Merge pull request #360 from LinuxForHealth/Example-and-test-of-custo…

…m-messages

Example and test of custom messages

src/test/java/custom_packages/2.6

@@ -0,0 +1,2 @@
+# This is path to custom HL7 message implementations so HL7 parser can validate them.
+org.foo.hl7.custom

src/test/java/io/github/linuxforhealth/hl7/message/Hl7CustomMessageTest.java

@@ -0,0 +1,137 @@
+/*
+ * (C) Copyright IBM Corp. 2020, 2021
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package io.github.linuxforhealth.hl7.message;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import java.io.FileOutputStream;
+import java.util.Properties;
+
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.ResourceType;
+
+import io.github.linuxforhealth.core.config.ConverterConfiguration;
+import io.github.linuxforhealth.fhir.FHIRContext;
+import io.github.linuxforhealth.hl7.ConverterOptions;
+import io.github.linuxforhealth.hl7.ConverterOptions.Builder;
+import io.github.linuxforhealth.hl7.HL7ToFHIRConverter;
+import io.github.linuxforhealth.hl7.resource.ResourceReader;
+import io.github.linuxforhealth.hl7.segments.util.ResourceUtils;
+
+// This shows how and tests the ability to create a custom Hl7 class
+// Detailed documentation about how this works is found here: 
+// http://javadox.com/ca.uhn.hapi/hapi-base/2.1/ca/uhn/hl7v2/parser/DefaultModelClassFactory.html#packageList(java.lang.String)
+// In this test, the custom class which HL7 uses for validation is placed in src/test/java/org/foo/hl7/custom/message/CUSTOM_PAT.java
+// The custom message is placed in src/test/resources/additional_custom_resources/hl7/message/CUSTOM_PAT.yml
+// The custom packages class is placed in src/test/java/custom_packages/2.6 and references the custom package /org/foo/hl7/custom/
+
+public class Hl7CustomMessageTest {
+
+    // # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+    // NOTE VALIDATION IS INTENTIONALLY NOT USED BECAUSE WE ARE CREATING RESOURCES THAT ARE NOT STANDARD
+    private static final ConverterOptions OPTIONS = new Builder().withPrettyPrint().build();
+    // # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+
+    private static final String CONF_PROP_HOME = "hl7converter.config.home";
+
+    @TempDir
+    static File folder;
+
+    static String originalConfigHome;
+
+    @BeforeAll
+    public static void saveConfigHomeProperty() {
+      originalConfigHome = System.getProperty(CONF_PROP_HOME);
+      ConverterConfiguration.reset();
+      ResourceReader.reset();
+    }
+
+    @AfterEach
+    public void reset() {
+      System.clearProperty(CONF_PROP_HOME);
+      ConverterConfiguration.reset();
+      ResourceReader.reset();
+    }
+
+    @AfterAll
+    public static void reloadPreviousConfigurations() {
+      if (originalConfigHome != null)
+        System.setProperty(CONF_PROP_HOME, originalConfigHome);
+      else
+        System.clearProperty(CONF_PROP_HOME);
+    }
+
+    @Test
+    public void testCustomPatMessage() throws IOException {
+
+        // Set up the config file
+    	  commonConfigFileSetup();
+
+        String hl7message = 
+            "MSH|^~\\&|||||20211005105125||CUSTOM^PAT|1a3952f1-38fe-4d55-95c6-ce58ebfc7f10|P|2.6\n"
+            + "PID|1|100009^^^FAC^MR|100009^^^FAC^MR||DOE^JANE||195001010000|M|||||5734421788|||U\n"
+            + "PRB|1|20211005|10281^LYMPHOID LEUKEMIA NEC^ICD9||||201208061011||201208061011|||||||201208061011\n"
+            + "PRB|2|20211005|11334^ABNORMALITIES OF HAIR^ICD9||||201208071000||201208071000|||||||201208071000\n"
+            + "AL1|50|DA|penicillin|MO||20210629\n"
+            + "AL1|50|MA|cat dander|SV|hives\\R\\ difficult breathing|20210629\n"
+            ;
+
+        List<BundleEntryComponent> e = getBundleEntryFromHL7Message(hl7message);
+
+        // Check for the expected resources 1 patient, 2 conditions, 2 allergies
+        List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
+        assertThat(patientResource).hasSize(1); // From PID
+
+        List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
+        assertThat(conditionResource).hasSize(2);  // From 2x PRB
+
+        List<Resource> allergyIntoleranceResource = ResourceUtils.getResourceList(e, ResourceType.AllergyIntolerance);
+        assertThat(allergyIntoleranceResource).hasSize(2);  // From 2x AL1
+
+        // Confirm that no extra resources are created
+        assertThat(e.size()).isEqualTo(5);
+    }
+
+    private static void commonConfigFileSetup() throws IOException {
+        File configFile = new File(folder, "config.properties");
+        Properties prop = new Properties();
+        prop.put("base.path.resource", "src/main/resources");
+        prop.put("supported.hl7.messages", "*");  // Must use wild card so the custom resources are found.
+        prop.put("default.zoneid", "+08:00");
+        prop.put("additional.resources.location", "src/test/resources/additional_custom_resources");  // Location of custom resources
+        prop.store(new FileOutputStream(configFile), null);
+        System.setProperty(CONF_PROP_HOME, configFile.getParent());
+    }
+
+    // Need custom convert sequence with options that turn off FHIR validation.
+    private static List<BundleEntryComponent> getBundleEntryFromHL7Message(String hl7message)  {
+        HL7ToFHIRConverter ftv = new HL7ToFHIRConverter();
+        String json = ftv.convert(hl7message, OPTIONS);  // Need custom options that turn off FHIR validation.
+        assertThat(json).isNotNull();
+        FHIRContext context = new FHIRContext();
+        IBaseResource bundleResource = context.getParser().parseResource(json);
+        assertThat(bundleResource).isNotNull();
+        Bundle b = (Bundle) bundleResource;
+        return b.getEntry();
+    }
+
+}
+
+

src/test/java/org/foo/hl7/custom/message/CUSTOM_PAT.java

@@ -0,0 +1,220 @@
+/*
+ * (C) Copyright IBM Corp. 2020, 2021
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+//########################################################################
+// Used for testing only. Not used in production.
+//########################################################################
+
+package org.foo.hl7.custom.message;
+
+import ca.uhn.hl7v2.model.v26.segment.*;
+
+import ca.uhn.hl7v2.HL7Exception;
+import ca.uhn.hl7v2.parser.ModelClassFactory;
+import ca.uhn.hl7v2.parser.DefaultModelClassFactory;
+import ca.uhn.hl7v2.model.*;
+
+/**
+ * <p>
+ * Represents a CUSTOM_PAT message structure. This structure
+ * contains the following elements:
+ * </p>
+ * <ul>
+ * <li>MSH (Message Header) <b> </b></li>
+ * <li>PID (Patient Identification) <b> </b></li>
+ * <li>PRB (Problem Details) <b>optional repeating</b></li>
+ * <li>AL1 (Allergy) <b>optional repeating</b></li>
+ * </ul>
+ *
+ * Sample Message:
+ * MSH|^~\\&|||||20210709162149||HIST^PAT|20210709162149|P|2.6
+ * PID|1|100021^^^FAC|100021^^^FAC||DOE^JANE||196705270000|F|||||5733551967|||U 
+ * PRB|1|20210726|11334^ABNORMALITIES OF HAIR^ICD9||||201208070948||201208070948|||||||201208070948
+ * AL1|90|MA|dog|MO|itch|20210629
+ */
+
+public class CUSTOM_PAT extends AbstractMessage {
+
+	/**
+	 * Creates a new CUSTOM_PAT message with DefaultModelClassFactory.
+	 */
+	public CUSTOM_PAT() {
+		this(new DefaultModelClassFactory());
+	}
+
+	/**
+	 * Creates a new CUSTOM_PAT message with custom ModelClassFactory.
+	 */
+	public CUSTOM_PAT(ModelClassFactory factory) {
+		super(factory);
+		init(factory);
+	}
+
+	private void init(ModelClassFactory factory) {
+		try {
+			// parms: ClassName, required, repeats
+			this.add(MSH.class, true, false);
+			this.add(PID.class, true, false);
+			this.add(PRB.class, false, true);
+			this.add(AL1.class, false, true);
+		} catch (HL7Exception e) {
+			log.error("Unexpected error creating CUSTOM_PAT - this is probably a bug in the source code generator.");
+		}
+	}
+
+	/**
+	 * Returns the version.
+	 */
+	public String getVersion() {
+		return "2.6";
+	}
+
+	/**
+	 * Returns MSH (Message Header) - creates it if necessary
+	 */
+	public MSH getMSH() {
+		return getTyped("MSH", MSH.class);
+	}
+
+	/**
+	 * Returns PID (Patient Identification) - creates it if necessary
+	 */
+	public PID getPID() {
+		return getTyped("PID", PID.class);
+	}
+
+	/**
+	 * Returns the first repetition of PRB (Problem Details) - creates it if
+	 * necessary
+	 */
+	public PRB getPRB() {
+		return getTyped("PRB", PRB.class);
+	}
+
+	/**
+	 * Returns a specific repetition of PRB (Problem Details) - creates it if
+	 * necessary
+	 *
+	 * @param rep The repetition index (0-indexed, i.e. the first repetition is at
+	 *            index 0)
+	 * @throws HL7Exception if the repetition requested is more than one greater
+	 *                      than the number of existing repetitions.
+	 */
+	public PRB getPRB(int rep) {
+		return getTyped("PRB", rep, PRB.class);
+	}
+
+	/**
+	 * Returns the number of existing repetitions of PRB
+	 */
+	public int getPRBReps() {
+		return getReps("PRB");
+	}
+
+	/**
+	 * Returns a non-modifiable List containing all current existing repetitions of
+	 * PRB.
+	 * Note that unlike {@link #getPRB()}, this method will not create any reps if
+	 * none are already present, so an empty list may be returned.
+	 */
+	public java.util.List<PRB> getPRBAll() throws HL7Exception {
+		return getAllAsList("PRB", PRB.class);
+	}
+
+	/**
+	 * Inserts a specific repetition of PRB (Problem Details)
+	 * *
+	 * @see AbstractGroup#insertRepetition(Structure, int)
+	 */
+	public void insertPRB(PRB structure, int rep) throws HL7Exception {
+		super.insertRepetition("PRB", structure, rep);
+	}
+
+	/**
+	 * Inserts a specific repetition of PRB (Problem Details)
+	 *
+	 * @see AbstractGroup#insertRepetition(Structure, int)
+	 */
+	public PRB insertPRB(int rep) throws HL7Exception {
+		return (PRB) super.insertRepetition("PRB", rep);
+	}
+
+	/**
+	 * Removes a specific repetition of PRB (Problem Details)
+	 *
+	 * @see AbstractGroup#removeRepetition(String, int)
+	 */
+	public PRB removePRB(int rep) throws HL7Exception {
+		return (PRB) super.removeRepetition("PRB", rep);
+	}
+
+	/**
+	 * Returns the first repetition of AL1 (Patient Allergy Information) - creates
+	 * it if necessary
+	 */
+	public AL1 getAL1() {
+		return getTyped("AL1", AL1.class);
+	}
+
+	/**
+	 * Returns a specific repetition of AL1 (Patient Allergy Information) - creates
+	 * it if necessary
+ 	 * @param rep The repetition index (0-indexed, i.e. the first repetition is at
+	 *            index 0)
+	 * @throws HL7Exception if the repetition requested is more than one greater
+	 *                      than the number of existing repetitions.
+	 */
+	public AL1 getAL1(int rep) {
+		return getTyped("AL1", rep, AL1.class);
+	}
+
+	/**
+	 * Returns the number of existing repetitions of AL1
+	 */
+	public int getAL1Reps() {
+		return getReps("AL1");
+	}
+
+	/**
+	 * Returns a non-modifiable List containing all current existing repetitions of
+	 * AL1.
+	 * 
+	 * Note that unlike {@link #getAL1()}, this method will not create any reps if
+	 * none are already present, so an empty list may be returned.
+	 *
+	 */
+	public java.util.List<AL1> getAL1All() throws HL7Exception {
+		return getAllAsList("AL1", AL1.class);
+	}
+
+	/**
+	 * Inserts a specific repetition of AL1 (Patient Allergy Information)
+	 *
+	 * @see AbstractGroup#insertRepetition(Structure, int)
+	 */
+	public void insertAL1(AL1 structure, int rep) throws HL7Exception {
+		super.insertRepetition("AL1", structure, rep);
+	}
+
+	/**
+	 * Inserts a specific repetition of AL1 (Patient Allergy Information)
+	 *
+	 * @see AbstractGroup#insertRepetition(Structure, int)
+	 */
+	public AL1 insertAL1(int rep) throws HL7Exception {
+		return (AL1) super.insertRepetition("AL1", rep);
+	}
+
+	/**
+	 * Removes a specific repetition of AL1 (Patient Allergy Information)
+	 *
+	 * @see AbstractGroup#removeRepetition(String, int)
+	 */
+	public AL1 removeAL1(int rep) throws HL7Exception {
+		return (AL1) super.removeRepetition("AL1", rep);
+	}
+
+}