Merge branch 'main' into remove-la-obr-except-54089-8

CDCgov · Nov 22, 2024 · abda88c · abda88c
2 parents 07fee0c + a289884
commit abda88c
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,4 +1,4 @@
-# Add a PR title
+# Description
 
 Describe what changed in this PR at a high level.
 

diff --git a/.github/renovate.json b/.github/renovate.json
@@ -36,7 +36,7 @@
         },
         {
             "matchPackageNames": ["com.azure:azure-identity"],
-            "allowedVersions": "!/^1\\.14\\.0$/"
+            "allowedVersions": "!/^1\\.14\\.[0-1]$/"
         }],
     "pinDigests": false
 }
diff --git a/.github/workflows/automated-staging-test-run.yml b/.github/workflows/automated-staging-test-run.yml
@@ -2,7 +2,7 @@ name: Automated Staging Test - Run integration tests
 
 on:
   schedule:
-    - cron: "0 2 * * 2-6"  # Tuesday to Saturday at 2am UTC - two hours after `automated-staging-test-submit` runs
+    - cron: "0 7 * * 2-6"  # Tuesday to Saturday at 2am EST (7am UTC) - two hours after `automated-staging-test-submit` runs
   workflow_dispatch:
 
 jobs:
@@ -17,3 +17,12 @@ jobs:
         env:
           AZURE_STORAGE_CONNECTION_STRING: ${{ secrets.AUTOMATED_TEST_AZURE_STORAGE_CONNECTION_STRING }}
         run: ./gradlew rs-e2e:clean rs-e2e:automatedTest
+
+      - name: Send slack notification on test failure
+        if: failure()
+        uses: slackapi/[email protected]
+        with:
+          webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
+          webhook-type: incoming-webhook
+          payload: |
+            text: "Automated Staging RS Integration Test Failed!: https://github.com/CDCgov/trusted-intermediary/actions/runs/${{ github.run_id }}"
diff --git a/.github/workflows/automated-staging-test-submit.yml b/.github/workflows/automated-staging-test-submit.yml
@@ -2,7 +2,7 @@ name: Automated Staging Test - Submit Messages
 
 on:
   schedule:
-    - cron: "0 0 * * 2-6"  # Tuesday to Saturday at Midnight UTC
+    - cron: "0 5 * * 2-6"  # Tuesday to Saturday at Midnight EST (5am UTC)
   workflow_dispatch:
 
 jobs:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -117,7 +117,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Run Db migration
-        uses: liquibase-github-actions/update@v4.29.2
+        uses: liquibase-github-actions/update@v4.30.0
         with:
           changelogFile: ./etor/databaseMigrations/root.yml
           url: "jdbc:postgresql://postgres:5432/testdb"

diff --git a/.secrets.baseline b/.secrets.baseline
@@ -218,7 +218,7 @@
         "filename": "operations/template/db.tf",
         "hashed_secret": "7cb6efb98ba5972a9b5090dc2e517fe14d12cb04",
         "is_verified": false,
-        "line_number": 20,
+        "line_number": 16,
         "is_secret": false
       }
     ],
@@ -243,5 +243,5 @@
       }
     ]
   },
-  "generated_at": "2024-05-28T21:15:26Z"
+  "generated_at": "2024-11-21T18:04:15Z"
 }
diff --git a/app/build.gradle b/app/build.gradle
@@ -25,10 +25,10 @@ dependencies {
 
     implementation 'io.javalin:javalin:6.3.0'
 
-    testImplementation 'org.apache.groovy:groovy:4.0.23'
+    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:3.17.1'
+    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.3'
 }
 
 jacocoTestCoverageVerification {

diff --git a/build.gradle b/build.gradle
@@ -14,7 +14,7 @@ plugins {
     id 'com.diffplug.spotless' version '6.25.0'
     id 'com.github.johnrengelman.shadow' version '8.1.1'
     id 'org.cyclonedx.bom' version '1.10.0'
-    id 'org.sonarqube' version '5.1.0.4882'
+    id 'org.sonarqube' version '6.0.0.5145'
 }
 
 dependencies {

diff --git a/docs/database.md b/docs/database.md
@@ -81,8 +81,10 @@ To revert changes in the Azure database we use The Github Actions runner.
 2. Select Run workflow
 3. Run the workflow (Example inputs below)
    - Use workflow from: Always Main
-   - Number of migrations to rollback, an integer that is specific to the file input
-   - File with migrations you want to roll back: This should be the file containing the specific sub-file in the `databaseMigrations` directory you want to rollback from EX: `./etor/databaseMigrations/metadata.yml`
+   - Number of migrations to rollback, an integer that is specific to the file input [liquibase-documentation](https://docs.liquibase.com/commands/rollback/rollback-count.html)
+   - File with migrations you want to roll back: This should be the file containing the specific sub-file in the `databaseMigrations` directory 
+     you want to rollback from. Generally you want to pick the root migration because it takes all the migrations into account so the number of 
+     migrations is applied to all the migrations. EX: `./etor/databaseMigrations/root.yml`
    - Azure environment to rollback on: Select the environment you want to see the changes reverted from
 4. Once you have the inputs entered select Run Workflow on the tab and the workflow should start up
 

diff --git a/e2e/build.gradle b/e2e/build.gradle
@@ -25,7 +25,7 @@ dependencies {
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:7.4.5'
     implementation 'org.fhir:ucum:1.0.8'
 
-    testImplementation 'org.apache.groovy:groovy:4.0.23'
+    testImplementation 'org.apache.groovy:groovy:4.0.24'
     testImplementation 'org.spockframework:spock-core:2.3-groovy-4.0'
 }
 

diff --git a/etor/build.gradle b/etor/build.gradle
@@ -13,13 +13,13 @@ dependencies {
     implementation project(':shared')
     testImplementation testFixtures(project(':shared'))
 
-    implementation 'com.azure:azure-storage-blob:12.28.1'
-    implementation 'com.azure:azure-identity:1.13.3'
+    implementation 'com.azure:azure-storage-blob:12.29.0'
+    implementation 'com.azure:azure-identity:1.14.2'
 
-    testImplementation 'org.apache.groovy:groovy:4.0.23'
+    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:3.17.1'
+    testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.17.3'
 }
 
 jacocoTestCoverageVerification {

diff --git a/etor/src/main/resources/transformation_definitions.json b/etor/src/main/resources/transformation_definitions.json
@@ -187,7 +187,7 @@
     },
     {
       "name": "ucsdOruUpdateUniversalServiceIdentifier",
-      "description": "Overrides the values of Name of Coding System (OBR-4.3) and Alternate Identifier (OBR-4.4) in Universal Type Code (OBR-4)",
+      "description": "Updates the coding system name (OBR-4.3) for ORU orders to the expected value",
       "message": "",
       "conditions": [
         "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.where(extension.value = 'HD.1').value in ('R797' | 'R508')",

diff --git a/examples/Test/Automated/008_ORU_R01_micro_character_encoding.hl7 b/examples/Test/Automated/008_ORU_R01_micro_character_encoding.hl7
@@ -0,0 +1,6 @@
+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||ORU^R01^ORU_R01|008|N|2.5.1||||||||||
+PID|1||80008836^^^&NPI^MR||CDPHSIX^BOY  MOMSIX^^^^^B|||M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||N|1
+NK1|1|CDPHSIX|MTH^Mother|132 ST^^SAN DIEGO^CA^92126^USA
+ORC|RE|7181233072^FormNumber||189430284^HospOrdNumber||||||||^ROSEN^REBECCA|||||||||UCSD JACOBS MEDICAL CENTER^^^^^^^^^R797| 2961DR YLLUT^^SAN DIEGO^CA^99999-9999
+OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
+OBX|1|NM|47633-3^Glycine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20240212103049
diff --git a/examples/Test/Automated/009_CA_ORU_R01_remove_99717-5_OBX.hl7 b/examples/Test/Automated/009_CA_ORU_R01_remove_99717-5_OBX.hl7
@@ -0,0 +1,7 @@
+MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|009|N|2.5.1||||||||||
+PID|1||80008836^^^&NPI^MR||CDPHSIX^BOY  MOMSIX^^^^^B|||M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||N|1
+NK1|1|CDPHSIX|MTH^Mother|132 ST^^SAN DIEGO^CA^92126^USA
+ORC|RE|7181233072^FormNumber||189430284^HospOrdNumber||||||||^ROSEN^REBECCA|||||||||UCSD JACOBS MEDICAL CENTER^^^^^^^^^R797| 2961DR YLLUT^^SAN DIEGO^CA^99999-9999
+OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
+OBX|1|CE|57721-3^Reason for lab test in Dried blood spot^LN|1|LA12421-6^Initial screen^LN|||N|||F|||20240226034304
+OBX|2|TX|^^^99717-5^Accession Number^L|1|045-89-477/21-2024-21|||N|||F|||20240226034304
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

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 = "4.7.0"
+      version = "4.10.0"
     }
   }
 

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 = "4.7.0"
+      version = "4.10.0"
     }
   }
 

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 = "4.7.0"
+      version = "4.10.0"
     }
   }
 

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 = "4.7.0"
+      version = "4.10.0"
     }
   }
 

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 = "4.7.0"
+      version = "4.10.0"
     }
   }