From f7580e4c6e34a883d874e3f75b94d483eeb92eb2 Mon Sep 17 00:00:00 2001 From: etanb Date: Thu, 10 Oct 2024 09:26:56 -0700 Subject: [PATCH 1/9] swap out service link across site --- frontend-react/src/config/index.ts | 57 +++------ .../reportstream-api/ReportStreamApi.mdx | 2 +- .../managing-your-connection/index.mdx | 4 +- frontend-react/src/content/site.json | 108 +++++++++--------- frontend-react/src/content/support/index.mdx | 6 +- 5 files changed, 76 insertions(+), 101 deletions(-) diff --git a/frontend-react/src/config/index.ts b/frontend-react/src/config/index.ts index 9a49ef6286b..b2e2c35ca16 100644 --- a/frontend-react/src/config/index.ts +++ b/frontend-react/src/config/index.ts @@ -1,15 +1,5 @@ -import { - IConfig, - IConfiguration, - SeverityLevel, -} from "@microsoft/applicationinsights-web"; -import { - AccessToken, - AuthState, - IDToken, - OktaAuthOptions, - RefreshToken, -} from "@okta/okta-auth-js"; +import { IConfig, IConfiguration, SeverityLevel } from "@microsoft/applicationinsights-web"; +import { AccessToken, AuthState, IDToken, OktaAuthOptions, RefreshToken } from "@okta/okta-auth-js"; import { WidgetOptions } from "@okta/okta-signin-widget"; import type { Feature } from "@okta/okta-signin-widget"; import type { IIdleTimerProps } from "react-idle-timer"; @@ -23,9 +13,7 @@ const envVars = { MODE: import.meta.env.MODE, }; -const DEFAULT_FEATURE_FLAGS = import.meta.env.VITE_FEATURE_FLAGS - ? import.meta.env.VITE_FEATURE_FLAGS.split(",") - : []; +const DEFAULT_FEATURE_FLAGS = import.meta.env.VITE_FEATURE_FLAGS ? import.meta.env.VITE_FEATURE_FLAGS.split(",") : []; const OKTA_ISSUER = `${envVars.OKTA_URL}/oauth2/default`; @@ -41,9 +29,7 @@ const config = { IS_PREVIEW: envVars.MODE !== "production", API_ROOT: `${envVars.RS_API_URL}/api`, APPLICATION_INSIGHTS: { - connectionString: - import.meta.env.VITE_APPLICATIONINSIGHTS_CONNECTION_STRING ?? - "instrumentationKey=test", + connectionString: import.meta.env.VITE_APPLICATIONINSIGHTS_CONNECTION_STRING ?? "instrumentationKey=test", loggingLevelConsole: import.meta.env.NODE_ENV === "development" ? 2 : 0, disableFetchTracking: false, enableAutoRouteTracking: true, @@ -54,19 +40,12 @@ const config = { enableCorsCorrelation: true, enableRequestHeaderTracking: true, enableResponseHeaderTracking: true, - disableTelemetry: !import.meta.env - .VITE_APPLICATIONINSIGHTS_CONNECTION_STRING, + disableTelemetry: !import.meta.env.VITE_APPLICATIONINSIGHTS_CONNECTION_STRING, excludeRequestFromAutoTrackingPatterns: ["google-analytics.com"], } as const satisfies IConfiguration & IConfig, RSCONSOLE: { // Debug ignored by default - reportableLevels: [ - "assert", - "error", - "info", - "trace", - "warn", - ] as ConsoleLevel[], + reportableLevels: ["assert", "error", "info", "trace", "warn"] as ConsoleLevel[], severityLevels: { info: SeverityLevel.Information, warn: SeverityLevel.Warning, @@ -96,17 +75,16 @@ const config = { }, async transformAuthState(oktaAuth, authState) { let finalAuthState: AuthState = structuredClone(authState); - const tokens = [ - authState.accessToken, - authState.idToken, - authState.refreshToken, - ].filter(Boolean) as (AccessToken | IDToken | RefreshToken)[]; + const tokens = [authState.accessToken, authState.idToken, authState.refreshToken].filter(Boolean) as ( + | AccessToken + | IDToken + | RefreshToken + )[]; // Prevent pulling incorrect token from a different okta environment if ( tokens.find( (t) => - ("issuer" in t && t.issuer !== OKTA_ISSUER) || - ("claims" in t && t.claims.iss !== OKTA_ISSUER), + ("issuer" in t && t.issuer !== OKTA_ISSUER) || ("claims" in t && t.claims.iss !== OKTA_ISSUER), ) ) { oktaAuth.clearStorage(); @@ -140,7 +118,7 @@ const config = { } satisfies Partial>, useClassicEngine: false, helpLinks: { - help: "https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599", + help: "https://app.smartsheetgov.com/b/form/95d2f16b772c42d8aaa0ef5db28a6838", }, i18n: { // Overriding English properties @@ -155,8 +133,7 @@ const config = { "error.username.required": "Please enter a username. Your username should be the email address you registered with. Check your activation email.", "password.reset": "Reset password", - "password.forgot.question.title": - "Answer forgotten password challenge", + "password.forgot.question.title": "Answer forgotten password challenge", "password.forgot.question.submit": "Reset password", "password.forgot.emailSent.title": "Email sent", "password.forgot.emailSent.desc": @@ -172,8 +149,7 @@ const config = { "Your account is locked because of too many failed attempts. Check your email for next steps to unlock.", "errors.E0000004": "Unable to sign in. Check your username and password. Your account will be locked after 5 failed attempts.", - "account.unlock.email.or.username.placeholder": - "Username or email", + "account.unlock.email.or.username.placeholder": "Username or email", "account.unlock.email.or.username.tooltip": "Username or email", }, }, @@ -185,8 +161,7 @@ const config = { openGraph: { image: { src: import.meta.env.VITE_OPENGRAPH_DEFAULT_IMAGE_SRC, - altText: import.meta.env - .VITE_OPENGRAPH_DEFAULT_IMAGE_ALTTEXT, + altText: import.meta.env.VITE_OPENGRAPH_DEFAULT_IMAGE_ALTTEXT, }, }, }, diff --git a/frontend-react/src/content/developer-resources/reportstream-api/ReportStreamApi.mdx b/frontend-react/src/content/developer-resources/reportstream-api/ReportStreamApi.mdx index 5b98851e37f..542649590a9 100644 --- a/frontend-react/src/content/developer-resources/reportstream-api/ReportStreamApi.mdx +++ b/frontend-react/src/content/developer-resources/reportstream-api/ReportStreamApi.mdx @@ -40,7 +40,7 @@ import site from "../../site.json"; ## Onboarding overview We’ll give you and your team resources and support as you begin connecting with ReportStream’s API. [Learn more](getting-started) about setting up your connection and formatting your data. - If you haven’t connected with us yet, [contact us](https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599) to set up your kickoff call. + If you haven’t connected with us yet, contact us to set up your kickoff call. diff --git a/frontend-react/src/content/managing-your-connection/index.mdx b/frontend-react/src/content/managing-your-connection/index.mdx index 3b9ea7354f5..7a1b3e1e87d 100644 --- a/frontend-react/src/content/managing-your-connection/index.mdx +++ b/frontend-react/src/content/managing-your-connection/index.mdx @@ -35,7 +35,7 @@ import site from "../../content/site.json"; * [Manage your public key](/manage-public-key) * [View your submission history](/submissions) - [Login](/login) or [contact us](https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599) to create an account. + [Login](/login) or contact us to create an account. @@ -46,7 +46,7 @@ import site from "../../content/site.json"; * [Refer healthcare organizations](/managing-your-connection/refer-healthcare-organizations) * [View your dashboard](/daily-data) - [Login](/login) or [contact us](https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599) to create an account. + [Login](/login) or contact us to create an account. diff --git a/frontend-react/src/content/site.json b/frontend-react/src/content/site.json index 77485c73e4d..745dcc70b7a 100644 --- a/frontend-react/src/content/site.json +++ b/frontend-react/src/content/site.json @@ -1,57 +1,57 @@ { - "imgPath": "/assets/", - "pdfPath": "/assets/pdf/", - "documentationPath": "/documentation/", - "orgs": { - "CDC": { - "name": "Centers for Disease Control and Prevention", - "url": "https://cdc.gov", - "email": "no-reply@cdc.gov" - }, - "PRIME": { - "name": "Pandemic Ready Interoperability Modernization Effort", - "email": "usds@cdc.gov", - "url": "https://www.cdc.gov/surveillance/projects/pandemic-ready-it-systems.html" - }, - "RS": { - "name": "ReportStream", - "url": "https://reportstream.cdc.gov", - "email": "reportstream@cdc.gov" - }, - "SR": { - "name": "SimpleReport", - "url": "https://simplereport.gov", - "email": "support@simplereport.gov" - }, - "USDS": { - "name": "U.S. Digital Service", - "url": "https://usds.gov", - "email": "USDS@omb.eop.gov" - } - }, - "forms": { - "intakeElr": { - "name": "ELR intake form", - "url": "https://app.smartsheetgov.com/b/form/b0935d5d1e924c57b2d293b4ed0f2cd5" - }, - "connectWithRS": { - "name": "Connect with ReportStream", - "url": "https://app.smartsheetgov.com/b/form/48f580abb9b440549b1a9cf996ba6957" - }, - "contactUs": { - "name": "Contact us", - "url": "https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599" - } - }, - "assets": { - "standardCsv": { - "path": "/assets/csv/ReportStream-StandardCSV-ExampleData-20220509.csv" - }, - "programmersGuidePdf": { - "path": "/assets/pdf/ReportStream-Programmers-Guide-v4.6.pdf" - }, - "exampleHl7": { - "path": "/assets/hl7/Example-hl7-file.hl7" - } + "imgPath": "/assets/", + "pdfPath": "/assets/pdf/", + "documentationPath": "/documentation/", + "orgs": { + "CDC": { + "name": "Centers for Disease Control and Prevention", + "url": "https://cdc.gov", + "email": "no-reply@cdc.gov" + }, + "PRIME": { + "name": "Pandemic Ready Interoperability Modernization Effort", + "email": "usds@cdc.gov", + "url": "https://www.cdc.gov/surveillance/projects/pandemic-ready-it-systems.html" + }, + "RS": { + "name": "ReportStream", + "url": "https://reportstream.cdc.gov", + "email": "reportstream@cdc.gov" + }, + "SR": { + "name": "SimpleReport", + "url": "https://simplereport.gov", + "email": "support@simplereport.gov" + }, + "USDS": { + "name": "U.S. Digital Service", + "url": "https://usds.gov", + "email": "USDS@omb.eop.gov" + } + }, + "forms": { + "intakeElr": { + "name": "ELR intake form", + "url": "https://app.smartsheetgov.com/b/form/b0935d5d1e924c57b2d293b4ed0f2cd5" + }, + "connectWithRS": { + "name": "Connect with ReportStream", + "url": "https://app.smartsheetgov.com/b/form/48f580abb9b440549b1a9cf996ba6957" + }, + "contactUs": { + "name": "Contact us", + "url": "https://app.smartsheetgov.com/b/form/95d2f16b772c42d8aaa0ef5db28a6838" + } + }, + "assets": { + "standardCsv": { + "path": "/assets/csv/ReportStream-StandardCSV-ExampleData-20220509.csv" + }, + "programmersGuidePdf": { + "path": "/assets/pdf/ReportStream-Programmers-Guide-v4.6.pdf" + }, + "exampleHl7": { + "path": "/assets/hl7/Example-hl7-file.hl7" } + } } diff --git a/frontend-react/src/content/support/index.mdx b/frontend-react/src/content/support/index.mdx index 6af0709fae8..2c26c9d1c5c 100644 --- a/frontend-react/src/content/support/index.mdx +++ b/frontend-react/src/content/support/index.mdx @@ -69,7 +69,7 @@ import site from "../../content/site.json"; ## Support request -

For issues with an existing connection, [submit a ticket](https://app.smartsheetgov.com/b/form/da894779659b45768079200609b3a599).
+

For issues with an existing connection, submit a ticket.
Our support team will respond as soon as possible to keep your data flowing.

@@ -183,7 +183,7 @@ import site from "../../content/site.json"; title: "How do I register for a ReportStream account?", content: (
  1. Request an account.
    - Submit a service request with information about your organization and explaining that you would like a ReportStream account.
  2. + Submit a service request with information about your organization and explaining that you would like a ReportStream account.
  3. Accept the terms of service.
    A ReportStream team member will process your request and confirm that you accept our terms of service.
  4. Activate your account.
    @@ -369,7 +369,7 @@ import site from "../../content/site.json"; headingLevel: "h4", title: "How do I manage team member accounts?", content: (

    - ReportStream manually manages user accounts for your team. To add or remove team members, contact us. + ReportStream manually manages user accounts for your team. To add or remove team members, contact us.

    ) }, ]} /> From d2700cbf6c2d8dc8e63bacdc408206698ca23bba Mon Sep 17 00:00:00 2001 From: Matt Date: Wed, 16 Oct 2024 15:54:04 -0700 Subject: [PATCH 2/9] add timeouts to other instances of azurerm_storage_account --- .../modules/storage/candidate_slot.tf | 18 ++++++++++++++++-- .../app/terraform/modules/storage/main.tf | 6 +++--- .../modules/storage/trial_frontends.tf | 9 ++++++++- 3 files changed, 27 insertions(+), 6 deletions(-) diff --git a/operations/app/terraform/modules/storage/candidate_slot.tf b/operations/app/terraform/modules/storage/candidate_slot.tf index 6fa9feadd23..4750011c859 100644 --- a/operations/app/terraform/modules/storage/candidate_slot.tf +++ b/operations/app/terraform/modules/storage/candidate_slot.tf @@ -8,7 +8,7 @@ resource "azurerm_storage_account" "storage_account_candidate" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false network_rules { @@ -38,6 +38,13 @@ resource "azurerm_storage_account" "storage_account_candidate" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } module "storageaccount_candidate_blob_private_endpoint" { @@ -155,7 +162,7 @@ resource "azurerm_storage_account" "storage_partner_candidate" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false network_rules { @@ -191,6 +198,13 @@ resource "azurerm_storage_account" "storage_partner_candidate" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } # Grant the storage account Key Vault access, to access encryption keys diff --git a/operations/app/terraform/modules/storage/main.tf b/operations/app/terraform/modules/storage/main.tf index 1170df1cf1b..db07e43d920 100644 --- a/operations/app/terraform/modules/storage/main.tf +++ b/operations/app/terraform/modules/storage/main.tf @@ -8,7 +8,7 @@ resource "azurerm_storage_account" "storage_account" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false network_rules { @@ -173,7 +173,7 @@ resource "azurerm_storage_account" "storage_public" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false static_website { @@ -223,7 +223,7 @@ resource "azurerm_storage_account" "storage_partner" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false network_rules { diff --git a/operations/app/terraform/modules/storage/trial_frontends.tf b/operations/app/terraform/modules/storage/trial_frontends.tf index 0ff68c67d35..43b5ee7eda2 100644 --- a/operations/app/terraform/modules/storage/trial_frontends.tf +++ b/operations/app/terraform/modules/storage/trial_frontends.tf @@ -9,7 +9,7 @@ resource "azurerm_storage_account" "storage_trials" { account_replication_type = "LRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false - enable_https_traffic_only = true + https_traffic_only_enabled = true local_user_enabled = false static_website { @@ -28,4 +28,11 @@ resource "azurerm_storage_account" "storage_trials" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } From a5a4b64471631d5eb64ac26fef8b8d8d367db0a7 Mon Sep 17 00:00:00 2001 From: JessicaWNava <119880261+JessicaWNava@users.noreply.github.com> Date: Thu, 17 Oct 2024 09:24:23 -0400 Subject: [PATCH 3/9] Engagement/jessica/15896 radx mars deidentify (#16192) Updating the radx mars deidentification transform. Updating the integration test and fixing an error --- .../main/kotlin/cli/ProcessFhirCommands.kt | 5 +- .../ORU_R01/ORU_R01-deidentified.yml | 227 +++++++++++++++--- .../ORU_deidentified-expected.hl7 | 7 +- 3 files changed, 196 insertions(+), 43 deletions(-) diff --git a/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt b/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt index dbe6d5bf212..8cdfd6bc150 100644 --- a/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt +++ b/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt @@ -211,10 +211,7 @@ class ProcessFhirCommands : CliktCommand( } if (validationErrors.isNotEmpty()) { - return MessageOrBundle( - filterErrors = mutableListOf(validationErrors.joinToString("\n")), - filtersPassed = false - ) + throw CliktError(validationErrors.joinToString("\n")) } receiver.conditionFilter.forEach { conditionFilter -> diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-deidentified.yml b/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-deidentified.yml index 02cd668e272..60bc0323e23 100644 --- a/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-deidentified.yml +++ b/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-deidentified.yml @@ -8,87 +8,135 @@ constants: elements: # PID 3.1 - name: deidentified-patient-identifier - condition: '%patientPath.identifier[0].extension(%`rsext-cx-identifier`).extension.where(url = "CX.5").value != "PI"' - value: ['""'] + condition: '%patientPath.identifier[0].extension(%`rsext-cx-identifier`).extension.where(url = "CX.5").value != + "PI" and %patientPath.identifier[0].extension(%`rsext-cx-identifier`).extension.where(url = "CX.5").value != + "PT" and %patientPath.identifier[0].extension(%`rsext-cx-identifier`).extension.where(url = "CX.5").value != "SID"' + value: ['""'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-3-1] # PID 5.1 - name: patient-last-name condition: '%patientPath.name[0].family.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-5-1] # PID 5.2 - name: patient-first-name condition: '%patientPath.name[0].extension(%`rsext-xpn-human-name`).extension.where(url="XPN.2").value.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-5-2] # PID 5.3 - name: patient-middle-name condition: '%patientPath.name[0].extension(%`rsext-xpn-human-name`).extension.where(url="XPN.3").value.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-5-3] + # PID 5.4 + - name: patient-suffix + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/PATIENT/PID-5-4 ] + + # PID 5.7 + - name: patient-type-code + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/PATIENT/PID-5-7 ] + # # PID 7.1 - name: deidentified-patient-dob condition: '%patientPath.birthDate.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-7-1] # PID 11.1 - name: patient-address1 condition: '%patientPath.address[0].extension(%`rsext-xad-address`).extension.where(url = %`rsext-sad-address-line`).extension.where(url = "SAD.1").value.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-11-1] # PID 11.2 - name: patient-address2 condition: '%patientPath.address[0].extension(%`rsext-xad-address`).extension.where(url = "XAD.2").value.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-11-2] # PID 11.3 - name: patient-city condition: '%patientPath.address[0].city.empty().not()' - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-11-3] - # PID 11.5 - - name: patient-postal-code - condition: '%patientPath.address[0].postalCode.empty().not()' - value: [ '""' ] - hl7Spec: [ /PATIENT_RESULT/PATIENT/PID-11-5 ] - # PID 13.4 - name: patient-email condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`rsext-xtn-contact-point`).extension('XTN.4').value.empty().not()" - value: ['""'] + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-13-4] # PID 13.6 - name: patient-phone-area-code - condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`ext-contactpoint-area`).value.empty().not()" - value: ['""'] + condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`ext-contactpoint-area`).value.empty().not() and %patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`ext-contactpoint-area`).value != '111'" + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-13-6] # PID 13.7 - name: patient-local-phone - condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`rsext-xtn-contact-point`).extension('XTN.7').value.empty().not()" - value: ['""'] + condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`rsext-xtn-contact-point`).extension('XTN.7').value.empty().not() and %patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`rsext-xtn-contact-point`).extension('XTN.7').value != '1111111'" + value: ['"Deidentified"'] hl7Spec: [/PATIENT_RESULT/PATIENT/PID-13-7] - # PID 13.12 - - name: patient-unformatted-phone - condition: "%patientPath.telecom[0].where((use = 'home' or use = 'mobile')).extension(%`rsext-xtn-contact-point`).extension('XTN.12').value.empty().not()" - value: ['""'] - hl7Spec: [/PATIENT_RESULT/PATIENT/PID-13-12] - # ORC 3.1 - name: orc-filler-order-number value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/ORC-3-1] + # ORC 1 + - name: order-control + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-1 ] + + # ORC 2 + - name: placer-order-number-orc-2 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-2 ] + + # ORC 3.1 + - name: filler-order-number-orc-3-1 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-3 ] + + # ORC 3.2 + - name: orc-3-2 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-3-2 ] + + # ORC 3.3 + - name: orc-3-3 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-3-3 ] + + # ORC 3.4 + - name: orc-3-4 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-3-4 ] + + # ORC 4 + - name: placer-group-number-orc-4 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-4 ] + + # ORC 9 + - name: datetime-of-order-event + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-9 ] + + # ORC 12 + - name: ordering-provider-from-practitioner + condition: 'false' + + # ORC 12 + - name: ordering-provider-from-practitioner-role + condition: 'false' + # ORC 12.1 - name: orc-ordering-provider-id value: ['""'] @@ -104,6 +152,16 @@ elements: value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/ORC-12-3] + # ORC 14 + - name: call-back-phone-number-ocr-14 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-14 ] + + # ORC 21 + - name: ordering-facility-name-orc-21 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-21-1 ] + # ORC 22.1 - name: ordering-facility-street1 value: ['""'] @@ -169,6 +227,14 @@ elements: value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/ORC-24-4] + # ORC 24 + - name: ordering-provider-address-from-practitioner + condition: 'false' + + # ORC 24 + - name: ordering-provider-address-from-practitioner-role + condition: 'false' + # ORC 24.5 - name: ordering-provider-zip value: ['""'] @@ -179,16 +245,35 @@ elements: value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/ORC-24-9] + # ORC 25 + - name: order-status-modifier-orc-25 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-25 ] + + # ORC 29 + - name: order-type-orc-29 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-29 ] + + # ORC 33 + - name: alternate-placer-order-number-orc-33 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-33 ] + + # ORC ext + - name: orc-extension + condition: 'false' + + # OBR 2.1 + - name: placer-order-number-obr-2-1 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-2-1 ] + # OBR 3.1 - name: obr-filler-order-number value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/OBR-3-1] - # OBR 7.1 - - name: observation-result-date - value: ['""'] - hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/OBR-7-1] - # OBR 16.1 - name: obr-ordering-provider-id value: ['""'] @@ -204,10 +289,80 @@ elements: value: ['""'] hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/OBR-16-3] - # OBR 22.1 - - name: results-change-date - value: ['""'] - hl7Spec: [/PATIENT_RESULT/ORDER_OBSERVATION/OBR-22-1] + # OBR 17.2 + - name: obr-order-callback-telecom-use-code + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-17-2 ] + + # OBR 17.3 + - name: obr-order-callback-telecom-equipment-type + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-17-3 ] + + # OBR 17.4 + - name: obr-order-callback-email + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-17-4 ] + + # OBR 17.6 + - name: obr-order-callback-phone-area-code + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-17-6 ] + + # OBR 17.7 + - name: obr-order-callback-local-phone + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBR-17-7 ] + + # OBX 14.1 + - name: obx-observation-date-time + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-14-1 ] + + # OBX 24.1 + - name: obx-test-performing-org-street-addr + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-1 ] + + # OBX 24.2 + - name: obx-test-performing-org-street-addr-2 + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-2 ] + + # OBX 24.3 + - name: obx-test-performing-org-city + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-3 ] + + # OBX 24.4 + - name: obx-test-performing-org-state + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-4 ] + + # OBX 24.5 + - name: obx-test-performing-org-zip-code + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-5 ] + + # OBX 24.6 + - name: obx-test-performing-org-country + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-6 ] + + # OBX 24.7 + - name: obx-test-performing-org-address-type + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-7 ] + + # OBX 24.8 + - name: obx-test-performing-org-or-geo-dest + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-8 ] + + # OBX 24.9 + - name: obx-test-performing-org-county + value: [ '""' ] + hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION/OBX-24-9 ] # Suppress all notes as they may contain PII data - name: patient-note @@ -218,3 +373,5 @@ elements: - name: order-note condition: 'false' + + diff --git a/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/ORU_deidentified-expected.hl7 b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/ORU_deidentified-expected.hl7 index 52a48dbf6e8..11c0691cf00 100644 --- a/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/ORU_deidentified-expected.hl7 +++ b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/ORU_deidentified-expected.hl7 @@ -1,9 +1,8 @@ MSH|^~\&|MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|CAREEVOLUTION^00Z0000024^CLIA|AIMS.INTEGRATION.STG^2.16.840.1.114222.4.3.15.2^ISO|AIMS.PLATFORM^2.16.840.1.114222.4.1.217446^ISO|20240412110603-0500||ORU^R01^ORU_R01|20240412110603_ff98cc992d5146e7916a5f0b873e534f|T|2.5.1|||NE|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO SFT|CAREEVOLUTION|2022|MMTC.STAG|16948||20240311 -PID|1||92041f50874c4595955d47f7ae4981c5^^^MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO^PI||^^^^^^S||||||^^^PIDSTATE!^^USA^^^PIDCOUNTY!||^^^^^^^^^^^ -ORC|RE||^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO||||||||||||||||||SA.OTCSelfReport -OBR|1||^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|97097-0^SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay^LN^^^^2.71|||||||||||||||||||||F -OBX|1|CWE|97097-0^SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BD Veritor At-Home COVID-19 Test_Becton, Dickinson and Company (BD)_EUA^^99ELR^^^^Vunknown||20240412230603||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake City +PID|1||92041f50874c4595955d47f7ae4981c5^^^MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO^PI||Deidentified^Deidentified^Deidentified||Deidentified||||Deidentified^Deidentified^Deidentified^PIDSTATE!^PIDPOSTAL!^USA^^^PIDCOUNTY!||^^^Deidentified^^Deidentified^Deidentified^^^^^PIDUNFORMATPHONE! +OBR|1||^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|97097-0^SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay^LN^^^^2.71|||DATE!|||||||||||||||DATE!|||F +OBX|1|CWE|97097-0^SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BD Veritor At-Home COVID-19 Test_Becton, Dickinson and Company (BD)_EUA^^99ELR^^^^Vunknown||20240412230603||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042 OBX|2|NM|35659-2^Age at specimen collection^LN^^^^2.71||44|a^year^UCUM^^^^2.1|||||F||||00Z0000042||||||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake City|||||QST OBX|3|CWE|95419-8^Whether patient has symptoms related to condition of interest^LN^^^^2.71||Y^Yes^HL70136^^^^2.5.1||||||F||||00Z0000042||||||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake City|||||QST OBX|4|DT|65222-2^Date and time of symptom onset^LN^^^^2.71||20240411||||||F||||00Z0000042||||||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake City|||||QST From 819ab5d409415b99397c7b5ad784ce552a32afd1 Mon Sep 17 00:00:00 2001 From: Matt Date: Thu, 17 Oct 2024 11:28:54 -0700 Subject: [PATCH 4/9] addding timeouts, addressing some drift --- .../app/terraform/modules/sftp/storage.tf | 22 ++++++++++++++++ .../app/terraform/modules/sftp/~inputs.tf | 25 +++++++++++++++++++ .../app/terraform/modules/storage/main.tf | 1 + 3 files changed, 48 insertions(+) diff --git a/operations/app/terraform/modules/sftp/storage.tf b/operations/app/terraform/modules/sftp/storage.tf index 5284414739e..f712935cfa0 100644 --- a/operations/app/terraform/modules/sftp/storage.tf +++ b/operations/app/terraform/modules/sftp/storage.tf @@ -7,6 +7,7 @@ resource "azurerm_storage_account" "sftp" { account_replication_type = "GRS" min_tls_version = "TLS1_2" allow_nested_items_to_be_public = false + large_file_share_enabled = false network_rules { default_action = "Allow" @@ -19,6 +20,13 @@ resource "azurerm_storage_account" "sftp" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } # SSH host keys share @@ -26,6 +34,13 @@ resource "azurerm_storage_share" "sftp_admin" { name = "${var.resource_prefix}-sftp-admin-share" storage_account_name = azurerm_storage_account.sftp.name quota = 1 + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } # SFTP startup scripts share @@ -33,6 +48,13 @@ resource "azurerm_storage_share" "sftp_scripts" { name = "${var.resource_prefix}-sftp-scripts-share" storage_account_name = azurerm_storage_account.sftp.name quota = 1 + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } # SFTP startup script diff --git a/operations/app/terraform/modules/sftp/~inputs.tf b/operations/app/terraform/modules/sftp/~inputs.tf index 5b460dbcfea..3d5bdb1e6f4 100644 --- a/operations/app/terraform/modules/sftp/~inputs.tf +++ b/operations/app/terraform/modules/sftp/~inputs.tf @@ -60,3 +60,28 @@ variable "sshinstances" { variable "sftp_dir" { description = "SFTP Script Directory" } + +# TF timeouts for storage operations +variable "timeout_create" { + description = "Timeout for create operations" + type = string + default = "60m" # module default 30m +} + +variable "timeout_read" { + description = "Timeout for read operations" + type = string + default = "60m" # module default 5m +} + +variable "timeout_update" { + description = "Timeout for update operations" + type = string + default = "60m" # module default 30m +} + +variable "timeout_delete" { + description = "Timeout for delete operations" + type = string + default = "60m" # module default 30m +} \ No newline at end of file diff --git a/operations/app/terraform/modules/storage/main.tf b/operations/app/terraform/modules/storage/main.tf index db07e43d920..201bbe55632 100644 --- a/operations/app/terraform/modules/storage/main.tf +++ b/operations/app/terraform/modules/storage/main.tf @@ -175,6 +175,7 @@ resource "azurerm_storage_account" "storage_public" { allow_nested_items_to_be_public = false https_traffic_only_enabled = true local_user_enabled = false + large_file_share_enabled = false static_website { index_document = "index.html" From 58332ab0837c46909585353716fb85eaab8bb093 Mon Sep 17 00:00:00 2001 From: Gabriel Dorsch Date: Thu, 17 Oct 2024 17:36:22 -0400 Subject: [PATCH 5/9] Check submission table when computing submission history (#16200) * Check submission table when computing submission history * Added mocks to fix 2 test failures --------- Co-authored-by: Arnej <118766341+arnejduranovic@users.noreply.github.com> --- .../history/azure/ReportFileFunction.kt | 14 +++++-- .../history/azure/DeliveryFunctionTests.kt | 7 ++++ .../SubmissionFunctionIntegrationTests.kt | 39 +++++++++++++++++++ .../history/azure/SubmissionFunctionTests.kt | 7 ++++ .../prime/reportstream/shared/Submission.kt | 12 +++++- 5 files changed, 74 insertions(+), 5 deletions(-) diff --git a/prime-router/src/main/kotlin/history/azure/ReportFileFunction.kt b/prime-router/src/main/kotlin/history/azure/ReportFileFunction.kt index cf88c750881..c3f6827c0b9 100644 --- a/prime-router/src/main/kotlin/history/azure/ReportFileFunction.kt +++ b/prime-router/src/main/kotlin/history/azure/ReportFileFunction.kt @@ -8,6 +8,7 @@ import gov.cdc.prime.router.CustomerStatus import gov.cdc.prime.router.RESTTransportType import gov.cdc.prime.router.azure.DataAccessTransaction import gov.cdc.prime.router.azure.HttpUtilities +import gov.cdc.prime.router.azure.SubmissionTableService import gov.cdc.prime.router.azure.WorkflowEngine import gov.cdc.prime.router.azure.db.tables.pojos.Action import gov.cdc.prime.router.history.ReportHistory @@ -161,10 +162,15 @@ abstract class ReportFileFunction( } catch (e: DataAccessException) { logger.error("Unable to fetch history for ID $id", e) return HttpUtilities.internalErrorResponse(request) - } catch (ex: IllegalStateException) { - logger.error(ex) - // Errors above are actionId or UUID not found errors. - return HttpUtilities.notFoundResponse(request, ex.message) + } catch (ex: IllegalStateException) { // actionId or UUID not found + val submission = SubmissionTableService.getInstance().getSubmission(id, "Received") + + return if (submission == null) { + logger.error(ex) + HttpUtilities.notFoundResponse(request, ex.message) + } else { + HttpUtilities.okJSONResponse(request, submission) + } } } diff --git a/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt b/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt index ec054de8d1c..b059d88242f 100644 --- a/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt +++ b/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt @@ -23,6 +23,7 @@ import gov.cdc.prime.router.azure.ApiSearchResult import gov.cdc.prime.router.azure.DatabaseAccess import gov.cdc.prime.router.azure.MockHttpRequestMessage import gov.cdc.prime.router.azure.MockSettings +import gov.cdc.prime.router.azure.SubmissionTableService import gov.cdc.prime.router.azure.WorkflowEngine import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.pojos.Action @@ -461,6 +462,12 @@ class DeliveryFunctionTests : Logging { every { AuthenticatedClaims.authenticate(any()) } returns AuthenticatedClaims.generateTestClaims() + val submissionTableService = mockk() + every { submissionTableService.getSubmission(any(), any()) } returns null + + mockkObject(SubmissionTableService.Companion) + every { SubmissionTableService.getInstance() } returns submissionTableService + // Invalid id: not a UUID nor a Long var response = function.getDeliveryDetails(mockRequest, "bad") assertThat(response.status).isEqualTo(HttpStatus.NOT_FOUND) diff --git a/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt b/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt index 34bd4b30719..421070fcf08 100644 --- a/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt +++ b/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt @@ -3,6 +3,7 @@ package gov.cdc.prime.router.history.azure import assertk.assertThat import assertk.assertions.isEqualTo import assertk.assertions.isNotNull +import gov.cdc.prime.reportstream.shared.Submission import gov.cdc.prime.router.ActionLog import gov.cdc.prime.router.ActionLogLevel import gov.cdc.prime.router.FileSettings @@ -11,6 +12,7 @@ import gov.cdc.prime.router.Metadata import gov.cdc.prime.router.MimeFormat import gov.cdc.prime.router.Topic import gov.cdc.prime.router.azure.MockHttpRequestMessage +import gov.cdc.prime.router.azure.SubmissionTableService import gov.cdc.prime.router.azure.WorkflowEngine import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.common.BaseEngine @@ -26,6 +28,7 @@ import gov.cdc.prime.router.tokens.oktaSystemAdminGroup import gov.cdc.prime.router.unittest.UnitTestUtils import io.mockk.clearAllMocks import io.mockk.every +import io.mockk.mockk import io.mockk.mockkObject import io.mockk.unmockkAll import org.junit.jupiter.api.AfterEach @@ -33,6 +36,8 @@ import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Test import org.junit.jupiter.api.extension.ExtendWith import org.testcontainers.junit.jupiter.Testcontainers +import java.time.OffsetDateTime +import java.time.ZoneOffset @Testcontainers @ExtendWith(ReportStreamTestDatabaseSetupExtension::class) @@ -69,6 +74,40 @@ class SubmissionFunctionIntegrationTests { assertThat(historyNode.get("warnings").size()).isEqualTo(0) } + @Test + fun `it should return a history for a submission received by the submissions microservice`() { + val timestamp = OffsetDateTime.now(ZoneOffset.UTC) + val submissionId = "some-submission-id" + val submissionTableService = mockk() + every { submissionTableService.getSubmission(any(), any()) } returns Submission( + submissionId, + "Received", + "some-url", + "some-detail", + timestamp + ) + + mockkObject(SubmissionTableService.Companion) + every { SubmissionTableService.getInstance() } returns submissionTableService + + val httpRequestMessage = MockHttpRequestMessage() + + val func = setupSubmissionFunction() + + val history = func.getReportDetailedHistory(httpRequestMessage, submissionId) + assertThat(history).isNotNull() + + val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) + assertThat(historyNode.fieldNames().asSequence().toList()).isEqualTo( + listOf("submissionId", "overallStatus", "timestamp") + ) + assertThat(historyNode.get("submissionId").asText()).isEqualTo(submissionId) + assertThat(historyNode.get("overallStatus").asText()).isEqualTo("Received") + assertThat(historyNode.get("timestamp").asText()).isEqualTo( + timestamp.format(JacksonMapperUtilities.timestampFormatter) + ) + } + @Test fun `it should return a history for partially delivered submission`() { val submittedReport = reportGraph { diff --git a/prime-router/src/test/kotlin/history/azure/SubmissionFunctionTests.kt b/prime-router/src/test/kotlin/history/azure/SubmissionFunctionTests.kt index ba80055acb5..caa067dcdea 100644 --- a/prime-router/src/test/kotlin/history/azure/SubmissionFunctionTests.kt +++ b/prime-router/src/test/kotlin/history/azure/SubmissionFunctionTests.kt @@ -22,6 +22,7 @@ import gov.cdc.prime.router.TranslatorConfiguration import gov.cdc.prime.router.azure.DatabaseAccess import gov.cdc.prime.router.azure.MockHttpRequestMessage import gov.cdc.prime.router.azure.MockSettings +import gov.cdc.prime.router.azure.SubmissionTableService import gov.cdc.prime.router.azure.WorkflowEngine import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.pojos.Action @@ -440,6 +441,12 @@ class SubmissionFunctionTests : Logging { every { AuthenticatedClaims.authenticate(any()) } returns AuthenticatedClaims.generateTestClaims() + val submissionTableService = mockk() + every { submissionTableService.getSubmission(any(), any()) } returns null + + mockkObject(SubmissionTableService.Companion) + every { SubmissionTableService.getInstance() } returns submissionTableService + // Invalid id: not a UUID nor a Long var response = function.getReportDetailedHistory(mockRequest, "bad") assertThat(response.status).isEqualTo(HttpStatus.NOT_FOUND) diff --git a/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt b/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt index a16924e6e6a..33b44311ee9 100644 --- a/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt +++ b/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt @@ -1,6 +1,10 @@ package gov.cdc.prime.reportstream.shared import com.azure.data.tables.models.TableEntity +import com.fasterxml.jackson.annotation.JsonIgnore +import com.fasterxml.jackson.annotation.JsonProperty +import com.fasterxml.jackson.annotation.JsonPropertyOrder +import java.time.OffsetDateTime /** * Represents a submission entity to be stored in Azure Table Storage. @@ -10,11 +14,16 @@ import com.azure.data.tables.models.TableEntity * @property bodyURL The URL pointing to the body of the submission. * @property detail Optional additional details about the submission. */ +@JsonPropertyOrder(value = ["submissionId", "overallStatus", "timestamp"]) data class Submission( val submissionId: String, + @JsonProperty("overallStatus") val status: String, + @JsonIgnore val bodyURL: String, + @JsonIgnore val detail: String? = null, + val timestamp: OffsetDateTime? = null ) { companion object { /** @@ -28,7 +37,8 @@ data class Submission( submissionId = tableEntity.partitionKey, status = tableEntity.rowKey, bodyURL = tableEntity.getProperty("body_url") as String, - detail = tableEntity.getProperty("detail") as String? + detail = tableEntity.getProperty("detail") as String?, + timestamp = tableEntity.timestamp ) } } From 632c6e0e0c8278e9d859dbd66ec0cc9e3665aabd Mon Sep 17 00:00:00 2001 From: Lucero Velasco <165824244+lucero-v@users.noreply.github.com> Date: Fri, 18 Oct 2024 10:11:10 -0600 Subject: [PATCH 6/9] added schema for observation fields with rule to suppress QST (#16249) added the new schema to MO, OH, & WA. fixed translation tests for those senders --- prime-router/settings/STLTs/MO/mo-phd.yml | 5 +- .../observation-fields/observation-fields.yml | 9 + .../STLTs/MD/MD-receiver-transform.yml | 3 + .../STLTs/MO/MO-receiver-transform.yml | 22 +- .../STLTs/OH/OH-observation-fields.yml | 7 - .../STLTs/OH/OH-receiver-transform.yml | 5 +- .../STLTs/WA/WA-observation-fields.yml | 7 - .../STLTs/WA/WA-receiver-transform.yml | 5 +- .../FHIR_to_HL7/sample_MO_20240628-0001.fhir | 4356 +++++++++++++++-- .../FHIR_to_HL7/sample_MO_20240628-0001.hl7 | 13 +- .../FHIR_to_HL7/sample_OH_20240718-0001.fhir | 2213 ++++++++- .../FHIR_to_HL7/sample_OH_20240718-0001.hl7 | 2 +- .../FHIR_to_HL7/sample_WA_20240719-0001.fhir | 1865 ++++++- .../FHIR_to_HL7/sample_WA_20240719-0001.hl7 | 24 +- .../datatests/translation-test-config.csv | 6 +- .../resources/settings/organizations.yml | 1 - 16 files changed, 7894 insertions(+), 649 deletions(-) create mode 100644 prime-router/src/main/resources/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml delete mode 100644 prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-observation-fields.yml delete mode 100644 prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-observation-fields.yml diff --git a/prime-router/settings/STLTs/MO/mo-phd.yml b/prime-router/settings/STLTs/MO/mo-phd.yml index f68d5886964..78413606360 100644 --- a/prime-router/settings/STLTs/MO/mo-phd.yml +++ b/prime-router/settings/STLTs/MO/mo-phd.yml @@ -33,7 +33,6 @@ replaceUnicodeWithAscii: false useBlankInsteadOfUnknown: null truncateHDNamespaceIds: true - truncateHl7Fields: "MSH-3-1, PID-3-3, PID-3-6-1, ORC-2-2, ORC-7-10-5, OBR-2-2, OBR-3-2, SPM-2-1-2, SPM-2-2-2, ORC-21-1, OBX-23-1, OBX-15-1, OBX-23-10 " usePid14ForPatientEmail: false convertTimestampToDateTime: null cliaForOutOfStateTesting: null @@ -86,8 +85,8 @@ processingModeFilter: [] reverseTheQualityFilter: false conditionFilter: - # Accept COVID only - - "(%resource.code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('840539006')).exists())" + # Positive COVID (840539006), Positive COVID-antibody (895448002) Positive MPOX (414015000) + - "%resource.where(interpretation.coding.code = 'A').code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('840539006'|'895448002'|'414015000')).exists()" mappedConditionFilter: [] deidentify: false deidentifiedValue: "" diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml new file mode 100644 index 00000000000..1f67a758714 --- /dev/null +++ b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml @@ -0,0 +1,9 @@ +constants: + OBX: '/PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION(%{resultIndex})/OBX' + +elements: + + - name: suppress-qst-for-aoe + condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.code = "AOE"' + value: [ '""' ] + hl7Spec: [ '%{OBX}-29' ] \ No newline at end of file diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MD/MD-receiver-transform.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MD/MD-receiver-transform.yml index 9821b6a49a7..38745f1b4d9 100644 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MD/MD-receiver-transform.yml +++ b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MD/MD-receiver-transform.yml @@ -31,3 +31,6 @@ elements: condition: '%resource.code.exists()' value: [ '%resource.system.getCodingSystemMapping()' ] hl7Spec: [ '%{PID}-10-3' ] + + - name: observation-result-with-aoe + resource: '%resource.result.resolve()' diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml index 0f6a4584e8d..98ed2c6759b 100644 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml +++ b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml @@ -14,12 +14,24 @@ elements: value: [ '%resource.system.getCodingSystemMapping()' ] hl7Spec: [ '%{PID}-10-3' ] + - name: mo-sending-facility-namespace-id + value: [ '"CDC Prime"' ] + hl7Spec: [ 'MSH-4-1' ] + + - name: mo-sending-application-universal-id + value: [ '"11D2030855"' ] + hl7Spec: [ 'MSH-4-2' ] + + - name: mo-sending-application-universal-id-type + value: [ '"CLIA"' ] + hl7Spec: [ 'MSH-4-3' ] + - name: mo-sender-facility-namespace-Id value: [ '"MOELR"' ] hl7Spec: [ 'MSH-5-1' ] - name: mo-sender-facility-universal-Id - value: [ '"2.16.840.1.114222.4.3.3.36"' ] + value: [ '"2.16.840.1.114222.4.3.3.10.1.1"' ] hl7Spec: [ 'MSH-5-2' ] - name: mo-sender-facility-universal-id-type @@ -40,4 +52,10 @@ elements: - name: mo-unwanted-fields value: [ '""' ] - hl7Spec: [ 'MSH-19-3', '%{PID}-13-12', '%{PID}-15-3', '%{ORC}-14-1', '%{OBR}-17-1' ] \ No newline at end of file + hl7Spec: [ 'MSH-19-3', '%{PID}-15-3', '%{ORC}-14-1', '%{OBR}-17-1' ] + + - name: mo-observation + resource: 'Bundle.entry.resource.ofType(Observation)' + schema: classpath:/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml + resourceIndex: resultIndex + diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-observation-fields.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-observation-fields.yml deleted file mode 100644 index e61120f780e..00000000000 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-observation-fields.yml +++ /dev/null @@ -1,7 +0,0 @@ -constants: - OBX: '/PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION(%{resultIndex})/OBX' - -elements: - - name: oh-suppress-qst-for-aoe - value: [ '""' ] - hl7Spec: [ '%{OBX}-29' ] \ No newline at end of file diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml index faaedba46ed..0cd8e27b0e1 100644 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml +++ b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml @@ -68,7 +68,6 @@ elements: hl7Spec: [ '%{PID}-10-1' , '%{PID}-10-2' , '%{PID}-10-3' , '%{PID}-10-7' , '%{PID}-10-9' ] - name: oh-observation - resource: Bundle.entry.resource.ofType(Observation) - condition: 'Bundle.entry.resource.ofType(Observation).code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.code = "AOE"' - schema: classpath:/metadata/hl7_mapping/receivers/STLTs/OH/OH-observation-fields.yml + resource: 'Bundle.entry.resource.ofType(Observation)' + schema: classpath:/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml resourceIndex: resultIndex \ No newline at end of file diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-observation-fields.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-observation-fields.yml deleted file mode 100644 index 7e1763a7c49..00000000000 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-observation-fields.yml +++ /dev/null @@ -1,7 +0,0 @@ -constants: - OBX: '/PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION(%{resultIndex})/OBX' - -elements: - - name: wa-suppress-qst-for-aoe - value: [ '""' ] - hl7Spec: [ '%{OBX}-29' ] \ No newline at end of file diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml index 61a616fcff4..8d233b16b8d 100644 --- a/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml +++ b/prime-router/src/main/resources/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml @@ -127,9 +127,8 @@ elements: hl7Spec: [ '%{PID}-22-7' ] - name: wa-observation - resource: Bundle.entry.resource.ofType(Observation) - condition: 'Bundle.entry.resource.ofType(Observation).code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.code = "AOE"' - schema: classpath:/metadata/hl7_mapping/receivers/STLTs/WA/WA-observation-fields.yml + resource: 'Bundle.entry.resource.ofType(Observation)' + schema: classpath:/metadata/hl7_mapping/receivers/Common/observation-fields/observation-fields.yml resourceIndex: resultIndex - name: wa-unwanted-fields diff --git a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_MO_20240628-0001.fhir b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_MO_20240628-0001.fhir index 86057d32469..6926b084fa0 100644 --- a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_MO_20240628-0001.fhir +++ b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_MO_20240628-0001.fhir @@ -1,151 +1,450 @@ { "resourceType": "Bundle", + "id": "1727929833139202000.aaea56b1-36c2-4e99-885e-b0a2fc4adc3b", + "meta": { + "lastUpdated": "2024-10-02T22:30:33.139-06:00" + }, "identifier": { - "value": "0bab3f94-feb4-4915-939d-1adc5da201f3" + "system": "https://reportstream.cdc.gov/prime-router", + "value": "3268e1d6-cb84-459b-8640-e7930369d34d" }, "type": "message", - "timestamp": "2024-06-05T18:55:01.277Z", + "timestamp": "2024-02-26T14:40:38.000-07:00", "entry": [ { - "fullUrl": "MessageHeader/5cbae40a-675e-49d4-b12a-04271de671a6", + "fullUrl": "MessageHeader/1727929833143119000.d5ff98a8-6425-447b-8f21-95c394693856", "resource": { "resourceType": "MessageHeader", - "id": "5cbae40a-675e-49d4-b12a-04271de671a6", + "id": "1727929833143119000.d5ff98a8-6425-447b-8f21-95c394693856", "meta": { "tag": [ { "system": "http://terminology.hl7.org/CodeSystem/v2-0103", - "code": "P", - "display": "Production" + "code": "T" } ] }, + "language": "ENG", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/character-set", + "valueString": "UNICODE UTF-8" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/msh-message-header", + "extension": [ + { + "url": "MSH.7", + "valueString": "20240226214038+0000" + }, + { + "url": "MSH.15", + "valueString": "NE" + }, + { + "url": "MSH.16", + "valueString": "NE" + }, + { + "url": "MSH.19", + "valueCodeableConcept": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "ISO" + } + ], + "code": "ENG", + "display": "English" + } + ] + } + }, + { + "url": "MSH.21", + "valueIdentifier": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "ELR_Receiver" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.113883.9.11" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "ISO" + } + ] + } + ], + "value": "PHLabReport-NoAck" + } + } + ] + } + ], "eventCoding": { "system": "http://terminology.hl7.org/CodeSystem/v2-0003", "code": "R01", - "display": "ORU/ACK - Unsolicited transmission of an observation message" + "display": "ORU^R01^ORU_R01" }, - "destination": [ - { - "name": "PRIME ReportStream", - "endpoint": "https://prime.cdc.gov/api/reports?option=SkipInvalidItems" - } - ], "sender": { - "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + "reference": "Organization/1727929833141261000.09e1e9c5-9153-465b-8096-f2010f7accf5" }, "source": { "extension": [ { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-binary-id", - "valueString": "d5de310" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "CDC PRIME - Atlanta" }, { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-install-date", - "valueInstant": "2024-06-05T15:42:52Z" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.114222.4.1.237821" }, { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-vendor-org", - "valueReference": { - "reference": "Organization/07640c5d-87cd-488b-9343-a226c5166539" - } + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueString": "ISO" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "MSH.3" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-binary-id", + "valueString": "0.2-SNAPSHOT" } ], - "software": "PRIME SimpleReport", - "version": "d5de310", - "endpoint": "https://simplereport.gov" - }, - "focus": [ + "name": "CDC PRIME - Atlanta: 2.16.840.1.114222.4.1.237821", + "software": "PRIME ReportStream", + "version": "0.2-SNAPSHOT", + "endpoint": "urn:oid:2.16.840.1.114222.4.1.237821" + } + } + }, + { + "fullUrl": "Organization/1727929833141261000.09e1e9c5-9153-465b-8096-f2010f7accf5", + "resource": { + "resourceType": "Organization", + "id": "1727929833141261000.09e1e9c5-9153-465b-8096-f2010f7accf5", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xon-organization", + "extension": [ + { + "url": "XON.10", + "valueString": "Testing Lab" + } + ] + } + ], + "identifier": [ { - "reference": "Provenance/d0dd19cd-76a0-4e16-ab1d-dc5838247b61" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.2,HD.3" + } + ], + "value": "Testing Lab" }, { - "reference": "DiagnosticReport/0bab3f94-feb4-4915-939d-1adc5da201f3" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.1" + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0301", + "code": "CLIA" + } + ] + }, + "value": "12D4567890" + } + ], + "address": [ + { + "country": "USA" } ] } }, { - "fullUrl": "Provenance/d0dd19cd-76a0-4e16-ab1d-dc5838247b61", + "fullUrl": "Provenance/1727929833147767000.180a12ca-0f33-4654-9e47-314771be2fad", "resource": { "resourceType": "Provenance", - "id": "d0dd19cd-76a0-4e16-ab1d-dc5838247b61", - "recorded": "2024-06-05T18:55:01.277Z", + "id": "1727929833147767000.180a12ca-0f33-4654-9e47-314771be2fad", + "target": [ + { + "reference": "MessageHeader/1727929833143119000.d5ff98a8-6425-447b-8f21-95c394693856" + }, + { + "reference": "DiagnosticReport/1727929833367956000.c65caf72-e07d-4311-8bfa-71c40af4fc92" + } + ], + "recorded": "2024-02-26T21:40:38Z", "activity": { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v2-0003", - "code": "R01", - "display": "ORU/ACK - Unsolicited transmission of an observation message" + "display": "ORU^R01^ORU_R01" } ] }, "agent": [ { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/provenance-participant-type", + "code": "author" + } + ] + }, "who": { - "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + "reference": "Organization/1727929833146941000.c466947f-1dd e-436e-be73-c74bbe73d7f1" + } + } + ], + "entity": [ + { + "role": "source", + "what": { + "reference": "Device/1727929833166211000.8bf87d48-698a-4e35-9b31-e196c17431cc" } } ] } }, { - "fullUrl": "DiagnosticReport/0bab3f94-feb4-4915-939d-1adc5da201f3", + "fullUrl": "Organization/1727929833146941000.c466947f-1dde-436e-be73-c74bbe73d7f1", "resource": { - "resourceType": "DiagnosticReport", - "id": "0bab3f94-feb4-4915-939d-1adc5da201f3", + "resourceType": "Organization", + "id": "1727929833146941000.c466947f-1dde-436e-be73-c74bbe73d7f1", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xon-organization", + "extension": [ + { + "url": "XON.10", + "valueString": "Testing Lab" + } + ] + } + ], "identifier": [ { - "value": "0bab3f94-feb4-4915-939d-1adc5da201f3" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.1" + } + ], + "value": "Testing Lab" + }, + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.2,HD.3" + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0301", + "code": "CLIA" + } + ] + }, + "value": "12D4567890" + } + ] + } + }, + { + "fullUrl": "Organization/1727929833165997000.423c7b09-5687-4762-b3ab-3264ad28a66d", + "resource": { + "resourceType": "Organization", + "id": "1727929833165997000.423c7b09-5687-4762-b3ab-3264ad28a66d", + "name": "Centers for Disease Control and Prevention" + } + }, + { + "fullUrl": "Device/1727929833166211000.8bf87d48-698a-4e35-9b31-e196c17431cc", + "resource": { + "resourceType": "Device", + "id": "1727929833166211000.8bf87d48-698a-4e35-9b31-e196c17431cc", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-vendor-org", + "valueReference": { + "reference": "Organization/1727929833165997000.423c7b09-5687-4762-b3ab-3264ad28a66d" + } } ], - "basedOn": [ + "manufacturer": "Centers for Disease Control and Prevention", + "deviceName": [ { - "reference": "ServiceRequest/185170f3-4361-48ff-85e1-808a66624470" + "name": "PRIME ReportStream", + "type": "manufacturer-name" } ], - "status": "final", - "code": { + "modelNumber": "0.2-SNAPSHOT", + "version": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-install-date", + "valueDateTime": "2024-02-23T15:13:35Z", + "_valueDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueString": "20240223151335+0000" + } + ] + } + } + ], + "value": "0.2-SNAPSHOT" + } + ] + } + }, + { + "fullUrl": "Provenance/1727929833167753000.7111b9a0-2d30-4e48-8f82-b5a8ebb259a9", + "resource": { + "resourceType": "Provenance", + "id": "1727929833167753000.7111b9a0-2d30-4e48-8f82-b5a8ebb259a9", + "recorded": "2024-10-02T22:30:33Z", + "policy": [ + "http://hl7.org/fhir/uv/v2mappings/message-oru-r01-to-bundle" + ], + "activity": { "coding": [ { - "system": "http://loinc.org", - "code": "94531-1" + "code": "v2-FHIR transformation" } ] }, - "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" - }, - "effectiveDateTime": "2024-06-05T18:39:58+00:00", - "issued": 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(Dekalb)^2.16.840.1.114222.4.1.237821^ISO|CDC PRIME^36DSMP9999^CLIA|OHDOH^2.16.840.1.114222.4.1.3674^ISO|OHDOH^2.16.840.1.114222.4.1.3674^ISO|20240815124718+0000||ORU^R01^ORU_R01|12256b9a-0ca9-47ed-95b4-0d4ca60c4324|P|2.5.1|||NE|NE|USA|UNICODE UTF-8|||PHLabReport-NoAck^ELR_Receiver^2.16.840.1.113883.9.11^ISO SFT|Centers for Disease Control and Prevention|0.2-SNAPSHOT|PRIME ReportStream|0.2-SNAPSHOT||20240812210736+0000 PID|1||10083d1d-dc8b-4ea0-91fa-8744cf0f013b^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Wolf^Karolann^^^^^L||19700201|F||1002-5^native^HL70005^^^^2.5.1^^native|123 Main St^^Tamuning^ND^55987^USA||(800) 232 4636^PRS^CP^^1^800^2324636^^^^^(800) 232 4636~^NET^Internet^wolf@test.com|||||||||H^Hispanic or Latino^HL70189^^^^2.9^^Hispanic or Latino||||||||N ORC|RE|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI||(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|20240815124718+0000||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|321 Ocean Drive^^Denver^CO^80210^USA OBR|1|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay^LN|||20240815123218+0000|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|||||20240815124718+0000|||F OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay^LN^^^^^^COVID-19||260373001^Detected^SCT|||A^Abnormal^HL70078^^^^2.7|||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc.^BinaxNOW COVID-19 Ag 2 Card^^^^^^^BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc.|No Equipment|20240815124718+0000||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA OBX|2|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69^^Has symptoms related to condition of interest||N^No^HL70136||||||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA OBX|3|CWE|82810-3^Pregnancy status^LN^^^^2.68^^Pregnancy status||60001007^Not pregnant^SCT||||||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA OBX|4|CWE|95418-0^Employed in a healthcare setting^LN^^^^2.69^^Employed in a healthcare setting||Y^Yes^HL70136||||||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA OBX|5|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69^^Resides in a congregate care setting||Y^Yes^HL70136||||||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA OBX|6|CWE|76691-5^Gender identity^LN^^^^^^Gender identity||UNK^Non-binary gender identity^NULLFL||||||F|||20240815123218+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA SPM|1|12256b9a-0ca9-47ed-95b4-0d4ca60c4324&Testing Lab&12D4567890&CLIA^12256b9a-0ca9-47ed-95b4-0d4ca60c4324&Testing Lab&12D4567890&CLIA||433801000124107^Nasopharyngeal and oropharyngeal swab^SCT^^^^2.67^^Nasopharyngeal and oropharyngeal swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240815123218+0000|20240815123218+0000 \ No newline at end of file diff --git a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.fhir b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.fhir index 51f4372d48b..1b639e36739 100644 --- a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.fhir +++ b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.fhir @@ -1,16 +1,16 @@ { "resourceType": "Bundle", "identifier": { - "value": "0bab3f94-feb4-4915-939d-1adc5da201f3" + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" }, "type": "message", - "timestamp": "2024-06-05T18:55:01.277Z", + "timestamp": "2024-08-15T12:47:18.310Z", "entry": [ { - "fullUrl": "MessageHeader/5cbae40a-675e-49d4-b12a-04271de671a6", + "fullUrl": "MessageHeader/59845db6-6210-4008-8369-67cb166bc651", "resource": { "resourceType": "MessageHeader", - "id": "5cbae40a-675e-49d4-b12a-04271de671a6", + "id": "59845db6-6210-4008-8369-67cb166bc651", "meta": { "tag": [ { @@ -20,10 +20,79 @@ } ] }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/msh-message-header", + "extension": [ + { + "url": "MSH.15", + "valueString": "NE" + }, + { + "url": "MSH.16", + "valueString": "NE" + }, + { + "url": "MSH.19", + "valueCodeableConcept": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "ISO" + } + ], + "code": "ENG", + "display": "English" + } + ] + } + }, + { + "url": "MSH.21", + "valueIdentifier": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "ELR_Receiver" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.113883.9.11" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueString": "ISO" + } + ] + } + ], + "value": "PHLabReport-NoAck" + } + }, + { + "url": "MSH.7", + "valueInstant": "2024-08-15T12:47:18.310Z" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/character-set", + "valueString": "UNICODE UTF-8" + } + ], "eventCoding": { "system": "http://terminology.hl7.org/CodeSystem/v2-0003", "code": "R01", - "display": "ORU/ACK - Unsolicited transmission of an observation message" + "display": "ORU^R01^ORU_R01" }, "destination": [ { @@ -38,39 +107,56 @@ "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-binary-id", - "valueString": "d5de310" + "valueString": "0.2-SNAPSHOT" }, { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-install-date", - "valueInstant": "2024-06-05T15:42:52Z" + "valueInstant": "2024-08-12T21:07:36Z" }, { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/software-vendor-org", "valueReference": { "reference": "Organization/07640c5d-87cd-488b-9343-a226c5166539" } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "CDC PRIME - Atlanta" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.114222.4.1.237821" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueString": "ISO" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "MSH.3" } ], - "software": "PRIME SimpleReport", - "version": "d5de310", - "endpoint": "https://simplereport.gov" + "name": "CDC PRIME - Atlanta: 2.16.840.1.114222.4.1.237821", + "software": "PRIME ReportStream", + "version": "0.2-SNAPSHOT", + "endpoint": "urn:oid:2.16.840.1.114222.4.1.237821" }, "focus": [ { - "reference": "Provenance/d0dd19cd-76a0-4e16-ab1d-dc5838247b61" + "reference": "Provenance/342b0559-0c77-4bb0-9c98-bae5a6cf17d6" }, { - "reference": "DiagnosticReport/0bab3f94-feb4-4915-939d-1adc5da201f3" + "reference": "DiagnosticReport/12256b9a-0ca9-47ed-95b4-0d4ca60c4324" } ] } }, { - "fullUrl": "Provenance/d0dd19cd-76a0-4e16-ab1d-dc5838247b61", + "fullUrl": "Provenance/342b0559-0c77-4bb0-9c98-bae5a6cf17d6", "resource": { "resourceType": "Provenance", - "id": "d0dd19cd-76a0-4e16-ab1d-dc5838247b61", - "recorded": "2024-06-05T18:55:01.277Z", + "id": "342b0559-0c77-4bb0-9c98-bae5a6cf17d6", + "recorded": "2024-08-15T12:47:18.310Z", "activity": { "coding": [ { @@ -90,18 +176,82 @@ } }, { - "fullUrl": "DiagnosticReport/0bab3f94-feb4-4915-939d-1adc5da201f3", + "fullUrl": "DiagnosticReport/12256b9a-0ca9-47ed-95b4-0d4ca60c4324", "resource": { "resourceType": "DiagnosticReport", - "id": "0bab3f94-feb4-4915-939d-1adc5da201f3", + "id": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324", "identifier": [ { - "value": "0bab3f94-feb4-4915-939d-1adc5da201f3" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.3" + } + ], + "type": { + "coding": [ + { + "code": "FILL" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + }, + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.2" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PLAC" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" } ], "basedOn": [ { - "reference": "ServiceRequest/185170f3-4361-48ff-85e1-808a66624470" + "reference": "ServiceRequest/5b0a1598-edcb-4a5d-af54-8acd393f734e" } ], "status": "final", @@ -109,43 +259,67 @@ "coding": [ { "system": "http://loinc.org", - "code": "94531-1" + "code": "94558-4" } ] }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] + }, + "issued": "2024-08-15T12:47:18+00:00", + "_issued": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueInstant": "2024-08-15T12:47:18+00:00" + } + ] }, - "effectiveDateTime": "2024-06-05T18:39:58+00:00", - "issued": "2024-06-05T18:55:01+00:00", "specimen": [ { - "reference": "Specimen/dc7af370-fc07-4b00-abc7-9b5dd87cf4d2" + "reference": "Specimen/baf09fcd-95d1-48d7-9b12-3f52d57d69f4" } ], "result": [ { - "reference": "Observation/5ab37a34-59f5-421f-92bd-baffaf26bb72" + "reference": "Observation/cf10c0e9-3050-4eeb-a7e0-0dfe76f46af3" } ] } }, { - "fullUrl": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67", + "fullUrl": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b", "resource": { "resourceType": "Patient", - "id": "7c0d1de9-270e-4d9c-a4ec-af92560cec67", + "id": "10083d1d-dc8b-4ea0-91fa-8744cf0f013b", "extension": [ { "url": "http://ibm.com/fhir/cdm/StructureDefinition/local-race-cd", "valueCodeableConcept": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ], "system": "http://terminology.hl7.org/CodeSystem/v3-Race", - "code": "2028-9" + "version": "2.5.1", + "code": "1002-5", + "display": "native" } ], - "text": "asian" + "text": "native" } }, { @@ -153,45 +327,168 @@ "valueCodeableConcept": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70189" + } + ], "system": "http://terminology.hl7.org/CodeSystem/v2-0189", - "code": "N", - "display": "Not Hispanic or Latino" + "version": "2.9", + "code": "H", + "display": "Hispanic or Latino" } ], - "text": "Not Hispanic or Latino" + "text": "Hispanic or Latino" } } ], "identifier": [ { - "value": "7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "PID.3" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cx-identifier", + "extension": [ + { + "url": "CX.5", + "valueString": "PI" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-facility", + "valueReference": { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + } + ], + "value": "10083d1d-dc8b-4ea0-91fa-8744cf0f013b", + "assigner": { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } } ], "name": [ { - "family": "Granger", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xpn-human-name", + "extension": [ + { + "url": "XPN.2", + "valueString": "Karolann" + } + ] + } + ], + "use": "official", + "family": "Wolf", "given": [ - "Hermione" + "Karolann" ] } ], "telecom": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.1", + "valueString": "(800) 232 4636" + }, + { + "url": "XTN.2", + "valueString": "PRS" + }, + { + "url": "XTN.3", + "valueString": "CP" + }, + { + "url": "XTN.7", + "valueInteger": 2324636 + }, + { + "url": "XTN.12", + "valueString": "(800) 232 4636" + } + ] + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-country", + "valueInteger": 1 + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-area", + "valueInteger": 800 + } + ], "system": "phone", - "value": "(212) 555 1234", + "value": "(800) 232 4636", "use": "mobile" + }, + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.2", + "valueString": "NET" + }, + { + "url": "XTN.3", + "valueString": "Internet" + }, + { + "url": "XTN.4", + "valueString": "wolf@test.com" + } + ] + } + ], + "system": "email", + "value": "wolf@test.com", + "use": "home" } ], "gender": "female", - "birthDate": "1990-07-21", + "birthDate": "1970-02-01", + "deceasedBoolean": false, "address": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xad-address", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/sad-address-line", + "extension": [ + { + "url": "SAD.1", + "valueString": "123 Main St" + } + ] + } + ] + } + ], "line": [ - "53 Buttonwood Ave" + "123 Main St" ], - "city": "Brooklyn", - "state": "WA", - "postalCode": "11224", + "city": "Tamuning", + "state": "ND", + "postalCode": "55987", "country": "USA" } ], @@ -205,8 +502,127 @@ "resource": { "resourceType": "Organization", "id": "719ec8ad-cf59-405a-9832-c4065945c130", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/organization-name-type", + "valueCoding": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueCodeableConcept": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "XON.2" + } + ], + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ], + "code": "L" + } + ] + } + } + ], + "code": "L" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.25" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.15" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.15" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.15" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.15" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "OBX.15" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization", + "valueCodeableConcept": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueCode": "CLIA" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ], + "code": "12D4567890", + "display": "Testing Lab" + } + ] + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xon-organization", + "extension": [ + { + "url": "XON.10", + "valueString": "12D4567890" + } + ] + } + ], "identifier": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.2,HD.3" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.113883.4.7" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueString": "ISO" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "CLIA" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/coding-system", + "valueCodeableConcept": { + "coding": [ + { + "code": "CLIA" + } + ] + } + } + ], "use": "official", "type": { "coding": [ @@ -217,11 +633,63 @@ ] }, "value": "12D4567890" + }, + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "HD.1" + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "XX" + } + ] + }, + "value": "Testing Lab" } ], "name": "Testing Lab", "telecom": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.1", + "valueString": "(530) 867 5309" + }, + { + "url": "XTN.2", + "valueString": "WPN" + }, + { + "url": "XTN.3", + "valueString": "PH" + }, + { + "url": "XTN.7", + "valueInteger": 8675309 + }, + { + "url": "XTN.12", + "valueString": "(530) 867 5309" + } + ] + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-country", + "valueInteger": 1 + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-area", + "valueInteger": 530 + } + ], "system": "phone", "value": "(530) 867 5309", "use": "work" @@ -229,11 +697,27 @@ ], "address": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xad-address", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/sad-address-line", + "extension": [ + { + "url": "SAD.1", + "valueString": "123 Beach Way" + } + ] + } + ] + } + ], "line": [ "123 Beach Way" ], "city": "Denver", - "state": "WA", + "state": "CO", "postalCode": "80210", "country": "USA" } @@ -245,9 +729,62 @@ "resource": { "resourceType": "Practitioner", "id": "ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xcn-practitioner", + "extension": [ + { + "url": "XCN.10", + "valueString": "L" + }, + { + "url": "XCN.3", + "valueString": "Phil" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.12" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "NPI" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "2.16.840.1.113883.4.6" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueString": "ISO" + } + ] + } + ], "identifier": [ { - "system": "http://hl7.org/fhir/sid/us-npi", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "NPI" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "urn:oid:2.16.840.1.113883.4.6" + } + ], + "type": { + "coding": [ + { + "code": "NPI" + } + ] + }, + "system": "NPI", "value": "1245319599" } ], @@ -261,6 +798,41 @@ ], "telecom": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.1", + "valueString": "(530) 867 5309" + }, + { + "url": "XTN.2", + "valueString": "WPN" + }, + { + "url": "XTN.3", + "valueString": "PH" + }, + { + "url": "XTN.7", + "valueInteger": 8675309 + }, + { + "url": "XTN.12", + "valueString": "(530) 867 5309" + } + ] + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-country", + "valueInteger": 1 + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-area", + "valueInteger": 530 + } + ], "system": "phone", "value": "(530) 867 5309", "use": "work" @@ -268,11 +840,27 @@ ], "address": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xad-address", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/sad-address-line", + "extension": [ + { + "url": "SAD.1", + "valueString": "321 Ocean Drive" + } + ] + } + ] + } + ], "line": [ "321 Ocean Drive" ], "city": "Denver", - "state": "WA", + "state": "CO", "postalCode": "80210", "country": "USA" } @@ -280,35 +868,105 @@ } }, { - "fullUrl": "Specimen/dc7af370-fc07-4b00-abc7-9b5dd87cf4d2", + "fullUrl": "Specimen/baf09fcd-95d1-48d7-9b12-3f52d57d69f4", "resource": { "resourceType": "Specimen", - "id": "dc7af370-fc07-4b00-abc7-9b5dd87cf4d2", + "id": "baf09fcd-95d1-48d7-9b12-3f52d57d69f4", "identifier": [ { - "value": "80ed36a0-4bd1-42c3-bb56-81ea4ac1e75a" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Component", + "valueString": "SPM.2.1" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/filler-assigned-identifier", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/entity-identifier", + "valueId": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PGN" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" } ], "type": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "SCT" + } + ], "system": "http://snomed.info/sct", - "code": "258500001" + "version": "2.67", + "code": "433801000124107", + "display": "Nasopharyngeal and oropharyngeal swab" } ], - "text": "Nasopharyngeal swab" + "text": "Nasopharyngeal and oropharyngeal swab" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" }, - "receivedTime": "2024-06-05T18:39:58+00:00", + "receivedTime": "2024-08-15T12:32:18+00:00", "collection": { - "collectedDateTime": "2024-06-05T18:39:58+00:00", + "collectedDateTime": "2024-08-15T12:32:18+00:00", "bodySite": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "SCT" + } + ], "system": "http://snomed.info/sct", - "code": "87100004" + "code": "87100004", + "display": "Topography unknown (body structure)" } ], "text": "Topography unknown (body structure)" @@ -317,10 +975,10 @@ } }, { - "fullUrl": "ServiceRequest/185170f3-4361-48ff-85e1-808a66624470", + "fullUrl": "ServiceRequest/5b0a1598-edcb-4a5d-af54-8acd393f734e", "resource": { "resourceType": "ServiceRequest", - "id": "185170f3-4361-48ff-85e1-808a66624470", + "id": "5b0a1598-edcb-4a5d-af54-8acd393f734e", "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/order-control", @@ -335,79 +993,350 @@ }, { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/order-effective-date", - "valueDateTime": "2024-06-05T18:54:58+00:00" - } - ], - "status": "completed", - "intent": "order", - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "94531-1" - } - ] - }, - "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" - }, - "requester": { - "reference": "PractitionerRole/57a1a000-16e5-461a-930a-2e4779944bc2" - }, - "performer": [ - { - "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" - } - ], - "supportingInfo": [ - { - "reference": "Observation/dd5369b2-91e7-32d9-8c7f-884cad6b0391" - }, - { - "reference": "Observation/fdf748f4-b187-31c6-b08d-334afc1c6a49" + "valueDateTime": "2024-08-15T12:47:18+00:00" }, { - "reference": "Observation/4c669397-3b8b-3448-a7c8-d2fb8c5afde5" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/business-event", + "valueCode": "RE" }, { - "reference": "Observation/4456d162-bfd8-37f3-aafe-1e6444c53934" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obr-observation-request", + "extension": [ + { + "url": "OBR.2", + "valueIdentifier": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.2" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PLAC" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + } + }, + { + "url": "OBR.3", + "valueIdentifier": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.3" + } + ], + "type": { + "coding": [ + { + "code": "FILL" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + } + }, + { + "url": "OBR.16", + "valueReference": { + "reference": "Practitioner/ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/callback-number", + "valueContactPoint": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.1", + "valueString": "(530) 867 5309" + }, + { + "url": "XTN.2", + "valueString": "WPN" + }, + { + "url": "XTN.3", + "valueString": "PH" + }, + { + "url": "XTN.7", + "valueInteger": 8675309 + }, + { + "url": "XTN.12", + "valueString": "(530) 867 5309" + } + ] + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-country", + "valueInteger": 1 + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-area", + "valueInteger": 530 + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.14" + } + ], + "system": "phone", + "value": "(530) 867 5309", + "use": "work" + } + }, + { + "url": "OBR.25", + "valueString": "F" + } + ] }, { - "reference": "Observation/0042a1cb-8473-3181-9b65-fcb08dc112a3" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/orc-common-order", + "extension": [ + { + "url": "ORC.15", + "valueDateTime": "2024-08-15T12:47:18+00:00" + } + ] } - ] - } - }, - { - "fullUrl": "Device/d303372c-70cb-46b7-bf74-23f4dc91e661", - "resource": { - "resourceType": "Device", - "id": "d303372c-70cb-46b7-bf74-23f4dc91e661", + ], "identifier": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.2" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + } + ], + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PLAC" + } + ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + }, + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id", + "valueString": "Testing Lab" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id", + "valueString": "12D4567890" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type", + "valueCode": "CLIA" + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.3" + } + ], "type": { "coding": [ { - "code": "MNI" + "code": "FILL" } ] + }, + "value": "12256b9a-0ca9-47ed-95b4-0d4ca60c4324" + } + ], + "status": "completed", + "intent": "order", + "code": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], + "system": "http://loinc.org", + "code": "94558-4", + "display": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay" + } + ] + }, + "subject": { + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "requester": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/callback-number", + "valueContactPoint": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xtn-contact-point", + "extension": [ + { + "url": "XTN.1", + "valueString": "(530) 867 5309" + }, + { + "url": "XTN.2", + "valueString": "WPN" + }, + { + "url": "XTN.3", + "valueString": "PH" + }, + { + "url": "XTN.7", + "valueInteger": 8675309 + }, + { + "url": "XTN.12", + "valueString": "(530) 867 5309" + } + ] + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-country", + "valueInteger": 1 + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/contactpoint-area", + "valueInteger": 530 + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field", + "valueString": "ORC.14" + } + ], + "system": "phone", + "value": "(530) 867 5309", + "use": "work" + } } + ], + "reference": "PractitionerRole/8fc81c25-0c0f-46bc-8692-efab10e4c19f" + }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], + "supportingInfo": [ + { + "reference": "Observation/e704237f-1c4a-38ca-ba72-a6b683f68f16" + }, + { + "reference": "Observation/fb84b03d-e40a-3b93-8c11-d63dafab905e" + }, + { + "reference": "Observation/40079ae2-599d-39ff-bb44-4838c90888da" + }, + { + "reference": "Observation/b4848674-cbd7-33ff-91a0-999df0c72987" + }, + { + "reference": "Observation/dfee47a9-6993-36de-b041-9aa6baaa4519" + } + ] + } + }, + { + "fullUrl": "Device/65006a82-d9ac-45b3-8ca1-67dc16010555", + "resource": { + "resourceType": "Device", + "id": "65006a82-d9ac-45b3-8ca1-67dc16010555", + "identifier": [ + { + "value": "No Equipment" } ], - "manufacturer": "Access Bio, Inc.", + "manufacturer": "Abbott Diagnostics Scarborough, Inc.", "deviceName": [ { - "name": "CareStart COVID-19 MDx RT-PCR", + "name": "BinaxNOW COVID-19 Ag 2 Card", "type": "model-name" } ] } }, { - "fullUrl": "PractitionerRole/57a1a000-16e5-461a-930a-2e4779944bc2", + "fullUrl": "PractitionerRole/8fc81c25-0c0f-46bc-8692-efab10e4c19f", "resource": { "resourceType": "PractitionerRole", - "id": "57a1a000-16e5-461a-930a-2e4779944bc2", + "id": "8fc81c25-0c0f-46bc-8692-efab10e4c19f", "practitioner": { "reference": "Practitioner/ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9" }, @@ -421,28 +1350,93 @@ "resource": { "resourceType": "Organization", "id": "07640c5d-87cd-488b-9343-a226c5166539", - "name": "SimpleReport" + "name": "Centers for Disease Control and Prevention" } }, { - "fullUrl": "Observation/5ab37a34-59f5-421f-92bd-baffaf26bb72", + "fullUrl": "Observation/cf10c0e9-3050-4eeb-a7e0-0dfe76f46af3", "resource": { "resourceType": "Observation", - "id": "5ab37a34-59f5-421f-92bd-baffaf26bb72", + "id": "cf10c0e9-3050-4eeb-a7e0-0dfe76f46af3", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.17", + "valueCodeableConcept": { + "coding": [ + { + "display": "BinaxNOW COVID-19 Ag 2 Card" + } + ] + } + } + ] + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/analysis-date-time", + "valueInstant": "2024-08-15T12:47:18.249Z", + "_valueInstant": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueInstant": "2024-08-15T12:47:18.249Z" + } + ] + } + } + ], "status": "final", "code": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", + "valueCoding": { + "system": "SNOMEDCT", + "code": "840539006", + "display": "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], "system": "http://loinc.org", - "code": "94500-6" + "code": "94558-4", + "display": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay" } ], "text": "COVID-19" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] }, - "issued": "2024-06-05T18:54:58.594Z", + "issued": "2024-08-15T12:47:18.249Z", "performer": [ { "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" @@ -451,6 +1445,16 @@ "valueCodeableConcept": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "SCT" + } + ], "system": "http://snomed.info/sct", "code": "260373001", "display": "Detected" @@ -461,7 +1465,18 @@ { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70078" + } + ], "system": "http://terminology.hl7.org/CodeSystem/v2-0078", + "version": "2.7", "code": "A", "display": "Abnormal" } @@ -473,29 +1488,63 @@ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/testkit-name-id", "valueCoding": { - "code": "CareStart COVID-19 MDx RT-PCR_Access Bio, Inc." + "code": "BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc." } } ], "coding": [ { - "display": "CareStart COVID-19 MDx RT-PCR" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ], + "code": "BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc.", + "display": "BinaxNOW COVID-19 Ag 2 Card" } - ] + ], + "text": "BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc." }, "specimen": { - "reference": "Specimen/dc7af370-fc07-4b00-abc7-9b5dd87cf4d2" + "reference": "Specimen/baf09fcd-95d1-48d7-9b12-3f52d57d69f4" }, "device": { - "reference": "Device/d303372c-70cb-46b7-bf74-23f4dc91e661" + "reference": "Device/65006a82-d9ac-45b3-8ca1-67dc16010555" } } }, { - "fullUrl": "Observation/dd5369b2-91e7-32d9-8c7f-884cad6b0391", + "fullUrl": "Observation/e704237f-1c4a-38ca-ba72-a6b683f68f16", "resource": { "resourceType": "Observation", - "id": "dd5369b2-91e7-32d9-8c7f-884cad6b0391", + "id": "e704237f-1c4a-38ca-ba72-a6b683f68f16", + "meta": { + "tag": [ + { + "code": "AOE" + } + ] + }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.29", + "valueString": "QST" + } + ] + } + ], "identifier": [ { "use": "official", @@ -514,9 +1563,6 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "95419-8", - "display": "Has symptoms related to condition of interest", "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", @@ -525,31 +1571,119 @@ "code": "AOE", "display": "Ask at order entry question" } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" } - ] + ], + "system": "http://loinc.org", + "version": "2.69", + "code": "95419-8", + "display": "Has symptoms related to condition of interest" } ], "text": "Has symptoms related to condition of interest" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], "valueCodeableConcept": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70136" + } + ], "system": "http://terminology.hl7.org/ValueSet/v2-0136", - "code": "Y", - "display": "Yes" + "code": "N", + "display": "No" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] + } + ], + "method": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] } ] } } }, { - "fullUrl": "Observation/fdf748f4-b187-31c6-b08d-334afc1c6a49", + "fullUrl": "Observation/fb84b03d-e40a-3b93-8c11-d63dafab905e", "resource": { "resourceType": "Observation", - "id": "fdf748f4-b187-31c6-b08d-334afc1c6a49", + "id": "fb84b03d-e40a-3b93-8c11-d63dafab905e", + "meta": { + "tag": [ + { + "code": "AOE" + } + ] + }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.29", + "valueString": "QST" + } + ] + } + ], "identifier": [ { "use": "official", @@ -558,17 +1692,7 @@ { "system": "http://loinc.org", "code": "81959-9", - "display": "Public health laboratory ask at order entry panel", - "extension": [ - { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", - "valueCoding": { - "system": "ReportStream", - "code": "AOE", - "display": "Ask at order entry question" - } - } - ] + "display": "Public health laboratory ask at order entry panel" } ] } @@ -578,43 +1702,136 @@ "code": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", + "valueCoding": { + "system": "ReportStream", + "code": "AOE", + "display": "Ask at order entry question" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], "system": "http://loinc.org", - "code": "11368-8", - "display": "Illness or injury onset date and time" + "version": "2.68", + "code": "82810-3", + "display": "Pregnancy status" } ], - "text": "Illness or injury onset date and time" + "text": "Pregnancy status" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" }, - "valueDateTime": "2024-06-01" - } - }, - { - "fullUrl": "Observation/4c669397-3b8b-3448-a7c8-d2fb8c5afde5", - "resource": { - "resourceType": "Observation", - "id": "4c669397-3b8b-3448-a7c8-d2fb8c5afde5", - "identifier": [ - { - "use": "official", - "type": { + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] + }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], + "valueCodeableConcept": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "SCT" + } + ], + "system": "http://snomed.info/sct", + "code": "60001007", + "display": "Not pregnant" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] + } + ], + "method": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] + } + } + }, + { + "fullUrl": "Observation/40079ae2-599d-39ff-bb44-4838c90888da", + "resource": { + "resourceType": "Observation", + "id": "40079ae2-599d-39ff-bb44-4838c90888da", + "meta": { + "tag": [ + { + "code": "AOE" + } + ] + }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.29", + "valueString": "QST" + } + ] + } + ], + "identifier": [ + { + "use": "official", + "type": { "coding": [ { "system": "http://loinc.org", "code": "81959-9", - "display": "Public health laboratory ask at order entry panel", - "extension": [ - { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", - "valueCoding": { - "system": "ReportStream", - "code": "AOE", - "display": "Ask at order entry question" - } - } - ] + "display": "Public health laboratory ask at order entry panel" } ] } @@ -624,30 +1841,89 @@ "code": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", + "valueCoding": { + "system": "ReportStream", + "code": "AOE", + "display": "Ask at order entry question" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], "system": "http://loinc.org", - "code": "82810-3", - "display": "Pregnancy status" + "version": "2.69", + "code": "95418-0", + "display": "Employed in a healthcare setting" } ], - "text": "Pregnancy status" + "text": "Employed in a healthcare setting" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] + }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], "valueCodeableConcept": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "60001007", - "display": "Not pregnant", "extension": [ { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", - "valueCoding": { - "system": "ReportStream", - "code": "AOE", - "display": "Ask at order entry question" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70136" + } + ], + "system": "http://terminology.hl7.org/ValueSet/v2-0136", + "code": "Y", + "display": "Yes" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" } + ] + } + ] + } + ], + "method": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" } ] } @@ -656,10 +1932,36 @@ } }, { - "fullUrl": "Observation/4456d162-bfd8-37f3-aafe-1e6444c53934", + "fullUrl": "Observation/b4848674-cbd7-33ff-91a0-999df0c72987", "resource": { "resourceType": "Observation", - "id": "4456d162-bfd8-37f3-aafe-1e6444c53934", + "id": "b4848674-cbd7-33ff-91a0-999df0c72987", + "meta": { + "tag": [ + { + "code": "AOE" + } + ] + }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.29", + "valueString": "QST" + } + ] + } + ], "identifier": [ { "use": "official", @@ -668,17 +1970,7 @@ { "system": "http://loinc.org", "code": "81959-9", - "display": "Public health laboratory ask at order entry panel", - "extension": [ - { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", - "valueCoding": { - "system": "ReportStream", - "code": "AOE", - "display": "Ask at order entry question" - } - } - ] + "display": "Public health laboratory ask at order entry panel" } ] } @@ -688,32 +1980,127 @@ "code": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", + "valueCoding": { + "system": "ReportStream", + "code": "AOE", + "display": "Ask at order entry question" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], "system": "http://loinc.org", - "code": "95418-0", - "display": "Employed in a healthcare setting" + "version": "2.69", + "code": "95421-4", + "display": "Resides in a congregate care setting" } ], - "text": "Employed in a healthcare setting" + "text": "Resides in a congregate care setting" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], "valueCodeableConcept": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70136" + } + ], "system": "http://terminology.hl7.org/ValueSet/v2-0136", "code": "Y", "display": "Yes" } ] + }, + "interpretation": [ + { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] + } + ], + "method": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] } } }, { - "fullUrl": "Observation/0042a1cb-8473-3181-9b65-fcb08dc112a3", + "fullUrl": "Observation/dfee47a9-6993-36de-b041-9aa6baaa4519", "resource": { "resourceType": "Observation", - "id": "0042a1cb-8473-3181-9b65-fcb08dc112a3", + "id": "dfee47a9-6993-36de-b041-9aa6baaa4519", + "meta": { + "tag": [ + { + "code": "AOE" + } + ] + }, + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", + "extension": [ + { + "url": "OBX.2", + "valueString": "CWE" + }, + { + "url": "OBX.11", + "valueString": "F" + }, + { + "url": "OBX.29", + "valueString": "QST" + } + ] + } + ], "identifier": [ { "use": "official", @@ -722,17 +2109,7 @@ { "system": "http://loinc.org", "code": "81959-9", - "display": "Public health laboratory ask at order entry panel", - "extension": [ - { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", - "valueCoding": { - "system": "ReportStream", - "code": "AOE", - "display": "Ask at order entry question" - } - } - ] + "display": "Public health laboratory ask at order entry panel" } ] } @@ -742,22 +2119,90 @@ "code": { "coding": [ { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", + "valueCoding": { + "system": "ReportStream", + "code": "AOE", + "display": "Ask at order entry question" + } + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "LN" + } + ], "system": "http://loinc.org", - "code": "95421-4", - "display": "Resides in a congregate care setting" + "code": "76691-5", + "display": "Gender identity" } ], - "text": "Resides in a congregate care setting" + "text": "Gender identity" }, "subject": { - "reference": "Patient/7c0d1de9-270e-4d9c-a4ec-af92560cec67" + "reference": "Patient/10083d1d-dc8b-4ea0-91fa-8744cf0f013b" + }, + "effectiveDateTime": "2024-08-15T12:32:18+00:00", + "_effectiveDateTime": { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", + "valueDateTime": "2024-08-15T12:32:18+00:00" + } + ] }, + "performer": [ + { + "reference": "Organization/719ec8ad-cf59-405a-9832-c4065945c130" + } + ], "valueCodeableConcept": { "coding": [ { - "system": "http://terminology.hl7.org/ValueSet/v2-0136", - "code": "Y", - "display": "Yes" + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "NULLFL" + } + ], + "system": "http://terminology.hl7.org/CodeSystem/v3-NullFlavor", + "code": "UNK", + "display": "Non-binary gender identity" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] + } + ] + } + ], + "method": { + "coding": [ + { + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + } + ] } ] } diff --git a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.hl7 b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.hl7 index 23c61256495..94859fda75e 100644 --- a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.hl7 +++ b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_WA_20240719-0001.hl7 @@ -1,12 +1,12 @@ -MSH|^~\&|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|Testing Lab^12D4567890^CLIA|WADOHPHRED^2.16.840.1.113883.3.237.4.2^ISO|dn1fro00^1.3.6.1.4.1.38630.2.1.1.19^ISO|20240605115501||ORU^R01^ORU_R01|0bab3f94-feb4-4915-939d-1adc5da201f3|P|2.5.1|||NE|NE|USA|UNICODE UTF-8|ENG^English^ISO||PHLabReport-NoAck^ELR_Receiver^2.16.840.1.113883.9.11^ISO -SFT|Centers for Disease Control and Prevention|0.2-SNAPSHOT|PRIME ReportStream|0.2-SNAPSHOT||20240605154252 -PID|1||7c0d1de9-270e-4d9c-a4ec-af92560cec67^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Granger^Hermione^^^^^L||19900721|F||2028-9^asian^HL70005^^^^2.5.1^^asian|53 Buttonwood Ave^^Brooklyn^WA^11224^USA||2125551234^PRS^CP^^1^212^5551234^^^^^2125551234||333^Unknown^99WA_LANG^^^^1|||||||N^Not Hispanic or Latino^HL70189^^^^2.9^^Not Hispanic or Latino||||||||N -ORC|RE|0bab3f94-feb4-4915-939d-1adc5da201f3^Testing Lab^12D4567890^CLIA|0bab3f94-feb4-4915-939d-1adc5da201f3^Testing Lab^12D4567890^CLIA|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI||^WPN^PH^^1^530^8675309|20240605115458||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA|^WPN^PH^^1^530^8675309|321 Ocean Drive^^Denver^WA^80210^USA -OBR|1|0bab3f94-feb4-4915-939d-1adc5da201f3^Testing Lab^12D4567890^CLIA|0bab3f94-feb4-4915-939d-1adc5da201f3^Testing Lab^12D4567890^CLIA|94531-1^SARS-CoV-2 (COVID-19) RNA panel - Respiratory system specimen by NAA with probe detection^LN|||20240605113958|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI|^WPN^PH^^1^530^8675309|||||20240605115501|||F -OBX|1|CWE|94500-6^SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection^LN^^^^^^COVID-19||260373001^Detected^SCT|||A^Abnormal^HL70078^^^^2.7|||F|||20240605113958|12D4567890^Testing Lab^CLIA||CareStart COVID-19 MDx RT-PCR_Access Bio, Inc.^CareStart COVID-19 MDx RT-PCR^^^^^^^CareStart COVID-19 MDx RT-PCR_Access Bio, Inc.|^^MNI|20240605115458||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -OBX|2|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69^^Has symptoms related to condition of interest||Y^Yes^HL70136||||||F|||20240605113958|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -OBX|3|DT|11368-8^Illness or injury onset date and time^LN^^^^^^Illness or injury onset date and time||20240601000000||||||F|||20240605113958|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -OBX|4|CWE|82810-3^Pregnancy status^LN^^^^2.68^^Pregnancy status||60001007^Not pregnant^SCT||||||F|||20240605113958|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -OBX|5|CWE|95418-0^Employed in a healthcare setting^LN^^^^2.69^^Employed in a healthcare setting||Y^Yes^HL70136||||||F|||20240605113958|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -OBX|6|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69^^Resides in a congregate care setting||Y^Yes^HL70136||||||F|||20240605113958|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^WA^80210^USA -SPM|1|0bab3f94-feb4-4915-939d-1adc5da201f3&Testing Lab&12D4567890&CLIA^0bab3f94-feb4-4915-939d-1adc5da201f3&Testing Lab&12D4567890&CLIA||258500001^Nasopharyngeal swab^SCT^^^^2.67^^Nasopharyngeal swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240605113958|20240605113958 +MSH|^~\&|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|Testing Lab^12D4567890^CLIA|WADOHPHRED^2.16.840.1.113883.3.237.4.2^ISO|dn1fro00^1.3.6.1.4.1.38630.2.1.1.19^ISO|20240815054718||ORU^R01^ORU_R01|12256b9a-0ca9-47ed-95b4-0d4ca60c4324|P|2.5.1|||NE|NE|USA|UNICODE UTF-8|ENG^English^ISO||PHLabReport-NoAck^ELR_Receiver^2.16.840.1.113883.9.11^ISO +SFT|Centers for Disease Control and Prevention|0.2-SNAPSHOT|PRIME ReportStream|0.2-SNAPSHOT||20240812210736 +PID|1||10083d1d-dc8b-4ea0-91fa-8744cf0f013b^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Wolf^Karolann^^^^^L||19700201|F||1002-5^native^HL70005^^^^2.5.1^^native|123 Main St^^Tamuning^ND^55987^USA||8002324636^PRS^CP^^1^800^2324636^^^^^8002324636~^NET^Internet^wolf@test.com||333^Unknown^99WA_LANG^^^^1|||||||H^Hispanic or Latino^HL70189^^^^2.9^^Hispanic or Latino||||||||N +ORC|RE|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI||^WPN^PH^^1^530^8675309|20240815054718||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|^WPN^PH^^1^530^8675309|321 Ocean Drive^^Denver^CO^80210^USA +OBR|1|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|12256b9a-0ca9-47ed-95b4-0d4ca60c4324^Testing Lab^12D4567890^CLIA|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay^LN|||20240815053218|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI|^WPN^PH^^1^530^8675309|||||20240815054718|||F +OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay^LN^^^^^^COVID-19||260373001^Detected^SCT|||A^Abnormal^HL70078^^^^2.7|||F|||20240815053218|12D4567890^Testing Lab^CLIA||BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc.^BinaxNOW COVID-19 Ag 2 Card^^^^^^^BinaxNOW COVID-19 Ag 2 Card_Abbott Diagnostics Scarborough, Inc.|No Equipment|20240815054718||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +OBX|2|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69^^Has symptoms related to condition of interest||N^No^HL70136||||||F|||20240815053218|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +OBX|3|CWE|82810-3^Pregnancy status^LN^^^^2.68^^Pregnancy status||60001007^Not pregnant^SCT||||||F|||20240815053218|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +OBX|4|CWE|95418-0^Employed in a healthcare setting^LN^^^^2.69^^Employed in a healthcare setting||Y^Yes^HL70136||||||F|||20240815053218|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +OBX|5|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69^^Resides in a congregate care setting||Y^Yes^HL70136||||||F|||20240815053218|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +OBX|6|CWE|76691-5^Gender identity^LN^^^^^^Gender identity||UNK^Non-binary gender identity^NULLFL||||||F|||20240815053218|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA +SPM|1|12256b9a-0ca9-47ed-95b4-0d4ca60c4324&Testing Lab&12D4567890&CLIA^12256b9a-0ca9-47ed-95b4-0d4ca60c4324&Testing Lab&12D4567890&CLIA||433801000124107^Nasopharyngeal and oropharyngeal swab^SCT^^^^2.67^^Nasopharyngeal and oropharyngeal swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240815053218|20240815053218 \ No newline at end of file diff --git a/prime-router/src/testIntegration/resources/datatests/translation-test-config.csv b/prime-router/src/testIntegration/resources/datatests/translation-test-config.csv index 9ce4f334d15..d63ebd3de62 100644 --- a/prime-router/src/testIntegration/resources/datatests/translation-test-config.csv +++ b/prime-router/src/testIntegration/resources/datatests/translation-test-config.csv @@ -48,7 +48,7 @@ FHIR_to_HL7/sample_AL_20240624-0001.fhir,,FHIR_to_HL7/sample_AL_20240624-0001.hl FHIR_to_HL7/sample_ID_20240624-0001.fhir,,FHIR_to_HL7/sample_ID_20240624-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/ID/ID-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_PR_20240624-0001.fhir,,FHIR_to_HL7/sample_PR_20240624-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/PR/PR-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_OK_20240628-0001.fhir,,FHIR_to_HL7/sample_OK_20240628-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/OK/OK-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" -FHIR_to_HL7/sample_MO_20240628-0001.fhir,,FHIR_to_HL7/sample_MO_20240628-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","mo-phd.full-elr","","" +FHIR_to_HL7/sample_MO_20240628-0001.fhir,,FHIR_to_HL7/sample_MO_20240628-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/MO/MO-receiver-transform.yml,HL7,PASS,"","","","mo-phd.full-elr","","" FHIR_to_HL7/sample_TN_20240701-0001.fhir,,FHIR_to_HL7/sample_TN_20240701-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/TN/TN-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_VT_20240628-0001.fhir,,FHIR_to_HL7/sample_VT_20240628-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/VT/VT-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","vt-doh.full-elr","","" FHIR_to_HL7/sample_MH_20240701-0001.fhir,,FHIR_to_HL7/sample_MH_20240701-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/MH/MH-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" @@ -59,8 +59,8 @@ FHIR_to_HL7/sample_OR_20240724-0001.fhir,,FHIR_to_HL7/sample_OR_20240724-0001.hl FHIR_to_HL7/sample_SR_20240729-0001.fhir,,FHIR_to_HL7/sample_CA_20240729-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/CA/CA-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_NH_20240716-0001.fhir,,FHIR_to_HL7/sample_NH_202407016-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/NH/NH-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_IL_20240802-0001.fhir,,FHIR_to_HL7/sample_IL_20240802-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/IL/IL-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" -FHIR_to_HL7/sample_WA_20240719-0001.fhir,,FHIR_to_HL7/sample_WA_20240719-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","wa-phd.full-elr","","" -FHIR_to_HL7/sample_OH_20240718-0001.fhir,,FHIR_to_HL7/sample_OH_20240718-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" +FHIR_to_HL7/sample_WA_20240719-0001.fhir,,FHIR_to_HL7/sample_WA_20240719-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/WA/WA-receiver-transform.yml,HL7,PASS,"","","","wa-phd.full-elr","","" +FHIR_to_HL7/sample_OH_20240718-0001.fhir,,FHIR_to_HL7/sample_OH_20240718-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/OH/OH-receiver-transform.yml,HL7,PASS,"","","","","","" FHIR_to_HL7/sample_NJ_20240719-0001.fhir,,FHIR_to_HL7/sample_NJ_20240719-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/NJ/NJ-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","nj-doh.full-elr","","classpath:/metadata/fhir_transforms/common/suppress-device-information.yml" FHIR_to_HL7/sample_ND_20240819-0001.fhir,,FHIR_to_HL7/sample_ND_20240819-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/ND/ND-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/sample_LA_20240806-0001.fhir,,FHIR_to_HL7/sample_LA_20240806-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/LA/LA-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","classpath:/metadata/fhir_transforms/receivers/reference-range-enrichment.yml" diff --git a/prime-router/src/testIntegration/resources/settings/organizations.yml b/prime-router/src/testIntegration/resources/settings/organizations.yml index e2ab115bb0c..051dc525b70 100644 --- a/prime-router/src/testIntegration/resources/settings/organizations.yml +++ b/prime-router/src/testIntegration/resources/settings/organizations.yml @@ -812,7 +812,6 @@ replaceUnicodeWithAscii: false useBlankInsteadOfUnknown: null truncateHDNamespaceIds: true - truncateHl7Fields: "MSH-3-1, PID-3-3, PID-3-6, ORC-2-2, ORC-7-10-5, OBR-2-2, OBR-3-2, SPM-2-1-2, SPM-2-2-2, ORC-21-1, OBX-23-1, OBX-15-1, OBX-23-10 " usePid14ForPatientEmail: false convertTimestampToDateTime: null cliaForOutOfStateTesting: null From b76a964f36fc0eb42cb9df034a91da2b09bd1a93 Mon Sep 17 00:00:00 2001 From: kant Date: Fri, 18 Oct 2024 04:16:27 -0700 Subject: [PATCH 7/9] unifying local and in memory azure event service classes into one --- .../observability/event/AzureEventService.kt | 21 ++++++-------- .../event/InMemoryAzureEventService.kt | 28 ------------------- .../event/ReportEventServiceTest.kt | 6 ++-- .../azure/FHIRConverterIntegrationTests.kt | 4 +-- .../FHIRDestinationFilterIntegrationTests.kt | 4 +-- .../FHIRReceiverFilterIntegrationTests.kt | 4 +-- .../azure/FHIRReceiverIntegrationTests.kt | 4 +-- .../azure/FHIRTranslatorIntegrationTests.kt | 4 +-- .../engine/FhirDestinationFilterTests.kt | 6 ++-- .../engine/FhirReceiverFilterTests.kt | 18 ++++++------ .../prime/reportstream/shared/Submission.kt | 2 +- 11 files changed, 34 insertions(+), 67 deletions(-) delete mode 100644 prime-router/src/test/kotlin/azure/observability/event/InMemoryAzureEventService.kt diff --git a/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt b/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt index 93e268635c2..1b5865e9025 100644 --- a/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt +++ b/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt @@ -39,27 +39,22 @@ class AzureEventServiceImpl( } } -// TODO: https://github.com/CDCgov/prime-reportstream/issues/15337 -/** - * Local storage of azure events (only used for testing) - */ -class LocalAzureEventServiceImpl( - val events: MutableList = mutableListOf(), - val reportStreamEvents: MutableMap> = mutableMapOf(), -) : AzureEventService, Logging { +class InMemoryAzureEventService : AzureEventService, Logging { + + val events: MutableList = mutableListOf() + val reportStreamEvents = mutableMapOf>() - /** - * Send event to Azure AppInsights using the Azure TelemetryClient - */ override fun trackEvent(event: AzureCustomEvent) { val name = event.javaClass.simpleName - logger.debug("Recording'$name' event in memory.") + logger.debug("Recording '$name' event in memory.") events.add(event) } override fun trackEvent(eventName: ReportStreamEventName, event: AzureCustomEvent) { + logger.debug("Recording '$eventName' event in memory.") reportStreamEvents.getOrPut(eventName) { - mutableListOf() + mutableListOf() }.add(event) + events.add(event) } } \ No newline at end of file diff --git a/prime-router/src/test/kotlin/azure/observability/event/InMemoryAzureEventService.kt b/prime-router/src/test/kotlin/azure/observability/event/InMemoryAzureEventService.kt deleted file mode 100644 index 1789a828a7b..00000000000 --- a/prime-router/src/test/kotlin/azure/observability/event/InMemoryAzureEventService.kt +++ /dev/null @@ -1,28 +0,0 @@ -package gov.cdc.prime.router.azure.observability.event - -import java.util.Collections - -// TODO: https://github.com/CDCgov/prime-reportstream/issues/15337 -/** - * Simple Event service that holds on to tracked events in-memory for test assertions - */ -class InMemoryAzureEventService : AzureEventService { - - private val events = mutableListOf() - - override fun trackEvent(event: AzureCustomEvent) { - events.add(event) - } - - override fun trackEvent(eventName: ReportStreamEventName, event: AzureCustomEvent) { - events.add(event) - } - - fun getEvents(): List { - return Collections.unmodifiableList(events) - } - - fun clear() { - events.clear() - } -} \ No newline at end of file diff --git a/prime-router/src/test/kotlin/azure/observability/event/ReportEventServiceTest.kt b/prime-router/src/test/kotlin/azure/observability/event/ReportEventServiceTest.kt index 526c409cc1b..2604cffdee4 100644 --- a/prime-router/src/test/kotlin/azure/observability/event/ReportEventServiceTest.kt +++ b/prime-router/src/test/kotlin/azure/observability/event/ReportEventServiceTest.kt @@ -71,7 +71,7 @@ class ReportEventServiceTest { val reportEventService = ReportStreamEventService( ReportStreamTestDatabaseContainer.testDatabaseAccess, - LocalAzureEventServiceImpl(), + InMemoryAzureEventService(), ReportService( ReportGraph(ReportStreamTestDatabaseContainer.testDatabaseAccess), ReportStreamTestDatabaseContainer.testDatabaseAccess @@ -115,7 +115,7 @@ class ReportEventServiceTest { val reportEventService = ReportStreamEventService( ReportStreamTestDatabaseContainer.testDatabaseAccess, - LocalAzureEventServiceImpl(), + InMemoryAzureEventService(), ReportService( ReportGraph(ReportStreamTestDatabaseContainer.testDatabaseAccess), ReportStreamTestDatabaseContainer.testDatabaseAccess @@ -193,7 +193,7 @@ class ReportEventServiceTest { val reportEventService = ReportStreamEventService( ReportStreamTestDatabaseContainer.testDatabaseAccess, - LocalAzureEventServiceImpl(), + InMemoryAzureEventService(), ReportService( ReportGraph(ReportStreamTestDatabaseContainer.testDatabaseAccess), ReportStreamTestDatabaseContainer.testDatabaseAccess diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt index 772dcec6796..d4c0a390c46 100644 --- a/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt @@ -30,8 +30,8 @@ import gov.cdc.prime.router.azure.db.tables.pojos.Action import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile import gov.cdc.prime.router.azure.observability.bundleDigest.BundleDigestLabResult import gov.cdc.prime.router.azure.observability.event.AzureEventUtils +import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService import gov.cdc.prime.router.azure.observability.event.ItemEventData -import gov.cdc.prime.router.azure.observability.event.LocalAzureEventServiceImpl import gov.cdc.prime.router.azure.observability.event.ReportEventData import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties @@ -100,7 +100,7 @@ class FHIRConverterIntegrationTests { ) ) - val azureEventService = LocalAzureEventServiceImpl() + val azureEventService = InMemoryAzureEventService() private fun createFHIRFunctionsInstance(): FHIRFunctions { val settings = FileSettings().loadOrganizations(universalPipelineOrganization) diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt index f86cc54a2bf..f587d95106d 100644 --- a/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt @@ -28,8 +28,8 @@ import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.observability.bundleDigest.BundleDigestLabResult import gov.cdc.prime.router.azure.observability.event.AzureEventService import gov.cdc.prime.router.azure.observability.event.AzureEventUtils +import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService import gov.cdc.prime.router.azure.observability.event.ItemEventData -import gov.cdc.prime.router.azure.observability.event.LocalAzureEventServiceImpl import gov.cdc.prime.router.azure.observability.event.ReportEventData import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties @@ -84,7 +84,7 @@ class FHIRDestinationFilterIntegrationTests : Logging { ) ) - val azureEventsService = LocalAzureEventServiceImpl() + val azureEventsService = InMemoryAzureEventService() @BeforeEach fun beforeEach() { diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt index e35dbd95155..5e921089b91 100644 --- a/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt @@ -34,8 +34,8 @@ import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.observability.bundleDigest.BundleDigestLabResult import gov.cdc.prime.router.azure.observability.event.AzureEventService import gov.cdc.prime.router.azure.observability.event.AzureEventUtils +import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService import gov.cdc.prime.router.azure.observability.event.ItemEventData -import gov.cdc.prime.router.azure.observability.event.LocalAzureEventServiceImpl import gov.cdc.prime.router.azure.observability.event.ReportEventData import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties @@ -174,7 +174,7 @@ class FHIRReceiverFilterIntegrationTests : Logging { ) ) - val azureEventService = LocalAzureEventServiceImpl() + val azureEventService = InMemoryAzureEventService() @BeforeEach fun beforeEach() { diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverIntegrationTests.kt index df8c56b8e7b..a3f4e2be2db 100644 --- a/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverIntegrationTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverIntegrationTests.kt @@ -21,7 +21,7 @@ import gov.cdc.prime.router.azure.db.Tables import gov.cdc.prime.router.azure.db.enums.ActionLogType import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile -import gov.cdc.prime.router.azure.observability.event.LocalAzureEventServiceImpl +import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService import gov.cdc.prime.router.azure.observability.event.ReportEventData import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties @@ -71,7 +71,7 @@ class FHIRReceiverIntegrationTests { ) ) - private val azureEventService = LocalAzureEventServiceImpl() + private val azureEventService = InMemoryAzureEventService() private lateinit var submissionTableService: SubmissionTableService private fun createFHIRFunctionsInstance(): FHIRFunctions { diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRTranslatorIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRTranslatorIntegrationTests.kt index d4d3d517d6b..e74ad4939b9 100644 --- a/prime-router/src/test/kotlin/fhirengine/azure/FHIRTranslatorIntegrationTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/azure/FHIRTranslatorIntegrationTests.kt @@ -21,7 +21,7 @@ import gov.cdc.prime.router.azure.QueueAccess import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.Task import gov.cdc.prime.router.azure.observability.event.AzureEventService -import gov.cdc.prime.router.azure.observability.event.LocalAzureEventServiceImpl +import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService import gov.cdc.prime.router.cli.tests.CompareData import gov.cdc.prime.router.common.TestcontainersUtils import gov.cdc.prime.router.common.UniversalPipelineTestUtils @@ -65,7 +65,7 @@ class FHIRTranslatorIntegrationTests : Logging { ) ) - val azureEventService = LocalAzureEventServiceImpl() + val azureEventService = InMemoryAzureEventService() @BeforeEach fun beforeEach() { diff --git a/prime-router/src/test/kotlin/fhirengine/engine/FhirDestinationFilterTests.kt b/prime-router/src/test/kotlin/fhirengine/engine/FhirDestinationFilterTests.kt index d6546d3eb8f..964308c2ed6 100644 --- a/prime-router/src/test/kotlin/fhirengine/engine/FhirDestinationFilterTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/engine/FhirDestinationFilterTests.kt @@ -260,7 +260,7 @@ class FhirDestinationFilterTests { actionHistory.reportsIn.clear() actionHistory.reportsOut.clear() actionHistory.actionLogs.clear() - azureEventService.clear() + azureEventService.events.clear() clearAllMocks() } @@ -325,7 +325,7 @@ class FhirDestinationFilterTests { assertThat(actionHistory.reportsIn).hasSize(1) assertThat(actionHistory.reportsOut).hasSize(1) - val azureEvents = azureEventService.getEvents() + val azureEvents = azureEventService.events assertThat(azureEvents).hasSize(1) assertThat(azureEvents.first()) @@ -491,7 +491,7 @@ class FhirDestinationFilterTests { assertThat(actionHistory.reportsIn).hasSize(1) assertThat(actionHistory.reportsOut).hasSize(1) - val azureEvents = azureEventService.getEvents() + val azureEvents = azureEventService.events assertThat(azureEvents).hasSize(1) assertThat(azureEvents.first()) .isInstanceOf(ReportStreamItemEvent::class) diff --git a/prime-router/src/test/kotlin/fhirengine/engine/FhirReceiverFilterTests.kt b/prime-router/src/test/kotlin/fhirengine/engine/FhirReceiverFilterTests.kt index d71ad140e10..a6c989e9a66 100644 --- a/prime-router/src/test/kotlin/fhirengine/engine/FhirReceiverFilterTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/engine/FhirReceiverFilterTests.kt @@ -173,7 +173,7 @@ class FhirReceiverFilterTests { actionHistory.reportsOut.clear() actionHistory.reportsReceived.clear() actionHistory.actionLogs.clear() - azureEventService.clear() + azureEventService.events.clear() mockkObject(BlobAccess) clearAllMocks() } @@ -225,7 +225,7 @@ class FhirReceiverFilterTests { } // assert - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -284,7 +284,7 @@ class FhirReceiverFilterTests { } } - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -346,7 +346,7 @@ class FhirReceiverFilterTests { } // assert - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -408,7 +408,7 @@ class FhirReceiverFilterTests { } // assert - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -463,7 +463,7 @@ class FhirReceiverFilterTests { val messages = engine.run(message, actionLogger, actionHistory, txn) assertThat(messages).isEmpty() - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -706,7 +706,7 @@ class FhirReceiverFilterTests { assertThat(actionHistory.reportsIn).hasSize(1) assertThat(actionHistory.reportsOut).hasSize(1) - val actualEvents = azureEventService.getEvents() + val actualEvents = azureEventService.events assertThat(actualEvents).hasSize(0) } @@ -798,7 +798,7 @@ class FhirReceiverFilterTests { val messages = engine.run(message, actionLogger, actionHistory, txn) assertThat(messages).isEmpty() - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { @@ -871,7 +871,7 @@ class FhirReceiverFilterTests { } // assert - azureEventService.getEvents().forEach { event -> + azureEventService.events.forEach { event -> assertThat(event) .isInstanceOf() .matchesPredicate { diff --git a/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt b/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt index 33b44311ee9..8d8dd2e11d2 100644 --- a/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt +++ b/shared/src/main/kotlin/gov/cdc/prime/reportstream/shared/Submission.kt @@ -23,7 +23,7 @@ data class Submission( val bodyURL: String, @JsonIgnore val detail: String? = null, - val timestamp: OffsetDateTime? = null + val timestamp: OffsetDateTime? = null, ) { companion object { /** From 1956fe03de5ae940fe639c57c80d4a8a522769a7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 13:09:15 -0500 Subject: [PATCH 8/9] Bump @okta/okta-signin-widget (#16264) Bumps the okta group with 1 update in the /frontend-react directory: [@okta/okta-signin-widget](https://github.com/okta/okta-signin-widget). Updates `@okta/okta-signin-widget` from 7.23.0 to 7.24.2 - [Release notes](https://github.com/okta/okta-signin-widget/releases) - [Changelog](https://github.com/okta/okta-signin-widget/blob/master/webpack.release.config.js) - [Commits](https://github.com/okta/okta-signin-widget/compare/okta-signin-widget-7.23.0...okta-signin-widget-7.24.2) --- updated-dependencies: - dependency-name: "@okta/okta-signin-widget" dependency-type: direct:production update-type: version-update:semver-minor dependency-group: okta ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- frontend-react/package.json | 2 +- frontend-react/yarn.lock | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/frontend-react/package.json b/frontend-react/package.json index 47d201b9a26..bfaf9ceafa2 100644 --- a/frontend-react/package.json +++ b/frontend-react/package.json @@ -8,7 +8,7 @@ "@microsoft/applicationinsights-react-js": "^17.3.2", "@microsoft/applicationinsights-web": "^3.3.2", "@okta/okta-react": "^6.9.0", - "@okta/okta-signin-widget": "^7.23.0", + "@okta/okta-signin-widget": "^7.24.2", "@rest-hooks/rest": "^3.0.3", "@tanstack/react-query": "^5.55.4", "@tanstack/react-query-devtools": "^5.55.4", diff --git a/frontend-react/yarn.lock b/frontend-react/yarn.lock index c22b4708f09..f0df3d183dd 100644 --- a/frontend-react/yarn.lock +++ b/frontend-react/yarn.lock @@ -2438,9 +2438,9 @@ __metadata: languageName: node linkType: hard -"@okta/okta-signin-widget@npm:^7.23.0": - version: 7.23.0 - resolution: "@okta/okta-signin-widget@npm:7.23.0" +"@okta/okta-signin-widget@npm:^7.24.2": + version: 7.24.2 + resolution: "@okta/okta-signin-widget@npm:7.24.2" dependencies: "@okta/okta-auth-js": ^7.8.0 "@sindresorhus/to-milliseconds": ^1.0.0 @@ -2464,7 +2464,7 @@ __metadata: dependenciesMeta: fsevents: optional: true - checksum: 5b55d5fc39412778505d262810ab3a87c2bf557a55a59e4f041f77393b6344e35a96477603a40e80cae325f0bd534aa61c95f0b154b659e647b35e55346d4b90 + checksum: 5f444bb83fefd76eb34a5f35953f3aa09323c72c07628e893cc3bddcf56c887a1ccce1ed462c7e730ee387fa0de4e15050d0dce294f8de7bc8459e54f9145288 languageName: node linkType: hard @@ -12196,7 +12196,7 @@ __metadata: "@microsoft/applicationinsights-react-js": ^17.3.2 "@microsoft/applicationinsights-web": ^3.3.2 "@okta/okta-react": ^6.9.0 - "@okta/okta-signin-widget": ^7.23.0 + "@okta/okta-signin-widget": ^7.24.2 "@playwright/test": ^1.47.0 "@rest-hooks/rest": ^3.0.3 "@rest-hooks/test": ^7.3.1 From 26f3f274a6fb6a5ffb9e661a6ae0fff1b3b7a1b0 Mon Sep 17 00:00:00 2001 From: Joseph Andersen <12385932+jpandersen87@users.noreply.github.com> Date: Mon, 21 Oct 2024 15:40:02 -0500 Subject: [PATCH 9/9] Manually resolve @okta/okta-auth-js to >=7.8.1 to fix security advisory (#16291) --- frontend-react/package.json | 3 +- frontend-react/yarn.lock | 452 ++---------------------------------- 2 files changed, 24 insertions(+), 431 deletions(-) diff --git a/frontend-react/package.json b/frontend-react/package.json index bfaf9ceafa2..4c8c5330e94 100644 --- a/frontend-react/package.json +++ b/frontend-react/package.json @@ -196,7 +196,8 @@ "vitest": "^2.0.5" }, "resolutions": { - "@types/react": "18.3.5" + "@types/react": "18.3.5", + "@okta/okta-auth-js": ">=7.8.1" }, "engines": { "node": "^20.15" diff --git a/frontend-react/yarn.lock b/frontend-react/yarn.lock index f0df3d183dd..e6777c2130d 100644 --- a/frontend-react/yarn.lock +++ b/frontend-react/yarn.lock @@ -19,17 +19,7 @@ __metadata: languageName: node linkType: hard -"@ampproject/remapping@npm:^2.2.0": - version: 2.2.1 - resolution: "@ampproject/remapping@npm:2.2.1" - dependencies: - "@jridgewell/gen-mapping": ^0.3.0 - "@jridgewell/trace-mapping": ^0.3.9 - checksum: 03c04fd526acc64a1f4df22651186f3e5ef0a9d6d6530ce4482ec9841269cf7a11dbb8af79237c282d721c5312024ff17529cd72cc4768c11e999b58e2302079 - languageName: node - linkType: hard - -"@ampproject/remapping@npm:^2.3.0": +"@ampproject/remapping@npm:^2.2.0, @ampproject/remapping@npm:^2.3.0": version: 2.3.0 resolution: "@ampproject/remapping@npm:2.3.0" dependencies: @@ -359,16 +349,7 @@ __metadata: languageName: node linkType: hard -"@babel/parser@npm:^7.1.0, @babel/parser@npm:^7.20.7, @babel/parser@npm:^7.23.0, @babel/parser@npm:^7.23.9, @babel/parser@npm:^7.24.7": - version: 7.24.7 - resolution: "@babel/parser@npm:7.24.7" - bin: - parser: ./bin/babel-parser.js - checksum: fc9d2c4c8712f89672edc55c0dc5cf640dcec715b56480f111f85c2bc1d507e251596e4110d65796690a96ac37a4b60432af90b3e97bb47e69d4ef83872dbbd6 - languageName: node - linkType: hard - -"@babel/parser@npm:^7.24.4": +"@babel/parser@npm:^7.1.0, @babel/parser@npm:^7.20.7, @babel/parser@npm:^7.23.0, @babel/parser@npm:^7.23.9, @babel/parser@npm:^7.24.4, @babel/parser@npm:^7.24.7": version: 7.24.8 resolution: "@babel/parser@npm:7.24.8" bin: @@ -2055,7 +2036,7 @@ __metadata: languageName: node linkType: hard -"@jridgewell/gen-mapping@npm:^0.3.0, @jridgewell/gen-mapping@npm:^0.3.5": +"@jridgewell/gen-mapping@npm:^0.3.5": version: 0.3.5 resolution: "@jridgewell/gen-mapping@npm:0.3.5" dependencies: @@ -2097,7 +2078,7 @@ __metadata: languageName: node linkType: hard -"@jridgewell/trace-mapping@npm:^0.3.23, @jridgewell/trace-mapping@npm:^0.3.24, @jridgewell/trace-mapping@npm:^0.3.25, @jridgewell/trace-mapping@npm:^0.3.9": +"@jridgewell/trace-mapping@npm:^0.3.23, @jridgewell/trace-mapping@npm:^0.3.24, @jridgewell/trace-mapping@npm:^0.3.25": version: 0.3.25 resolution: "@jridgewell/trace-mapping@npm:0.3.25" dependencies: @@ -2399,9 +2380,9 @@ __metadata: languageName: node linkType: hard -"@okta/okta-auth-js@npm:^7.8.0": - version: 7.8.0 - resolution: "@okta/okta-auth-js@npm:7.8.0" +"@okta/okta-auth-js@npm:>=7.8.1": + version: 7.8.1 + resolution: "@okta/okta-auth-js@npm:7.8.1" dependencies: "@babel/runtime": ^7.12.5 "@peculiar/webcrypto": ^1.4.0 @@ -2413,13 +2394,12 @@ __metadata: cross-fetch: ^3.1.5 fast-text-encoding: ^1.0.6 js-cookie: ^3.0.1 - jsonpath-plus: ^6.0.1 node-cache: ^5.1.2 p-cancelable: ^2.0.0 tiny-emitter: 1.1.0 webcrypto-shim: ^0.1.5 xhr2: 0.1.3 - checksum: faeac22381a46784381e3757c1f5193bb7dc821ea39fdd5d58952dc744cf0a64788e979aa3ce4a2551dd29f6b49e9e7eda756bafc3737386ec4c6d2b3277582c + checksum: f71a09539fe249b25991fd5a7581f6078a6abc2ac1db5f147ce1d44d20350987e45f7dbbabbd80c65a6da6989fa07322c7ce6a96f40c18959315e2f3c99698d2 languageName: node linkType: hard @@ -2656,13 +2636,6 @@ __metadata: languageName: node linkType: hard -"@rollup/rollup-android-arm-eabi@npm:4.13.0": - version: 4.13.0 - resolution: "@rollup/rollup-android-arm-eabi@npm:4.13.0" - conditions: os=android & cpu=arm - languageName: node - linkType: hard - "@rollup/rollup-android-arm-eabi@npm:4.21.2": version: 4.21.2 resolution: "@rollup/rollup-android-arm-eabi@npm:4.21.2" @@ -2670,13 +2643,6 @@ __metadata: languageName: node linkType: hard -"@rollup/rollup-android-arm64@npm:4.13.0": - version: 4.13.0 - resolution: "@rollup/rollup-android-arm64@npm:4.13.0" - conditions: os=android & cpu=arm64 - languageName: node - linkType: hard - "@rollup/rollup-android-arm64@npm:4.21.2": version: 4.21.2 resolution: "@rollup/rollup-android-arm64@npm:4.21.2" @@ -2684,13 +2650,6 @@ __metadata: languageName: node linkType: hard -"@rollup/rollup-darwin-arm64@npm:4.13.0": - version: 4.13.0 - resolution: "@rollup/rollup-darwin-arm64@npm:4.13.0" - conditions: os=darwin & cpu=arm64 - languageName: node - linkType: hard - "@rollup/rollup-darwin-arm64@npm:4.21.2": version: 4.21.2 resolution: "@rollup/rollup-darwin-arm64@npm:4.21.2" @@ -2698,13 +2657,6 @@ __metadata: languageName: node linkType: hard -"@rollup/rollup-darwin-x64@npm:4.13.0": - version: 4.13.0 - 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