Merge pull request #51 from UCLH-DHCT/jeremy/hf-data

Generate real HL7 in the synth generator. Parse real HL7 in reader.
SAFEHR-data · Aug 27, 2024 · 3b901f3 · 3b901f3
2 parents ddbfc4e + fd45fed
commit 3b901f3
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diff --git a/.github/workflows/emap-tests.yaml b/.github/workflows/emap-tests.yaml
@@ -18,6 +18,7 @@ jobs:
       emap-interchange: ${{ steps.filter.outputs.emap-interchange }}
       core: ${{ steps.filter.outputs.core }}
       hl7-reader: ${{ steps.filter.outputs.hl7-reader }}
+      waveform-reader: ${{ steps.filter.outputs.waveform-reader }}
     steps:
       - uses: actions/checkout@v3
       - uses: dorny/paths-filter@v2
@@ -44,6 +45,11 @@ jobs:
               - 'emap-interchange/**'
               - 'emap-star/**'
               - 'hl7-reader/**'
+            waveform-reader:
+              - '.github/**'
+              - 'emap-checker.xml'
+              - 'emap-interchange/**'
+              - 'waveform-reader/**'
   emap-star-tests:
     needs: [filter]
     runs-on: ubuntu-latest
@@ -138,3 +144,26 @@ jobs:
         if: success() || failure()
         with:
           report_paths: '**/target/surefire-reports/TEST-*.xml'
+  waveform-reader-tests:
+    needs: [filter]
+    runs-on: ubuntu-latest
+    if: needs.filter.outputs.waveform-reader == 'true'
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up java
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+          cache: 'maven'
+      - name: Build emap-interchange
+        working-directory: emap-interchange
+        run: mvn clean install
+      - name: Run waveform-reader tests
+        working-directory: waveform-reader
+        run: mvn clean test
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v2
+        if: success() || failure()
+        with:
+          report_paths: '**/target/surefire-reports/TEST-*.xml'
diff --git a/waveform-generator/pom.xml b/waveform-generator/pom.xml
@@ -54,6 +54,12 @@
       </exclusions>
     </dependency>
 
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-text</artifactId>
+      <version>1.12.0</version>
+    </dependency>
+
     <dependency>
       <groupId>org.junit.jupiter</groupId>
       <artifactId>junit-jupiter-engine</artifactId>

diff --git a/...ator/src/main/java/uk/ac/ucl/rits/inform/datasources/waveform_generator/Hl7Generator.java b/...ator/src/main/java/uk/ac/ucl/rits/inform/datasources/waveform_generator/Hl7Generator.java
@@ -1,5 +1,7 @@
 package uk.ac.ucl.rits.inform.datasources.waveform_generator;
 
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.text.StringSubstitutor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
@@ -10,11 +12,15 @@
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.time.Instant;
+import java.time.ZoneId;
 import java.time.ZoneOffset;
 import java.time.format.DateTimeFormatter;
 import java.time.temporal.ChronoUnit;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.Random;
 import java.util.stream.Collectors;
 
 @Component
@@ -98,21 +104,75 @@ public void generateMessages() throws IOException {
         }
     }
 
+    private String applyHl7Template(long samplingRate, String locationId, Instant observationDatetime,
+                                    String messageId, List<ImmutablePair<String, List<Double>>> valuesByStreamId) {
+        // lines in HL7 messages must be CR terminated
+        final String templateStr = """
+                MSH|^~\\&|DATACAPTOR||||${messageDatetime}||ORU^R01|${messageId}|P|2.3||||||UNICODE UTF-8|\r\
+                PID|\r\
+                PV1||I|${locationId}|\r\
+                OBR|||||||${obsDatetime}|||${locationId}|||${locationId}|\r\
+                """;
+        final String obxTemplate = """
+                OBX|${obxI}|${dataType}|${streamId}||${valuesAsStr}||||||F||20|${obsDatetime}|\r\
+                """;
+        ZoneId hospitalTimezone = ZoneId.of("Europe/London");
+        DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyyMMddHHmmss.SSSZZ");
+        String obsDatetime = formatter.format(observationDatetime.atZone(hospitalTimezone));
+        // go for something vaguely realistic
+        int milliSecondDelay = new Random().nextInt(50, 150);
+        Instant messageDatetime = observationDatetime.plusMillis(milliSecondDelay);
+        String messageDatetimeStr = formatter.format(messageDatetime.atZone(hospitalTimezone));
+        Map<String, String> parameters = new HashMap<>();
+        parameters.put("locationId", locationId);
+        parameters.put("obsDatetime", obsDatetime);
+        parameters.put("messageDatetime", messageDatetimeStr);
+        parameters.put("messageId", messageId);
+
+        StringSubstitutor stringSubstitutor = new StringSubstitutor(parameters);
+        StringBuilder obrMsg = new StringBuilder(stringSubstitutor.replace(templateStr));
+        for (int obxI = 0; obxI < valuesByStreamId.size(); obxI++) {
+            var streamValuePair = valuesByStreamId.get(obxI);
+            List<Double> values = streamValuePair.getRight();
+            String valuesAsStr = values.stream().map(d -> String.format("%.3f", d)).collect(Collectors.joining("^"));
+            String dataType;
+            if (values.size() == 1) {
+                dataType = "NM";
+            } else if (values.size() > 1) {
+                dataType = "NA";
+            } else {
+                logger.error("Empty value array, why?");
+                dataType = "";
+            }
+            parameters.put("obxI", Integer.toString(obxI + 1));
+            parameters.put("streamId", streamValuePair.getLeft());
+            parameters.put("dataType", dataType);
+            parameters.put("valuesAsStr", valuesAsStr);
+            obrMsg.append(stringSubstitutor.replace(obxTemplate));
+        }
+        String obrMsgStr = obrMsg.toString();
+        if (obrMsgStr.contains("\n")) {
+            throw new RuntimeException("HL7 message contains LF char; lines must be CR terminated");
+        }
+        return obrMsgStr;
+    }
 
     /**
      * Make synthetic HL7 messages for a single patient and single machine, max one second per message.
+     * @param locationId where the data originates from (machine/bed location)
+     * @param streamId identifier for the stream
      * @param samplingRate in samples per second
      * @param numMillis number of milliseconds to produce data for
-     * @param locationId where the data originates from (machine/bed location)
      * @param startTime observation time of the beginning of the period that the messages are to cover
      * @param millisPerMessage max time per message (will split into multiple if needed)
      * @return all messages
      */
-    private List<String> makeSyntheticWaveformMsgs(String locationId,
-                                                            final long samplingRate,
-                                                            final long numMillis,
-                                                            final Instant startTime,
-                                                            final long millisPerMessage
+    private List<String> makeSyntheticWaveformMsgs(final String locationId,
+                                                   final String streamId,
+                                                   final long samplingRate,
+                                                   final long numMillis,
+                                                   final Instant startTime,
+                                                   final long millisPerMessage
     ) {
         List<String> allMessages = new ArrayList<>();
         final long numSamples = numMillis * samplingRate / 1000;
@@ -123,13 +183,6 @@ private List<String> makeSyntheticWaveformMsgs(String locationId,
             String timeStr = DateTimeFormatter.ofPattern("HHmmss").format(startTime.atOffset(ZoneOffset.UTC));
             String messageId = String.format("%s_t%s_msg%05d", locationId, timeStr, overallSampleIdx);
 
-            // XXX: make this into real HL7
-            StringBuilder hl7Template = new StringBuilder();
-            hl7Template.append("/samplingRate/").append(samplingRate).append("/");
-            hl7Template.append("/locationId/").append(locationId).append("/");
-            hl7Template.append("/messageStartTime/").append(messageStartTime).append("/");
-            hl7Template.append("/messageId/").append(messageId).append("/");
-
             var values = new ArrayList<Double>();
             long samplesPerMessage = samplingRate * millisPerMessage / 1000;
             for (long valueIdx = 0;
@@ -138,10 +191,12 @@ private List<String> makeSyntheticWaveformMsgs(String locationId,
                 // a sine wave between maxValue and -maxValue
                 values.add(2 * maxValue * Math.sin(overallSampleIdx * 0.01) - maxValue);
             }
-            String valuesAsStr = values.stream().map(d -> String.format("%.3f", d)).collect(Collectors.joining(","));
-            hl7Template.append("/values/").append(valuesAsStr).append("/");
 
-            allMessages.add(hl7Template.toString());
+            // Only one stream ID per HL7 message for the time being
+            List<ImmutablePair<String, List<Double>>> valuesByStreamId = new ArrayList<>();
+            valuesByStreamId.add(new ImmutablePair<>(streamId, values));
+            String fullHl7message = applyHl7Template(samplingRate, locationId, messageStartTime, messageId, valuesByStreamId);
+            allMessages.add(fullHl7message);
         }
         return allMessages;
     }
@@ -159,14 +214,15 @@ public List<String> makeSyntheticWaveformMsgsAllPatients(
             Instant startTime, long numPatients, long numMillis) {
         List<String> waveformMsgs = new ArrayList<>();
         for (int p = 0; p < numPatients; p++) {
-            var machine1Str = String.format("P%03d_mach1", p);
-            var machine2Str = String.format("P%03d_mach2", p);
+            var location = String.format("Bed%03d", p);
+            String streamId1 = "52912";
+            String streamId2 = "52913";
             final long millisPerMessage = 10000;
             int sizeBefore = waveformMsgs.size();
             waveformMsgs.addAll(makeSyntheticWaveformMsgs(
-                    machine1Str, 50, numMillis, startTime, millisPerMessage));
+                    location, streamId1, 50, numMillis, startTime, millisPerMessage));
             waveformMsgs.addAll(makeSyntheticWaveformMsgs(
-                    machine2Str, 300, numMillis, startTime, millisPerMessage));
+                    location, streamId2, 300, numMillis, startTime, millisPerMessage));
             int sizeAfter = waveformMsgs.size();
             logger.debug("Patient {}, generated {} messages", p, sizeAfter - sizeBefore);
         }

diff --git a/waveform-reader/pom.xml b/waveform-reader/pom.xml
@@ -74,6 +74,13 @@
       </exclusions>
     </dependency>
 
+    <dependency>
+      <groupId>com.h2database</groupId>
+      <artifactId>h2</artifactId>
+      <scope>test</scope>
+    </dependency>
+
+
     <dependency>
       <groupId>org.junit.jupiter</groupId>
       <artifactId>junit-jupiter-engine</artifactId>
@@ -120,6 +127,11 @@
       <optional>true</optional>
     </dependency>
 
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-test</artifactId>
+    </dependency>
+
 
   </dependencies>
   <build>

diff --git a/...rm-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/waveform/Hl7ListenerConfig.java b/...rm-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/waveform/Hl7ListenerConfig.java
@@ -13,6 +13,7 @@
 import org.springframework.integration.ip.tcp.connection.TcpNetServerConnectionFactory;
 import org.springframework.integration.ip.tcp.serializer.TcpCodecs;
 import org.springframework.messaging.Message;
+import uk.ac.ucl.rits.inform.datasources.waveform.hl7parse.Hl7ParseException;
 
 import java.net.Socket;
 import java.nio.charset.StandardCharsets;
@@ -87,14 +88,13 @@ public TcpReceivingChannelAdapter inbound(TcpNetServerConnectionFactory connecti
     /**
      * Message handler. Source IP check has passed if we get here. No reply is expected.
      * @param msg the incoming message
-     * @throws InterruptedException .
+     * @throws InterruptedException if publisher send is interrupted
+     * @throws Hl7ParseException .
      */
     @ServiceActivator(inputChannel = "hl7Stream")
-    public void handler(Message<byte[]> msg) throws InterruptedException {
+    public void handler(Message<byte[]> msg) throws InterruptedException, Hl7ParseException {
         byte[] asBytes = msg.getPayload();
         String asStr = new String(asBytes, StandardCharsets.UTF_8);
-        logger.trace("received message = {}", asStr);
-        logger.info("MESSAGE of size {}", asStr.length());
         // parse message from HL7 to interchange message, send to publisher
         hl7ParseAndSend.parseAndSend(asStr);
     }