From 39f290cf79ff64bbbc2a4684990b71681e603c03 Mon Sep 17 00:00:00 2001
From: dbojicic <148293341+dbojicic@users.noreply.github.com>
Date: Thu, 16 Jan 2025 21:43:11 +1000
Subject: [PATCH] QA fixes in StructureDefinitions (#312)

* Removed comments from gender identity and individual pronouns

* Removed short and definition from the identifier

* Rreorder invariants, correct invariant expressions, and align with FHIR-43848 changes

* Remove short from Observation.status and reorder invariants
---
 input/resources/au-core-bloodpressure.xml        |  2 +-
 input/resources/au-core-bodytemp.xml             | 12 ++++++------
 .../resources/au-core-diagnosticresult-path.xml  | 11 +++++------
 input/resources/au-core-diagnosticresult.xml     | 13 ++++++-------
 input/resources/au-core-heartrate.xml            |  2 +-
 input/resources/au-core-location.xml             |  2 --
 input/resources/au-core-patient.xml              |  2 --
 input/resources/au-core-procedure.xml            |  2 +-
 input/resources/au-core-resprate.xml             | 12 ++++++------
 input/resources/au-core-smokingstatus.xml        | 16 ++++++++--------
 input/resources/au-core-waistcircum.xml          | 12 ++++++------
 11 files changed, 40 insertions(+), 46 deletions(-)

diff --git a/input/resources/au-core-bloodpressure.xml b/input/resources/au-core-bloodpressure.xml
index bfed0aad..4bfadfd5 100644
--- a/input/resources/au-core-bloodpressure.xml
+++ b/input/resources/au-core-bloodpressure.xml
@@ -248,7 +248,7 @@
       <constraint>
         <key value="au-core-obs-01"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-bloodpressure"/>
diff --git a/input/resources/au-core-bodytemp.xml b/input/resources/au-core-bodytemp.xml
index 6f91c0e2..2f6a3767 100644
--- a/input/resources/au-core-bodytemp.xml
+++ b/input/resources/au-core-bodytemp.xml
@@ -21,7 +21,7 @@
       <definition value="Measurement of a patient's body temperature at a point in time."/>
       <comment value="Body temperature observation using a LOINC code, a SNOMED CT code and a metric UCUM unit of measure."/>
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="At least value or data absent reason shall be present"/>
         <expression value="dataAbsentReason.exists() or value.exists()"/>
@@ -250,7 +250,7 @@
       </extension>
       <path value="Observation.valueQuantity"/>
       <short value="Body temperature"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element>
     <element id="Observation.valueQuantity.value">
       <extension url="http://hl7.org/fhir/StructureDefinition/obligation">
@@ -361,15 +361,15 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element>
     <element id="Observation.bodySite">
       <path value="Observation.bodySite" />
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodytemp"/>
diff --git a/input/resources/au-core-diagnosticresult-path.xml b/input/resources/au-core-diagnosticresult-path.xml
index 10f8ef36..f0aceafb 100644
--- a/input/resources/au-core-diagnosticresult-path.xml
+++ b/input/resources/au-core-diagnosticresult-path.xml
@@ -18,7 +18,7 @@
     <element id="Observation">
       <path value="Observation"/>
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="If there is no component or hasMember element then at least value or data absent reason shall be present"/>
         <expression value="(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())"/>
@@ -44,7 +44,6 @@
         </extension>
       </extension>
       <path value="Observation.status"/>
-      <short value="preliminary | final | amended +"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.category">
@@ -136,9 +135,9 @@
       </extension>
       <path value="Observation.effective[x]"/>
       <short value="Time of specimen collection"/>
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
         <human value="Date shall be at least to day or, if not available, the Data Absent Reason extension shall be present"/>
         <expression value="(($this is dateTime implies $this.toString().length() >= 10) and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists().not()) xor ($this is dateTime implies ($this.hasValue().not() and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists()))"/>
@@ -193,7 +192,7 @@
         </extension>
       </extension>
       <path value="Observation.value[x]"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.dataAbsentReason">
@@ -214,7 +213,7 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.interpretation">
diff --git a/input/resources/au-core-diagnosticresult.xml b/input/resources/au-core-diagnosticresult.xml
index 7643c746..01a813a4 100644
--- a/input/resources/au-core-diagnosticresult.xml
+++ b/input/resources/au-core-diagnosticresult.xml
@@ -18,7 +18,7 @@
     <element id="Observation">
       <path value="Observation"/>
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="If there is no component or hasMember element then at least value or data absent reason shall be present"/>
         <expression value="(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())"/>
@@ -44,7 +44,6 @@
         </extension>
       </extension>
       <path value="Observation.status"/>
-      <short value="preliminary | final | amended +"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.category">
@@ -133,9 +132,9 @@
       </extension>
       <path value="Observation.effective[x]"/>
       <min value="1"/>
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
         <human value="Date shall be at least to day or, if not available, the Data Absent Reason extension shall be present"/>
         <expression value="(($this is dateTime implies $this.toString().length() >= 10) and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists().not()) xor ($this is dateTime implies ($this.hasValue().not() and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists()))"/>
@@ -190,7 +189,7 @@
         </extension>
       </extension>
       <path value="Observation.value[x]"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.dataAbsentReason">
@@ -211,7 +210,7 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
     </element>
     <element id="Observation.bodySite">
@@ -236,7 +235,7 @@
       <constraint>
         <key value="au-core-obs-04"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult"/>
diff --git a/input/resources/au-core-heartrate.xml b/input/resources/au-core-heartrate.xml
index 001b1e95..e53c0418 100644
--- a/input/resources/au-core-heartrate.xml
+++ b/input/resources/au-core-heartrate.xml
@@ -345,7 +345,7 @@
       <constraint>
         <key value="au-core-obs-01"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-heartrate"/>
diff --git a/input/resources/au-core-location.xml b/input/resources/au-core-location.xml
index 55eb4f2d..d9d3e6c9 100644
--- a/input/resources/au-core-location.xml
+++ b/input/resources/au-core-location.xml
@@ -29,8 +29,6 @@
     </element>
     <element id="Location.identifier">
       <path value="Location.identifier"/>
-      <short value="Unique code or number identifying the location to its users" />
-      <definition value="Unique code or number identifying the location to its users." />
       <condition value="au-core-loc-01"/>
     </element>
     <element id="Location.name">
diff --git a/input/resources/au-core-patient.xml b/input/resources/au-core-patient.xml
index 8ede23b8..1df6f51c 100644
--- a/input/resources/au-core-patient.xml
+++ b/input/resources/au-core-patient.xml
@@ -77,7 +77,6 @@
       <path value="Patient.extension" />
       <sliceName value="genderIdentity" />
       <short value="Gender identity shall be a member of the Gender Identity Response value set if any codes within that value set can apply"/>
-      <comment value="Individual Gender identity [Gender Identity Response](https://healthterminologies.gov.au/fhir/ValueSet/gender-identity-response-1) ([Extensible](http://hl7.org/fhir/R4/terminologies.html#extensible)). See [Australian Bureau of Statics (ABS) Standard for Sex, Gender, Variations of Sex Characteristics and Sexual Orientation Variables, 2020](https://www.abs.gov.au/statistics/standards/standard-sex-gender-variations-sex-characteristics-and-sexual-orientation-variables/latest-release#gender) for further materials."/>
       <mustSupport value="true"/>
     </element>
     <element id="Patient.extension:individualPronouns">
@@ -100,7 +99,6 @@
       <path value="Patient.extension"/>
       <sliceName value="individualPronouns"/>
       <short value="Pronouns shall be a member of the Australian Pronouns value set if any codes within that value set can apply"/>
-      <comment value="Individual Pronouns [Australian Pronouns](https://healthterminologies.gov.au/fhir/ValueSet/australian-pronouns-1) ([Extensible](http://hl7.org/fhir/R4/terminologies.html#extensible))."/>
       <mustSupport value="true"/>
     </element>
     <element id="Patient.identifier">
diff --git a/input/resources/au-core-procedure.xml b/input/resources/au-core-procedure.xml
index 86af503a..dbb0b34e 100644
--- a/input/resources/au-core-procedure.xml
+++ b/input/resources/au-core-procedure.xml
@@ -190,7 +190,7 @@
       <constraint>
         <key value="au-core-pro-01"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-procedure"/>
diff --git a/input/resources/au-core-resprate.xml b/input/resources/au-core-resprate.xml
index 1c2d2465..e3041b51 100644
--- a/input/resources/au-core-resprate.xml
+++ b/input/resources/au-core-resprate.xml
@@ -21,7 +21,7 @@
       <definition value="Measurement of a patient's respiration rate at a point in time."/>
       <comment value="Respiration rate observation using a LOINC code and a SNOMED CT code."/>
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="At least value or data absent reason shall be present"/>
         <expression value="dataAbsentReason.exists() or value.exists()"/>
@@ -250,7 +250,7 @@
       </extension>
       <path value="Observation.valueQuantity"/>
       <short value="Respiration rate"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element>
     <element id="Observation.valueQuantity.value">
       <extension url="http://hl7.org/fhir/StructureDefinition/obligation">
@@ -346,15 +346,15 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element>
     <element id="Observation.bodySite">
       <path value="Observation.bodySite" />
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-resprate"/>
diff --git a/input/resources/au-core-smokingstatus.xml b/input/resources/au-core-smokingstatus.xml
index ff4409fb..2806080b 100644
--- a/input/resources/au-core-smokingstatus.xml
+++ b/input/resources/au-core-smokingstatus.xml
@@ -20,7 +20,7 @@
       <short value="Smoking status" />
       <definition value="An observation of smoking status, i.e. current behaviour for all types of tobacco smoking, at a point in time." />
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="At least value or data absent reason shall be present"/>
         <expression value="dataAbsentReason.exists() or value.exists()"/>
@@ -193,13 +193,13 @@
       <type>
         <code value="dateTime" />
       </type>
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
-        <human value="Date shall be at least to day"/>
-        <expression value="$this is DateTime implies $this.toString().length() &gt;= 8"/>
-        <xpath value="f:matches(effectiveDateTime,/\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d([+-][0-2]\d:[0-5]\d|Z)/)"/>
+        <human value="Date shall be at least to day or, if not available, the Data Absent Reason extension shall be present"/>
+        <expression value="(($this is dateTime implies $this.toString().length() >= 10) and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists().not()) xor ($this is dateTime implies ($this.hasValue().not() and extension('http://hl7.org/fhir/StructureDefinition/data-absent-reason').value.exists()))"/>
+        <xpath value="((self::dateTime and string-length(.) >= 10 and not(extension[@url='http://hl7.org/fhir/StructureDefinition/data-absent-reason'])) xor (self::dateTime and not(.) and extension[@url='http://hl7.org/fhir/StructureDefinition/data-absent-reason']))"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-smokingstatus"/>
       </constraint>
       <mustSupport value="true"/>
@@ -225,7 +225,7 @@
       <type>
         <code value="CodeableConcept" />
       </type>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
       <binding>
         <strength value="extensible" />
@@ -250,7 +250,7 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
       <mustSupport value="true"/>
     </element>
   </differential>
diff --git a/input/resources/au-core-waistcircum.xml b/input/resources/au-core-waistcircum.xml
index 114a108f..b4617ffc 100644
--- a/input/resources/au-core-waistcircum.xml
+++ b/input/resources/au-core-waistcircum.xml
@@ -21,7 +21,7 @@
       <definition value="Measurement of a patient's waist circumference at a point in time."/>
       <comment value="Waist circumference observation using a LOINC code, a SNOMED CT code and a metric UCUM unit of measure."/>
       <constraint>
-        <key value="au-core-obs-02"/>
+        <key value="au-core-obs-01"/>
         <severity value="error"/>
         <human value="At least value or data absent reason shall be present"/>
         <expression value="dataAbsentReason.exists() or value.exists()"/>
@@ -279,7 +279,7 @@
       </extension>
       <path value="Observation.valueQuantity"/> 
       <short value="Waist circumference"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element> 
     <element id="Observation.valueQuantity.value">
       <path value="Observation.valueQuantity.value"/> 
@@ -349,15 +349,15 @@
         </extension>
       </extension>
       <path value="Observation.dataAbsentReason"/>
-      <condition value="au-core-obs-02"/>
+      <condition value="au-core-obs-01"/>
     </element>
     <element id="Observation.bodySite">
       <path value="Observation.bodySite" />
-      <condition value="au-core-obs-01"/>
+      <condition value="au-core-obs-02"/>
       <constraint>
-        <key value="au-core-obs-01"/>
+        <key value="au-core-obs-02"/>
         <severity value="error"/>
-        <human value="If a coded body site is provided, at least one code shall be from SNOMED CT"/>
+        <human value="If a coded body site is provided, at least one coding shall be from SNOMED CT"/>
         <expression value="coding.exists() implies coding.where(system='http://snomed.info/sct').exists()"/>
         <xpath value="not(exists(f:coding/f:system)) or exists(f:coding/f:system[@value='http://snomed.info/sct'])"/>
         <source value="http://hl7.org.au/fhir/core/StructureDefinition/au-core-waistcircum"/>