open_ehr 0.6.1 → 0.9.0

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-OBSERVATION.body_mass_index.v1.adl

@@ -0,0 +1,166 @@
+archetype (adl_version=1.4)
+	openEHR-EHR-OBSERVATION.body_mass_index.v1
+
+concept
+	[at0000]	-- Body mass index
+language
+	original_language = <[ISO_639-1::en]>
+description
+	original_author = <
+		["name"] = <"Sam Heard">
+		["organisation"] = <"Ocean Informatics">
+		["email"] = <"sam.heard@oceaninformatics.com">
+		["date"] = <"22/03/2006">
+	>
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"To record the Body Mass Index (BMI) of a person.
+Body Mass Index is a calculated ratio describing how an individual's body weight relates to the weight that is regarded as normal, or desirable, for the individual's height. ">
+			use = <"Use to record the Body Mass Index of both adults and children.  
+Use to enter the Body Mass Index either manually (ie calculated and directly entered by the clinician), or automatically (ie calculation and entry is done automatically by a software application, based on separate height and weight measurements).
+Formulas: Body Mass Index is commonly calculated as weight (kg) / [height (m) squared]. This is the assumed formula unless otherwise specified in the Formula element within Protocol. Alternatively estimate Body Mass Index using pounds and inches: weight (lb) / [height (in) squared] x 703 (with ounces (oz) and fractions changed to decimal values).
+In some situations the Body Mass Index formula is corrected eg for use in amputees - this specific formula can be recorded as part of the protocol.  Alternatively the common Body Mass Index calculation can be used with amputees and similar injuries or disabilities if using adjusted height and/or adjusted weight, as appropriate, rather than actual height and weight.   See openEHR-EHR-OBSERVATION.height-adjusted and openEHR-EHR-OBSERVATION.body_weight-adjusted.
+See WHO reference re adjusting height/length for Body Mass Index in paediatrics. 
+In children and teens, BMI needs to be assessed using age-related reference charts. 
+">
+			keywords = <"obesity", "index", "body mass", "BMI", "anorexia", "Quetelet", "malnutrition", "failure to thrive", "bulimia">
+			misuse = <"Not intended to record information regarding Body Mass Index percentiles - these will be recorded in separate archetypes.">
+			copyright = <"copyright (c) 2009 openEHR Foundation">
+		>
+	>
+	lifecycle_state = <"Initial">
+	other_contributors = <"Marja Buur, Medisch Centrum Alkmaar, Netherlands", "Rong Chen, Cambio Healthcare Systems, Sweden", "Angela de Zwart, Orion Health, New Zealand", "Paul Donaldson, Nursing Informatics Australia, Australia", "Sebastian Garde, Ocean Informatics, Germany", "Heather Grain, Llewelyn Grain Informatics, Australia", "Anne Harbison, CPCER, Australia", "Sam Heard, Ocean Informatics, Australia", "Andrew James, University of Toronto, Canada", "Shinji Kobayashi, Ehime University, Japan", "Heather Leslie, Ocean Informatics, Australia (Editor)", "Rikard Lovstrom, Swedish Medical Association, Sweden", "Ian McNicoll, Ocean Informatics, United Kingdom">
+	other_details = <
+		["MD5-CAM-1.0.1"] = <"1605E211E9BFB4093A72CCE7A9792FF9">
+		["references"] = <"Clinical Guidelines on the Identification, Evaluation, and Treatment of Overweight and Obesity in Adults: The Evidence Report [Internet]. Bethesda (MD): National Heart, Lung, and Blood Institute; NIH Publication No. 98-4083, Sep 1998, [cited 2009 July 02]. Available from: http://www.nhlbi.nih.gov/guidelines/obesity/
+
+About BMI for Children and Teens [Internet]. Atlanta (GA): Division of Nutrition, Physical Activity and Obesity, Centers for Disease Control and Prevention; 2009 Jan 27 [cited 2009 Jul 28 ]. Available from: http://www.cdc.gov/healthyweight/assessing/bmi/childrens_BMI/about_childrens_BMI.html
+
+WHO Child Growth Standards: Length/height-for-age, weight-for-age, weight-for-length, weight-for-height and body mass index-for-age: Methods and development. [Internet] Geneva, Switzerland: WHO Multicentre Growth Reference Study Group, World Health Organization; 2006 [cited 2009 July 02].  Chapter 6, BMI-for-age standards. Available from: http://www.who.int/childgrowth/standards/Chap_6.pdf.
+
+Obesity: Preventing and Managing the Global Epidemic: Report of a WHO Consultation [Internet]. Geneva, Switzerland: World Health Organisation; 2000 [cited 2009 Jul 28]. Available from: http://www.who.int/nutrition/publications/obesity/WHO_TRS_894/en/index.html
+
+Tzamaloukas AH, Patron A, Malhotra D. Body Mass Index in Amputees. Journal of Parenteral and Enteral Nutrition [Internet]. 1994 [cited 2009 Jul 28]; 18 (4): 355. Available from: http://pen.sagepub.com/cgi/content/abstract/18/4/355  
+
+
+
+">
+	>
+
+definition
+	OBSERVATION[at0000] matches {	-- Body mass index
+		data matches {
+			HISTORY[at0001] matches {	-- history
+				events cardinality matches {1..*; unordered} matches {
+					EVENT[at0002] occurrences matches {1..*} matches {	-- Any event
+						data matches {
+							ITEM_TREE[at0003] matches {	-- Single
+								items cardinality matches {1..*; unordered} matches {
+									ELEMENT[at0004] matches {	-- Body Mass Index
+										value matches {
+											C_DV_QUANTITY <
+												property = <[openehr::349]>
+												list = <
+													["1"] = <
+														units = <"kg/m2">
+														magnitude = <|0.0..<1000.0|>
+														precision = <|1|>
+													>
+													["2"] = <
+														units = <"lb/in2">
+														magnitude = <|0.0..<1000.0|>
+														precision = <|1|>
+													>
+												>
+											>
+										}
+									}
+								}
+							}
+						}
+					}
+				}
+			}
+		}
+		protocol matches {
+			ITEM_LIST[at0005] matches {	-- List
+				items cardinality matches {0..*; ordered} matches {
+					ELEMENT[at0006] occurrences matches {0..1} matches {	-- Method
+						value matches {
+							DV_CODED_TEXT matches {
+								defining_code matches {
+									[local::
+									at0007, 	-- Automatic entry
+									at0008]	-- Direct entry
+								}
+							}
+						}
+					}
+					ELEMENT[at0010] occurrences matches {0..1} matches {	-- Formula
+						value matches {
+							DV_TEXT matches {*}
+						}
+					}
+					ELEMENT[at0011] occurrences matches {0..1} matches {	-- Comment
+						value matches {
+							DV_TEXT matches {*}
+						}
+					}
+				}
+			}
+		}
+	}
+
+
+ontology
+	term_definitions = <
+		["en"] = <
+			items = <
+				["at0000"] = <
+					text = <"Body mass index">
+					description = <"Calculated measurement which compares a person's weight and height.">
+				>
+				["at0001"] = <
+					text = <"history">
+					description = <"@ internal @">
+				>
+				["at0002"] = <
+					text = <"Any event">
+					description = <"Any timed recording of Body Mass Index.">
+				>
+				["at0003"] = <
+					text = <"Single">
+					description = <"@ internal @">
+				>
+				["at0004"] = <
+					text = <"Body Mass Index">
+					description = <"Index describing ratio of weight to height.">
+				>
+				["at0005"] = <
+					text = <"List">
+					description = <"@ internal @">
+				>
+				["at0006"] = <
+					text = <"Method">
+					description = <"The method of entering the Body Mass Index.">
+				>
+				["at0007"] = <
+					text = <"Automatic entry">
+					description = <"Body Mass Index calculated and entered automatically without user intervention.">
+				>
+				["at0008"] = <
+					text = <"Direct entry">
+					description = <"Body Mass Index calculated and entered directly by user.">
+				>
+				["at0010"] = <
+					text = <"Formula">
+					description = <"Formula used to derive the Body Mass Index.">
+				>
+				["at0011"] = <
+					text = <"Comment">
+					description = <"Comment about the Body Mass Index measurement eg noting that the measurements used were adjusted weight/height.">
+				>
+			>
+		>
+	>

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-SECTION.findings.v1.adl

@@ -0,0 +1,47 @@
+archetype (adl_version=1.4)
+	openEHR-EHR-SECTION.findings.v1
+
+concept
+	[at0000]	-- Clinical findings
+language
+	original_language = <[ISO_639-1::en]>
+description
+	original_author = <
+		["name"] = <"Sam Heard">
+		["organisation"] = <"Ocean Informatics">
+		["date"] = <"9/01/2007">
+		["email"] = <"sam.heard@oceaninformatics.biz">
+	>
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"A heading to contain clinical findings">
+			use = <"A section which only contains observations">
+			keywords = <"findings", ...>
+			misuse = <"">
+		>
+	>
+	lifecycle_state = <"Initial">
+	other_contributors = <>
+
+definition
+	SECTION[at0000] matches {	-- Clinical findings
+		items cardinality matches {0..*; unordered} matches {
+			allow_archetype OBSERVATION occurrences matches {0..1} matches {
+				include
+					archetype_id/value matches {/.*/}
+			}
+		}
+	}
+
+ontology
+	term_definitions = <
+		["en"] = <
+			items = <
+				["at0000"] = <
+					description = <"The findings at this contact">
+					text = <"Clinical findings">
+				>
+			>
+		>
+	>

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-SECTION.reason_for_encounter.v1.adl

@@ -0,0 +1,51 @@
+archetype (adl_version=1.4)
+	openEHR-EHR-SECTION.reason_for_encounter.v1
+
+concept
+	[at0000]	-- Reason for encounter
+language
+	original_language = <[ISO_639-1::en]>
+description
+	original_author = <
+		["name"] = <"Sam Heard">
+		["organisation"] = <"Ocean Informatics">
+		["date"] = <"9/01/2007">
+		["email"] = <"sam.heard@oceaninformatics.biz">
+	>
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"A heading to display the reason for encounter">
+			use = <"To record a symptom, problem or other reason for encounter">
+			keywords = <"rfe", "reason">
+			misuse = <"">
+		>
+	>
+	lifecycle_state = <"Initial">
+	other_contributors = <>
+
+definition
+	SECTION[at0000] matches {	-- Reason for encounter
+		items cardinality matches {0..*; unordered} matches {
+			allow_archetype OBSERVATION occurrences matches {1..*} matches {
+				include
+					archetype_id/value matches {/.*/}
+			}
+			allow_archetype EVALUATION occurrences matches {0..1} matches {
+				include
+					archetype_id/value matches {/.*/}
+			}
+		}
+	}
+
+ontology
+	term_definitions = <
+		["en"] = <
+			items = <
+				["at0000"] = <
+					description = <"The reason(s) for this particular encounter">
+					text = <"Reason for encounter">
+				>
+			>
+		>
+	>

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-SECTION.summary.v1.adl

@@ -0,0 +1,52 @@
+archetype (adl_version=1.4)
+	openEHR-EHR-SECTION.summary.v1
+
+concept
+	[at0000]	-- Summary
+language
+	original_language = <[ISO_639-1::en]>
+description
+	original_author = <
+		["name"] = <"Sam Heard">
+		["organisation"] = <"Ocean Informatics">
+		["date"] = <"9/01/2007">
+		["email"] = <"sam.heard@oceaninformatics.biz">
+	>
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"A heading containing summary information based on particular evaluation entries">
+			use = <"A heading for organising clinical data under a heading of summary">
+			keywords = <"review", "conclusions", "risk">
+			misuse = <"">
+		>
+	>
+	lifecycle_state = <"Initial">
+	other_contributors = <>
+
+definition
+	SECTION[at0000] matches {	-- Summary
+		items cardinality matches {0..*; unordered} matches {
+			allow_archetype EVALUATION occurrences matches {0..1} matches {
+				include
+					archetype_id/value matches {/clinical_synopsis\.v1/}
+					archetype_id/value matches {/problem\.v1/}
+					archetype_id/value matches {/problem-diagnosis\.v1/}
+					archetype_id/value matches {/problem-diagnosis-histological\.v1/}
+					archetype_id/value matches {/problem-genetic\.v1/}
+					archetype_id/value matches {/risk\.v1/}
+			}
+		}
+	}
+
+ontology
+	term_definitions = <
+		["en"] = <
+			items = <
+				["at0000"] = <
+					description = <"A heading for conclusions and other evaluations">
+					text = <"Summary">
+				>
+			>
+		>
+	>

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-SECTION.vital_signs.v1.adl

@@ -0,0 +1,54 @@
+archetype (adl_version=1.4)
+	openEHR-EHR-SECTION.vital_signs.v1
+
+concept
+	[at0000]	-- Vital signs
+language
+	original_language = <[ISO_639-1::en]>
+description
+	original_author = <
+		["name"] = <"Sam Heard">
+		["organisation"] = <"Ocean Informatics">
+		["date"] = <"14/03/2006">
+		["email"] = <"sam.heard@oceaninformatics.biz">
+	>
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"A heading or section which can only contain observations considered to be vital signs. This group of observations is a common set in medicine, and while these often occur separately in health records, when they are measured together this is a significant assessment of wellbeing.">
+			use = <"An organisational heading for vital signs">
+			keywords = <"blood pressure", "temperature", "pulse", "oxygen saturation", "respirations", "observations", "vital", "signs">
+			misuse = <"Does not need to be used to record these entries separately">
+		>
+	>
+	lifecycle_state = <"AuthorDraft">
+	other_contributors = <>
+
+definition
+	SECTION[at0000] matches {	-- Vital signs
+		items cardinality matches {0..*; unordered} matches {
+			allow_archetype OBSERVATION occurrences matches {1..5} matches {
+				include
+					archetype_id/value matches {/blood_pressure\.v1/}
+					archetype_id/value matches {/heart_rate-pulse\.v1/}
+					archetype_id/value matches {/respiration\.v1/}
+					archetype_id/value matches {/body_temperature\.v1/}
+					archetype_id/value matches {/oximetry\.v1/}
+					archetype_id/value matches {/heart_rate\.v1/}
+				exclude
+					archetype_id/value matches {/.*/}
+			}
+		}
+	}
+
+ontology
+	term_definitions = <
+		["en"] = <
+			items = <
+				["at0000"] = <
+					description = <"A group of observations that are recorded at the same time and record the blood pressure, pulse, temperature and other readings">
+					text = <"Vital signs">
+				>
+			>
+		>
+	>

data/spec/lib/open_ehr/parser/adl/openEHR-EHR-cadl_sample.v1.adl

@@ -0,0 +1,9 @@
+SECTION[at0000] matches {	-- Summary
+	items cardinality matches {0..*; unordered} matches {
+		allow_archetype EVALUATION occurrences matches {0..1} matches {
+			include
+				archetype_id/value matches {/clinical_synopsis\.v1/}				archetype_id/value matches {/problem\.v1/}					archetype_id/value matches {/problem-diagnosis\.v1/}
+				archetype_id/value matches {/problem-diagnosis-histological\.v1/}
+				archetype_id/value matches {/problem-genetic\.v1/}
+	}
+}

data/spec/lib/open_ehr/parser/adl_parser_spec.rb

@@ -0,0 +1,210 @@
+require File.dirname(__FILE__) + '/../../../spec_helper'
+include OpenEHR::Parser
+include OpenEHR::AM::Archetype::ConstraintModel
+include OpenEHR::AM::Archetype::Assertion
+
+describe ADLParser do
+
+  before (:all) do
+    @adl_dir = File.dirname(__FILE__) + '/adl/'
+  end
+
+  context 'openEHR-EHR-SECTION-summary.v1.adl' do
+    before(:all) do
+      @ap = OpenEHR::Parser::ADLParser.new(@adl_dir + 'openEHR-EHR-SECTION.summary.v1.adl')
+    end
+
+    it 'is an instance fo ADLParser' do
+      @ap.should be_an_instance_of ADLParser
+    end
+
+    context 'openEHR-EHR-SECTION.summary.v1 parse' do
+      context 'ADL parser generates archetype from ADL' do
+        before(:all) do
+          @archetype = @ap.parse
+        end
+
+        it 'archetype_id should be openEHR-EHR-SECTION-summary' do
+          @archetype.archetype_id.should == 'openEHR-EHR-SECTION.summary.v1'
+        end
+
+        it 'adl_version should be 1.4' do
+          @archetype.adl_version.should == '1.4'
+        end
+
+        it 'concept should be at0000]' do
+          @archetype.concept.should == 'at0000'
+        end
+
+        it 'original language is ISO_639-1::en' do
+          @archetype.original_language.should == 'ISO_639-1::en'
+        end
+
+        context 'description' do
+          before(:all) do
+            @description = @archetype.description
+          end
+
+          context 'original author' do
+            before(:all) do
+              @original_author = @description[:original_author]
+            end
+
+            it 'name is Sam Heard' do
+              @original_author[:name].should == 'Sam Heard'
+            end
+
+            it 'organisation is Ocean Informatics' do
+              @original_author[:organisation].should == 'Ocean Informatics'
+            end
+
+            it 'date is 9/01/2007' do
+              @original_author[:date].should == '9/01/2007'
+            end
+
+            it 'email is sam.heard@oceaninformatics.biz' do
+              @original_author[:email].should == 'sam.heard@oceaninformatics.biz'
+            end
+          end
+
+          context 'details' do
+            before(:all) do
+              @details = @description[:details]
+            end
+
+            context 'en details' do
+              before(:all) do
+                @en = @details[:en]
+              end
+
+              it 'language is ISO_639-1::en' do
+                @en[:language].should == 'ISO_639-1::en'
+              end 
+
+              it 'purpose is A heading...' do
+                @en[:purpose].should == "A heading containing summary information based on particular evaluation entries"
+              end
+
+              it 'use is A heading for...' do
+                @en[:use].should == "A heading for organising clinical data under a heading of summary"
+              end
+
+              it 'keywords are review, conclusions, risk' do
+                @en[:keywords].should == ['review', 'conclusions', 'risk']
+              end
+
+              it 'misuse should empty' do
+                @en[:misuse].should == ''
+              end
+            end
+
+            it 'lifecycle_state is Initial' do
+              @description[:lifecycle_state].should == 'Initial'
+            end
+
+            it 'other_contributors is nil' do
+              @description[:other_contributors].should be_nil
+            end
+          end # of details
+        end # of description
+
+        context 'definition section' do
+          before(:all) do
+            @definition = @archetype.definition
+          end
+
+          it 'rm_type is SECTION' do
+            @definition.rm_type_name.should == 'SECTION'
+          end
+
+          it 'node_id is at0000' do
+            @definition.node_id.should == 'at0000'
+          end
+
+          it 'root path is /' do
+            @definition.path.should == '/'
+          end
+
+          it 'not any allowed' do
+            @definition.any_allowed?.should == false
+          end
+
+          context 'c_attribute specs' do
+            before(:all) do
+              @attribute = @definition.attributes[0]
+            end
+
+            it 'attribute is instance of CMultipleAttribute' do
+              @attribute.should be_an_instance_of CMultipleAttribute
+            end
+
+            it 'rm_attribute_name is items' do
+              @attribute.rm_attribute_name.should == 'items'
+            end
+
+            it 'path is /items' do
+              @attribute.path.should == '/items'
+            end
+
+            it 'cardinarity is unorderd' do
+              @attribute.cardinality.should_not be_ordered
+            end
+
+            it 'lower interval of cardinality is 0' do
+              @attribute.cardinality.interval.lower.should be 0
+            end
+
+            it 'interval of cardinality is upper unbounded' do
+              @attribute.cardinality.interval.should be_upper_unbounded
+            end
+            context 'children archetype slot specs' do
+              before(:all) do
+                @archetype_slot = @attribute.children[0]
+              end
+
+              it 'is an instance of ArchetypeSlot' do
+                @archetype_slot.should be_an_instance_of ArchetypeSlot
+              end
+
+              it 's rm type name is EVALUATION' do
+                @archetype_slot.rm_type_name.should == 'EVALUATION'
+              end
+
+              it 's lower of occurrences should be 0' do
+                @archetype_slot.occurrences.lower.should be 0
+              end
+
+              it 's upper of occurrences should be 1' do
+                @archetype_slot.occurrences.upper.should be 1
+              end
+
+              context 'assertions' do
+                before(:all) do
+                  @includes = @archetype_slot.includes
+                end
+
+                context '1st assertion' do
+                  before(:all) do
+                    @assertion0 = @includes[0]
+                  end
+
+                  it 'assertion0 should be an instance of assertion' do
+                    @assertion0.should be_an_instance_of Assertion
+                  end
+
+                  it 'expression type of assertion0 is Boolean' do
+                    @assertion0.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of assertion0 is /clinical_synopsis\.v1/' do
+                    @assertion0.expression.item.pattern.should == '/clinical_synopsis\.v1/'
+                  end
+                end
+              end
+            end
+          end
+        end #definition
+      end
+    end
+  end
+end

data/spec/lib/open_ehr/parser/base_spec.rb

@@ -0,0 +1,19 @@
+require File.dirname(__FILE__) + '/../../../spec_helper'
+include OpenEHR::Parser
+
+describe Base do
+  context 'create an instance' do
+    before do
+      adl_dir = File.dirname(__FILE__)+'/adl/'
+      @bp = Base.new(adl_dir + 'openEHR-EHR-SECTION.summary.v1.adl')
+    end
+
+    it 'creates an instance' do
+      @bp.should be_an_instance_of Base
+    end
+
+    it 'returns filename' do
+      @bp.filename.should match /openEHR-EHR-SECTION.summary.v1.adl$/
+    end
+  end
+end

data/spec/spec.opts

@@ -1,5 +1,6 @@
 --drm
 --colour
 --format specdoc
---loadby mtime
 --reverse
+
+#--loadby mtime

data/spec/spec_helper.rb

@@ -1,5 +1,8 @@
 require 'rubygems'
 require 'spork'
+require 'simplecov'
+
+SimpleCov.start
 
 Spork.prefork do
   # Loading more in this block will cause your tests to run faster. However,