health-data-standards 3.2.10 → 3.2.11

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/health-data-standards/export/helper/scooped_view_helper.rb

@@ -92,6 +92,10 @@ module HealthDataStandards
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.63')
               when  '2.16.840.1.113883.3.560.1.63' 
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.6')
+              when '2.16.840.1.113883.3.560.1.3' 
+                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.11')
+              when  '2.16.840.1.113883.3.560.1.11' 
+                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.3')
               end
  
             codes = (value_set_map(patient["bundle_id"])[data_criteria.code_list_id] || [])

data/lib/health-data-standards/ext/node.rb

@@ -0,0 +1,46 @@
+# This is a freedom patch that will only be applied when using JRuby
+# Currently, Nokogiri does not properly handle namespace prefixes
+# when they are set on the document root and then used in XPath
+# expressions. We should be able to remove this patch if/when
+# Rob's pull request is accepted:
+# https://github.com/sparklemotion/nokogiri/pull/959
+if RUBY_PLATFORM.include?('java')
+  module Nokogiri
+    module XML
+      NAMESPACES = {'cda' => 'urn:hl7-org:v3',
+                'sdtc' => 'urn:hl7-org:sdtc',
+                'gc32' => 'urn:hl7-org:greencda:c32',
+                'ccr' => 'urn:astm-org:CCR',
+                'vs' => 'urn:ihe:iti:svs:2008',
+                'xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
+                'hrf-md' => 'http://www.hl7.org/schemas/hdata/2009/11/metadata',
+                'nlm' => 'urn:ihe:iti:svs:2008'
+                }
+      class Node
+        alias_method :old_at_xpath, :at_xpath
+        alias_method :old_xpath, :xpath
+
+        def xpath(*args)
+          old_xpath(*args, NAMESPACES)
+        end
+
+        def at_xpath(*args)
+          old_at_xpath(*args, NAMESPACES)
+        end
+      end
+
+      class NodeSet
+        alias_method :old_at_xpath, :at_xpath
+        alias_method :old_xpath, :xpath
+
+        def xpath(*args)
+          old_xpath(*args, NAMESPACES)
+        end
+
+        def at_xpath(*args)
+          old_at_xpath(*args, NAMESPACES)
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cda/provider_importer.rb

@@ -32,7 +32,7 @@ module HealthDataStandards
           provider = {}
           entity = performer.xpath(entity_path)
           
-          name = entity.xpath("./cda:assignedPerson/cda:name")
+          name = entity.at_xpath("./cda:assignedPerson/cda:name")
           provider[:title]        = extract_data(name, "./cda:prefix")
           provider[:given_name]   = extract_data(name, "./cda:given[1]")
           provider[:family_name]  = extract_data(name, "./cda:family")
@@ -51,6 +51,7 @@ module HealthDataStandards
           provider[:telecoms] = performer.xpath("./cda:assignedEntity/cda:telecom").try(:map) {|te| import_telecom(te)}
           
           provider[:npi] = npi if Provider.valid_npi?(npi)
+          
           provider
         end
       
@@ -61,7 +62,7 @@ module HealthDataStandards
       
         # Returns nil if result is an empty string, block allows text munging of result if there is one
         def extract_data(subject, query)
-          result = subject.xpath(query).text
+          result = subject.try(:xpath,query).try(:text)
           if result == ""
             nil
           else

data/lib/health-data-standards/tasks/bundle.rake

@@ -3,6 +3,32 @@ require 'health-data-standards'
 db_name = ENV['DB_NAME'] || 'test'
 
 namespace :bundle do
+
+  desc 'Activate/Inactivate a measure bundle'
+  task :activate,[:version,:active] => [:environment] do |task, args|
+    bundle = Bundle.where({version: args.version})
+    if bundle.count == 0
+      puts "Cannot find bundle with version number #{args.version}"
+      return
+    end
+
+    bundle.each do |b|
+      b.active = (args.active == "true")
+      b.save
+      puts "Bundle #{b.title} - #{b.version}  active: #{b.active}"
+    end
+
+  end
+
+
+  desc 'List bundles'
+  task :list  => [:environment] do 
+     Bundle.where({}).each do |b|
+      puts "Bundle #{b.title} - #{b.version}  active: #{b.active}"
+     end
+  end
+
+
   desc 'Import a quality bundle into the database.'
   task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes] => [:environment] do |task, args|
     raise "The path to the measures zip file must be specified" unless args.bundle_path

data/lib/health-data-standards.rb

@@ -12,6 +12,7 @@ require 'memoist'
 # Freedom patches
 require_relative 'health-data-standards/ext/symbol'
 require_relative 'health-data-standards/ext/string'
+require_relative 'health-data-standards/ext/node'
 
 require_relative 'health-data-standards/util/hl7_helper'
 require_relative 'health-data-standards/util/code_system_helper'

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.11.cat1.erb

@@ -14,7 +14,7 @@
       <!-- Attribute: discharge datetime -->
       <high <%= value_or_null_flavor(entry.end_time) %>/>
     </effectiveTime>
-    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :reason_oids=>field_oids["ORDINALITY"]}) %>
+    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :reason_oids=>field_oids["ORDINAL"]}) %>
     
     <%== code_display(entry, {'tag_name' => 'value', 'value_set_map' => value_set_map,'preferred_code_sets' => ['LOINC', 'SNOMED-CT', 'ICD-9-CM', 'ICD-10-CM'],
                                                     'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\""}) %>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.13.cat1.erb

@@ -15,7 +15,7 @@
     <!-- Attribute: Stop Datetime -->
     <high <%= value_or_null_flavor(entry.end_time) %>/>
   </effectiveTime>
-  <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINALITY"]}) %>
+  <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINAL"]}) %>
 
   <%== code_display(entry, 'value_set_map' => value_set_map,'tag_name' => 'value', 'preferred_code_sets' => ['SNOMED-CT', 'ICD-9-CM', 'ICD-10-CM', 'LOINC'], 'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
   <!-- Status -->

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.14.cat1.erb

@@ -14,7 +14,7 @@
       <!-- Attribute: Stop Datetime -->
       <high <%= value_or_null_flavor(entry.end_time) %>/>
     </effectiveTime>
-    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINALITY"]}}) %>
+    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINAL"]}}) %>
 
     <%== code_display(entry, 'value_set_map' => value_set_map,'tag_name' => 'value', 'preferred_code_sets' => ['SNOMED-CT', 'ICD-9-CM', 'ICD-10-CM', 'CPT'],
                              'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.64.cat1.erb

@@ -12,7 +12,7 @@
       <low <%= value_or_null_flavor(entry.start_time) %>/>
       <high <%= value_or_null_flavor(entry.end_time) %>/>
     </effectiveTime>
-    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINALITY"]}) %>
+    <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINAL"]}) %>
     <%== render(:partial => 'reason', :locals => {:entry => entry, :reason_oids=>field_oids["REASON"]}) %>
     <% if entry.respond_to?(:incision_time) && entry.incision_time.present? -%>
     <entryRelationship typeCode="REFR">

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 3.2.10
+  version: 3.2.11
 platform: ruby
 authors:
 - Andy Gregorowicz
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-28 00:00:00.000000000 Z
+date: 2013-09-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -180,6 +180,7 @@ files:
 - lib/health-data-standards/export/rendering_context.rb
 - lib/health-data-standards/export/template_helper.rb
 - lib/health-data-standards/export/view_helper.rb
+- lib/health-data-standards/ext/node.rb
 - lib/health-data-standards/ext/string.rb
 - lib/health-data-standards/ext/symbol.rb
 - lib/health-data-standards/import/bundle/importer.rb
@@ -505,7 +506,8 @@ files:
 - Rakefile
 - VERSION
 homepage: https://github.com/projectcypress/health-data-standards
-licenses: []
+licenses:
+- APL 2.0
 metadata: {}
 post_install_message: 
 rdoc_options: []