Refactor rs-e2e project to remove Hapi HL7 library

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

@@ -0,0 +1,54 @@
+package gov.hhs.cdc.trustedintermediary.rse2e;
+
+import gov.hhs.cdc.trustedintermediary.wrappers.HealthData;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Pattern;
+
+/**
+ * Represents a HAPI HL7 message that implements the HealthData interface. This class provides a
+ * wrapper around the HAPI Message object.
+ */
+public class HL7Message implements HealthData<HL7Message> {
+
+    private final Map<String, List<String>> segments;
+    private final char[] delimiters;
+
+    public HL7Message(Map<String, List<String>> segments, char[] delimiters) {
+        this.segments = segments;
+        this.delimiters = delimiters;
+    }
+
+    public List<String> getSegment(String segment) {
+        return segments.get(segment);
+    }
+
+    public String getValue(String segmentName, int... indices) {
+        List<String> fields = segments.get(segmentName);
+        if (fields == null || indices[0] > fields.size()) {
+            return null;
+        }
+
+        String value = fields.get(indices[0] - 1);
+        for (int i = 1; i < indices.length; i++) {
+            value = splitAndGet(value, delimiters[i - 1], indices[i]);
+            if (value == null) return null;
+        }
+        return value;
+    }
+
+    private String splitAndGet(String value, char delimiter, int index) {
+        String[] parts = value.split(Pattern.quote(String.valueOf(delimiter)));
+        return index <= parts.length ? parts[index - 1] : null;
+    }
+
+    @Override
+    public HL7Message getUnderlyingData() {
+        return this;
+    }
+
+    @Override
+    public String getIdentifier() {
+        return getValue("MSH", 10);
+    }
+}

rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/HL7Parser.java

@@ -0,0 +1,42 @@
+package gov.hhs.cdc.trustedintermediary.rse2e;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.regex.Pattern;
+
+public class HL7Parser {
+
+    private static final HL7Parser INSTANCE = new HL7Parser();
+
+    private static final String NEWLINE_REGEX = "\\r?\\n|\\r";
+    private static final char DEFAULT_FIELD_SEPARATOR = '|';
+
+    private HL7Parser() {}
+
+    public static HL7Parser getInstance() {
+        return INSTANCE;
+    }
+
+    public static HL7Message parse(String content) {
+        Map<String, List<String>> segments = new HashMap<>();
+        char[] encodingCharacters = null;
+        String[] lines = content.split(NEWLINE_REGEX);
+        for (String line : lines) {
+            if (line.trim().isEmpty()) continue;
+            String[] fields = line.split(Pattern.quote(String.valueOf(DEFAULT_FIELD_SEPARATOR)));
+            String segmentName = fields[0];
+            List<String> segmentFields =
+                    new ArrayList<>(Arrays.asList(fields).subList(1, fields.length));
+            if (Objects.equals(segmentName, "MSH")) {
+                encodingCharacters = fields[1].toCharArray();
+                segmentFields.add(0, String.valueOf(DEFAULT_FIELD_SEPARATOR));
+            }
+            segments.put(segmentName, segmentFields);
+        }
+        return new HL7Message(segments, encodingCharacters);
+    }
+}

rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7ExpressionEvaluator.java

@@ -56,6 +56,7 @@ public final boolean evaluateExpression(String expression, HealthData<?>... data
         String rightOperand =
                 matcher.group(3); // e.g. MSH-5.1, input.MSH-5.1, 'EPIC', ('EPIC', 'CERNER'), 2
 
+        // TODO: replace with our own Message implementation
         Message outputMessage = (Message) data[0].getUnderlyingData();
         Message inputMessage = (data.length > 1) ? (Message) data[1].getUnderlyingData() : null;
 

rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcher.java

@@ -1,12 +1,9 @@
 package gov.hhs.cdc.trustedintermediary.rse2e.external.hapi;
 
-import ca.uhn.hl7v2.DefaultHapiContext;
-import ca.uhn.hl7v2.HL7Exception;
-import ca.uhn.hl7v2.HapiContext;
-import ca.uhn.hl7v2.model.Message;
-import ca.uhn.hl7v2.parser.Parser;
 import com.google.common.collect.Sets;
 import gov.hhs.cdc.trustedintermediary.rse2e.HL7FileStream;
+import gov.hhs.cdc.trustedintermediary.rse2e.HL7Message;
+import gov.hhs.cdc.trustedintermediary.rse2e.HL7Parser;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
@@ -31,13 +28,13 @@ public static HapiHL7FileMatcher getInstance() {
         return INSTANCE;
     }
 
-    public Map<HapiHL7Message, HapiHL7Message> matchFiles(
+    public Map<HL7Message, HL7Message> matchFiles(
             List<HL7FileStream> outputFiles, List<HL7FileStream> inputFiles)
             throws HapiHL7FileMatcherException {
         // We pair up output and input files based on the control ID, which is in MSH-10
         // Any files (either input or output) that don't have a match are logged
-        Map<String, HapiHL7Message> inputMap = parseAndMapMessageByControlId(inputFiles);
-        Map<String, HapiHL7Message> outputMap = parseAndMapMessageByControlId(outputFiles);
+        Map<String, HL7Message> inputMap = parseAndMapMessageByControlId(inputFiles);
+        Map<String, HL7Message> outputMap = parseAndMapMessageByControlId(outputFiles);
 
         Set<String> inputKeys = inputMap.keySet();
         Set<String> outputKeys = outputMap.keySet();
@@ -54,37 +51,31 @@ public Map<HapiHL7Message, HapiHL7Message> matchFiles(
         return inputKeys.stream().collect(Collectors.toMap(inputMap::get, outputMap::get));
     }
 
-    public Map<String, HapiHL7Message> parseAndMapMessageByControlId(List<HL7FileStream> files)
+    public Map<String, HL7Message> parseAndMapMessageByControlId(List<HL7FileStream> files)
             throws HapiHL7FileMatcherException {
 
-        Map<String, HapiHL7Message> messageMap = new HashMap<>();
+        Map<String, HL7Message> messageMap = new HashMap<>();
 
-        try (HapiContext context = new DefaultHapiContext()) {
-            Parser parser = context.getPipeParser();
-
-            for (HL7FileStream hl7FileStream : files) {
-                String fileName = hl7FileStream.fileName();
-                try (InputStream inputStream = hl7FileStream.inputStream()) {
-                    String content = new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
-                    Message message = parser.parse(content);
-                    HapiHL7Message hapiHL7Message = new HapiHL7Message(message);
-                    String msh10 = hapiHL7Message.getIdentifier();
-                    if (msh10 == null || msh10.isEmpty()) {
-                        throw new HapiHL7FileMatcherException(
-                                String.format("MSH-10 is empty for file: %s", fileName));
-                    }
-                    messageMap.put(msh10, hapiHL7Message);
-                } catch (HL7Exception e) {
-                    throw new HapiHL7FileMatcherException(
-                            String.format("Failed to parse HL7 message from file: %s", fileName),
-                            e);
-                } catch (IOException e) {
+        for (HL7FileStream hl7FileStream : files) {
+            String fileName = hl7FileStream.fileName();
+            try (InputStream inputStream = hl7FileStream.inputStream()) {
+                String content = new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
+                HL7Message message = HL7Parser.parse(content);
+                String msh10 = message.getIdentifier();
+                if (msh10 == null || msh10.isEmpty()) {
                     throw new HapiHL7FileMatcherException(
-                            String.format("Failed to read file: %s", fileName), e);
+                            String.format("MSH-10 is empty for file: %s", fileName));
                 }
+                messageMap.put(msh10, message);
+                //                } catch (HL7Exception e) {
+                //                    throw new HapiHL7FileMatcherException(
+                //                            String.format("Failed to parse HL7 message from file:
+                // %s", fileName),
+                //                            e);
+            } catch (IOException e) {
+                throw new HapiHL7FileMatcherException(
+                        String.format("Failed to read file: %s", fileName), e);
             }
-        } catch (IOException e) {
-            throw new HapiHL7FileMatcherException("Failed to close input stream", e);
         }
 
         return messageMap;

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/HL7ParserTest.groovy

@@ -0,0 +1,24 @@
+package gov.hhs.cdc.trustedintermediary.rse2e
+
+import spock.lang.Specification
+
+class HL7ParserTest extends Specification {
+
+    def "test defined assertions on relevant messages"() {
+        given:
+        def content = """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^automated-staging-test-receiver-id^DNS|20230101010000-0000||ORM^O01^ORM_O01|001|N|2.5.1||||||||||
+PID|1||1300974^^^Baptist East^MR||ONE^TESTCASE||202402210152-0500|F^Female^HL70001||2106-3^White^HL70005|1234 GPCS WAY^^MONTGOMERY^Alabama^36117^USA^home^^Montgomery|||||||2227600015||||N^Not Hispanic or Latino^HL70189|||1|||||
+NK1|1|ONE^MOMFIRST|MTH^Mother^HL70063||^^^^^804^5693861||||||||||||||||||||||||||||123456789^^^Medicaid&2.16.840.1.113883.4.446&ISO^MD||||000-00-0000^^^ssn&2.16.840.1.113883.4.1&ISO^SS
+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
+"""
+
+        when:
+        HL7Message message = HL7Parser.parse(content)
+        String value = message.getValue("PID", 3, 4)
+
+        then:
+        value == "Baptist East"
+    }
+}

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7MessageTest.groovy → rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HL7MessageTest.groovy

@@ -3,14 +3,15 @@ package gov.hhs.cdc.trustedintermediary.rse2e.external.hapi
 import ca.uhn.hl7v2.model.Message
 import ca.uhn.hl7v2.model.v251.message.ORU_R01
 import ca.uhn.hl7v2.model.v251.segment.MSH
+import gov.hhs.cdc.trustedintermediary.rse2e.HL7Message
 import spock.lang.Specification
 
-class HapiHL7MessageTest extends Specification {
+class HL7MessageTest extends Specification {
 
     def "getUnderlyingData should correctly initialize and return underlying data"() {
         given:
         def mockMessage = Mock(Message)
-        def hl7Message = new HapiHL7Message(mockMessage)
+        def hl7Message = new HL7Message(mockMessage)
 
         expect:
         hl7Message.getUnderlyingData() == mockMessage
@@ -24,7 +25,7 @@ class HapiHL7MessageTest extends Specification {
         mshSegment.getMessageControlID().setValue(expectedIdentifier)
 
         and:
-        def hl7Message = new HapiHL7Message(oruMessage)
+        def hl7Message = new HL7Message(oruMessage)
 
         when:
         def name = hl7Message.getIdentifier()

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcherTest.groovy

@@ -2,6 +2,7 @@ package gov.hhs.cdc.trustedintermediary.rse2e.external.hapi
 
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
 import gov.hhs.cdc.trustedintermediary.rse2e.HL7FileStream
+import gov.hhs.cdc.trustedintermediary.rse2e.HL7Message
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger
 import spock.lang.Specification
 
@@ -30,10 +31,10 @@ class HapiHL7FileMatcherTest extends Specification {
             new HL7FileStream("outputFileStream1", Mock(InputStream)),
             new HL7FileStream("outputFileStream2", Mock(InputStream))
         ]
-        def mockInputMessage1 = Mock(HapiHL7Message)
-        def mockInputMessage2 = Mock(HapiHL7Message)
-        def mockOutputMessage1 = Mock(HapiHL7Message)
-        def mockOutputMessage2 = Mock(HapiHL7Message)
+        def mockInputMessage1 = Mock(HL7Message)
+        def mockInputMessage2 = Mock(HL7Message)
+        def mockOutputMessage1 = Mock(HL7Message)
+        def mockOutputMessage2 = Mock(HL7Message)
         spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": mockInputMessage1, "002": mockInputMessage2 ]
         spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": mockOutputMessage1, "002": mockOutputMessage2 ]
 
@@ -60,8 +61,8 @@ class HapiHL7FileMatcherTest extends Specification {
         mockOutputFiles = [
             new HL7FileStream("matchingOutputFileStream", Mock(InputStream))
         ]
-        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HapiHL7Message), "002": Mock(HapiHL7Message) ]
-        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HapiHL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HL7Message), "002": Mock(HL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HL7Message) ]
         spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
 
         then:
@@ -79,8 +80,8 @@ class HapiHL7FileMatcherTest extends Specification {
             new HL7FileStream("matchingOutputFileStream", Mock(InputStream)),
             new HL7FileStream("nonMatchingOutputFileStream", Mock(InputStream))
         ]
-        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HapiHL7Message) ]
-        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HapiHL7Message), "003": Mock(HapiHL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HL7Message), "003": Mock(HL7Message) ]
         spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
 
         then:

rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/ruleengine/AssertionRuleEngineTest.groovy

@@ -1,7 +1,7 @@
 package gov.hhs.cdc.trustedintermediary.rse2e.ruleengine
 
-import ca.uhn.hl7v2.model.Message
-import gov.hhs.cdc.trustedintermediary.rse2e.external.hapi.HapiHL7Message
+
+import gov.hhs.cdc.trustedintermediary.rse2e.HL7Message
 import gov.hhs.cdc.trustedintermediary.ruleengine.RuleLoader
 import gov.hhs.cdc.trustedintermediary.ruleengine.RuleLoaderException
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
@@ -85,7 +85,7 @@ class AssertionRuleEngineTest extends Specification {
         }
 
         when:
-        ruleEngine.runRules(Mock(HapiHL7Message), Mock(HapiHL7Message))
+        ruleEngine.runRules(Mock(HL7Message), Mock(HL7Message))
 
         then:
         1 * mockLogger.logError(_ as String, exception)
@@ -97,15 +97,15 @@ class AssertionRuleEngineTest extends Specification {
         mockRuleLoader.loadRules(_ as InputStream, _ as TypeReference) >> { throw exception }
 
         when:
-        ruleEngine.runRules(Mock(HapiHL7Message), Mock(HapiHL7Message))
+        ruleEngine.runRules(Mock(HL7Message), Mock(HL7Message))
 
         then:
         1 * mockLogger.logError(_ as String, exception)
     }
 
     def "runRules returns nothing when there are no rules"() {
         when:
-        def result = ruleEngine.runRules(Mock(HapiHL7Message), Mock(HapiHL7Message))
+        def result = ruleEngine.runRules(Mock(HL7Message), Mock(HL7Message))
 
         then:
         result.isEmpty()
@@ -117,7 +117,7 @@ class AssertionRuleEngineTest extends Specification {
         mockRuleLoader.loadRules(_ as InputStream, _ as TypeReference) >> [rule]
 
         when:
-        def result = ruleEngine.runRules(Mock(HapiHL7Message), Mock(HapiHL7Message))
+        def result = ruleEngine.runRules(Mock(HL7Message), Mock(HL7Message))
 
         then:
         result.size() == 1
@@ -130,7 +130,7 @@ class AssertionRuleEngineTest extends Specification {
         mockRuleLoader.loadRules(_ as InputStream, _ as TypeReference) >> [rule]
 
         when:
-        def result = ruleEngine.runRules(Mock(HapiHL7Message), Mock(HapiHL7Message))
+        def result = ruleEngine.runRules(Mock(HL7Message), Mock(HL7Message))
 
         then:
         result.isEmpty()