From 6d63c34778e373d237d779767ac04b012c318181 Mon Sep 17 00:00:00 2001
From: Peter Robinson <peter.robinson@jax.org>
Date: Thu, 24 Aug 2023 20:11:31 +0200
Subject: [PATCH] small revisions

---
 .../nejm/NejmCaseReportFromPdfFilterer.java              | 9 +++++++--
 .../phenopacket2prompt/querygen/TimePointParser.java     | 4 ++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/monarchinitiative/phenopacket2prompt/nejm/NejmCaseReportFromPdfFilterer.java b/src/main/java/org/monarchinitiative/phenopacket2prompt/nejm/NejmCaseReportFromPdfFilterer.java
index ab547ec..6a6e6e1 100644
--- a/src/main/java/org/monarchinitiative/phenopacket2prompt/nejm/NejmCaseReportFromPdfFilterer.java
+++ b/src/main/java/org/monarchinitiative/phenopacket2prompt/nejm/NejmCaseReportFromPdfFilterer.java
@@ -115,7 +115,9 @@ public NejmCaseReportFromPdfFilterer(String caseId, List<String> lines) {
                     line.startsWith("Pathological Diagnosis")){
                 inDifferentialDiagnosis = true;
             } else if (caseId.equalsIgnoreCase("PMID:33730458") &&
-                    line.startsWith("Pathological Discussion")){
+                    line.startsWith("Pathological Discussion")) {
+                inDifferentialDiagnosis = true;
+            } else if (caseId.equals("PMID:34437787") && line.startsWith("Dr. Andrew M. Crabbe")) {
                 inDifferentialDiagnosis = true;
             } else {
                 if (inCase && ! inDifferentialDiagnosis) {
@@ -133,6 +135,9 @@ public NejmCaseReportFromPdfFilterer(String caseId, List<String> lines) {
             } else if (line.strip().startsWith("Final Diagnosis")) {
                 inActualDiagnosis = true;
                 diagnosis = lines.get(index+1);
+            } else if (line.strip().startsWith("Anatomical Diagnosis")) {
+                inActualDiagnosis = true;
+                diagnosis = lines.get(index+1);
             }
 
 
@@ -159,7 +164,7 @@ public NejmCaseReportFromPdfFilterer(String caseId, List<String> lines) {
         int start=-1;
         int end=-1;
         while(matcher.find()) {
-            n_matched++;
+                n_matched++;
             if (n_matched==1){
                 start = matcher.end()+1;
             } else if (n_matched==2) {
diff --git a/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java b/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java
index b76fd53..6974bda 100644
--- a/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java
+++ b/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java
@@ -32,7 +32,7 @@ public class TimePointParser {
     private final Pattern pattern9 = Pattern.compile("After a \\b\\w+\\b[ -](weeks?|days?|months?|years?) admission",Pattern.CASE_INSENSITIVE);
     private final Pattern pattern10 = Pattern.compile("On admission to (the other|another) hospital",Pattern.CASE_INSENSITIVE);
     private final Pattern pattern11 = Pattern.compile("Over the next \\b\\w+\\b (hours?|days?|weeks?|months?|years?)",Pattern.CASE_INSENSITIVE);
-
+    private final Pattern pattern12 = Pattern.compile("3.5 years before the current evaluation");
 
     /** Note we do all searching in lower case */
     private final Set<String> fixedPatterns = Set.of("in the emergency department", "on examination", "in childhood", "examination was notable for",
@@ -55,7 +55,7 @@ public TimePointParser() {
         patternList.add(pattern8);
         patternList.add(pattern9);
         patternList.add(pattern10);
-       // patternList.add(pattern11);
+        patternList.add(pattern12);
 
     }