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NIAD-3304: Ensure correct ordering of originalText when mapping CodeableConcept to CD #1168

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MartinWheelerMT merged 4 commits into from
Mar 24, 2025
Merged

NIAD-3304: Ensure correct ordering of originalText when mapping CodeableConcept to CD #1168

MartinWheelerMT merged 4 commits into from
Mar 24, 2025

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@MartinWheelerMT
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@MartinWheelerMT MartinWheelerMT commented Mar 20, 2025 •
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What

  • Update CD template to ensure that originalText is always populated first.
  • Update tests to reflect the ordering change
  • Update CodeableConceptCdMapper to only add code translations when it is possible to map from URL to OID as anything other than an OID is not supported in the schema.
  • Update CodesSystemsUtil to return empty string if a mapping to known code system cannot be found.
  • Update test accordingly.
  • Update CodeableConceptCdMapper to create a new coding element for legacy codes, to avoid modifying an element whilst iterating a list.
  • Add test for an unknown code system.
  • SonarCube fix to remove public modifier on test class.
  • Fix error in "Medications" test file, where a legacy code contains a space, which is not valid according to the schema.

Why

The imports were failing on EMIS due to schema validation issues, looking at the schema:

   <xsd:complexContent>
            <xsd:extension base="ANY">
                <xsd:sequence>
                    <xsd:element name="originalText" type="ED" minOccurs="0">
                        <xsd:annotation>
                            <xsd:documentation> The text or phrase used as the basis for the coding. </xsd:documentation>
                            <xsd:appinfo />
                        </xsd:annotation>
                    </xsd:element>
                    <xsd:element name="qualifier" type="CR" minOccurs="0" maxOccurs="unbounded">
                        <xsd:annotation>
                            <xsd:documentation> Specifies additional codes that increase the
                                specificity of the primary code. </xsd:documentation>
                            <xsd:appinfo />
                        </xsd:annotation>
                    </xsd:element>
                    <xsd:element name="group" minOccurs="0" maxOccurs="unbounded">
                        <xsd:complexType>
                            <xsd:sequence>
                                <xsd:element name="qualifier" type="CR" maxOccurs="unbounded" />
                            </xsd:sequence>
                        </xsd:complexType>
                    </xsd:element>
                    <xsd:element name="translation" type="CD" minOccurs="0" maxOccurs="unbounded">
                        <xsd:annotation>
                            <xsd:documentation> A set of other concept descriptors that translate
                                this concept descriptor into other code systems. </xsd:documentation>
                            <xsd:appinfo />
                        </xsd:annotation>
                    </xsd:element>
                </xsd:sequence>
...

It appears that the originalText field should be appearing first in the sequence ahead of the translations.

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)

Checklist:

  • I have performed a self-review of my code
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes

@MartinWheelerMT
NIAD-3304: Fix issue with ordering of originalText when mapping to …
ebd4f0e 
…CD XML

* Update CD template to ensure that `originalText` is always populated first.
* Update tests to reflect the ordering change
@MartinWheelerMT MartinWheelerMT changed the title NIAD-3304: NIAD-3304: Ensure correct ordering of originalText when mapping CodeableConcept to CD Mar 20, 2025
@MartinWheelerMT
NIAD-3304: Fix issue with ordering of originalText when mapping to …
c2a8fe5 
…CD XML

* Update `CodeableConceptCdMapper` to only add code translations when it is possible to map from URL to OID as anything other than an OID is not supported in the schema.
* Update CodesSystemsUtil to return empty string if a mapping to known code system cannot be found.
* Update test accordingly.
@MartinWheelerMT
NIAD-3304: Fix issue with ordering of originalText when mapping to …
7c44bc2 
…CD XML

* Update `CodeableConceptCdMapper` to create a new coding element for legacy codes, to avoid modifying an element whilst iterating a list.
@MartinWheelerMT
NIAD-3304: Fix issue with ordering of originalText when mapping to …
7a9800d 
…CD XML

* Add test for an unknown code system.
* SonarCube fix to remove public modifier on test class.
* Fix error in "Medications" test file, where a legacy code contains a space, which is not valid according to the schema.
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github-actions bot commented Mar 21, 2025

Looks good. All 5 mutations in this change were killed.

class surviving killed
💯uk.nhs.adaptors.gp2gp.ehr.mapper.CodeableConceptCdMapper 0 4
💯uk.nhs.adaptors.gp2gp.ehr.utils.CodeSystemsUtil 0 1

See https://pitest.org

@sonarqubecloud
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sonarqubecloud bot commented Mar 21, 2025

Quality Gate Passed Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@MartinWheelerMT MartinWheelerMT enabled auto-merge (squash) March 21, 2025 11:54
@MartinWheelerMT MartinWheelerMT merged commit 74c048e into main Mar 24, 2025
15 checks passed
@MartinWheelerMT MartinWheelerMT deleted the fix-ordering-of-original-text-in-cd-xml branch March 24, 2025 09:50
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@MartinWheelerMT @ORybak5