From 9d8e69b4c0e59d97a92627f4f0250f2a4f076b50 Mon Sep 17 00:00:00 2001
From: Dylan Mendelowitz <dmendelowitz@mitre.org>
Date: Fri, 15 Sep 2023 12:59:53 -0400
Subject: [PATCH] Adding Encounter Extractor

---
 package-lock.json                             | 20 +++++++++----------
 src/ICARECSVClient.js                         |  3 +++
 .../encounter-information.csv                 |  4 ++++
 3 files changed, 17 insertions(+), 10 deletions(-)
 create mode 100644 test/sample-client-data/encounter-information.csv

diff --git a/package-lock.json b/package-lock.json
index f6690e3..b6b38d5 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1104,9 +1104,9 @@
       "dev": true
     },
     "@types/triple-beam": {
-      "version": "1.3.2",
-      "resolved": "https://registry.npmjs.org/@types/triple-beam/-/triple-beam-1.3.2.tgz",
-      "integrity": "sha512-txGIh+0eDFzKGC25zORnswy+br1Ha7hj5cMVwKIU7+s0U2AxxJru/jZSMU6OC9MJWP6+pc/hc6ZjyZShpsyY2g=="
+      "version": "1.3.3",
+      "resolved": "https://registry.npmjs.org/@types/triple-beam/-/triple-beam-1.3.3.tgz",
+      "integrity": "sha512-6tOUG+nVHn0cJbVp25JFayS5UE6+xlbcNF9Lo9mU7U0zk3zeUShZied4YEQZjy1JBF043FSkdXw8YkUJuVtB5g=="
     },
     "@types/yargs": {
       "version": "15.0.15",
@@ -5749,7 +5749,7 @@
       }
     },
     "mcode-extraction-framework": {
-      "version": "git+https://github.com/mcode/mcode-extraction-framework.git#b82ba0eee7d571c696a1c6dd6afb2b244ada9b20",
+      "version": "git+https://github.com/mcode/mcode-extraction-framework.git#9e9659494a15b19e64f3331e8c95513544e2f44a",
       "from": "git+https://github.com/mcode/mcode-extraction-framework.git",
       "requires": {
         "ajv": "^6.12.6",
@@ -7750,9 +7750,9 @@
       }
     },
     "triple-beam": {
-      "version": "1.3.0",
-      "resolved": "https://registry.npmjs.org/triple-beam/-/triple-beam-1.3.0.tgz",
-      "integrity": "sha512-XrHUvV5HpdLmIj4uVMxHggLbFSZYIn7HEWsqePZcI50pco+MPqJ50wMGY794X7AOOhxOBAjbkqfAbEe/QMp2Lw=="
+      "version": "1.4.1",
+      "resolved": "https://registry.npmjs.org/triple-beam/-/triple-beam-1.4.1.tgz",
+      "integrity": "sha512-aZbgViZrg1QNcG+LULa7nhZpJTZSLm/mXnHXnbAbjmN5aSa0y7V+wvv6+4WaBtpISJzThKy+PIPxc1Nq1EJ9mg=="
     },
     "tsconfig-paths": {
       "version": "3.14.1",
@@ -8086,9 +8086,9 @@
       }
     },
     "winston": {
-      "version": "3.9.0",
-      "resolved": "https://registry.npmjs.org/winston/-/winston-3.9.0.tgz",
-      "integrity": "sha512-jW51iW/X95BCW6MMtZWr2jKQBP4hV5bIDq9QrIjfDk6Q9QuxvTKEAlpUNAzP+HYHFFCeENhph16s0zEunu4uuQ==",
+      "version": "3.10.0",
+      "resolved": "https://registry.npmjs.org/winston/-/winston-3.10.0.tgz",
+      "integrity": "sha512-nT6SIDaE9B7ZRO0u3UvdrimG0HkB7dSTAgInQnNR2SOPJ4bvq5q79+pXLftKmP52lJGW15+H5MCK0nM9D3KB/g==",
       "requires": {
         "@colors/colors": "1.5.0",
         "@dabh/diagnostics": "^2.0.2",
diff --git a/src/ICARECSVClient.js b/src/ICARECSVClient.js
index b11dffe..65a9939 100644
--- a/src/ICARECSVClient.js
+++ b/src/ICARECSVClient.js
@@ -7,6 +7,7 @@ const {
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVCTCAdverseEventExtractor,
+  CSVEncounterExtractor,
   CSVObservationExtractor,
   CSVPatientExtractor,
   CSVProcedureExtractor,
@@ -27,6 +28,7 @@ class ICARECSVClient extends BaseClient {
       CSVClinicalTrialInformationExtractor,
       CSVConditionExtractor,
       CSVCTCAdverseEventExtractor,
+      CSVEncounterExtractor,
       CSVObservationExtractor,
       CSVPatientExtractor,
       CSVProcedureExtractor,
@@ -49,6 +51,7 @@ class ICARECSVClient extends BaseClient {
       { type: 'CSVObservationExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVEncounterExtractor', dependencies: ['CSVPatientExtractor'] },
     ];
     // Sort extractors based on order and dependencies
     this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);
diff --git a/test/sample-client-data/encounter-information.csv b/test/sample-client-data/encounter-information.csv
new file mode 100644
index 0000000..eb108cb
--- /dev/null
+++ b/test/sample-client-data/encounter-information.csv
@@ -0,0 +1,4 @@
+mrn,encounterId,status,classCode,classSystem,typeCode,typeSystem,startDate,endDate
+123,encounterId-1,arrived,AMB,http://terminology.hl7.org/CodeSystem/v3-ActCode,11429006,http://snomed.info/sct,2020-01-10,2020-01-10
+456,encounterId-2,planned,AMB,http://terminology.hl7.org/CodeSystem/v3-ActCode,270427003,http://snomed.info/sct,2021-02-10,2021-05-12
+789,encounterId-3,cancelled,IMP,http://terminology.hl7.org/CodeSystem/v3-ActCode,,,,
\ No newline at end of file