From 8a090dfa8d4e9c9d00ed7ca6effbd021b45f9813 Mon Sep 17 00:00:00 2001
From: emmastephenson <80282552+emmastephenson@users.noreply.github.com>
Date: Tue, 17 Oct 2023 14:32:38 -0700
Subject: [PATCH] Check for RR field presence before merging RR to eCR (#866)

Avoids unnecessary work if an RR has already been merged with its eICR.
---
 phdi/fhir/conversion/convert.py               |  4 +++
 .../rr_extraction/merged_eICR.xml             | 17 ++++++++++++
 tests/fhir/conversion/test_conversion.py      | 27 +++++++++++++++++++
 3 files changed, 48 insertions(+)
 create mode 100644 tests/assets/fhir-converter/rr_extraction/merged_eICR.xml

diff --git a/phdi/fhir/conversion/convert.py b/phdi/fhir/conversion/convert.py
index 6511b33218..7cafc6cb7f 100644
--- a/phdi/fhir/conversion/convert.py
+++ b/phdi/fhir/conversion/convert.py
@@ -48,6 +48,10 @@ def add_rr_data_to_eicr(rr, ecr):
     rr = etree.fromstring(rr)
     ecr = etree.fromstring(ecr)
 
+    if ecr.xpath('//*[@codeSystem="2.16.840.1.113883.6.1"]'):
+        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",
diff --git a/tests/assets/fhir-converter/rr_extraction/merged_eICR.xml b/tests/assets/fhir-converter/rr_extraction/merged_eICR.xml
new file mode 100644
index 0000000000..26ea65fa86
--- /dev/null
+++ b/tests/assets/fhir-converter/rr_extraction/merged_eICR.xml
@@ -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>
\ No newline at end of file
diff --git a/tests/fhir/conversion/test_conversion.py b/tests/fhir/conversion/test_conversion.py
index 6e6e6a8a01..85d0e88a73 100644
--- a/tests/fhir/conversion/test_conversion.py
+++ b/tests/fhir/conversion/test_conversion.py
@@ -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