small revisions

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) {

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);
 
  }