quality-measure-engine 3.1.2 → 3.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.travis.yml +12 -5
- data/Gemfile +3 -4
- data/Gemfile.lock +76 -96
- data/LICENSE +201 -0
- data/lib/qme/database_access.rb +1 -1
- data/lib/qme/map/map_reduce_executor.rb +31 -18
- data/lib/qme/quality_report.rb +4 -3
- data/lib/qme/version.rb +1 -1
- data/lib/quality-measure-engine.rb +0 -1
- data/quality-measure-engine.gemspec +11 -10
- data/test/mongoid.yml +1 -1
- data/test/test_helper.rb +46 -14
- data/test/unit/qme/map/map_reduce_builder_test.rb +1 -1
- data/test/unit/qme/map/map_reduce_executor_test.rb +5 -5
- data/test/unit/qme/map/measure_calculation_job_test.rb +4 -4
- data/test/unit/qme/quality_measure_test.rb +3 -3
- data/test/unit/qme/quality_report_test.rb +46 -44
- metadata +28 -47
- data/LICENSE.txt +0 -13
checksums.yaml
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---
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SHA1:
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metadata.gz: 54f1d94d1b3c43ee810b625b40c6082208812a30
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data.tar.gz: 3c5283e6e770e9b7e278c4fe99cdf62a5929cdf4
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SHA512:
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metadata.gz: 58370f38f783d1ea5e014cf812611faf2cc0f7884a09664c4e2d4c27100e84931f870bb4d4af5dff87811ddfa5492177e5451ac3380aaedec806bdd5952f367b
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data.tar.gz: 38a9fd3db563f81e183d7862aa8c80698c1fca4285f715dc93e20aee609f55887453dcadb289b77fe9320a6849f89a9d19259d7620579e357f2cd0c593f7b5cc
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data/.travis.yml
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language: ruby
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rvm:
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dist: precise
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addons:
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apt:
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sources:
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- sourceline: 'deb http://repo.mongodb.org/apt/ubuntu precise/mongodb-org/3.4 multiverse'
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key_url: 'http://keyserver.ubuntu.com/pks/lookup?op=get&fingerprint=on&search=0x9ECBEC467F0CEB10'
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packages:
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- mongodb-org-server=3.4.5
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script: bundle exec rake test
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services:
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data/Gemfile
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PATH
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remote: .
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specs:
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BUNDLED WITH
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1.15.4
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data/LICENSE
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Apache License
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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|
data/lib/qme/database_access.rb
CHANGED
@@ -51,10 +51,13 @@ module QME
|
|
51
51
|
if (filters['genders'] && filters['genders'].size > 0)
|
52
52
|
match['value.gender'] = {'$in' => filters['genders']}
|
53
53
|
end
|
54
|
+
if (filters['patients'] && filters['patients'].size > 0)
|
55
|
+
match['value.patient_id'] = {'$in' => filters['patients']}
|
56
|
+
end
|
54
57
|
if (filters['providers'] && filters['providers'].size > 0)
|
55
58
|
providers = filters['providers'].map { |pv| {'providers' => BSON::ObjectId.from_string(pv) } }
|
56
|
-
pipeline.concat [{'$project' => {'value' => 1, 'providers' => "$value.provider_performances.provider_id"}},
|
57
|
-
{'$unwind' => '$providers'},
|
59
|
+
pipeline.concat [{'$project' => {'value' => 1, 'providers' => "$value.provider_performances.provider_id"}},
|
60
|
+
{'$unwind' => '$providers'},
|
58
61
|
{'$match' => {'$or' => providers}},
|
59
62
|
{'$group' => {"_id" => "$_id", "value" => {"$first" => "$value"}}}]
|
60
63
|
end
|
@@ -87,19 +90,23 @@ module QME
|
|
87
90
|
supplemental_data = Hash[*keys.map{|k| [k,{QME::QualityReport::RACE => {},
|
88
91
|
QME::QualityReport::ETHNICITY => {},
|
89
92
|
QME::QualityReport::SEX => {},
|
90
|
-
QME::QualityReport::PAYER => {}}]}.flatten]
|
91
|
-
|
93
|
+
QME::QualityReport::PAYER => {}}]}.flatten]
|
92
94
|
keys.each do |pop_id|
|
93
|
-
|
95
|
+
pline = build_query
|
96
|
+
|
97
|
+
_match = pline[0]["$match"]
|
94
98
|
_match["value.#{pop_id}"] = {"$gt" => 0}
|
95
99
|
SUPPLEMENTAL_DATA_ELEMENTS.each_pair do |supp_element,location|
|
96
100
|
group1 = {"$group" => { "_id" => { "id" => "$_id", "val" => location}}}
|
97
101
|
group2 = {"$group" => {"_id" => "$_id.val", "val" =>{"$sum" => 1} }}
|
98
|
-
pipeline =
|
99
|
-
|
102
|
+
pipeline = pline.clone
|
103
|
+
pipeline << group1
|
104
|
+
pipeline << group2
|
100
105
|
|
106
|
+
aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => pipeline)
|
107
|
+
aggregate_document = aggregate.documents[0]
|
101
108
|
v = {}
|
102
|
-
(
|
109
|
+
(aggregate_document["result"] || []).each do |entry|
|
103
110
|
code = entry["_id"].nil? ? "UNK" : entry["_id"]
|
104
111
|
v[code] = entry["val"]
|
105
112
|
end
|
@@ -127,14 +134,16 @@ module QME
|
|
127
134
|
QME::QualityReport::EXCLUSIONS => {"$sum" => "$value.#{QME::QualityReport::EXCLUSIONS}"},
|
128
135
|
QME::QualityReport::EXCEPTIONS => {"$sum" => "$value.#{QME::QualityReport::EXCEPTIONS}"},
|
129
136
|
QME::QualityReport::MSRPOPL => {"$sum" => "$value.#{QME::QualityReport::MSRPOPL}"},
|
137
|
+
QME::QualityReport::MSRPOPLEX => {"$sum" => "$value.#{QME::QualityReport::MSRPOPLEX}"},
|
130
138
|
QME::QualityReport::CONSIDERED => {"$sum" => 1}
|
131
139
|
}}
|
132
140
|
|
133
141
|
aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => pipeline)
|
134
|
-
|
142
|
+
aggregate_document = aggregate.documents[0]
|
143
|
+
if !aggregate.successful?
|
135
144
|
raise RuntimeError, "Aggregation Failed"
|
136
|
-
elsif
|
137
|
-
|
145
|
+
elsif aggregate_document['result'].size !=1
|
146
|
+
aggregate_document['result'] =[{"defaults" => true,
|
138
147
|
QME::QualityReport::POPULATION => 0,
|
139
148
|
QME::QualityReport::DENOMINATOR => 0,
|
140
149
|
QME::QualityReport::NUMERATOR =>0,
|
@@ -142,6 +151,7 @@ module QME
|
|
142
151
|
QME::QualityReport::EXCLUSIONS => 0,
|
143
152
|
QME::QualityReport::EXCEPTIONS => 0,
|
144
153
|
QME::QualityReport::MSRPOPL => 0,
|
154
|
+
QME::QualityReport::MSRPOPLEX => 0,
|
145
155
|
QME::QualityReport::CONSIDERED => 0}]
|
146
156
|
end
|
147
157
|
|
@@ -155,7 +165,7 @@ module QME
|
|
155
165
|
result[QME::QualityReport::OBSERVATION] = aggregated_value
|
156
166
|
end
|
157
167
|
|
158
|
-
agg_result =
|
168
|
+
agg_result = aggregate_document['result'].first
|
159
169
|
agg_result.reject! {|k, v| k == '_id'} # get rid of the group id the Mongo forced us to use
|
160
170
|
# result['exclusions'] += get_db['patient_cache'].find(base_query.merge({'value.manual_exclusion'=>true})).count
|
161
171
|
agg_result.merge!(execution_time: (Time.now.to_i - @parameter_values['start_time'].to_i)) if @parameter_values['start_time']
|
@@ -179,11 +189,12 @@ module QME
|
|
179
189
|
cv_pipeline << {'$group' => {'_id' => '$value.values', 'count' => {'$sum' => 1}}}
|
180
190
|
|
181
191
|
aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => cv_pipeline)
|
192
|
+
aggregate_document = aggregate.documents[0]
|
182
193
|
|
183
|
-
raise RuntimeError, "Aggregation Failed" if
|
194
|
+
raise RuntimeError, "Aggregation Failed" if aggregate_document['ok'] != 1
|
184
195
|
|
185
196
|
frequencies = {}
|
186
|
-
|
197
|
+
aggregate_document['result'].each do |freq_count_pair|
|
187
198
|
frequencies[freq_count_pair['_id']] = freq_count_pair['count']
|
188
199
|
end
|
189
200
|
QME::MapReduce::CVAggregator.send(@measure_def.aggregator.parameterize, frequencies)
|
@@ -224,15 +235,17 @@ module QME
|
|
224
235
|
# result is returned directly.
|
225
236
|
def get_patient_result(patient_id)
|
226
237
|
measure = Builder.new(get_db(), @measure_def, @parameter_values)
|
227
|
-
|
238
|
+
operation = get_db().command(:mapreduce => 'records',
|
228
239
|
:map => measure.map_function,
|
229
240
|
:reduce => "function(key, values){return values;}",
|
230
241
|
:out => {:inline => true},
|
231
|
-
:raw => true,
|
242
|
+
# :raw => true,
|
232
243
|
:query => {:medical_record_number => patient_id, :test_id => @parameter_values["test_id"]})
|
233
244
|
|
234
|
-
|
235
|
-
|
245
|
+
|
246
|
+
raise operation.documents[0]['err'] if !operation.successful?
|
247
|
+
return nil if operation.documents[0]['results'].empty?
|
248
|
+
operation.documents[0]['results'][0]['value']
|
236
249
|
end
|
237
250
|
|
238
251
|
|
data/lib/qme/quality_report.rb
CHANGED
@@ -47,6 +47,7 @@ module QME
|
|
47
47
|
EXCLUSIONS = 'DENEX'
|
48
48
|
EXCEPTIONS = 'DENEXCEP'
|
49
49
|
MSRPOPL = 'MSRPOPL'
|
50
|
+
MSRPOPLEX = 'MSRPOPLEX'
|
50
51
|
OBSERVATION = 'OBSERV'
|
51
52
|
ANTINUMERATOR = 'antinumerator'
|
52
53
|
CONSIDERED = 'considered'
|
@@ -100,13 +101,13 @@ module QME
|
|
100
101
|
end
|
101
102
|
|
102
103
|
def self.queue_staged_rollups(measure_id,sub_id,effective_date)
|
103
|
-
query = Mongoid.
|
104
|
+
query = Mongoid.default_client["rollup_buffer"].find({measure_id: measure_id, sub_id: sub_id, effective_date: effective_date})
|
104
105
|
query.each do |options|
|
105
106
|
if QME::QualityReport.where("_id" => options["quality_report_id"]).count == 1
|
106
107
|
QME::QualityReport.enque_job(options,:rollup)
|
107
108
|
end
|
108
109
|
end
|
109
|
-
query.
|
110
|
+
query.delete_many
|
110
111
|
end
|
111
112
|
|
112
113
|
# Determines whether the quality report has been calculated for the given
|
@@ -149,7 +150,7 @@ module QME
|
|
149
150
|
self.status["state"] = "stagged"
|
150
151
|
self.save
|
151
152
|
options.merge!( {measure_id: self.measure_id, sub_id: self.sub_id, effective_date: self.effective_date })
|
152
|
-
Mongoid.
|
153
|
+
Mongoid.default_client["rollup_buffer"].insert_one(options)
|
153
154
|
else
|
154
155
|
# queue the job for calculation
|
155
156
|
QME::QualityReport.enque_job(options,:calculation)
|
data/lib/qme/version.rb
CHANGED
@@ -6,23 +6,24 @@ require 'qme/version'
|
|
6
6
|
Gem::Specification.new do |gem|
|
7
7
|
gem.name = "quality-measure-engine"
|
8
8
|
gem.version = QME::VERSION
|
9
|
-
gem.authors = ["
|
10
|
-
gem.email = ["
|
9
|
+
gem.authors = ["The MITRE Corporation"]
|
10
|
+
gem.email = ["tacoma-list@lists.mitre.org"]
|
11
11
|
gem.description = %q{A library for running clinical quality measures}
|
12
12
|
gem.summary = %q{This library can run JavaScript based clinical quality measures on a repository of patients stored in MongoDB}
|
13
|
-
gem.homepage = "
|
13
|
+
gem.homepage = "https://github.com/projectcypress/quality-measure-engine"
|
14
|
+
gem.license = 'Apache-2.0'
|
14
15
|
|
15
16
|
gem.files = `git ls-files`.split($/)
|
16
17
|
gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
|
17
18
|
gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
|
18
19
|
gem.require_paths = ["lib"]
|
19
20
|
|
20
|
-
gem.add_dependency '
|
21
|
-
gem.add_dependency '
|
22
|
-
gem.add_dependency '
|
23
|
-
gem.add_dependency 'delayed_job_mongoid', '~> 2.
|
21
|
+
gem.add_dependency 'mongoid', '~> 5.0'
|
22
|
+
gem.add_dependency 'rubyzip', '~> 1.0'
|
23
|
+
gem.add_dependency 'zip-zip', "~> 0.3"
|
24
|
+
gem.add_dependency 'delayed_job_mongoid', '~> 2.2'
|
24
25
|
|
25
|
-
gem.add_development_dependency "minitest", "~> 5.4
|
26
|
-
gem.add_development_dependency "simplecov", "~> 0.9
|
27
|
-
gem.add_development_dependency "rails", "~> 4.1
|
26
|
+
gem.add_development_dependency "minitest", "~> 5.4"
|
27
|
+
gem.add_development_dependency "simplecov", "~> 0.9"
|
28
|
+
gem.add_development_dependency "rails", "~> 4.1"
|
28
29
|
end
|
data/test/mongoid.yml
CHANGED
data/test/test_helper.rb
CHANGED
@@ -1,39 +1,71 @@
|
|
1
1
|
require 'simplecov_setup'
|
2
2
|
require 'minitest/autorun'
|
3
3
|
require 'quality-measure-engine'
|
4
|
-
require 'pry-nav'
|
5
4
|
|
5
|
+
Mongo::Logger.logger.level = Logger::WARN
|
6
6
|
Mongoid.load!(File.join(File.dirname(__FILE__),"mongoid.yml"), :test)
|
7
7
|
|
8
8
|
class MiniTest::Unit::TestCase
|
9
9
|
|
10
10
|
def load_system_js
|
11
|
-
Mongoid.
|
11
|
+
Mongoid.default_client['system.js'].delete_many({})
|
12
12
|
Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', "library_functions", '*.js')).each do |json_fixture_file|
|
13
13
|
name = File.basename(json_fixture_file,".*")
|
14
14
|
fn = "function () {\n #{File.read(json_fixture_file)} \n }"
|
15
|
-
Mongoid.
|
15
|
+
Mongoid.default_client['system.js'].update_one({
|
16
|
+
"_id" => name},
|
16
17
|
{
|
17
18
|
"_id" => name,
|
18
19
|
"value" => BSON::Code.new(fn)
|
19
|
-
}
|
20
|
+
},{upsert: true}
|
20
21
|
)
|
21
22
|
end
|
22
23
|
|
23
24
|
end
|
24
25
|
|
25
|
-
# Add more helper methods to be used by all tests here...
|
26
26
|
|
27
|
-
def
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
fixture_json[attr] = BSON::ObjectId.from_string(fixture_json[attr])
|
27
|
+
def value_or_bson(v)
|
28
|
+
if v.is_a? Hash
|
29
|
+
if v['$oid']
|
30
|
+
BSON::ObjectId.from_string(v['$oid'])
|
31
|
+
else
|
32
|
+
map_bson_ids(v)
|
34
33
|
end
|
34
|
+
else
|
35
|
+
v
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
def map_array(arr)
|
40
|
+
ret = []
|
41
|
+
arr.each do |v|
|
42
|
+
ret << value_or_bson(v)
|
43
|
+
end
|
44
|
+
ret
|
45
|
+
end
|
35
46
|
|
36
|
-
|
47
|
+
def map_bson_ids(json)
|
48
|
+
json.each_pair do |k, v|
|
49
|
+
if v.is_a? Hash
|
50
|
+
json[k] = value_or_bson(v)
|
51
|
+
elsif v.is_a? Array
|
52
|
+
json[k] = map_array(v)
|
53
|
+
elsif k == 'create_at' || k == 'updated_at'
|
54
|
+
json[k] = Time.at.local(v).in_time_zone
|
55
|
+
end
|
56
|
+
end
|
57
|
+
json
|
58
|
+
end
|
59
|
+
|
60
|
+
def collection_fixtures(*collections)
|
61
|
+
collections.each do |collection|
|
62
|
+
get_db()[collection].drop
|
63
|
+
Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', collection, '*.json')).each do |json_fixture_file|
|
64
|
+
fixture_json = JSON.parse(File.read(json_fixture_file), max_nesting: 250)
|
65
|
+
fixture_json['_id'] = BSON::ObjectId.from_string(fixture_json['_id']) if fixture_json['_id']
|
66
|
+
map_bson_ids(fixture_json)
|
67
|
+
Mongoid.default_client[collection].insert_one(fixture_json)
|
68
|
+
end
|
37
69
|
end
|
38
70
|
end
|
39
|
-
end
|
71
|
+
end
|
@@ -4,7 +4,7 @@ class MapReduceBuilderTest < MiniTest::Unit::TestCase
|
|
4
4
|
include QME::DatabaseAccess
|
5
5
|
|
6
6
|
def setup
|
7
|
-
collection_fixtures(
|
7
|
+
collection_fixtures('measures')
|
8
8
|
@measure_json = QME::QualityMeasure.where({"nqf_id" => '0043'}).first
|
9
9
|
load_system_js
|
10
10
|
end
|
@@ -7,9 +7,9 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
|
|
7
7
|
|
8
8
|
get_db['query_cache'].drop()
|
9
9
|
get_db['patient_cache'].drop()
|
10
|
-
collection_fixtures(
|
11
|
-
collection_fixtures(
|
12
|
-
collection_fixtures(
|
10
|
+
collection_fixtures('measures')
|
11
|
+
collection_fixtures('records')
|
12
|
+
collection_fixtures('bundles')
|
13
13
|
options = {'measure_id' => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8",
|
14
14
|
'effective_date' => Time.gm(2011, 1, 15).to_i}
|
15
15
|
@quality_report =QME::QualityReport.find_or_create_by(options)
|
@@ -117,7 +117,7 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
|
|
117
117
|
def test_get_patient_result_with_bundle_id
|
118
118
|
measure_id = "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8"
|
119
119
|
bundle_id = get_db()['bundles'].find.first
|
120
|
-
get_db()['measures'].
|
120
|
+
get_db()['measures'].update_many({'id' => measure_id}, {:$set => {'bundle_id' => bundle_id}})
|
121
121
|
executor = QME::MapReduce::Executor.new(measure_id, nil,
|
122
122
|
'effective_date' => Time.gm(2011, 1, 15).to_i, 'bundle_id' => bundle_id)
|
123
123
|
result = executor.get_patient_result("12345")
|
@@ -125,4 +125,4 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
|
|
125
125
|
assert result[QME::QualityReport::NUMERATOR]
|
126
126
|
end
|
127
127
|
|
128
|
-
end
|
128
|
+
end
|
@@ -6,9 +6,9 @@ class MapCalculationJobTest < MiniTest::Unit::TestCase
|
|
6
6
|
def setup
|
7
7
|
get_db['query_cache'].drop()
|
8
8
|
get_db['patient_cache'].drop()
|
9
|
-
collection_fixtures(
|
10
|
-
collection_fixtures(
|
11
|
-
collection_fixtures(
|
9
|
+
collection_fixtures('measures')
|
10
|
+
collection_fixtures('records')
|
11
|
+
collection_fixtures('bundles')
|
12
12
|
load_system_js
|
13
13
|
|
14
14
|
Delayed::Worker.delay_jobs = false
|
@@ -21,4 +21,4 @@ class MapCalculationJobTest < MiniTest::Unit::TestCase
|
|
21
21
|
job = Delayed::Job.enqueue(QME::MapReduce::MeasureCalculationJob.new({'quality_report_id' => qr.id,"oid_dictionary"=>{}}))
|
22
22
|
assert job
|
23
23
|
end
|
24
|
-
end
|
24
|
+
end
|
@@ -4,8 +4,8 @@ class QualityMeasureTest < MiniTest::Unit::TestCase
|
|
4
4
|
include QME::DatabaseAccess
|
5
5
|
def setup
|
6
6
|
|
7
|
-
collection_fixtures(
|
8
|
-
collection_fixtures(
|
7
|
+
collection_fixtures('measures')
|
8
|
+
collection_fixtures('bundles')
|
9
9
|
load_system_js
|
10
10
|
end
|
11
11
|
|
@@ -14,4 +14,4 @@ class QualityMeasureTest < MiniTest::Unit::TestCase
|
|
14
14
|
assert_equal 5, all_measures.size
|
15
15
|
assert all_measures.where({"hqmf_id" => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8"}).first
|
16
16
|
end
|
17
|
-
end
|
17
|
+
end
|
@@ -5,50 +5,51 @@ class QualityReportTest < MiniTest::Unit::TestCase
|
|
5
5
|
|
6
6
|
def setup
|
7
7
|
load_system_js
|
8
|
-
collection_fixtures(
|
9
|
-
collection_fixtures(
|
10
|
-
collection_fixtures(
|
8
|
+
collection_fixtures('bundles')
|
9
|
+
collection_fixtures('records')
|
10
|
+
collection_fixtures('measures')
|
11
|
+
|
11
12
|
get_db()['query_cache'].drop()
|
12
13
|
get_db()['patient_cache'].drop()
|
13
|
-
get_db()['query_cache'].
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
|
14
|
+
get_db()['query_cache'].insert_one({
|
15
|
+
"measure_id" => "test2",
|
16
|
+
"sub_id" => "b",
|
17
|
+
"status" =>{"state" => "completed"},
|
18
|
+
"initialPopulation" => 4,
|
19
|
+
"result" => {
|
20
|
+
QME::QualityReport::NUMERATOR => 1,
|
21
|
+
QME::QualityReport::DENOMINATOR => 2,
|
22
|
+
QME::QualityReport::EXCLUSIONS => 1},
|
23
|
+
"effective_date" => Time.gm(2010, 9, 19).to_i}
|
23
24
|
)
|
24
|
-
get_db()['patient_cache'].
|
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
|
-
|
25
|
+
get_db()['patient_cache'].insert_one({
|
26
|
+
"value" => {
|
27
|
+
QME::QualityReport::POPULATION => 0,
|
28
|
+
QME::QualityReport::DENOMINATOR => 0,
|
29
|
+
QME::QualityReport::NUMERATOR => 0,
|
30
|
+
QME::QualityReport::EXCLUSIONS => 0,
|
31
|
+
QME::QualityReport::ANTINUMERATOR => 0,
|
32
|
+
"medical_record_id" => "0616911582",
|
33
|
+
"first" => "Mary",
|
34
|
+
"last" => "Edwards",
|
35
|
+
"gender" => "F",
|
36
|
+
"birthdate" => Time.gm(1940, 9, 19).to_i,
|
37
|
+
"test_id" => nil,
|
38
|
+
"provider_performances" => nil,
|
39
|
+
"race" => {
|
40
|
+
"code" => "2106-3",
|
41
|
+
"code_set" => "CDC-RE"
|
42
|
+
},
|
43
|
+
"ethnicity" => {
|
44
|
+
"code" => "2135-2",
|
45
|
+
"code_set" => "CDC-RE"
|
46
|
+
},
|
47
|
+
"measure_id" => "test2",
|
48
|
+
"sub_id" => "b",
|
49
|
+
"effective_date" => Time.gm(2010, 9, 19).to_i
|
50
|
+
}}
|
50
51
|
)
|
51
|
-
collection_fixtures(
|
52
|
+
collection_fixtures('delayed_backend_mongoid_jobs')
|
52
53
|
end
|
53
54
|
|
54
55
|
def test_calculated
|
@@ -86,6 +87,7 @@ class QualityReportTest < MiniTest::Unit::TestCase
|
|
86
87
|
def test_status
|
87
88
|
status = QME::MapReduce::MeasureCalculationJob.status('not really a job id')
|
88
89
|
assert_equal :complete, status
|
90
|
+
|
89
91
|
status = QME::MapReduce::MeasureCalculationJob.status("508aeff07042f9f88900000d")
|
90
92
|
assert_equal :queued, status
|
91
93
|
end
|
@@ -95,7 +97,7 @@ class QualityReportTest < MiniTest::Unit::TestCase
|
|
95
97
|
assert Delayed::Worker.delay_jobs
|
96
98
|
Delayed::Job.destroy_all
|
97
99
|
QME::QualityReport.destroy_all
|
98
|
-
Mongoid.
|
100
|
+
Mongoid.default_client["rollup_buffer"].delete_many({})
|
99
101
|
qr = QME::QualityReport.find_or_create('2E679CD2-3FEC-4A75-A75A-61403E5EFEE8', nil, "effective_date" => Time.gm(2011, 9, 19).to_i)
|
100
102
|
qr2 = QME::QualityReport.find_or_create('2E679CD2-3FEC-4A75-A75A-61403E5EFEE8', nil, {"effective_date" => Time.gm(2011, 9, 19).to_i,:filters=>{"providers"=>["a"]}})
|
101
103
|
assert !qr.calculated?
|
@@ -112,9 +114,9 @@ class QualityReportTest < MiniTest::Unit::TestCase
|
|
112
114
|
assert qr.calculation_queued_or_running?
|
113
115
|
assert qr2.calculation_queued_or_running?
|
114
116
|
|
115
|
-
assert_equal 0, Mongoid.
|
117
|
+
assert_equal 0, Mongoid.default_client["rollup_buffer"].count({})
|
116
118
|
qr2.calculate({"oid_dictionary"=>{}},true)
|
117
|
-
assert_equal 1, Mongoid.
|
119
|
+
assert_equal 1, Mongoid.default_client["rollup_buffer"].count({})
|
118
120
|
|
119
121
|
|
120
122
|
assert_equal 1, Delayed::Job.count()
|
@@ -127,6 +129,6 @@ class QualityReportTest < MiniTest::Unit::TestCase
|
|
127
129
|
job = Delayed::Job.where({}).first
|
128
130
|
assert_equal "rollup", job.queue
|
129
131
|
|
130
|
-
assert_equal 0, Mongoid.
|
132
|
+
assert_equal 0, Mongoid.default_client["rollup_buffer"].count({})
|
131
133
|
end
|
132
134
|
end
|
metadata
CHANGED
@@ -1,135 +1,116 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: quality-measure-engine
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.
|
5
|
-
prerelease:
|
4
|
+
version: 3.2.0
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
|
-
-
|
9
|
-
- Andy Gregorowicz
|
10
|
-
- Rob Dingwell
|
11
|
-
- Adam Goldstein
|
12
|
-
- Andre Quina
|
7
|
+
- The MITRE Corporation
|
13
8
|
autorequire:
|
14
9
|
bindir: bin
|
15
10
|
cert_chain: []
|
16
|
-
date:
|
11
|
+
date: 2017-11-13 00:00:00.000000000 Z
|
17
12
|
dependencies:
|
18
13
|
- !ruby/object:Gem::Dependency
|
19
|
-
name:
|
14
|
+
name: mongoid
|
20
15
|
requirement: !ruby/object:Gem::Requirement
|
21
|
-
none: false
|
22
16
|
requirements:
|
23
17
|
- - "~>"
|
24
18
|
- !ruby/object:Gem::Version
|
25
|
-
version:
|
19
|
+
version: '5.0'
|
26
20
|
type: :runtime
|
27
21
|
prerelease: false
|
28
22
|
version_requirements: !ruby/object:Gem::Requirement
|
29
|
-
none: false
|
30
23
|
requirements:
|
31
24
|
- - "~>"
|
32
25
|
- !ruby/object:Gem::Version
|
33
|
-
version:
|
26
|
+
version: '5.0'
|
34
27
|
- !ruby/object:Gem::Dependency
|
35
|
-
name:
|
28
|
+
name: rubyzip
|
36
29
|
requirement: !ruby/object:Gem::Requirement
|
37
|
-
none: false
|
38
30
|
requirements:
|
39
31
|
- - "~>"
|
40
32
|
- !ruby/object:Gem::Version
|
41
|
-
version:
|
33
|
+
version: '1.0'
|
42
34
|
type: :runtime
|
43
35
|
prerelease: false
|
44
36
|
version_requirements: !ruby/object:Gem::Requirement
|
45
|
-
none: false
|
46
37
|
requirements:
|
47
38
|
- - "~>"
|
48
39
|
- !ruby/object:Gem::Version
|
49
|
-
version:
|
40
|
+
version: '1.0'
|
50
41
|
- !ruby/object:Gem::Dependency
|
51
|
-
name:
|
42
|
+
name: zip-zip
|
52
43
|
requirement: !ruby/object:Gem::Requirement
|
53
|
-
none: false
|
54
44
|
requirements:
|
55
45
|
- - "~>"
|
56
46
|
- !ruby/object:Gem::Version
|
57
|
-
version: 0.
|
47
|
+
version: '0.3'
|
58
48
|
type: :runtime
|
59
49
|
prerelease: false
|
60
50
|
version_requirements: !ruby/object:Gem::Requirement
|
61
|
-
none: false
|
62
51
|
requirements:
|
63
52
|
- - "~>"
|
64
53
|
- !ruby/object:Gem::Version
|
65
|
-
version: 0.
|
54
|
+
version: '0.3'
|
66
55
|
- !ruby/object:Gem::Dependency
|
67
56
|
name: delayed_job_mongoid
|
68
57
|
requirement: !ruby/object:Gem::Requirement
|
69
|
-
none: false
|
70
58
|
requirements:
|
71
59
|
- - "~>"
|
72
60
|
- !ruby/object:Gem::Version
|
73
|
-
version: 2.
|
61
|
+
version: '2.2'
|
74
62
|
type: :runtime
|
75
63
|
prerelease: false
|
76
64
|
version_requirements: !ruby/object:Gem::Requirement
|
77
|
-
none: false
|
78
65
|
requirements:
|
79
66
|
- - "~>"
|
80
67
|
- !ruby/object:Gem::Version
|
81
|
-
version: 2.
|
68
|
+
version: '2.2'
|
82
69
|
- !ruby/object:Gem::Dependency
|
83
70
|
name: minitest
|
84
71
|
requirement: !ruby/object:Gem::Requirement
|
85
|
-
none: false
|
86
72
|
requirements:
|
87
73
|
- - "~>"
|
88
74
|
- !ruby/object:Gem::Version
|
89
|
-
version: 5.4
|
75
|
+
version: '5.4'
|
90
76
|
type: :development
|
91
77
|
prerelease: false
|
92
78
|
version_requirements: !ruby/object:Gem::Requirement
|
93
|
-
none: false
|
94
79
|
requirements:
|
95
80
|
- - "~>"
|
96
81
|
- !ruby/object:Gem::Version
|
97
|
-
version: 5.4
|
82
|
+
version: '5.4'
|
98
83
|
- !ruby/object:Gem::Dependency
|
99
84
|
name: simplecov
|
100
85
|
requirement: !ruby/object:Gem::Requirement
|
101
|
-
none: false
|
102
86
|
requirements:
|
103
87
|
- - "~>"
|
104
88
|
- !ruby/object:Gem::Version
|
105
|
-
version: 0.9
|
89
|
+
version: '0.9'
|
106
90
|
type: :development
|
107
91
|
prerelease: false
|
108
92
|
version_requirements: !ruby/object:Gem::Requirement
|
109
|
-
none: false
|
110
93
|
requirements:
|
111
94
|
- - "~>"
|
112
95
|
- !ruby/object:Gem::Version
|
113
|
-
version: 0.9
|
96
|
+
version: '0.9'
|
114
97
|
- !ruby/object:Gem::Dependency
|
115
98
|
name: rails
|
116
99
|
requirement: !ruby/object:Gem::Requirement
|
117
|
-
none: false
|
118
100
|
requirements:
|
119
101
|
- - "~>"
|
120
102
|
- !ruby/object:Gem::Version
|
121
|
-
version: 4.1
|
103
|
+
version: '4.1'
|
122
104
|
type: :development
|
123
105
|
prerelease: false
|
124
106
|
version_requirements: !ruby/object:Gem::Requirement
|
125
|
-
none: false
|
126
107
|
requirements:
|
127
108
|
- - "~>"
|
128
109
|
- !ruby/object:Gem::Version
|
129
|
-
version: 4.1
|
110
|
+
version: '4.1'
|
130
111
|
description: A library for running clinical quality measures
|
131
112
|
email:
|
132
|
-
-
|
113
|
+
- tacoma-list@lists.mitre.org
|
133
114
|
executables: []
|
134
115
|
extensions: []
|
135
116
|
extra_rdoc_files: []
|
@@ -138,7 +119,7 @@ files:
|
|
138
119
|
- ".travis.yml"
|
139
120
|
- Gemfile
|
140
121
|
- Gemfile.lock
|
141
|
-
- LICENSE
|
122
|
+
- LICENSE
|
142
123
|
- README.md
|
143
124
|
- Rakefile
|
144
125
|
- lib/qme/database_access.rb
|
@@ -180,29 +161,29 @@ files:
|
|
180
161
|
- test/unit/qme/map/measure_calculation_job_test.rb
|
181
162
|
- test/unit/qme/quality_measure_test.rb
|
182
163
|
- test/unit/qme/quality_report_test.rb
|
183
|
-
homepage:
|
184
|
-
licenses:
|
164
|
+
homepage: https://github.com/projectcypress/quality-measure-engine
|
165
|
+
licenses:
|
166
|
+
- Apache-2.0
|
167
|
+
metadata: {}
|
185
168
|
post_install_message:
|
186
169
|
rdoc_options: []
|
187
170
|
require_paths:
|
188
171
|
- lib
|
189
172
|
required_ruby_version: !ruby/object:Gem::Requirement
|
190
|
-
none: false
|
191
173
|
requirements:
|
192
174
|
- - ">="
|
193
175
|
- !ruby/object:Gem::Version
|
194
176
|
version: '0'
|
195
177
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
196
|
-
none: false
|
197
178
|
requirements:
|
198
179
|
- - ">="
|
199
180
|
- !ruby/object:Gem::Version
|
200
181
|
version: '0'
|
201
182
|
requirements: []
|
202
183
|
rubyforge_project:
|
203
|
-
rubygems_version:
|
184
|
+
rubygems_version: 2.6.12
|
204
185
|
signing_key:
|
205
|
-
specification_version:
|
186
|
+
specification_version: 4
|
206
187
|
summary: This library can run JavaScript based clinical quality measures on a repository
|
207
188
|
of patients stored in MongoDB
|
208
189
|
test_files:
|
data/LICENSE.txt
DELETED
@@ -1,13 +0,0 @@
|
|
1
|
-
Copyright (c) 2012 The MITRE Corporation
|
2
|
-
|
3
|
-
Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
-
you may not use this file except in compliance with the License.
|
5
|
-
You may obtain a copy of the License at
|
6
|
-
|
7
|
-
http://www.apache.org/licenses/LICENSE-2.0
|
8
|
-
|
9
|
-
Unless required by applicable law or agreed to in writing, software
|
10
|
-
distributed under the License is distributed on an "AS IS" BASIS,
|
11
|
-
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12
|
-
See the License for the specific language governing permissions and
|
13
|
-
limitations under the License.
|