set Developer"
OID_TITLE = 
"Value Set OID"
CONCEPT_TITLE = 
"Value Set Name"
CATEGORY_TITLE = 
"QDM Category"
CODE_SET_TITLE = 
"Code System"
VERSION_TITLE = 
"Code System Version"
CODE_TITLE = 
"Code"
DESCRIPTION_TITLE = 
"Descriptor"
CODE_SYSTEM_NORMALIZER = 
{
  'ICD-9'=>'ICD-9-CM',
  'ICD-10'=>'ICD-10-CM',
  'HL7 (2.16.840.1.113883.5.1)'=>'HL7'
}
IGNORED_CODE_SYSTEM_NAMES = 
['Grouping', 'GROUPING' ,'HL7', "Administrative Sex"]

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Parser

Returns a new instance of Parser.



29
30
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 29

def initialize()
end

Class Method Details

.get_format(file_path) ⇒ Object 



108
109
110
111
112
113
114
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 108

def self.get_format(file_path)
  if file_path =~ /xls$/
    :xls
  elsif file_path =~ /xlsx$/
    :xlsx
  end
end

Instance Method Details

#adopt_orphan(orphan) ⇒ Object 



78
79
80
81
82
83
84
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 78

def adopt_orphan(orphan)
  parent = orphan.dup
  parent["code_sets"] = [orphan]
  parent.delete("codes")
  parent.delete("code_set")
  parent
end

#cells_to_hashs_by_oid(array) ⇒ Object

take an excel matrix array and turn it into an array of db models



87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 87

def cells_to_hashs_by_oid(array)
  a = Array.new(array)                  # new variable for reentrant
  headers = a.shift.map {|i| i.to_s }   # because of this shift
  string_data = a.map {|row| row.map {|cell| cell.to_s } }
  array_of_hashes = string_data.map {|row| Hash[*headers.zip(row).flatten] }

  by_oid = {}
  array_of_hashes.each do |row|
    entry = convert_row(row)
    
    existing = by_oid[entry["oid"]]
    if (existing)
      existing["codes"].concat(entry["codes"])
    else
      by_oid[entry["oid"]] = entry
    end
  end
    
  by_oid
end

#collapse_groups(by_oid_ungrouped) ⇒ Object 



39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 39

def collapse_groups(by_oid_ungrouped)
    
  final = []
    
  # select the grouped code sets and fill in the children... also remove the children that are a
  # member of a group.  We remove the children so that we can create parent groups for the orphans
  (by_oid_ungrouped.select {|key,value| value["code_set"].upcase == GROUP_CODE_SET}).each do |key, value|
    # remove the group so that it is not in the orphan list
    by_oid_ungrouped.delete(value["oid"])
    codes = []
    value["codes"].each do |child_oid|
#            codes << by_oid_ungrouped.delete(child_oid)
      # do not delete the children of a group.  These may be referenced by other groups or directly by the measure
      code = by_oid_ungrouped[child_oid]
      puts "\tcode could not be found: #{child_oid}" unless code
      codes << code if code
      # for hierarchies we need to probably have codes be a hash that we select from if we don't find the
      # element in by_oid_ungrouped we may need to look for it in final
    end
    value["code_sets"] = codes
    value.delete("codes")
    value.delete("code_set")
    final << value
  end
    
  # fill out the orphans
  by_oid_ungrouped.each do |key, orphan|
    final << adopt_orphan(orphan)
  end
  
  deleted = []
  final.delete_if {|x| to_delete = x['code_sets'].nil? || x['code_sets'].empty?; deleted << x if to_delete; to_delete }
  deleted.each do |value|
    puts "\tDeleted value set with no code sets: #{value['oid']}"
  end
  final
    
end

#parse(file, options = {}) ⇒ Object

import an excel matrix array into mongo



33
34
35
36
37
 
# File 'lib/hqmf-parser/value_sets/value_set_parser.rb', line 33

def parse(file, options={})
  sheet_array = file_to_array(file, options)
  by_oid_ungrouped = cells_to_hashs_by_oid(sheet_array)
  collapse_groups(by_oid_ungrouped)
end