Merge branch 'main' into devex/1247-add_impact_sections_to_adrs_012-016

CDCgov · Dec 4, 2024 · 8c6aa19 · 8c6aa19
2 parents eeceec2 + 96fc5c3
commit 8c6aa19
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diff --git a/README.md b/README.md
@@ -56,7 +56,7 @@ creates a `.env` file in the resource folder with the required configuration
 
 ### Using a local database
 
-Use [docker-compose.postgres.yml](docker-compose.postgres.yml) to run your local DB. In IntelliJ, you can click the play arrow to start it
+Use [docker-compose.yml](docker-compose.yml) to run your local DB. In IntelliJ, you can click the play arrow to start it
 
 ![docker-postgres.png](images/docker-postgres.png)
 
@@ -466,3 +466,8 @@ Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
 for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
 [public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
 and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
+
+### Troubleshooting
+
+Error: copier: stat: "/app/build/libs/app-all.jar": no such file or directory
+Solution: Run ./gradlew shadowjar first
diff --git a/app/build.gradle b/app/build.gradle
@@ -28,7 +28,7 @@ dependencies {
     testImplementation 'org.apache.groovy:groovy:4.0.24'
     testImplementation 'org.spockframework:spock-core:2.3-groovy-4.0'
     testImplementation 'com.openpojo:openpojo:0.9.1'
-    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.3'
+    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.4'
 }
 
 jacocoTestCoverageVerification {

diff --git a/docker-compose.postgres.yml b/docker-compose.postgres.yml
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,3 +1,10 @@
+# Run the following to migrate...
+# liquibase update --changelog-file ./etor/databaseMigrations/root.yml --url jdbc:postgresql://localhost:5433/intermediary --username intermediary --password 'changeIT!' --label-filter '!azure'
+
+# Run the following to rollback...
+# liquibase rollback-count --changelog-file ./etor/databaseMigrations/root.yml --url jdbc:postgresql://localhost:5433/intermediary --username intermediary --password 'changeIT!' --count 2
+
+
 version: "3.7"
 services:
   router:
@@ -7,3 +14,18 @@ services:
     ports:
       - "8080:8080" # default api endpoint port
       - "6006:6006" # Java debug port
+
+  postgresql:
+    image: postgres:16
+    restart: unless-stopped
+    environment:
+      POSTGRES_DB: "intermediary"
+      POSTGRES_PASSWORD: "changeIT!" # pragma: allowlist secret
+      POSTGRES_USER: "intermediary"
+    ports:
+      - 5433:5432
+    volumes:
+      - ti_postgres_data:/var/lib/postgresql/data
+
+volumes:
+  ti_postgres_data:
diff --git a/e2e/build.gradle b/e2e/build.gradle
@@ -15,8 +15,8 @@ dependencies {
     implementation 'org.apache.httpcomponents.client5:httpclient5-fluent:5.4.1'
 
     //jackson
-    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.1'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.2'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.2'
 
     //fhir
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:7.6.0'

diff --git a/etor/build.gradle b/etor/build.gradle
@@ -19,7 +19,7 @@ dependencies {
     testImplementation 'org.apache.groovy:groovy:4.0.24'
     testImplementation 'org.spockframework:spock-core:2.3-groovy-4.0'
     testImplementation 'com.openpojo:openpojo:0.9.1'
-    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.3'
+    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.4'
 }
 
 jacocoTestCoverageVerification {

diff --git a/operations/environments/dev/main.tf b/operations/environments/dev/main.tf
@@ -2,7 +2,7 @@ terraform {
   required_providers {
     azurerm = {
       source  = "hashicorp/azurerm"
-      version = "4.11.0"
+      version = "4.12.0"
     }
   }
 

diff --git a/operations/environments/internal/main.tf b/operations/environments/internal/main.tf
@@ -2,7 +2,7 @@ terraform {
   required_providers {
     azurerm = {
       source  = "hashicorp/azurerm"
-      version = "4.11.0"
+      version = "4.12.0"
     }
   }
 

diff --git a/operations/environments/pr/main.tf b/operations/environments/pr/main.tf
@@ -2,7 +2,7 @@ terraform {
   required_providers {
     azurerm = {
       source  = "hashicorp/azurerm"
-      version = "4.11.0"
+      version = "4.12.0"
     }
   }
 

diff --git a/operations/environments/prd/main.tf b/operations/environments/prd/main.tf
@@ -2,7 +2,7 @@ terraform {
   required_providers {
     azurerm = {
       source  = "hashicorp/azurerm"
-      version = "4.11.0"
+      version = "4.12.0"
     }
   }
 

diff --git a/operations/environments/stg/main.tf b/operations/environments/stg/main.tf
@@ -2,7 +2,7 @@ terraform {
   required_providers {
     azurerm = {
       source  = "hashicorp/azurerm"
-      version = "4.11.0"
+      version = "4.12.0"
     }
   }
 

diff --git a/rs-e2e/build.gradle b/rs-e2e/build.gradle
@@ -14,8 +14,8 @@ dependencies {
     testImplementation testFixtures(project(':shared'))
 
     //jackson
-    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.1'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.2'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.2'
 
     // azure
     implementation 'com.azure:azure-storage-blob:12.29.0'

diff --git a/...src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcher.java b/...src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcher.java
@@ -4,7 +4,6 @@
 import ca.uhn.hl7v2.HL7Exception;
 import ca.uhn.hl7v2.HapiContext;
 import ca.uhn.hl7v2.model.Message;
-import ca.uhn.hl7v2.model.v251.segment.MSH;
 import ca.uhn.hl7v2.parser.Parser;
 import com.google.common.collect.Sets;
 import gov.hhs.cdc.trustedintermediary.rse2e.HL7FileStream;
@@ -32,13 +31,13 @@ public static HapiHL7FileMatcher getInstance() {
         return INSTANCE;
     }
 
-    public Map<Message, Message> matchFiles(
+    public Map<HapiHL7Message, HapiHL7Message> 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, Message> inputMap = mapMessageByControlId(inputFiles);
-        Map<String, Message> outputMap = mapMessageByControlId(outputFiles);
+        Map<String, HapiHL7Message> inputMap = parseAndMapMessageByControlId(inputFiles);
+        Map<String, HapiHL7Message> outputMap = parseAndMapMessageByControlId(outputFiles);
 
         Set<String> inputKeys = inputMap.keySet();
         Set<String> outputKeys = outputMap.keySet();
@@ -55,10 +54,10 @@ public Map<Message, Message> matchFiles(
         return inputKeys.stream().collect(Collectors.toMap(inputMap::get, outputMap::get));
     }
 
-    public Map<String, Message> mapMessageByControlId(List<HL7FileStream> files)
+    public Map<String, HapiHL7Message> parseAndMapMessageByControlId(List<HL7FileStream> files)
             throws HapiHL7FileMatcherException {
 
-        Map<String, Message> messageMap = new HashMap<>();
+        Map<String, HapiHL7Message> messageMap = new HashMap<>();
 
         try (HapiContext context = new DefaultHapiContext()) {
             Parser parser = context.getPipeParser();
@@ -68,13 +67,13 @@ public Map<String, Message> mapMessageByControlId(List<HL7FileStream> files)
                 try (InputStream inputStream = hl7FileStream.inputStream()) {
                     String content = new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
                     Message message = parser.parse(content);
-                    MSH mshSegment = (MSH) message.get("MSH");
-                    String msh10 = mshSegment.getMessageControlID().getValue();
+                    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, message);
+                    messageMap.put(msh10, hapiHL7Message);
                 } catch (HL7Exception e) {
                     throw new HapiHL7FileMatcherException(
                             String.format("Failed to parse HL7 message from file: %s", fileName),

diff --git a/rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7Message.java b/rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7Message.java
@@ -1,6 +1,8 @@
 package gov.hhs.cdc.trustedintermediary.rse2e.external.hapi;
 
+import ca.uhn.hl7v2.HL7Exception;
 import ca.uhn.hl7v2.model.Message;
+import ca.uhn.hl7v2.model.v251.segment.MSH;
 import gov.hhs.cdc.trustedintermediary.wrappers.HealthData;
 
 /**
@@ -21,7 +23,12 @@ public Message getUnderlyingData() {
     }
 
     @Override
-    public String getName() {
-        return underlyingData.getName();
+    public String getIdentifier() {
+        try {
+            MSH mshSegment = (MSH) underlyingData.get("MSH");
+            return mshSegment.getMessageControlID().getValue();
+        } catch (HL7Exception e) {
+            return null;
+        }
     }
 }
diff --git a/rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/ruleengine/AssertionRule.java b/rs-e2e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/ruleengine/AssertionRule.java
@@ -46,7 +46,7 @@ public final void runRule(HealthData<?>... data) {
                                     + "': "
                                     + assertion
                                     + " ("
-                                    + outputData.getName()
+                                    + outputData.getIdentifier()
                                     + ")");
                 }
             } catch (Exception e) {

diff --git a/...e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/ruleengine/AssertionRuleEngine.java b/...e/src/main/java/gov/hhs/cdc/trustedintermediary/rse2e/ruleengine/AssertionRuleEngine.java
@@ -1,9 +1,8 @@
 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.ruleengine.RuleLoader;
 import gov.hhs.cdc.trustedintermediary.ruleengine.RuleLoaderException;
+import gov.hhs.cdc.trustedintermediary.wrappers.HealthData;
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
 import gov.hhs.cdc.trustedintermediary.wrappers.formatter.TypeReference;
 import java.io.IOException;
@@ -64,21 +63,18 @@ public List<AssertionRule> getRules() {
         return assertionRules;
     }
 
-    public Set<AssertionRule> runRules(Message outputMessage, Message inputMessage) {
+    public Set<AssertionRule> runRules(HealthData<?> outputMessage, HealthData<?> inputMessage) {
         try {
             ensureRulesLoaded();
         } catch (RuleLoaderException e) {
             logger.logError("Failed to load rules definitions", e);
             return Set.of();
         }
 
-        HapiHL7Message outputHapiMessage = new HapiHL7Message(outputMessage);
-        HapiHL7Message inputHapiMessage = new HapiHL7Message(inputMessage);
-
         Set<AssertionRule> runRules = new HashSet<>();
         for (AssertionRule rule : assertionRules) {
-            if (rule.shouldRun(outputHapiMessage)) {
-                rule.runRule(outputHapiMessage, inputHapiMessage);
+            if (rule.shouldRun(outputMessage)) {
+                rule.runRule(outputMessage, inputMessage);
                 runRules.add(rule);
             }
         }

diff --git a/rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/AutomatedTest.groovy b/rs-e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/rse2e/AutomatedTest.groovy
@@ -1,6 +1,5 @@
 package gov.hhs.cdc.trustedintermediary.rse2e
 
-import ca.uhn.hl7v2.model.Message
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
 import gov.hhs.cdc.trustedintermediary.rse2e.external.hapi.HapiHL7FileMatcher
 import gov.hhs.cdc.trustedintermediary.rse2e.external.hapi.HapiHL7ExpressionEvaluator
@@ -65,8 +64,8 @@ class AutomatedTest extends Specification  {
 
         when:
         for (messagePair in matchedFiles) {
-            Message inputMessage = messagePair.getKey() as Message
-            Message outputMessage = messagePair.getValue() as Message
+            def inputMessage = messagePair.getKey()
+            def outputMessage = messagePair.getValue()
             def evaluatedRules = engine.runRules(outputMessage, inputMessage)
             rulesToEvaluate.removeAll(evaluatedRules)
         }

diff --git a/.../groovy/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcherTest.groovy b/.../groovy/gov/hhs/cdc/trustedintermediary/rse2e/external/hapi/HapiHL7FileMatcherTest.groovy
@@ -1,6 +1,5 @@
 package gov.hhs.cdc.trustedintermediary.rse2e.external.hapi
 
-import ca.uhn.hl7v2.model.Message
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
 import gov.hhs.cdc.trustedintermediary.rse2e.HL7FileStream
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger
@@ -31,15 +30,15 @@ class HapiHL7FileMatcherTest extends Specification {
             new HL7FileStream("outputFileStream1", Mock(InputStream)),
             new HL7FileStream("outputFileStream2", Mock(InputStream))
         ]
-        def mockInputMessage1 = Mock(Message)
-        def mockInputMessage2 = Mock(Message)
-        def mockOutputMessage1 = Mock(Message)
-        def mockOutputMessage2 = Mock(Message)
-        spyFileMatcher.mapMessageByControlId(mockInputFiles) >> [ "001": mockInputMessage1, "002": mockInputMessage2 ]
-        spyFileMatcher.mapMessageByControlId(mockOutputFiles) >> [ "001": mockOutputMessage1, "002": mockOutputMessage2 ]
+        def mockInputMessage1 = Mock(HapiHL7Message)
+        def mockInputMessage2 = Mock(HapiHL7Message)
+        def mockOutputMessage1 = Mock(HapiHL7Message)
+        def mockOutputMessage2 = Mock(HapiHL7Message)
+        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": mockInputMessage1, "002": mockInputMessage2 ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": mockOutputMessage1, "002": mockOutputMessage2 ]
 
         when:
-        def result =spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
+        def result = spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
 
         then:
         result.size() == 2
@@ -61,8 +60,8 @@ class HapiHL7FileMatcherTest extends Specification {
         mockOutputFiles = [
             new HL7FileStream("matchingOutputFileStream", Mock(InputStream))
         ]
-        spyFileMatcher.mapMessageByControlId(mockInputFiles) >> [ "001": Mock(Message), "002": Mock(Message) ]
-        spyFileMatcher.mapMessageByControlId(mockOutputFiles) >> [ "001": Mock(Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HapiHL7Message), "002": Mock(HapiHL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HapiHL7Message) ]
         spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
 
         then:
@@ -80,8 +79,8 @@ class HapiHL7FileMatcherTest extends Specification {
             new HL7FileStream("matchingOutputFileStream", Mock(InputStream)),
             new HL7FileStream("nonMatchingOutputFileStream", Mock(InputStream))
         ]
-        spyFileMatcher.mapMessageByControlId(mockInputFiles) >> [ "001": Mock(Message) ]
-        spyFileMatcher.mapMessageByControlId(mockOutputFiles) >> [ "001": Mock(Message), "003": Mock(Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockInputFiles) >> ["001": Mock(HapiHL7Message) ]
+        spyFileMatcher.parseAndMapMessageByControlId(mockOutputFiles) >> ["001": Mock(HapiHL7Message), "003": Mock(HapiHL7Message) ]
         spyFileMatcher.matchFiles(mockOutputFiles, mockInputFiles)
 
         then:
@@ -110,14 +109,16 @@ class HapiHL7FileMatcherTest extends Specification {
         ]
 
         when:
-        def result = fileMatcher.mapMessageByControlId(mockFiles)
+        def result = fileMatcher.parseAndMapMessageByControlId(mockFiles)
 
         then:
         result.size() == 2
-        result[file1Msh10] != null
-        file1MshSegment == result[file1Msh10].encode().trim()
-        result[file2Msh10] != null
-        file2MshSegment == result[file2Msh10].encode().trim()
+        def message1 = result[file1Msh10]
+        def message2 = result[file2Msh10]
+        message1 != null
+        message2 != null
+        file1MshSegment == message1.getUnderlyingData().encode().trim()
+        file2MshSegment == message2.getUnderlyingData().encode().trim()
     }
 
     def "should throw HapiHL7FileMatcherException when MSH-10 is empty"() {
@@ -130,7 +131,7 @@ class HapiHL7FileMatcherTest extends Specification {
         def hl7FileStream = new HL7FileStream("file1", inputStream)
 
         when:
-        fileMatcher.mapMessageByControlId([hl7FileStream])
+        fileMatcher.parseAndMapMessageByControlId([hl7FileStream])
 
         then:
         thrown(HapiHL7FileMatcherException)
@@ -142,7 +143,7 @@ class HapiHL7FileMatcherTest extends Specification {
         def hl7FileStream = new HL7FileStream("badFile", inputStream)
 
         when:
-        fileMatcher.mapMessageByControlId([hl7FileStream])
+        fileMatcher.parseAndMapMessageByControlId([hl7FileStream])
 
         then:
         thrown(HapiHL7FileMatcherException)