minor bug fixes

monarch-initiative · Aug 23, 2023 · b744f70 · b744f70
1 parent 43f378b
commit b744f70
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java b/src/main/java/org/monarchinitiative/phenopacket2prompt/querygen/TimePointParser.java
@@ -9,7 +9,7 @@ public class TimePointParser {
 
 
     /** gets 2 dats before presentation, Two days before presentation etc.*/
-    private final Pattern pattern1 = Pattern.compile("\\b\\w+\\b\\s+(hours?|days?|weeks?|months?|years?|decades?) before presentation",Pattern.CASE_INSENSITIVE);
+    private final Pattern pattern1 = Pattern.compile("\\b\\w+\\b\\s+(hours?|days?|weeks?|months?|years?|decades?) before (the current )?presentation",Pattern.CASE_INSENSITIVE);
 
     private final Pattern pattern2 = Pattern.compile("\\b\\w+\\b\\s+(hours?|days?|weeks?|months?|years?|decades?) earlier",Pattern.CASE_INSENSITIVE);
 

diff --git a/...va/org/monarchinitiative/phenopacket2prompt/querygen/qfactory/AbstractQueryGenerator.java b/...va/org/monarchinitiative/phenopacket2prompt/querygen/qfactory/AbstractQueryGenerator.java
@@ -101,6 +101,8 @@ private String stripFamilyHistoryAndPmh(String originalSeg) {
         for (var line : lines) {
             if (line.toLowerCase().contains("family history")) continue;
             if (line.toLowerCase().contains("medical history")) continue;
+            if (line.toLowerCase().contains(" mother ")) continue; // e.g. the patient's mother had
+            if (line.toLowerCase().contains(" father ")) continue;
             validLines.add(line);
         }
         return String.join(". ", validLines);

diff --git a/...monarchinitiative/phenopacket2prompt/querygen/qfactory/TextWithManualAnnotsGenerator.java b/...monarchinitiative/phenopacket2prompt/querygen/qfactory/TextWithManualAnnotsGenerator.java
@@ -57,8 +57,6 @@ protected String getPhenopacketTextWithManualAdditions() {
         vignette = vignette.substring(ii + 1);
         List<TimePoint> timePointList = timePointParser.getTimePoints(vignette);
 
-
-
         try {
             Map<String, String> timeSegments = timeSegments(vignette, timePointList);
             for (var entry : timeSegments.entrySet()) {
@@ -85,6 +83,7 @@ protected String getPhenopacketTextWithManualAdditions() {
                     .append("\n");
         }
         if (familyHistory.size() > 0) {
+            sb.append("The family history was notable for the following. ");
             for (String item: familyHistory) {
                 sb.append(item).append("\n");
             }
@@ -150,8 +149,9 @@ protected String getPhenopacketBasedQuerySegmentWithAdditions(String presentatio
             capitalizedTimepoint = presentationTimeDescription.substring(0, 1).toUpperCase() + presentationTimeDescription.substring(1);
         }
 
-        sb.append(capitalizedTimepoint);
+        sb.append(capitalizedTimepoint).append(" ");
         boolean observedEmpty = true;
+        boolean needEmpty = true;
         if (!observed_terms.isEmpty()) {
             observedEmpty = false;
             if (capitalizedTimepoint.isEmpty()) {
@@ -166,20 +166,23 @@ protected String getPhenopacketBasedQuerySegmentWithAdditions(String presentatio
             sb.append(observedSymptoms).append(" \n");
         }
         if (!excluded_terms.isEmpty()) {
+            if (needEmpty) { sb.append(" "); needEmpty = false; }
             String excludededSymptoms = getOxfordCommaList(excluded_terms);
             if (observedEmpty) {
-                sb.append(", the following signs and symptoms were excluded: ");
+                sb.append("The following signs and symptoms were excluded: ");
             } else {
                 sb.append("The following signs and symptoms were excluded: ");
             }
             sb.append(excludededSymptoms).append("\n");
         }
         if (! diagnostics.isEmpty()) {
+            if (needEmpty) { sb.append(" "); needEmpty = false; }
             sb.append("The following diagnostic observations were made: ");
             sb.append(getOxfordCommaList(diagnostics));
             sb.append("\n");
         }
         if (! treatment.isEmpty()) {
+            if (needEmpty) { sb.append(" "); needEmpty = false; }
             sb.append("The following treatments were administered: ");
             sb.append(getOxfordCommaList(treatment));
             sb.append("\n");