Removed HL7Parser and moved message parsing logic to HL7Message to av…

…oid circular dependencies

rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/hl7/HL7FileMatcher.java

@@ -57,7 +57,7 @@ public Map<String, HL7Message> parseAndMapMessageByControlId(List<HL7FileStream>
             String fileName = hl7FileStream.fileName();
             try (InputStream inputStream = hl7FileStream.inputStream()) {
                 String content = new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
-                HL7Message message = HL7Parser.parseMessage(content);
+                HL7Message message = HL7Message.parse(content);
                 String msh10 = message.getIdentifier();
                 if (msh10 == null || msh10.isEmpty()) {
                     throw new HL7FileMatcherException(

rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/hl7/HL7Message.java

@@ -1,7 +1,10 @@
 package gov.hhs.cdc.trustedintermediary.rse2e.hl7;
 
 import gov.hhs.cdc.trustedintermediary.wrappers.HealthData;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.Objects;
 import java.util.regex.Pattern;
 
 /**
@@ -10,6 +13,9 @@
  */
 public class HL7Message implements HealthData<HL7Message> {
 
+    static final String MSH_SEGMENT_NAME = "MSH";
+    static final String NEWLINE_REGEX = "\\r?\\n|\\r";
+
     private final List<HL7Segment> segments;
     private final HL7Encoding encoding;
 
@@ -37,10 +43,32 @@ public String toString() {
         return String.join(
                 HL7Encoding.DEFAULT_SEGMENT_DELIMITER,
                 getSegments().stream()
-                        .map(segment -> HL7Parser.segmentToString(segment, this.encoding))
+                        .map(segment -> segmentToString(segment, this.encoding))
                         .toList());
     }
 
+    public static HL7Message parse(String content) {
+        List<HL7Segment> segments = new ArrayList<>();
+        String encodingCharactersField = null;
+        String[] lines = content.split(NEWLINE_REGEX);
+        for (String line : lines) {
+            if (line.trim().isEmpty()) continue;
+            String[] fields =
+                    line.split(
+                            Pattern.quote(String.valueOf(HL7Encoding.DEFAULT_FIELD_DELIMITER)), -1);
+            String segmentName = fields[0];
+            List<String> segmentFields =
+                    new ArrayList<>(Arrays.asList(fields).subList(1, fields.length));
+            if (Objects.equals(segmentName, MSH_SEGMENT_NAME)) {
+                encodingCharactersField = fields[1];
+                segmentFields.add(0, String.valueOf(HL7Encoding.DEFAULT_FIELD_DELIMITER));
+            }
+            segments.add(new HL7Segment(segmentName, segmentFields));
+        }
+
+        return new HL7Message(segments, HL7Encoding.fromEncodingField(encodingCharactersField));
+    }
+
     public List<HL7Segment> getSegments() {
         return this.segments;
     }
@@ -98,4 +126,16 @@ public String getValue(String path) throws HL7MessageException {
         }
         return value;
     }
+
+    protected static String segmentToString(HL7Segment segment, HL7Encoding encoding) {
+        String fieldSeparator = String.valueOf(encoding.getFieldDelimiter());
+
+        if (segment.name().equals(MSH_SEGMENT_NAME)) {
+            return segment.name()
+                    + segment.fields().get(0)
+                    + String.join(
+                            fieldSeparator, segment.fields().subList(1, segment.fields().size()));
+        }
+        return segment.name() + fieldSeparator + String.join(fieldSeparator, segment.fields());
+    }
 }

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/hl7/HL7ExpressionEvaluatorTest.groovy

@@ -18,7 +18,7 @@ class HL7ExpressionEvaluatorTest extends Specification {
 
         messageContent = """MSH|^~\\&|Sender Application^sender.test.com^DNS|Sender Facility^0.0.0.0.0.0.0.0^ISO|Receiver Application^0.0.0.0.0.0.0.0^ISO|Receiver Facility^simulated-lab-id^DNS|20230101010000-0000||ORM^O01^ORM_O01|111111|T|2.5.1
 PID|1||11102779^^^CR^MR||SMITH^BB SARAH^^^^^L"""
-        hl7Message = HL7Parser.parseMessage(messageContent)
+        hl7Message = HL7Message.parse(messageContent)
 
         TestApplicationContext.injectRegisteredImplementations()
     }

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/hl7/HL7MessageTest.groovy

@@ -15,7 +15,52 @@ ORC|NW|4560411583^ORDERID||||||||||12345^^^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L|
 OBR|1|4560411583^ORDERID||54089-8^Newborn screening panel AHIC^LN|||202402221854-0500|||||||||12345^^^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L||||||||
 OBX|1|ST|57723-9^Unique bar code number of Current sample^LN||123456||||||F|||202402221854-0500
 OBX|2|NM|||3122||||||F|||202402221854-0500||"""
-        message = HL7Parser.parseMessage(messageContent)
+        message = HL7Message.parse(messageContent)
+    }
+
+    def "parse should handle basic HL7 message"() {
+        given:
+        def content = """MSH|^~\\&|sending_app|sending_facility
+PID|||12345||Doe^John||19800101|M"""
+
+        when:
+        def message = HL7Message.parse(content)
+        def segments = message.getSegments()
+
+        then:
+        segments.size() == 2
+        segments[0].name() == "MSH"
+        segments[0].fields().size() == 4
+        segments[0].fields().get(0) == "|"
+        segments[0].fields().get(1) == "^~\\&"
+        segments[1].name() == "PID"
+        segments[1].fields().size() == 8
+        segments[1].fields().get(2) == "12345"
+        segments[1].fields().get(4) == "Doe^John"
+    }
+
+    def "parse should handle empty lines in message"() {
+        given:
+        def content = """MSH|^~\\&|sending_app
+
+PID|||12345"""
+
+        when:
+        def result = HL7Message.parse(content)
+
+        then:
+        result.getSegments().size() == 2
+    }
+
+    def "parse should preserve empty fields"() {
+        given:
+        def content = "MSH|^~\\&|sending_app||sending_facility"
+
+        when:
+        def result = HL7Message.parse(content)
+
+        then:
+        result.getSegments().get(0).fields().get(3) == ""
     }
 
     def "getUnderlyingData should correctly return itself"() {