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Check that RR isn't already present before attempting to merge with eICR #870

Merged
merged 6 commits into from
Oct 18, 2023
Merged

Check that RR isn't already present before attempting to merge with eICR #870

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51f8533
wip
emmastephenson Oct 13, 2023
585847e
wip
emmastephenson Oct 13, 2023
d9ea154
check for rr before merging
emmastephenson Oct 13, 2023
4f885fc
look for id instead of RR string
emmastephenson Oct 17, 2023
38b9617
use RR code...not LOINC codeSystem
emmastephenson Oct 17, 2023
451da0c
Merge branch 'main' into emma/844-rr-check
emmastephenson Oct 18, 2023
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4 changes: 4 additions & 0 deletions phdi/fhir/conversion/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,10 @@ def add_rr_data_to_eicr(rr, ecr):
rr = etree.fromstring(rr)
ecr = etree.fromstring(ecr)

if ecr.xpath('//*[@code="88085-6"]'):
print("This eCR has already been merged with RR data.")
return etree.tostring(ecr, encoding="unicode", method="xml")

# Create the tags for elements we'll be looking for
rr_tags = [
"templateId",
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17 changes: 17 additions & 0 deletions tests/assets/fhir-converter/rr_extraction/merged_eICR.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
<ClinicalDocument xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><section><templateId extension="2017-04-01" root="2.16.840.1.113883.10.20.15.2.1.2"/>
<id root="4efa0e5c-c34c-429f-b5de-f1a13aef4a28"/>
<code code="88085-6" codeSystem="2.16.840.1.113883.6.1" displayName="Reportability response report Document Public health"/>
<title>Reportability Response</title>
<effectiveTime value="20220228190403+0000"/>
<confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25" displayName="Normal"/>
<entry>
<act classCode="ACT" moodCode="EVN">
<templateId extension="2017-04-01" root="2.16.840.1.113883.10.20.15.2.3.29"/>
<id root="39d966b9-8a3a-4024-93d8-138e97d5898a"/>
<code code="RRVS19" codeSystem="2.16.840.1.114222.4.5.274" codeSystemName="PHIN VS (CDC Local Coding System)" displayName="eICR processed"/>
</act>
</entry>
<entry typeCode="DRIV">
<organizer classCode="CLUSTER" moodCode="EVN"/>
</entry>
</section></ClinicalDocument>
27 changes: 27 additions & 0 deletions tests/fhir/conversion/test_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -335,3 +335,30 @@ def test_add_rr_to_ecr():
assert temps is not None
assert temps.attrib["root"] == "2.16.840.1.113883.10.20.15.2.3.29"
assert "RRVS19" in status_code.attrib["code"]


def test_add_rr_to_ecr_rr_already_present(capfd):
with open(
pathlib.Path(__file__).parent.parent.parent
/ "assets"
/ "fhir-converter"
/ "rr_extraction"
/ "CDA_RR.xml"
) as fp:
rr = fp.read()

# This eICR has already been merged with an RR
with open(
pathlib.Path(__file__).parent.parent.parent
/ "assets"
/ "fhir-converter"
/ "rr_extraction"
/ "merged_eICR.xml"
) as fp:
ecr = fp.read()

merged_ecr = add_rr_data_to_eicr(rr, ecr)
assert merged_ecr == ecr

out, err = capfd.readouterr()
assert "This eCR has already been merged with RR data." in out
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