Merge branch 'main' into create-vpn-before-destroy

CDCgov · Oct 29, 2024 · fba0562 · fba0562
2 parents 3b561a1 + 36b9f1b
commit fba0562
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Showing 16 changed files with 102 additions and 21 deletions.
diff --git a/.github/renovate.json b/.github/renovate.json
@@ -33,6 +33,10 @@
                 "org.apache.httpcomponents.client5:httpclient5-fluent"
             ],
             "allowedVersions": "!/^5\\.3$/"
+        },
+        {
+            "matchPackageNames": ["com.azure:azure-identity"],
+            "allowedVersions": "!/^1\\.14\\.0$/"
         }],
     "pinDigests": false
 }
diff --git a/README.md b/README.md
@@ -347,12 +347,10 @@ with this option enabled.
 4. Run the `./cleanslate` script. For more information you can refer to the [ReportStream docs](https://github.com/CDCgov/prime-reportstream/blob/master/prime-router/docs/docs-deprecated/getting-started/getting-started.md#building-the-baseline)
 5. If attempting to access the metadata endpoint in ReportStream add the variable `ETOR_TI_baseurl="http://host.docker.internal:8080"` to `.prime-router/.vault/env/.env.local` file before building the container
 6. Run RS with `docker compose up --build -d`
-7. Edit `/settings/STLTs/Flexion/flexion.yml` to comment the lines related to staging settings, and uncomment the ones for local settings:
-   - `authTokenUrl`, `reportUrl`, `authHeaders.host` under REST `transport` in `receivers`
-   - `type` and `credentialName` under SFTP `transport` in `receivers`
-8. Run the `./reset.sh` script to reset the database
-9. Run the `./load-etor-org-settings.sh` to apply the ETOR organization settings
-10. Run the `./setup-local-vault.sh` script to set up the local vault secrets
+7. Run the `reset.sh` script to reset the database
+8. Run the `update_org_yaml.sh` script to update the RS organization settings
+9. Run the `load-etor-org-settings.sh` to apply the ETOR organization settings
+10. Run the `setup-local-vault.sh` script to set up the local vault secrets
     - You can verify that the script created the secrets successfully by going to `http://localhost:8200/` in your browser, use the token in `prime-router/.vault/env/.env.local` to authenticate, and then go to `Secrets engines` > `secret/` to check the available secrets
 
 #### Submit request to ReportStream

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:2.18.0'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.0'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.1'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
 
     //fhir
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:7.4.5'

diff --git a/etor/build.gradle b/etor/build.gradle
@@ -14,7 +14,7 @@ dependencies {
     testImplementation testFixtures(project(':shared'))
 
     implementation 'com.azure:azure-storage-blob:12.28.1'
-    implementation 'com.azure:azure-identity:1.14.0'
+    implementation 'com.azure:azure-identity:1.13.3'
 
     testImplementation 'org.apache.groovy:groovy:4.0.23'
     testImplementation 'org.spockframework:spock-core:2.3-groovy-4.0'

diff --git a/examples/Test/Automated/004_CA_ORU_R01_leading_zeroes.hl7 b/examples/Test/Automated/004_CA_ORU_R01_leading_zeroes.hl7
@@ -0,0 +1,6 @@
+MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|004|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||54079-9^Galactosemia newborn screening panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
+OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|05.100|enzyme units|>50|N|||F|||20240226034304
diff --git a/examples/Test/Automated/005_CA_ORU_R01_no_leading_zeroes.hl7 b/examples/Test/Automated/005_CA_ORU_R01_no_leading_zeroes.hl7
@@ -0,0 +1,6 @@
+MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|005|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||54079-9^Galactosemia newborn screening panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
+OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|0.6500|enzyme units|>50|N|||F|||20240226034304
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 = "4.6.0"
+      version = "4.7.0"
     }
   }
 

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 = "4.6.0"
+      version = "4.7.0"
     }
   }
 

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 = "4.6.0"
+      version = "4.7.0"
     }
   }
 

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 = "4.6.0"
+      version = "4.7.0"
     }
   }
 

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 = "4.6.0"
+      version = "4.7.0"
     }
   }
 

diff --git a/operations/template/alert.tf b/operations/template/alert.tf
@@ -260,6 +260,7 @@ resource "azurerm_monitor_scheduled_query_rules_alert" "ti-log-errors-alert" {
 
   query = <<-QUERY
       AppServiceConsoleLogs
+      | where _ResourceId !contains "pre-live"
       | project columnifexists("ResultDescription", 'default_value')
       | project  JsonResult = parse_json(ResultDescription)
       | evaluate bag_unpack(JsonResult) : (level: string, message: string)

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:2.18.0'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.0'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.1'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
 
     // azure
     implementation 'com.azure:azure-storage-blob:12.28.1'

diff --git a/rs-e2e/src/main/resources/assertion_definitions.json b/rs-e2e/src/main/resources/assertion_definitions.json
@@ -36,6 +36,24 @@
         "OBR-16 = ORC-12",
         "OBR.count() = 1"
       ]
+    },
+    {
+      "name": "CDPH leading zeros",
+      "conditions": [
+        "MSH-10 = '004'"
+      ],
+      "rules": [
+        "OBX-5 = '5.100'"
+      ]
+    },
+    {
+      "name": "CDPH no leading zeros",
+      "conditions": [
+        "MSH-10 = '005'"
+      ],
+      "rules": [
+        "OBX-5 = '0.6500'"
+      ]
     }
   ]
 }
diff --git a/scripts/rs/update_org_yaml.sh b/scripts/rs/update_org_yaml.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+source "$CDCTI_HOME/scripts/hurl/utils.sh"
+
+# This script updates the organization settings YAML files in RS to:
+# - use local REST transport settings for Flexion's etor-service-receiver receivers
+# - use local SFTP transport settings for Flexion's simulated-hospital and simulated-lab receivers
+# - use local SFTP transport settings for partner organizations
+
+# Requirements:
+# - yq (https://github.com/mikefarah/yq)
+# - This script should run inside the prime-router directory of the prime-reportstream codebase
+
+ORG_SETTINGS_DIR="settings/STLTs"
+
+check_installed_commands yq
+
+echo "Updating transport in Flexion org settings file..."
+yq eval '.[0].receivers[] |= (
+    select(.name == "simulated-hospital" or .name == "simulated-lab").transport = {
+        "type": "SFTP",
+        "host": "sftp",
+        "port": 22,
+        "filePath": "./upload",
+        "credentialName": "DEFAULT-SFTP"
+    } |
+    select(.name == "etor-service-receiver-orders") |= (
+        .transport.authTokenUrl = "http://host.docker.internal:8080/v1/auth/token" |
+        .transport.reportUrl = "http://host.docker.internal:8080/v1/etor/orders"
+    ) |
+    select(.name == "etor-service-receiver-results") |= (
+        .transport.authTokenUrl = "http://host.docker.internal:8080/v1/auth/token" |
+        .transport.reportUrl = "http://host.docker.internal:8080/v1/etor/results"
+    )
+)' -i "$ORG_SETTINGS_DIR/Flexion/flexion.yml"
+
+echo "Updating transport in partner org settings files..."
+for file in "$ORG_SETTINGS_DIR/CA/ucsd.yml" "$ORG_SETTINGS_DIR/LA/la-ochsner.yml" "$ORG_SETTINGS_DIR/LA/la-phl.yml"; do
+    yq eval '.[0].receivers[] |= select(.name == "etor-nbs-results" or .name == "etor-nbs-orders").transport = {
+        "type": "SFTP",
+        "host": "sftp",
+        "port": 22,
+        "filePath": "./upload",
+        "credentialName": "DEFAULT-SFTP"
+    }' -i "$file"
+done
+
+echo "Updates completed."
diff --git a/shared/build.gradle b/shared/build.gradle
@@ -22,10 +22,10 @@ dependencies {
     implementation 'net.logstash.logback:logstash-logback-encoder:8.0'
 
     //jackson
-    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.0'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.0'
-    implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.18.0'
-    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.18.0'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.18.1'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
+    implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.18.1'
+    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.18.1'
 
     // hapi fhir
     api 'ca.uhn.hapi.fhir:hapi-fhir-base:7.4.5'
@@ -49,7 +49,7 @@ dependencies {
 
     // azure sdk
     implementation 'com.azure:azure-security-keyvault-secrets:4.9.0'
-    implementation 'com.azure:azure-identity:1.14.0'
+    implementation 'com.azure:azure-identity:1.13.3'
 
     testImplementation 'org.apache.groovy:groovy:4.0.23'
     testFixturesImplementation 'org.apache.groovy:groovy:4.0.23'