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adding fixtures for data missing from tests since movin bundle import…

… code to HDS
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1 parent 5cfd89a commit d7e3da02ee05a4513a7c8c7159fb025b6be0042d @rdingwell rdingwell committed
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10 Gemfile.lock
@@ -4,7 +4,7 @@ PATH
quality-measure-engine (2.1.0)
delayed_job_mongoid (~> 2.0.0)
mongoid (~> 3.0)
- moped (~> 1.2.7)
+ moped (~> 1.4.2)
nokogiri (~> 1.5.5)
rubyXL (~> 1.2.10)
rubyzip (~> 0.9.9)
@@ -63,12 +63,12 @@ GEM
method_source (0.8.1)
mime-types (1.21)
minitest (4.1.0)
- mongoid (3.0.22)
- activemodel (~> 3.1)
- moped (~> 1.2)
+ mongoid (3.1.2)
+ activemodel (~> 3.2)
+ moped (~> 1.4.2)
origin (~> 1.0)
tzinfo (~> 0.3.22)
- moped (1.2.9)
+ moped (1.4.2)
multi_json (1.6.1)
nokogiri (1.5.6)
origin (1.0.11)
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10 test/fixtures/bundles/bundle.json
@@ -0,0 +1,10 @@
+{
+ "name": "Meaningful Use Stage 2 Clinical Quality Measures",
+ "license": "<p>Performance measures and related data specifications (the \"Measures\") are copyrighted by\nthe noted quality measure providers as indicated in the applicable Measure. Coding\nvocabularies are owned by their copyright owners. By using the Measures, a user\n(\"User\") agrees to these Terms of Use. Measures are not clinical guidelines and do not\nestablish a standard of medical care and quality measure providers are not responsible\nfor any use of or reliance on the Measures.</p>\n\n<p><strong>THE MEASURES AND SPECIFICATIONS ARE PROVIDED \"AS IS\" WITHOUT ANY WARRANTY OF\nANY KIND, AND ANY AND ALL IMPLIED WARRANTIES ARE HEREBY DISCLAIMED, INCLUDING ANY\nWARRANTY OF NON-INFRINGEMENT, ACCURACY, MERCHANTABILITY AND FITNESS FOR A PARTICULAR\nPURPOSE. NO QUALITY MEASURE PROVIDER, NOR ANY OF THEIR TRUSTEES, DIRECTORS, MEMBERS,\nAFFILIATES, OFFICERS, EMPLOYEES, SUCCESSORS AND/OR ASSIGNS WILL BE LIABLE TO YOU FOR\nANY DIRECT, INDIRECT, SPECIAL, EXEMPLARY, INCIDENTAL, PUNITIVE, AND/OR CONSEQUENTIAL\nDAMAGE OF ANY KIND, IN CONTRACT, TORT OR OTHERWISE, IN CONNECTION WITH THE USE OF THE\nPOPHEALTH TOOL OR THE MEASURES, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGE.\n</strong></p>\n\n<p>The Measures are licensed to a User for the limited purpose of using, reproducing and\ndistributing the Measures with the popHealth Tool as delivered to User, without any\nmodification, for commercial and noncommercial uses, but such uses are only permitted\nif the copies of the Measures contain this complete Copyright, Disclaimer and Terms\nof Use. Users of the Measures may not alter, enhance, or otherwise modify the Measures.</p>\n\n<p><strong>NOT A CONTRIBUTION</strong> - The Measures, including specifications and coding,\nas used in the popHealth Tool, are not a contribution under the Apache license. Coding\nin the Measures is provided for convenience only and necessary licenses for use should\nbe obtained from the copyright owners. Current Procedural Terminology \n(CPT<span class=\"reg\">&reg;</span>) &copy; 2004-2010 American Medical Association. \nLOINC<span class=\"reg\">&reg;</span> &copy; 2004 Regenstrief Institute,\nInc. SNOMED Clinical Terms<span class=\"reg\">&reg;</span> \n(SNOMED CT<span class=\"reg\">&reg;</span>) &copy; 2004-2010 International Health\nTerminology Standards Development Organization.</p>",
+ "extensions": [
+ "map_reduce_utils",
+ "underscore_min",
+ "hqmf_utils"
+ ],
+ "measures": []
+}
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5,146 test/fixtures/library_functions/hqmf_utils.js
5,146 additions, 0 deletions not shown because the diff is too large. Please use a local Git client to view these changes.
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45 test/fixtures/library_functions/map_reduce_utils.js
@@ -0,0 +1,45 @@
+// Adds common utility functions to the root JS object. These are then
+// available for use by the map-reduce functions for each measure.
+// lib/qme/mongo_helpers.rb executes this function on a database
+// connection.
+
+var root = this;
+
+root.map = function(record, population, denominator, numerator, exclusion, denexcep) {
+ var value = {IPP: 0, DENOM: 0, NUMER: 0, DENEXCEP: 0,
+ DENEX: 0, antinumerator: 0, patient_id: record._id,
+ medical_record_id: record.medical_record_number,
+ first: record.first, last: record.last, gender: record.gender,
+ birthdate: record.birthdate, test_id: record.test_id,
+ provider_performances: record.provider_performances,
+ race: record.race, ethnicity: record.ethnicity, languages: record.languages};
+ var ipp = population()
+ if (Specifics.validate(ipp)) {
+ value.IPP = 1;
+ if (Specifics.validate(denexcep(), ipp)) {
+ value.DENEXCP = 1;
+ } else {
+ denom = denominator();
+ if (Specifics.validate(denom, ipp)) {
+ value.DENOM = 1;
+ numer = numerator()
+ if (Specifics.validate(numer, denom, ipp)) {
+ value.NUMER = 1;
+ } else {
+ excl = exclusion()
+ if (Specifics.validate(excl, denom, ipp)) {
+ value.DENEX = 1;
+ value.DENOM = 0;
+ } else {
+ value.antinumerator = 1;
+ }
+ }
+ }
+ }
+ }
+
+
+ if (typeof Logger != 'undefined') value['logger'] = Logger.logger
+
+ emit(ObjectId(), value);
+};
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32 test/fixtures/library_functions/underscore_min.js
@@ -0,0 +1,32 @@
+// Underscore.js 1.3.3
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+(function(){function r(a,c,d){if(a===c)return 0!==a||1/a==1/c;if(null==a||null==c)return a===c;a._chain&&(a=a._wrapped);c._chain&&(c=c._wrapped);if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return!1;switch(e){case "[object String]":return a==""+c;case "[object Number]":return a!=+a?c!=+c:0==a?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
+c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if("object"!=typeof a||"object"!=typeof c)return!1;for(var f=d.length;f--;)if(d[f]==a)return!0;d.push(a);var f=0,g=!0;if("[object Array]"==e){if(f=a.length,g=f==c.length)for(;f--&&(g=f in a==f in c&&r(a[f],c[f],d)););}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return!1;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&r(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c,h)&&!f--)break;
+g=!f}}d.pop();return g}var s=this,I=s._,o={},k=Array.prototype,p=Object.prototype,i=k.slice,J=k.unshift,l=p.toString,K=p.hasOwnProperty,y=k.forEach,z=k.map,A=k.reduce,B=k.reduceRight,C=k.filter,D=k.every,E=k.some,q=k.indexOf,F=k.lastIndexOf,p=Array.isArray,L=Object.keys,t=Function.prototype.bind,b=function(a){return new m(a)};"undefined"!==typeof exports?("undefined"!==typeof module&&module.exports&&(exports=module.exports=b),exports._=b):s._=b;b.VERSION="1.3.3";var j=b.each=b.forEach=function(a,
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+a.reduce===A){e&&(c=b.bind(c,e));return f?a.reduce(c,d):a.reduce(c)}j(a,function(a,b,i){if(f)d=c.call(e,d,a,b,i);else{d=a;f=true}});if(!f)throw new TypeError("Reduce of empty array with no initial value");return d};b.reduceRight=b.foldr=function(a,c,d,e){var f=arguments.length>2;a==null&&(a=[]);if(B&&a.reduceRight===B){e&&(c=b.bind(c,e));return f?a.reduceRight(c,d):a.reduceRight(c)}var g=b.toArray(a).reverse();e&&!f&&(c=b.bind(c,e));return f?b.reduce(g,c,d,e):b.reduce(g,c)};b.find=b.detect=function(a,
+c,b){var e;G(a,function(a,g,h){if(c.call(b,a,g,h)){e=a;return true}});return e};b.filter=b.select=function(a,c,b){var e=[];if(a==null)return e;if(C&&a.filter===C)return a.filter(c,b);j(a,function(a,g,h){c.call(b,a,g,h)&&(e[e.length]=a)});return e};b.reject=function(a,c,b){var e=[];if(a==null)return e;j(a,function(a,g,h){c.call(b,a,g,h)||(e[e.length]=a)});return e};b.every=b.all=function(a,c,b){var e=true;if(a==null)return e;if(D&&a.every===D)return a.every(c,b);j(a,function(a,g,h){if(!(e=e&&c.call(b,
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+(e={value:a,computed:b})});return e.value};b.shuffle=function(a){var b=[],d;j(a,function(a,f){d=Math.floor(Math.random()*(f+1));b[f]=b[d];b[d]=a});return b};b.sortBy=function(a,c,d){var e=b.isFunction(c)?c:function(a){return a[c]};return b.pluck(b.map(a,function(a,b,c){return{value:a,criteria:e.call(d,a,b,c)}}).sort(function(a,b){var c=a.criteria,d=b.criteria;return c===void 0?1:d===void 0?-1:c<d?-1:c>d?1:0}),"value")};b.groupBy=function(a,c){var d={},e=b.isFunction(c)?c:function(a){return a[c]};
+j(a,function(a,b){var c=e(a,b);(d[c]||(d[c]=[])).push(a)});return d};b.sortedIndex=function(a,c,d){d||(d=b.identity);for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?e=g+1:f=g}return e};b.toArray=function(a){return!a?[]:b.isArray(a)||b.isArguments(a)?i.call(a):a.toArray&&b.isFunction(a.toArray)?a.toArray():b.values(a)};b.size=function(a){return b.isArray(a)?a.length:b.keys(a).length};b.first=b.head=b.take=function(a,b,d){return b!=null&&!d?i.call(a,0,b):a[0]};b.initial=function(a,b,d){return i.call(a,
+0,a.length-(b==null||d?1:b))};b.last=function(a,b,d){return b!=null&&!d?i.call(a,Math.max(a.length-b,0)):a[a.length-1]};b.rest=b.tail=function(a,b,d){return i.call(a,b==null||d?1:b)};b.compact=function(a){return b.filter(a,function(a){return!!a})};b.flatten=function(a,c){return b.reduce(a,function(a,e){if(b.isArray(e))return a.concat(c?e:b.flatten(e));a[a.length]=e;return a},[])};b.without=function(a){return b.difference(a,i.call(arguments,1))};b.uniq=b.unique=function(a,c,d){var d=d?b.map(a,d):a,
+e=[];a.length<3&&(c=true);b.reduce(d,function(d,g,h){if(c?b.last(d)!==g||!d.length:!b.include(d,g)){d.push(g);e.push(a[h])}return d},[]);return e};b.union=function(){return b.uniq(b.flatten(arguments,true))};b.intersection=b.intersect=function(a){var c=i.call(arguments,1);return b.filter(b.uniq(a),function(a){return b.every(c,function(c){return b.indexOf(c,a)>=0})})};b.difference=function(a){var c=b.flatten(i.call(arguments,1),true);return b.filter(a,function(a){return!b.include(c,a)})};b.zip=function(){for(var a=
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+i.call(arguments,1);c.length==0&&(c=b.functions(a));j(c,function(c){a[c]=b.bind(a[c],a)});return a};b.memoize=function(a,c){var d={};c||(c=b.identity);return function(){var e=c.apply(this,arguments);return b.has(d,e)?d[e]:d[e]=a.apply(this,arguments)}};b.delay=function(a,b){var d=i.call(arguments,2);return setTimeout(function(){return a.apply(null,d)},b)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(i.call(arguments,1)))};b.throttle=function(a,c){var d,e,f,g,h,i,j=b.debounce(function(){h=
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+return b.apply(this,d)}};b.compose=function(){var a=arguments;return function(){for(var b=arguments,d=a.length-1;d>=0;d--)b=[a[d].apply(this,b)];return b[0]}};b.after=function(a,b){return a<=0?b():function(){if(--a<1)return b.apply(this,arguments)}};b.keys=L||function(a){if(a!==Object(a))throw new TypeError("Invalid object");var c=[],d;for(d in a)b.has(a,d)&&(c[c.length]=d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=b.methods=function(a){var c=[],d;for(d in a)b.isFunction(a[d])&&
+c.push(d);return c.sort()};b.extend=function(a){j(i.call(arguments,1),function(b){for(var d in b)a[d]=b[d]});return a};b.pick=function(a){var c={};j(b.flatten(i.call(arguments,1)),function(b){b in a&&(c[b]=a[b])});return c};b.defaults=function(a){j(i.call(arguments,1),function(b){for(var d in b)a[d]==null&&(a[d]=b[d])});return a};b.clone=function(a){return!b.isObject(a)?a:b.isArray(a)?a.slice():b.extend({},a)};b.tap=function(a,b){b(a);return a};b.isEqual=function(a,b){return r(a,b,[])};b.isEmpty=
+function(a){if(a==null)return true;if(b.isArray(a)||b.isString(a))return a.length===0;for(var c in a)if(b.has(a,c))return false;return true};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=p||function(a){return l.call(a)=="[object Array]"};b.isObject=function(a){return a===Object(a)};b.isArguments=function(a){return l.call(a)=="[object Arguments]"};b.isArguments(arguments)||(b.isArguments=function(a){return!(!a||!b.has(a,"callee"))});b.isFunction=function(a){return l.call(a)=="[object Function]"};
+b.isString=function(a){return l.call(a)=="[object String]"};b.isNumber=function(a){return l.call(a)=="[object Number]"};b.isFinite=function(a){return b.isNumber(a)&&isFinite(a)};b.isNaN=function(a){return a!==a};b.isBoolean=function(a){return a===true||a===false||l.call(a)=="[object Boolean]"};b.isDate=function(a){return l.call(a)=="[object Date]"};b.isRegExp=function(a){return l.call(a)=="[object RegExp]"};b.isNull=function(a){return a===null};b.isUndefined=function(a){return a===void 0};b.has=function(a,
+b){return K.call(a,b)};b.noConflict=function(){s._=I;return this};b.identity=function(a){return a};b.times=function(a,b,d){for(var e=0;e<a;e++)b.call(d,e)};b.escape=function(a){return(""+a).replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/>/g,"&gt;").replace(/"/g,"&quot;").replace(/'/g,"&#x27;").replace(/\//g,"&#x2F;")};b.result=function(a,c){if(a==null)return null;var d=a[c];return b.isFunction(d)?d.call(a):d};b.mixin=function(a){j(b.functions(a),function(c){M(c,b[c]=a[c])})};var N=0;b.uniqueId=
+function(a){var b=N++;return a?a+b:b};b.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var u=/.^/,n={"\\":"\\","'":"'",r:"\r",n:"\n",t:"\t",u2028:"\u2028",u2029:"\u2029"},v;for(v in n)n[n[v]]=v;var O=/\\|'|\r|\n|\t|\u2028|\u2029/g,P=/\\(\\|'|r|n|t|u2028|u2029)/g,w=function(a){return a.replace(P,function(a,b){return n[b]})};b.template=function(a,c,d){d=b.defaults(d||{},b.templateSettings);a="__p+='"+a.replace(O,function(a){return"\\"+n[a]}).replace(d.escape||
+u,function(a,b){return"'+\n_.escape("+w(b)+")+\n'"}).replace(d.interpolate||u,function(a,b){return"'+\n("+w(b)+")+\n'"}).replace(d.evaluate||u,function(a,b){return"';\n"+w(b)+"\n;__p+='"})+"';\n";d.variable||(a="with(obj||{}){\n"+a+"}\n");var a="var __p='';var print=function(){__p+=Array.prototype.join.call(arguments, '')};\n"+a+"return __p;\n",e=new Function(d.variable||"obj","_",a);if(c)return e(c,b);c=function(a){return e.call(this,a,b)};c.source="function("+(d.variable||"obj")+"){\n"+a+"}";return c};
+b.chain=function(a){return b(a).chain()};var m=function(a){this._wrapped=a};b.prototype=m.prototype;var x=function(a,c){return c?b(a).chain():a},M=function(a,c){m.prototype[a]=function(){var a=i.call(arguments);J.call(a,this._wrapped);return x(c.apply(b,a),this._chain)}};b.mixin(b);j("pop,push,reverse,shift,sort,splice,unshift".split(","),function(a){var b=k[a];m.prototype[a]=function(){var d=this._wrapped;b.apply(d,arguments);var e=d.length;(a=="shift"||a=="splice")&&e===0&&delete d[0];return x(d,
+this._chain)}});j(["concat","join","slice"],function(a){var b=k[a];m.prototype[a]=function(){return x(b.apply(this._wrapped,arguments),this._chain)}});m.prototype.chain=function(){this._chain=true;return this};m.prototype.value=function(){return this._wrapped}}).call(this);
View
16 test/test_helper.rb
@@ -9,6 +9,22 @@
end
class MiniTest::Unit::TestCase
+
+ def load_system_js
+ Mongoid.default_session['system.js'].drop
+ Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', "library_functions", '*.js')).each do |json_fixture_file|
+ name = File.basename(json_fixture_file,".*")
+ fn = "function () {\n #{File.read(json_fixture_file)} \n }"
+ Mongoid.default_session['system.js'].find('_id' => name).upsert(
+ {
+ "_id" => name,
+ "value" => Moped::BSON::Code.new(fn)
+ }
+ )
+ end
+
+ end
+
# Add more helper methods to be used by all tests here...
def collection_fixtures(db, collection, *id_attributes)
View
1 test/unit/qme/map/map_reduce_builder_test.rb
@@ -6,6 +6,7 @@ class MapReduceBuilderTest < MiniTest::Unit::TestCase
def setup
raw_measure_json = File.read(File.join('test', 'fixtures', 'measures', 'measure_metadata.json'))
@measure_json = JSON.parse(raw_measure_json)
+ load_system_js
end
def test_extracting_measure_metadata
View
2 test/unit/qme/map/map_reduce_executor_test.rb
@@ -9,6 +9,8 @@ def setup
get_db['patient_cache'].drop()
collection_fixtures(get_db(), 'measures')
collection_fixtures(get_db(), 'records', '_id')
+ collection_fixtures(get_db(), 'bundles')
+ load_system_js
end
def test_map_records_into_measure_groups
View
2 test/unit/qme/map/measure_calculation_job_test.rb
@@ -8,6 +8,8 @@ def setup
get_db['patient_cache'].drop()
collection_fixtures(get_db(), 'measures')
collection_fixtures(get_db(), 'records', '_id')
+ collection_fixtures(get_db(), 'bundles')
+ load_system_js
Delayed::Worker.delay_jobs = false
end
View
3 test/unit/qme/quality_measure_test.rb
@@ -5,7 +5,8 @@ class QualityMeasureTest < MiniTest::Unit::TestCase
def setup
collection_fixtures(get_db(), 'measures')
-
+ collection_fixtures(get_db(), 'bundles')
+ load_system_js
end
def test_getting_all_measures
View
2 test/unit/qme/quality_report_test.rb
@@ -4,6 +4,8 @@ class QualityReportTest < MiniTest::Unit::TestCase
include QME::DatabaseAccess
def setup
+ load_system_js
+ collection_fixtures(get_db(), 'bundles')
get_db()['query_cache'].drop()
get_db()['patient_cache'].drop()
get_db()['query_cache'].insert(

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