diff --git a/.github/ISSUE_TEMPLATE/DevSecOps-issue.md b/.github/ISSUE_TEMPLATE/DevSecOps-issue.md new file mode 100644 index 00000000000..aa0dbad2787 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/DevSecOps-issue.md @@ -0,0 +1,69 @@ +--- +name: DevSecOps ticket +about: For new DevSecOps tickets on the board. +labels: ['DevSecOps', 'reportstream'] +--- +# DevSecOps Issue + +## Summary + +Context and description + +## Environment + +- [ ] Local +- [ ] Dev +- [ ] Stage +- [ ] Prod + +## Priority + +- [ ] **Critical** - affecting prod systems +- [ ] **Major** - blocking major functionality, deployment, etc +- [ ] **Minor** - improvements, bug fixes +- [ ] **Nice-to-have** - feature request + +### Blocks the following + +- List any blockers +- Link any Github relevant issues + +### Blocked by the following + +- Link to any tickets that add context, etc + +## Contact + +**Team**: + +**Slack Team Channel**: + +**Slack Contact (Full Name):** + +**Technical Team Lead:** + +## How to Reproduce + +### Screenshots, links, etc. for context + +## How to Test + +## Definition of Done + +- [ ] + +## Context Links + +**Git Repo:** + +**Relevant Code Links:** + +**Azure**: + +**Site URL**: + +**Other**: + +## Notes + +- \ No newline at end of file diff --git a/.github/workflows/deploy_terraform.yml b/.github/workflows/deploy_terraform.yml index 3112e70fc10..82f8ea619f2 100644 --- a/.github/workflows/deploy_terraform.yml +++ b/.github/workflows/deploy_terraform.yml @@ -11,7 +11,7 @@ on: jobs: pre_job: name: Set Build Environment - concurrency: + concurrency: group: ${{ github.workflow }}-${{ needs.pre_job.outputs.env_name }} cancel-in-progress: true runs-on: ubuntu-latest @@ -28,7 +28,7 @@ jobs: confirm_changes: name: Check Terraform Stats - ${{ needs.pre_job.outputs.env_name }} if: ${{ needs.pre_job.outputs.tf_change == 'true' }} - concurrency: + concurrency: group: ${{ github.workflow }}-${{ needs.pre_job.outputs.env_name }} cancel-in-progress: true needs: @@ -60,7 +60,7 @@ jobs: approve_deploy: name: Approve Deploy - ${{ needs.pre_job.outputs.env_name }} - concurrency: + concurrency: group: ${{ github.workflow }}-${{ needs.pre_job.outputs.env_name }} cancel-in-progress: true needs: @@ -75,7 +75,7 @@ jobs: run_deploy: name: Run Deploy - ${{ needs.pre_job.outputs.env_name }} - concurrency: + concurrency: group: ${{ github.workflow }}-${{ needs.pre_job.outputs.env_name }} cancel-in-progress: true needs: @@ -108,4 +108,7 @@ jobs: - name: Run Terraform run: | terraform init -input=false - terraform apply -input=false -no-color -lock-timeout=600s -auto-approve + terraform validate + terraform fmt -recursive + terraform plan -out ${{ needs.pre_job.outputs.env_name }}-tf.plan + # terraform apply -input=false -no-color -lock-timeout=600s -auto-approve ${{ needs.pre_job.outputs.env_name }}-tf.plan diff --git a/auth/build.gradle.kts b/auth/build.gradle.kts index f04d2619d62..9a8b9d8a923 100644 --- a/auth/build.gradle.kts +++ b/auth/build.gradle.kts @@ -1,7 +1,7 @@ apply(from = rootProject.file("buildSrc/shared.gradle.kts")) plugins { - id("org.springframework.boot") version "3.3.2" + id("org.springframework.boot") version "3.3.4" id("io.spring.dependency-management") version "1.1.6" id("reportstream.project-conventions") kotlin("plugin.spring") version "2.0.0" @@ -14,8 +14,8 @@ dependencies { implementation(project(":shared")) implementation("org.jetbrains.kotlin:kotlin-reflect") - implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.8.1") - implementation("org.jetbrains.kotlinx:kotlinx-coroutines-reactor:1.8.1") + implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.9.0") + implementation("org.jetbrains.kotlinx:kotlinx-coroutines-reactor:1.9.0") /** * Spring WebFlux was chosen for this project to be able to better handle periods of high traffic @@ -24,7 +24,7 @@ dependencies { implementation("org.springframework.cloud:spring-cloud-gateway-webflux") implementation("org.springframework.boot:spring-boot-starter-oauth2-resource-server") - runtimeOnly("com.nimbusds:oauth2-oidc-sdk:11.18") + runtimeOnly("com.nimbusds:oauth2-oidc-sdk:11.19.1") testImplementation("org.springframework.boot:spring-boot-starter-test") testImplementation("org.springframework.security:spring-security-test") @@ -45,7 +45,7 @@ configurations.all { dependencyManagement { imports { - mavenBom("com.azure.spring:spring-cloud-azure-dependencies:5.14.0") + mavenBom("com.azure.spring:spring-cloud-azure-dependencies:5.16.0") mavenBom("org.springframework.cloud:spring-cloud-dependencies:2023.0.3") } } diff --git a/frontend-react/e2e/spec/chromium-only/authenticated/daily-data-page-user-flow.spec.ts b/frontend-react/e2e/spec/chromium-only/authenticated/daily-data-page-user-flow.spec.ts index 1a7001cadde..c9aff20e410 100644 --- a/frontend-react/e2e/spec/chromium-only/authenticated/daily-data-page-user-flow.spec.ts +++ b/frontend-react/e2e/spec/chromium-only/authenticated/daily-data-page-user-flow.spec.ts @@ -206,7 +206,7 @@ test.describe( ); }); - test.skip("clears 'Report ID'", async ({ dailyDataPage }) => { + test("clears 'Report ID'", async ({ dailyDataPage }) => { // Search by Report ID const reportId = await tableDataCellValue(dailyDataPage.page, 0, 0); await searchInput(dailyDataPage.page).fill(reportId); @@ -289,7 +289,7 @@ test.describe( expect(await tableDataCellValue(dailyDataPage.page, 0, 0)).toEqual(reportId); }); - test.skip("returns match for Filename", async ({ dailyDataPage }) => { + test("returns match for Filename", async ({ dailyDataPage }) => { // Filename search is currently broken and being tracked // in ticket #15644 const fileName = await tableDataCellValue(dailyDataPage.page, 0, 4); @@ -302,7 +302,8 @@ test.describe( // Check filter status lists receiver value const filterStatusText = filterStatus([fileName]); - await expect(dailyDataPage.page.getByTestId("filter-status")).toContainText(filterStatusText); + const actualText = await dailyDataPage.page.getByTestId("filter-status").textContent(); + expect(filterStatusText).toContain(actualText); //Check table data matches search expect(await tableDataCellValue(dailyDataPage.page, 0, 4)).toEqual(fileName); diff --git a/frontend-react/package.json b/frontend-react/package.json index 47d201b9a26..59b314189ef 100644 --- a/frontend-react/package.json +++ b/frontend-react/package.json @@ -8,20 +8,20 @@ "@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", + "@tanstack/react-query": "^5.59.15", + "@tanstack/react-query-devtools": "^5.59.15", "@trussworks/react-uswds": "^9.1.0", "@uswds/uswds": "3.7.1", "axios": "^1.7.7", "classnames": "^2.5.1", "date-fns": "^3.6.0", - "date-fns-tz": "^3.1.3", + "date-fns-tz": "^3.2.0", "dompurify": "^3.1.6", "downloadjs": "^1.4.7", "export-to-csv-fix-source-map": "^0.2.1", - "focus-trap-react": "^10.2.3", + "focus-trap-react": "^10.3.0", "history": "^5.3.0", "html-to-text": "^9.0.5", "lodash": "^4.17.21", @@ -33,15 +33,15 @@ "react-loader-spinner": "^6.1.6", "react-markdown": "^9.0.1", "react-query-kit": "^3.3.0", - "react-router": "^6.26.1", - "react-router-dom": "^6.26.1", + "react-router": "^6.27.0", + "react-router-dom": "^6.27.0", "react-scroll-sync": "^0.11.2", - "react-toastify": "^10.0.5", + "react-toastify": "^10.0.6", "rehype-raw": "^7.0.0", "rehype-slug": "^5.1.0", "rest-hooks": "^6.1.7", "sanitize-html": "^2.13.0", - "tsx": "^4.19.0", + "tsx": "^4.19.1", "use-deep-compare-effect": "^1.8.1", "uuid": "^10.0.0", "web-vitals": "^3.4.0" @@ -110,8 +110,8 @@ ] }, "devDependencies": { - "@mdx-js/react": "^3.0.1", - "@mdx-js/rollup": "^3.0.1", + "@mdx-js/react": "^3.1.0", + "@mdx-js/rollup": "^3.1.0", "@playwright/test": "^1.47.0", "@rest-hooks/test": "^7.3.1", "@storybook/addon-a11y": "^8.2.9", @@ -128,7 +128,7 @@ "@storybook/testing-library": "^0.2.2", "@storybook/theming": "^8.2.9", "@testing-library/dom": "^10.4.0", - "@testing-library/jest-dom": "^6.5.0", + "@testing-library/jest-dom": "^6.6.2", "@testing-library/react": "^16.0.1", "@testing-library/user-event": "^14.5.2", "@types/dompurify": "^3.0.5", @@ -140,19 +140,19 @@ "@types/mdx": "^2.0.13", "@types/node": "^20.12.5", "@types/react": "18.3.5", - "@types/react-dom": "^18.3.0", + "@types/react-dom": "^18.3.1", "@types/react-router-dom": "^5.3.3", "@types/react-scroll-sync": "^0.9.0", "@types/sanitize-html": "^2.13.0", "@typescript-eslint/eslint-plugin": "^7.17.0", "@typescript-eslint/parser": "^7.17.0", - "@vitejs/plugin-react": "^4.3.1", - "@vitest/coverage-istanbul": "^2.0.5", - "@vitest/ui": "^2.0.5", + "@vitejs/plugin-react": "^4.3.3", + "@vitest/coverage-istanbul": "^2.1.3", + "@vitest/ui": "^2.1.3", "autoprefixer": "^10.4.20", "browserslist": "^4.23.3", "browserslist-useragent-regexp": "^4.1.3", - "chromatic": "^11.7.1", + "chromatic": "^11.12.6", "cross-env": "^7.0.3", "dotenv-flow": "^4.1.0", "eslint": "8.57", @@ -166,20 +166,20 @@ "eslint-plugin-react-hooks": "^4.6.2", "eslint-plugin-react-refresh": "^0.4.7", "eslint-plugin-storybook": "^0.8.0", - "eslint-plugin-testing-library": "^6.3.0", + "eslint-plugin-testing-library": "^6.4.0", "eslint-plugin-vitest": "^0.5.4", "husky": "^9.1.5", - "jsdom": "^25.0.0", + "jsdom": "^25.0.1", "lint-staged": "^15.2.10", "mockdate": "^3.0.5", - "msw": "^2.3.5", + "msw": "^2.4.11", "msw-storybook-addon": "beta", "npm-run-all": "^4.1.5", "otpauth": "^9.3.2", "patch-package": "^8.0.0", "postcss": "^8.4.45", "prettier": "^3.3.3", - "react-error-boundary": "^4.0.13", + "react-error-boundary": "^4.1.2", "remark-frontmatter": "^5.0.0", "remark-mdx-frontmatter": "^5.0.0", "remark-mdx-toc": "^0.3.1", @@ -189,14 +189,15 @@ "ts-node": "^10.9.2", "tslib": "^2.6.3", "typescript": "^5.5.4", - "undici": "^6.19.8", - "vite": "^5.4.3", + "undici": "^6.20.1", + "vite": "^5.4.9", "vite-plugin-checker": "^0.8.0", "vite-plugin-svgr": "^4.2.0", - "vitest": "^2.0.5" + "vitest": "^2.1.3" }, "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/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/about/roadmap.mdx b/frontend-react/src/content/about/roadmap.mdx index 94cce91a2c6..c5749c1e094 100644 --- a/frontend-react/src/content/about/roadmap.mdx +++ b/frontend-react/src/content/about/roadmap.mdx @@ -17,7 +17,7 @@ import site from "../../content/site.json" -

Last updated: August 05, 2024

+

Last updated: October 07, 2024

## Objectives for FY24 Learn about our goals and how we are measuring success for this fiscal year (FY), which runs from October 2023 through September 2024. @@ -46,7 +46,7 @@ Learn about our goals and how we are measuring success for this fiscal year (FY) tag: "recently-completed", body: (

- Arizona, Colorado, and Kansas are able to receive flu and RSV data from ReportStream. + Arkansas, Florida, Guam, Idaho, Illinois, Louisiana, Maine, Massachusetts, Minnesota, and Oklahoma are able to receive flu and RSV data from ReportStream.

), }, @@ -54,29 +54,29 @@ Learn about our goals and how we are measuring success for this fiscal year (FY) tag: "working-on-now", body: (

- Onboard or update connections for Arkansas, Connecticut, Florida, Idaho, Illinois, Iowa, Kentucky, Louisiana, Maine, Massachusetts, Michigan, Minnesota, Missouri, Montana, Oklahoma, Virginia, Washington D.C. + Onboard or update connections for Alabama, Connecticut, Delaware, Indiana, Iowa, Kentucky, Michigan, Mississippi, Missouri, Montana, New Hampshire, New Jersey, New Mexico, Ohio, Pennsylvania, Puerto Rico, Republic of Marshall Islands, South Dakota, Tennessee, Vermont, Virginia, Washington, Washington D.C., and Wyoming.

), }, { tag: "next", body: ( -

- Support remaining STLTs to connect or update their connections to be able to receive additional conditions. -

+

Support remaining STLTs to connect or update their connections to be able to receive additional conditions.

), }, { title:

Partner with SimpleReport to help nontraditional and lower-resourced testing sites and facilities report test results and send data to STLTs and the CDC.

, tag: "recently-completed", body: ( -

California, Nevada, and New York are receiving flu A/B or RSV data.

+

Contacted nontraditional and lower-resourced HIV senders in Texas as part of targeted health equity improvement work.

), }, { tag: "recently-completed", body: ( -

Identify nontraditional and lower-resourced HIV senders in Texas as part of targeted health equity improvement work.

+

+ Alaska, Arizona, California, Colorado, Florida, Hawaii, Idaho, Illinois, Louisiana, Massachusetts, Minnesota, Nevada, New York, and Rhode Island are receiving flu A/B or RSV data. +

), }, { @@ -86,45 +86,39 @@ Learn about our goals and how we are measuring success for this fiscal year (FY) ), }, { - tag: "next", + tag: "working-on-now", body: ( -

Identify more regions in California to exchange HIV test result data.

+

Add support for hepatitis C and other STI reporting through SimpleReport.

), }, { tag: "next", body: ( -

Add support for hepatitis C reporting through SimpleReport.

+

Add support for more conditions reporting through SimpleReport.

), }, { title:

Help at-home test takers and test manufacturers easily report results to STLTs and CDC.

, tag: "recently-completed", body: ( -

Support file validation against different HL7 profiles, starting with the RADx MARS custom NIST HL7 2.5.1 profile.

+

Route test results from MakeMyTestCount.org to one STLT in test environment.

), }, { tag: "working-on-now", body: ( -

Route test results from MakeMyTestCount.org to one STLT in test environment.

+

Route test results from MakeMyTestCount.org to one STLT in production.

), }, { tag: "next", body: ( -

Route test results from MakeMyTestCount.org to one STLT in production.

+

Route test results from another OTC testing (point-of-care) sender to one STLT in production.

), }, { title: "Facilitate electronic laboratory reporting (ELR) for the CDC infectious disease labs and transmit to STLTs. ", tag: "recently-completed", - body: ( -

Test data pipeline with two STLT partners to transmit test results.

- ), - }, - { - tag: "working-on-now", body: (

Complete final internal review of test result data transfer before moving to production.

), 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.

    ) }, ]} /> diff --git a/frontend-react/yarn.lock b/frontend-react/yarn.lock index c22b4708f09..265352b06f5 100644 --- a/frontend-react/yarn.lock +++ b/frontend-react/yarn.lock @@ -20,16 +20,6 @@ __metadata: 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": version: 2.3.0 resolution: "@ampproject/remapping@npm:2.3.0" dependencies: @@ -49,6 +39,16 @@ __metadata: languageName: node linkType: hard +"@babel/code-frame@npm:^7.25.7": + version: 7.25.7 + resolution: "@babel/code-frame@npm:7.25.7" + dependencies: + "@babel/highlight": ^7.25.7 + picocolors: ^1.0.0 + checksum: 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+86,29 @@ __metadata: languageName: node linkType: hard +"@babel/core@npm:^7.25.2": + version: 7.25.8 + resolution: "@babel/core@npm:7.25.8" + dependencies: + "@ampproject/remapping": ^2.2.0 + "@babel/code-frame": ^7.25.7 + "@babel/generator": ^7.25.7 + "@babel/helper-compilation-targets": ^7.25.7 + "@babel/helper-module-transforms": ^7.25.7 + "@babel/helpers": ^7.25.7 + "@babel/parser": ^7.25.8 + "@babel/template": ^7.25.7 + "@babel/traverse": ^7.25.7 + "@babel/types": ^7.25.8 + convert-source-map: ^2.0.0 + debug: ^4.1.0 + gensync: ^1.0.0-beta.2 + json5: ^2.2.3 + semver: ^6.3.1 + checksum: 77ddf693faf6997915e7bbe16e9f21ca1c0e58bc60ace9eac51c373b21d1b46ce50de650195c136a594b0e5fcb901ca17bb57c2d20bf175b3c325211138bcfde + languageName: node + linkType: hard + "@babel/generator@npm:^7.24.7": version: 7.24.7 resolution: "@babel/generator@npm:7.24.7" @@ -91,6 +121,18 @@ __metadata: languageName: node linkType: hard +"@babel/generator@npm:^7.25.7": + version: 7.25.7 + resolution: "@babel/generator@npm:7.25.7" + dependencies: + "@babel/types": ^7.25.7 + "@jridgewell/gen-mapping": ^0.3.5 + "@jridgewell/trace-mapping": ^0.3.25 + jsesc: ^3.0.2 + checksum: f81cf9dc0191ae4411d82978114382ad6e047bfb678f9a95942bac5034a41719d88f047679f5e2f51ba7728b54ebd1cc32a10df7b556215d8a6ab9bdd4f11831 + languageName: node + linkType: hard + "@babel/helper-annotate-as-pure@npm:^7.22.5, @babel/helper-annotate-as-pure@npm:^7.24.7": version: 7.24.7 resolution: "@babel/helper-annotate-as-pure@npm:7.24.7" @@ -123,6 +165,19 @@ __metadata: languageName: node linkType: hard +"@babel/helper-compilation-targets@npm:^7.25.7": + version: 7.25.7 + resolution: "@babel/helper-compilation-targets@npm:7.25.7" + dependencies: + "@babel/compat-data": ^7.25.7 + "@babel/helper-validator-option": ^7.25.7 + browserslist: ^4.24.0 + lru-cache: ^5.1.1 + semver: ^6.3.1 + checksum: 5b57e7d4b9302c07510ad3318763c053c3d46f2d40a45c2ea0c59160ccf9061a34975ae62f36a32f15d8d03497ecd5ca43a96417c1fd83eb8c035e77a69840ef + 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+15058,19 @@ __metadata: linkType: hard "vite@npm:^5.0.0": - version: 5.3.1 - resolution: "vite@npm:5.3.1" + version: 5.4.3 + resolution: "vite@npm:5.4.3" dependencies: esbuild: ^0.21.3 fsevents: ~2.3.3 - postcss: ^8.4.38 - rollup: ^4.13.0 + postcss: ^8.4.43 + rollup: ^4.20.0 peerDependencies: "@types/node": ^18.0.0 || >=20.0.0 less: "*" lightningcss: ^1.21.0 sass: "*" + sass-embedded: "*" stylus: "*" sugarss: "*" terser: ^5.4.0 @@ -15046,6 +15086,8 @@ __metadata: optional: true sass: optional: true + sass-embedded: + optional: true stylus: optional: true sugarss: @@ -15054,13 +15096,13 @@ __metadata: optional: true bin: vite: bin/vite.js - checksum: a06d35566338794a877538ddacccccfdac30df7e260546dc0513e77191b86a13398b86a8082bb6c842013b0d3062f951f624a3f800867cbf06aef89e49767d6c + checksum: 3a28bcb09345030d2dba41b93b6b8a3aac8f19a9336c50e7e5f5e30931fbb16193cdd97814c5c0d1b5ade3b3e763b329eb881ea5cfe6e422c669d21a304f3295 languageName: node linkType: hard -"vite@npm:^5.4.3": - version: 5.4.3 - resolution: "vite@npm:5.4.3" +"vite@npm:^5.4.9": + version: 5.4.9 + resolution: "vite@npm:5.4.9" dependencies: esbuild: ^0.21.3 fsevents: ~2.3.3 @@ -15097,38 +15139,38 @@ __metadata: optional: true bin: vite: bin/vite.js - checksum: 3a28bcb09345030d2dba41b93b6b8a3aac8f19a9336c50e7e5f5e30931fbb16193cdd97814c5c0d1b5ade3b3e763b329eb881ea5cfe6e422c669d21a304f3295 + checksum: d3229e0618ece284af0478ec09c474a7a70ac369920716afdb6ebed8e320fd17a17c60afddba0d436698fe4837474cccd057c3e7d8270281b57506b78c5fbb8c languageName: node linkType: hard -"vitest@npm:^2.0.5": - version: 2.0.5 - resolution: "vitest@npm:2.0.5" - dependencies: - "@ampproject/remapping": ^2.3.0 - "@vitest/expect": 2.0.5 - "@vitest/pretty-format": ^2.0.5 - "@vitest/runner": 2.0.5 - "@vitest/snapshot": 2.0.5 - "@vitest/spy": 2.0.5 - "@vitest/utils": 2.0.5 +"vitest@npm:^2.1.3": + version: 2.1.3 + resolution: "vitest@npm:2.1.3" + dependencies: + "@vitest/expect": 2.1.3 + "@vitest/mocker": 2.1.3 + "@vitest/pretty-format": ^2.1.3 + "@vitest/runner": 2.1.3 + "@vitest/snapshot": 2.1.3 + "@vitest/spy": 2.1.3 + "@vitest/utils": 2.1.3 chai: ^5.1.1 - debug: ^4.3.5 - execa: ^8.0.1 - magic-string: ^0.30.10 + debug: ^4.3.6 + magic-string: ^0.30.11 pathe: ^1.1.2 std-env: ^3.7.0 - tinybench: ^2.8.0 + tinybench: ^2.9.0 + tinyexec: ^0.3.0 tinypool: ^1.0.0 tinyrainbow: ^1.2.0 vite: ^5.0.0 - vite-node: 2.0.5 + vite-node: 2.1.3 why-is-node-running: ^2.3.0 peerDependencies: "@edge-runtime/vm": "*" "@types/node": ^18.0.0 || >=20.0.0 - "@vitest/browser": 2.0.5 - "@vitest/ui": 2.0.5 + "@vitest/browser": 2.1.3 + "@vitest/ui": 2.1.3 happy-dom: "*" jsdom: "*" peerDependenciesMeta: @@ -15146,7 +15188,7 @@ __metadata: optional: true bin: vitest: vitest.mjs - checksum: 4709e7678d89f957d9bd8e4dd2f99734857df03e22d38d9c3986a75f608205572b73c2faaf059ed41a2dccbc5c65f6717bf66594d6459cf2e57ab175be9aebc1 + checksum: c2e7159cfeb837d16dfd03acdcaff85c3bd234f1fd6a258dbd5202455b8e04b1c9f932567396b00cfe8d6fdba61857fa5f6663874fe56bf4cd084f516da1a86d languageName: node linkType: hard @@ -15496,7 +15538,7 @@ __metadata: languageName: node linkType: hard -"ws@npm:^8.18.0": +"ws@npm:^8.18.0, ws@npm:^8.2.3": version: 8.18.0 resolution: "ws@npm:8.18.0" peerDependencies: @@ -15511,21 +15553,6 @@ __metadata: languageName: node linkType: hard -"ws@npm:^8.2.3": - version: 8.17.1 - resolution: "ws@npm:8.17.1" - peerDependencies: - bufferutil: ^4.0.1 - utf-8-validate: ">=5.0.2" - peerDependenciesMeta: - bufferutil: - optional: true - utf-8-validate: - optional: true - checksum: 442badcce1f1178ec87a0b5372ae2e9771e07c4929a3180321901f226127f252441e8689d765aa5cfba5f50ac60dd830954afc5aeae81609aefa11d3ddf5cecf - languageName: node - linkType: hard - "xhr2@npm:0.1.3": version: 0.1.3 resolution: "xhr2@npm:0.1.3" @@ -15568,16 +15595,7 @@ __metadata: languageName: node linkType: hard -"yaml@npm:^2.0.0, yaml@npm:^2.2.2": - version: 2.4.2 - resolution: "yaml@npm:2.4.2" - bin: - yaml: bin.mjs - checksum: 90dda4485de04367251face9abb5c36927c94e44078f4e958e6468a07e74e7e92f89be20fc49860b6268c51ee5a5fc79ef89197d3f874bf24ef8921cc4ba9013 - languageName: node - linkType: hard - -"yaml@npm:~2.5.0": +"yaml@npm:^2.0.0, yaml@npm:^2.2.2, yaml@npm:~2.5.0": version: 2.5.0 resolution: "yaml@npm:2.5.0" bin: diff --git a/operations/app/terraform/modules/function_app/locals.tf b/operations/app/terraform/modules/function_app/locals.tf index 15daeed6e3f..c94c8ceaca7 100644 --- a/operations/app/terraform/modules/function_app/locals.tf +++ b/operations/app/terraform/modules/function_app/locals.tf @@ -19,6 +19,7 @@ locals { "RS_OKTA_ClientId" = var.RS_OKTA_clientId "ETOR_TI_baseurl" = var.etor_ti_base_url "cdctiautomated" = var.cdctiautomated_sa + "JAVA_OPTS" = var.JAVA_OPTS # Manage client secrets via a Key Vault "CREDENTIAL_STORAGE_METHOD" = "AZURE" "CREDENTIAL_KEY_VAULT_NAME" = var.client_config_key_vault_name diff --git a/operations/app/terraform/modules/function_app/~inputs.tf b/operations/app/terraform/modules/function_app/~inputs.tf index 5b20d635fb5..2504367d17e 100644 --- a/operations/app/terraform/modules/function_app/~inputs.tf +++ b/operations/app/terraform/modules/function_app/~inputs.tf @@ -93,6 +93,7 @@ variable "etor_ti_base_url" {} variable "cdctiautomated_sa" { default = "" } +variable "JAVA_OPTS" {} variable "subnets" { description = "A set of all available subnet combinations" 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/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 8ad6e5456e2..201bbe55632 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 { @@ -36,6 +36,13 @@ resource "azurerm_storage_account" "storage_account" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } resource "azurerm_storage_queue" "storage_queue" { @@ -166,8 +173,9 @@ 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 + large_file_share_enabled = false static_website { index_document = "index.html" @@ -189,6 +197,13 @@ resource "azurerm_storage_account" "storage_public" { tags = { environment = var.environment } + + timeouts { + create = var.timeout_create + read = var.timeout_read + delete = var.timeout_delete + update = var.timeout_update + } } resource "azurerm_storage_share" "gh_locks" { @@ -209,7 +224,7 @@ 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 { @@ -244,6 +259,13 @@ resource "azurerm_storage_account" "storage_partner" { 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/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 + } } diff --git a/operations/app/terraform/modules/storage/~inputs.tf b/operations/app/terraform/modules/storage/~inputs.tf index b992fc1a84f..092cdf1acb7 100644 --- a/operations/app/terraform/modules/storage/~inputs.tf +++ b/operations/app/terraform/modules/storage/~inputs.tf @@ -58,4 +58,29 @@ variable "storage_queue_name" { description = "Default storage queue names that will be created in the storage account." type = list(string) default = ["proces"] +} + +# TF timeouts for storage operations +variable "timeout_create" { + description = "Timeout for create operations" + type = string + default = "60m" # module default 60m +} + +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 60m +} + +variable "timeout_delete" { + description = "Timeout for delete operations" + type = string + default = "60m" # module default 60m } \ No newline at end of file diff --git a/operations/app/terraform/vars/demo/locals.tf b/operations/app/terraform/vars/demo/locals.tf index f5268b611a6..52e3441efa8 100644 --- a/operations/app/terraform/vars/demo/locals.tf +++ b/operations/app/terraform/vars/demo/locals.tf @@ -17,6 +17,7 @@ locals { RS_okta_redirect_url = "https://prime-data-hub-XXXXXXX.azurefd.net/download" RS_OKTA_scope = "reportstream_dev" etor_ti_base_url = "https://cdcti-stg-api.azurewebsites.net" + JAVA_OPTS = "-Dfile.encoding=UTF-8" } key_vault = { app_config_kv_name = "pdh${local.init.environment}-appconfig${local.init.random_id}" diff --git a/operations/app/terraform/vars/demo/main.tf b/operations/app/terraform/vars/demo/main.tf index 6f4b51614e8..4894ed6fbb5 100644 --- a/operations/app/terraform/vars/demo/main.tf +++ b/operations/app/terraform/vars/demo/main.tf @@ -183,6 +183,7 @@ module "function_app" { RS_OKTA_clientId = data.azurerm_key_vault_secret.RS_OKTA_clientId.value RS_OKTA_authKey = data.azurerm_key_vault_secret.RS_OKTA_authKey.value etor_ti_base_url = local.init.etor_ti_base_url + JAVA_OPTS = local.init.JAVA_OPTS } module "front_door" { diff --git a/operations/app/terraform/vars/prod/locals.tf b/operations/app/terraform/vars/prod/locals.tf index f1e2a953eb8..a64ee7953a8 100644 --- a/operations/app/terraform/vars/prod/locals.tf +++ b/operations/app/terraform/vars/prod/locals.tf @@ -16,7 +16,7 @@ locals { storage_queue_name = ["process"] sftp_container_module = false etor_ti_base_url = "https://cdcti-prd-api.azurewebsites.net" - + JAVA_OPTS = "-Dfile.encoding=UTF-8" } key_vault = { app_config_kv_name = "pdh${local.init.environment}-appconfig" diff --git a/operations/app/terraform/vars/prod/main.tf b/operations/app/terraform/vars/prod/main.tf index 6085b0a5afc..e9637d28fd9 100644 --- a/operations/app/terraform/vars/prod/main.tf +++ b/operations/app/terraform/vars/prod/main.tf @@ -161,6 +161,7 @@ module "function_app" { RS_OKTA_clientId = data.azurerm_key_vault_secret.RS_OKTA_clientId.value RS_OKTA_authKey = data.azurerm_key_vault_secret.RS_OKTA_authKey.value etor_ti_base_url = local.init.etor_ti_base_url + JAVA_OPTS = local.init.JAVA_OPTS } module "front_door" { diff --git a/operations/app/terraform/vars/staging/locals.tf b/operations/app/terraform/vars/staging/locals.tf index b194df91ba2..47066309e34 100644 --- a/operations/app/terraform/vars/staging/locals.tf +++ b/operations/app/terraform/vars/staging/locals.tf @@ -16,6 +16,7 @@ locals { storage_queue_name = ["process", "batch", "batch-poison", "elr-fhir-convert", "process-poison", "send", "send-poison", "elr-fhir-convert", "elr-fhir-convert-poison", "elr-fhir-route", "elr-fhir-translate", "elr-fhir-translate-poison", "process-elr"] sftp_container_module = true etor_ti_base_url = "https://cdcti-stg-api.azurewebsites.net" + JAVA_OPTS = "-Dfile.encoding=UTF-8" } key_vault = { app_config_kv_name = "pdh${local.init.environment}-appconfig" diff --git a/operations/app/terraform/vars/staging/main.tf b/operations/app/terraform/vars/staging/main.tf index 2ba317c6fc0..2f83e671976 100644 --- a/operations/app/terraform/vars/staging/main.tf +++ b/operations/app/terraform/vars/staging/main.tf @@ -161,6 +161,7 @@ module "function_app" { RS_OKTA_authKey = data.azurerm_key_vault_secret.RS_OKTA_authKey.value etor_ti_base_url = local.init.etor_ti_base_url cdctiautomated_sa = data.azurerm_key_vault_secret.cdctiautomated_sa.value + JAVA_OPTS = local.init.JAVA_OPTS } module "front_door" { diff --git a/operations/app/terraform/vars/test/locals.tf b/operations/app/terraform/vars/test/locals.tf index 2ad7f5012eb..b229fad36f0 100644 --- a/operations/app/terraform/vars/test/locals.tf +++ b/operations/app/terraform/vars/test/locals.tf @@ -16,6 +16,7 @@ locals { storage_queue_name = ["process"] sftp_container_module = true etor_ti_base_url = "https://cdcti-stg-api.azurewebsites.net" + JAVA_OPTS = "-Dfile.encoding=UTF-8" } key_vault = { app_config_kv_name = "pdh${local.init.environment}-app-config" diff --git a/operations/app/terraform/vars/test/main.tf b/operations/app/terraform/vars/test/main.tf index 9ebefd9a7f1..5a3a0162a0c 100644 --- a/operations/app/terraform/vars/test/main.tf +++ b/operations/app/terraform/vars/test/main.tf @@ -164,6 +164,7 @@ module "function_app" { RS_OKTA_clientId = data.azurerm_key_vault_secret.RS_OKTA_clientId.value RS_OKTA_authKey = data.azurerm_key_vault_secret.RS_OKTA_authKey.value etor_ti_base_url = local.init.etor_ti_base_url + JAVA_OPTS = local.init.JAVA_OPTS } module "front_door" { diff --git a/prime-router/build.gradle.kts b/prime-router/build.gradle.kts index 5705ce5bd18..c8dcd983c41 100644 --- a/prime-router/build.gradle.kts +++ b/prime-router/build.gradle.kts @@ -35,7 +35,7 @@ apply(from = rootProject.file("buildSrc/shared.gradle.kts")) plugins { val kotlinVersion by System.getProperties() id("reportstream.project-conventions") - id("org.flywaydb.flyway") version "10.18.0" + id("org.flywaydb.flyway") version "10.18.2" id("nu.studer.jooq") version "9.0" id("com.github.johnrengelman.shadow") version "8.1.1" id("com.microsoft.azure.azurefunctions") version "1.16.1" @@ -75,7 +75,7 @@ val javaVersion = when (appJvmTarget) { } val ktorVersion = "2.3.12" val kotlinVersion by System.getProperties() -val jacksonVersion = "2.17.2" +val jacksonVersion = "2.18.0" jacoco.toolVersion = "0.8.12" // Local database information, first one wins: @@ -839,7 +839,7 @@ buildscript { // will need to be removed once this issue is resolved in Maven. classpath("net.minidev:json-smart:2.5.1") // as per flyway v10 docs the postgres flyway module must be on the project buildpath - classpath("org.flywaydb:flyway-database-postgresql:10.18.0") + classpath("org.flywaydb:flyway-database-postgresql:10.18.2") } } @@ -867,7 +867,7 @@ dependencies { implementation("com.azure:azure-storage-queue:12.22.0") { exclude(group = "com.azure", module = "azure-core") } - implementation("com.azure:azure-security-keyvault-secrets:4.8.6") { + implementation("com.azure:azure-security-keyvault-secrets:4.8.7") { exclude(group = "com.azure", module = "azure-core") exclude(group = "com.azure", module = "azure-core-http-netty") } @@ -897,36 +897,36 @@ dependencies { branch = "master" } } - implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.2.2") + implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.4.2") // https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-caching-caffeine - implementation("ca.uhn.hapi.fhir:hapi-fhir-caching-caffeine:7.2.2") - implementation("ca.uhn.hapi.fhir:hapi-fhir-client:7.2.2") + implementation("ca.uhn.hapi.fhir:hapi-fhir-caching-caffeine:7.4.2") + implementation("ca.uhn.hapi.fhir:hapi-fhir-client:7.4.2") // pin - implementation("ca.uhn.hapi.fhir:org.hl7.fhir.utilities:6.3.24") + implementation("ca.uhn.hapi.fhir:org.hl7.fhir.utilities:6.3.29") implementation("ca.uhn.hapi.fhir:org.hl7.fhir.r4:6.3.24") implementation("ca.uhn.hapi:hapi-base:2.5.1") implementation("ca.uhn.hapi:hapi-structures-v251:2.5.1") implementation("ca.uhn.hapi:hapi-structures-v27:2.5.1") implementation("com.googlecode.libphonenumber:libphonenumber:8.13.46") implementation("org.thymeleaf:thymeleaf:3.1.2.RELEASE") - implementation("com.sendgrid:sendgrid-java:4.10.2") + implementation("com.sendgrid:sendgrid-java:4.10.3") implementation("com.okta.jwt:okta-jwt-verifier:0.5.7") implementation("org.json:json:20240303") // DO NOT INCREMENT SSHJ to a newer version without first thoroughly testing it locally. implementation("com.hierynomus:sshj:0.38.0") implementation("com.jcraft:jsch:0.1.55") implementation("org.apache.poi:poi:5.3.0") - implementation("org.apache.commons:commons-csv:1.11.0") + implementation("org.apache.commons:commons-csv:1.12.0") implementation("org.apache.commons:commons-lang3:3.15.0") implementation("org.apache.commons:commons-text:1.12.0") implementation("commons-codec:commons-codec:1.17.1") - implementation("commons-io:commons-io:2.16.1") + implementation("commons-io:commons-io:2.17.0") implementation("org.postgresql:postgresql:42.7.4") - implementation("com.zaxxer:HikariCP:5.1.0") - implementation("org.flywaydb:flyway-core:10.18.0") - implementation("org.flywaydb:flyway-database-postgresql:10.18.0") - implementation("org.commonmark:commonmark:0.22.0") - implementation("com.google.guava:guava:33.3.0-jre") + implementation("com.zaxxer:HikariCP:6.0.0") + implementation("org.flywaydb:flyway-core:10.18.2") + implementation("org.flywaydb:flyway-database-postgresql:10.18.2") + implementation("org.commonmark:commonmark:0.23.0") + implementation("com.google.guava:guava:33.3.1-jre") implementation("com.helger.as2:as2-lib:5.1.2") implementation("org.bouncycastle:bcprov-jdk15to18:1.78.1") implementation("org.bouncycastle:bcprov-jdk18on:1.78.1") @@ -950,7 +950,7 @@ dependencies { implementation("org.apache.poi:poi:5.3.0") implementation("org.apache.poi:poi-ooxml:5.3.0") implementation("org.apache.commons:commons-compress:1.27.1") - implementation("commons-io:commons-io:2.16.1") + implementation("commons-io:commons-io:2.17.0") implementation("com.anyascii:anyascii:0.3.2") // force jsoup since skrapeit-html-parser@1.2.1+ has not updated implementation("org.jsoup:jsoup:1.18.1") @@ -978,7 +978,7 @@ dependencies { implementation("xalan:xalan:2.7.3") // validations - implementation("com.networknt:json-schema-validator:1.5.1") + implementation("com.networknt:json-schema-validator:1.5.2") implementation("io.konform:konform-jvm:0.4.0") runtimeOnly("com.okta.jwt:okta-jwt-verifier-impl:0.5.7") diff --git a/prime-router/docs/api/reports.yml b/prime-router/docs/api/reports.yml index 2a860227aa8..3212c7f4e96 100644 --- a/prime-router/docs/api/reports.yml +++ b/prime-router/docs/api/reports.yml @@ -118,6 +118,51 @@ paths: $ref: '#/components/schemas/Report' '500': description: Internal Server Error + /reports/testing/test: + post: + summary: Evaluates a message based off of the receiver settings specified. Returns any errors, filtering, or the message. + security: + - OAuth2: [ system_admin ] + parameters: + - in: query + name: receiverName + description: The name of the receiver to look for in the current environment's settings + schema: + type: string + required: true + example: full-elr + - in: query + name: organizationName + description: The name of the organization to look for the receiver in the current environment's settings + required: true + schema: + type: string + example: me-phd + - in: query + name: senderSchema + description: The path to the sender schema + required: false + schema: + type: string + example: classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml + requestBody: + description: The message to process + required: true + content: + application/json: + schema: + $ref: '#/components/schemas/Report' + responses: + '200': + description: OK + content: + application/json: + schema: + $ref: '#/components/schemas/Report' + '400': + description: Error with one or more filters or finding the receiver. + '500': + description: Internal Server Error /reports/download: get: summary: Downloads a message based on the report id 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/kotlin/azure/ActionHistory.kt b/prime-router/src/main/kotlin/azure/ActionHistory.kt index 53c139c788b..3f620279a36 100644 --- a/prime-router/src/main/kotlin/azure/ActionHistory.kt +++ b/prime-router/src/main/kotlin/azure/ActionHistory.kt @@ -448,6 +448,22 @@ class ActionHistory( } } + /** + * Allows tracking of an empty report regardless of where it is generated in the pipeline + * @param report the details of the report + */ + fun trackEmptyReport(report: Report) { + generatingEmptyReport = true + val reportFile = ReportFile() + reportFile.reportId = report.id + reportFile.schemaTopic = report.schema.topic + reportFile.schemaName = "None" + reportFile.itemCount = 0 + reportFile.bodyFormat = report.bodyFormat.toString() + reportFile.nextAction = TaskAction.none + reportsOut[reportFile.reportId] = reportFile + } + /** * Use this to record history info about a newly generated empty [report] for sending to [receiver] that * has requested an empty batch. The [event] will be batch or send. diff --git a/prime-router/src/main/kotlin/azure/ReportFunction.kt b/prime-router/src/main/kotlin/azure/ReportFunction.kt index 65c5aaed0aa..9a97ed96533 100644 --- a/prime-router/src/main/kotlin/azure/ReportFunction.kt +++ b/prime-router/src/main/kotlin/azure/ReportFunction.kt @@ -1,8 +1,10 @@ package gov.cdc.prime.router.azure import com.fasterxml.jackson.databind.ObjectMapper +import com.fasterxml.jackson.databind.SerializationFeature import com.fasterxml.jackson.databind.json.JsonMapper import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule +import com.github.ajalt.clikt.core.CliktError import com.google.common.net.HttpHeaders import com.microsoft.azure.functions.HttpMethod import com.microsoft.azure.functions.HttpRequestMessage @@ -23,7 +25,6 @@ import gov.cdc.prime.router.Sender import gov.cdc.prime.router.Sender.ProcessingType import gov.cdc.prime.router.SubmissionReceiver import gov.cdc.prime.router.UniversalPipelineReceiver -import gov.cdc.prime.router.azure.BlobAccess.Companion.defaultBlobMetadata import gov.cdc.prime.router.azure.BlobAccess.Companion.getBlobContainer import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile @@ -32,6 +33,7 @@ import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties import gov.cdc.prime.router.azure.observability.event.ReportStreamEventService import gov.cdc.prime.router.cli.PIIRemovalCommands +import gov.cdc.prime.router.cli.ProcessFhirCommands import gov.cdc.prime.router.common.AzureHttpUtils.getSenderIP import gov.cdc.prime.router.common.Environment import gov.cdc.prime.router.common.JacksonMapperUtilities @@ -43,6 +45,7 @@ import gov.cdc.prime.router.tokens.authenticationFailure import gov.cdc.prime.router.tokens.authorizationFailure import kotlinx.serialization.json.Json import org.apache.logging.log4j.kotlin.Logging +import java.io.File import java.nio.charset.StandardCharsets import java.util.UUID @@ -120,6 +123,113 @@ class ReportFunction( return HttpUtilities.unauthorizedResponse(request) } + /** + * Run a message through the fhirdata cli + * + * @see ../../../docs/api/reports.yml + */ + @FunctionName("processFhirDataRequest") + fun processFhirDataRequest( + @HttpTrigger( + name = "processFhirDataRequest", + methods = [HttpMethod.POST], + authLevel = AuthorizationLevel.ANONYMOUS, + route = "reports/testing/test" + ) request: HttpRequestMessage, + ): HttpResponseMessage { + val claims = AuthenticatedClaims.authenticate(request) + if (claims != null && claims.authorized(setOf(Scope.primeAdminScope))) { + val receiverName = request.queryParameters["receiverName"] + val organizationName = request.queryParameters["organizationName"] + val senderSchema = request.queryParameters["senderSchema"] + if (receiverName.isNullOrBlank()) { + return HttpUtilities.badRequestResponse( + request, + "The receiver name is required" + ) + } + if (organizationName.isNullOrBlank()) { + return HttpUtilities.badRequestResponse( + request, + "The organization name is required" + ) + } + if (request.body.isNullOrBlank()) { + return HttpUtilities.badRequestResponse( + request, + "A message to process must be included in the body" + ) + } + val file = File("filename.fhir") + file.createNewFile() + file.bufferedWriter().use { out -> + out.write(request.body) + } + + try { + val result = ProcessFhirCommands().processFhirDataRequest( + file, + Environment.get().envName, + receiverName, + organizationName, + senderSchema, + false + ) + file.delete() + val message = if (result.message != null) { + result.message.toString() + } else { + null + } + val bundle = if (result.bundle != null) { + result.bundle.toString() + } else { + null + } + return HttpUtilities.okResponse( + request, + ObjectMapper().configure(SerializationFeature.FAIL_ON_SELF_REFERENCES, false).writeValueAsString( + MessageOrBundleStringified( + message, + bundle, + result.senderTransformPassed, + result.senderTransformErrors, + result.senderTransformWarnings, + result.enrichmentSchemaPassed, + result.enrichmentSchemaErrors, + result.senderTransformWarnings, + result.receiverTransformPassed, + result.receiverTransformErrors, + result.receiverTransformWarnings, + result.filterErrors, + result.filtersPassed + ) + ) + ) + } catch (exception: CliktError) { + file.delete() + return HttpUtilities.badRequestResponse(request, "${exception.message}") + } + } + return HttpUtilities.unauthorizedResponse(request) + } + + class MessageOrBundleStringified( + var message: String? = null, + var bundle: String? = null, + override var senderTransformPassed: Boolean = true, + override var senderTransformErrors: MutableList = mutableListOf(), + override var senderTransformWarnings: MutableList = mutableListOf(), + override var enrichmentSchemaPassed: Boolean = true, + override var enrichmentSchemaErrors: MutableList = mutableListOf(), + override var enrichmentSchemaWarnings: MutableList = mutableListOf(), + override var receiverTransformPassed: Boolean = true, + override var receiverTransformErrors: MutableList = mutableListOf(), + override var receiverTransformWarnings: MutableList = mutableListOf(), + override var filterErrors: MutableList = mutableListOf(), + override var filtersPassed: Boolean = true, + ) : ProcessFhirCommands.MessageOrBundleParent() + /** * Moved the logic to a separate function for testing purposes */ diff --git a/prime-router/src/main/kotlin/azure/SendFunction.kt b/prime-router/src/main/kotlin/azure/SendFunction.kt index e258e641c8e..1225af6da02 100644 --- a/prime-router/src/main/kotlin/azure/SendFunction.kt +++ b/prime-router/src/main/kotlin/azure/SendFunction.kt @@ -230,8 +230,12 @@ class SendFunction( val randomSeconds = Random.nextInt(ditherRetriesInSec * -1, ditherRetriesInSec) val nextRetryTime = OffsetDateTime.now().plusSeconds(waitMinutes * 60 + randomSeconds) val nextRetryToken = RetryToken(nextRetryCount, nextRetryItems) + val submittedReportIds = workflowEngine.reportService.getRootReports(report.reportId).map { + it.reportId + } val msg = "Send Failed. Will retry sending report: $report.reportId to ${receiver.fullName}" + - " in $waitMinutes minutes and $randomSeconds seconds at $nextRetryTime" + " in $waitMinutes minutes and $randomSeconds seconds at $nextRetryTime." + + " Corresponding submitted ReportIds: $submittedReportIds" logger.warn(msg) actionHistory.setActionType(TaskAction.send_warning) actionHistory.trackActionResult(msg) diff --git a/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt b/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt index 93e268635c2..1b5865e9025 100644 --- a/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt +++ b/prime-router/src/main/kotlin/azure/observability/event/AzureEventService.kt @@ -39,27 +39,22 @@ class AzureEventServiceImpl( } } -// TODO: https://github.com/CDCgov/prime-reportstream/issues/15337 -/** - * Local storage of azure events (only used for testing) - */ -class LocalAzureEventServiceImpl( - val events: MutableList = mutableListOf(), - val reportStreamEvents: MutableMap> = mutableMapOf(), -) : AzureEventService, Logging { +class InMemoryAzureEventService : AzureEventService, Logging { + + val events: MutableList = mutableListOf() + val reportStreamEvents = mutableMapOf>() - /** - * Send event to Azure AppInsights using the Azure TelemetryClient - */ override fun trackEvent(event: AzureCustomEvent) { val name = event.javaClass.simpleName - logger.debug("Recording'$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/main/kotlin/cli/ProcessFhirCommands.kt b/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt index 43bfa4ab2e7..8cdfd6bc150 100644 --- a/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt +++ b/prime-router/src/main/kotlin/cli/ProcessFhirCommands.kt @@ -31,7 +31,6 @@ import gov.cdc.prime.router.common.Environment import gov.cdc.prime.router.common.JacksonMapperUtilities import gov.cdc.prime.router.config.validation.OrganizationValidation import gov.cdc.prime.router.fhirengine.config.HL7TranslationConfig -import gov.cdc.prime.router.fhirengine.engine.FHIRConverter import gov.cdc.prime.router.fhirengine.engine.FHIRReceiverFilter import gov.cdc.prime.router.fhirengine.engine.FHIRReceiverFilter.ReceiverFilterEvaluationResult import gov.cdc.prime.router.fhirengine.engine.encodePreserveEncodingChars @@ -49,6 +48,7 @@ import org.hl7.fhir.r4.model.Base import org.hl7.fhir.r4.model.Bundle import org.hl7.fhir.r4.model.Extension import org.hl7.fhir.r4.model.Reference +import java.io.File import java.util.UUID /** @@ -100,28 +100,28 @@ class ProcessFhirCommands : CliktCommand( /** * Name of the receiver settings to use */ - private val receiverName by option( + private val receiverNameParam by option( "--receiver-name", help = "Name of the receiver settings to use" ) /** * Name of the org settings to use */ - private val orgName by option( + private val orgNameParam by option( "--org", help = "Name of the org settings to use" ) /** * Environment that specifies where to get the receiver settings */ - private val environment by option( + private val environmentParam by option( "--receiver-setting-env", help = "Environment that specifies where to get the receiver settings" ) /** * Sender schema location */ - private val senderSchema by option("-s", "--sender-schema", help = "Sender schema location") + private val senderSchemaParam by option("-s", "--sender-schema", help = "Sender schema location") private val inputSchema by option( "--input-schema", help = "Mapping schema for input file" @@ -130,35 +130,67 @@ class ProcessFhirCommands : CliktCommand( private val hl7DiffHelper = HL7DiffHelper() override fun run() { + val messageOrBundle = + processFhirDataRequest( + inputFile, + environmentParam, + receiverNameParam, + orgNameParam, + senderSchemaParam, + true + ) + if (messageOrBundle.message != null) { + outputResult(messageOrBundle.message!!) + } else if (messageOrBundle.bundle != null) { + outputResult(fhirResult = messageOrBundle.bundle!!, ActionLogger()) + } else { + throw CliktError("No result returned.") + } + } + + fun processFhirDataRequest( + inputFile: File, + environment: String?, + receiverName: String?, + orgName: String?, + senderSchema: String?, + isCli: Boolean, + ): MessageOrBundle { // Read the contents of the file val contents = inputFile.inputStream().readBytes().toString(Charsets.UTF_8) if (contents.isBlank()) throw CliktError("File ${inputFile.absolutePath} is empty.") - val actionLogger = ActionLogger() // Check on the extension of the file for supported operations val inputFileType = inputFile.extension.uppercase() - val receiver = getReceiver() + val receiver = if (!isCli) { + getReceiver(environment, receiverName, orgName, GetMultipleSettings(), isCli) + } else { + null + } // If there is a receiver, check the filters var bundle = FhirTranscoder.decode(contents) if (receiver != null) { - val reportStreamFilters = mutableListOf() - reportStreamFilters.add(receiver.jurisdictionalFilter) - reportStreamFilters.add(receiver.qualityFilter) - reportStreamFilters.add(receiver.routingFilter) - reportStreamFilters.add(receiver.processingModeFilter) + val reportStreamFilters = mutableListOf>() + reportStreamFilters.add(Pair("Jurisdictional Filter", receiver.jurisdictionalFilter)) + reportStreamFilters.add(Pair("Quality Filter", receiver.qualityFilter)) + reportStreamFilters.add(Pair("Routing Filter", receiver.routingFilter)) + reportStreamFilters.add(Pair("Processing Mode Filter", receiver.processingModeFilter)) val validationErrors = mutableListOf() reportStreamFilters.forEach { reportStreamFilter -> - reportStreamFilter.forEach { filter -> + reportStreamFilter.second.forEach { filter -> val validation = OrganizationValidation.validateFilter(filter) if (!validation) { - validationErrors.add("Filter '$filter' is not valid.") + validationErrors.add( + "Filter of type ${reportStreamFilter.first} is not valid. " + + "Value: '$filter'" + ) } else { val result = FhirPathUtils.evaluate( CustomContext( bundle, bundle, - FHIRConverter().loadFhirPathShorthandLookupTable(), + mutableMapOf(), CustomFhirPathFunctions() ), bundle, @@ -168,7 +200,11 @@ class ProcessFhirCommands : CliktCommand( if (result.isEmpty() || (result[0].isBooleanPrimitive && result[0].primitiveValue() == "false") ) { - throw CliktError("Filter '$filter' filtered out everything, nothing to return.") + return MessageOrBundle( + filterErrors = + mutableListOf("Filter '$filter' filtered out everything, nothing to return."), + filtersPassed = false + ) } } } @@ -181,81 +217,170 @@ class ProcessFhirCommands : CliktCommand( receiver.conditionFilter.forEach { conditionFilter -> val validation = OrganizationValidation.validateFilter(conditionFilter) if (!validation) { - throw CliktError("Condition filter '$conditionFilter' is not valid.") + return MessageOrBundle( + filterErrors = + mutableListOf("Condition filter '$conditionFilter' is not valid."), + filtersPassed = false + ) } } } + var messageOrBundle = MessageOrBundle() when { // HL7 to FHIR conversion inputFileType == "HL7" && ( - outputFormat == MimeFormat.FHIR.toString() || - (receiver != null && receiver.format == MimeFormat.FHIR) - ) -> { - var fhirMessage = convertHl7ToFhir(contents, receiver).first - fhirMessage = applyEnrichmentSchemas(fhirMessage) + (isCli && outputFormat == MimeFormat.FHIR.toString()) || + (receiver != null && receiver.format == MimeFormat.FHIR) + ) -> { + val fhirMessage = convertHl7ToFhir(contents, receiver).first + val enrichmentSchemaInfo = applyEnrichmentSchemas(fhirMessage, isCli) + setEnrichmentSchemaFields(messageOrBundle, enrichmentSchemaInfo) + if (receiver != null && receiver.enrichmentSchemaNames.isNotEmpty()) { receiver.enrichmentSchemaNames.forEach { currentSchema -> - fhirMessage = FhirTransformer(currentSchema).process(fhirMessage) + val transfromer = FhirTransformer(currentSchema) + val returnedBundle = + transfromer.process(messageOrBundle.bundle!!) + setEnrichmentSchemaFields( + messageOrBundle, + transfromer.warnings, + transfromer.errors, + returnedBundle + ) } } - outputResult( - handleSenderAndReceiverTransforms(fhirMessage), actionLogger - ) + return handleSenderAndReceiverTransforms(messageOrBundle, senderSchema, isCli) } // FHIR to HL7 conversion (inputFileType == "FHIR" || inputFileType == "JSON") && ( - outputFormat == MimeFormat.HL7.toString() || - (receiver != null && (receiver.format == MimeFormat.HL7 || receiver.format == MimeFormat.HL7_BATCH)) - ) -> { - if (receiver == null) { - return outputResult(convertFhirToHl7(contents)) - } + (isCli && outputFormat == MimeFormat.HL7.toString()) || + (receiver != null && (receiver.format == MimeFormat.HL7 || receiver.format == MimeFormat.HL7_BATCH)) + ) -> { + if (receiver == null) { + return convertFhirToHl7( + jsonString = contents, + senderSchema = senderSchema, + isCli = isCli + ) + } - bundle = FhirTranscoder.decode(contents) - if (receiver.enrichmentSchemaNames.isNotEmpty()) { - receiver.enrichmentSchemaNames.forEach { currentSchema -> - bundle = FhirTransformer(currentSchema).process(bundle) - } - } - outputResult( - convertFhirToHl7( - FhirTranscoder.encode(bundle), - receiver.translation as Hl7Configuration, - receiver + bundle = FhirTranscoder.decode(contents) + messageOrBundle.bundle = bundle + if (receiver.enrichmentSchemaNames.isNotEmpty()) { + receiver.enrichmentSchemaNames.forEach { currentSchema -> + val transformer = FhirTransformer(currentSchema) + val returnedBundle = + transformer.process(bundle) + setEnrichmentSchemaFields( + messageOrBundle, + transformer.warnings, + transformer.errors, + returnedBundle ) + } + } + + messageOrBundle = convertFhirToHl7( + FhirTranscoder.encode(messageOrBundle.bundle!!), + receiver.translation as Hl7Configuration, + receiver, + senderSchema, + isCli ) } // FHIR to FHIR conversion (inputFileType == "FHIR" || inputFileType == "JSON") && ( - outputFormat == MimeFormat.FHIR.toString() || - (receiver != null && receiver.format == MimeFormat.FHIR) - ) -> { - outputResult(convertFhirToFhir(FhirTranscoder.encode(bundle), receiver), actionLogger) + (isCli && outputFormat == MimeFormat.FHIR.toString()) || + (receiver != null && receiver.format == MimeFormat.FHIR) + ) -> { + return convertFhirToFhir(FhirTranscoder.encode(bundle), receiver, senderSchema, isCli) } // HL7 to FHIR to HL7 conversion inputFileType == "HL7" && ( - outputFormat == MimeFormat.HL7.toString() || - (receiver != null && (receiver.format == MimeFormat.HL7 || receiver.format == MimeFormat.HL7_BATCH)) - ) -> { + (isCli && outputFormat == MimeFormat.HL7.toString()) || + ( + receiver != null && + (receiver.format == MimeFormat.HL7 || receiver.format == MimeFormat.HL7_BATCH) + ) + ) -> { val (bundle2, inputMessage) = convertHl7ToFhir(contents, receiver) - val output = convertFhirToHl7(FhirTranscoder.encode(bundle2)) - outputResult(output) - if (diffHl7Output != null) { - val differences = hl7DiffHelper.diffHl7(output, inputMessage) + val output = convertFhirToHl7( + jsonString = FhirTranscoder.encode(bundle2), + senderSchema = senderSchema, + isCli = isCli + ) + if (diffHl7Output != null && isCli) { + val differences = hl7DiffHelper.diffHl7(output.message!!, inputMessage) echo("-------diff output") echo("There were ${differences.size} differences between the input and output") differences.forEach { echo(it.toString()) } } + return output } else -> throw CliktError("File extension ${inputFile.extension} is not supported.") } + return messageOrBundle + } + + private fun setEnrichmentSchemaFields( + messageOrBundle: MessageOrBundle, + enrichmentSchemaFields: FhirTransformer.BundleWithMessages, + ): MessageOrBundle { + messageOrBundle.enrichmentSchemaWarnings.addAll(enrichmentSchemaFields.warnings) + messageOrBundle.enrichmentSchemaErrors.addAll(enrichmentSchemaFields.errors) + messageOrBundle.enrichmentSchemaPassed = enrichmentSchemaFields.errors.isEmpty() + messageOrBundle.bundle = enrichmentSchemaFields.bundle + return messageOrBundle + } + + private fun setEnrichmentSchemaFields( + messageOrBundle: MessageOrBundle, + warnings: MutableList, + errors: MutableList, + bundle: Bundle, + ): MessageOrBundle { + messageOrBundle.enrichmentSchemaWarnings.addAll(warnings) + messageOrBundle.enrichmentSchemaErrors.addAll(errors) + messageOrBundle.enrichmentSchemaPassed = errors.isEmpty() + messageOrBundle.bundle = bundle + return messageOrBundle } + abstract class MessageOrBundleParent( + open var senderTransformPassed: Boolean = true, + open var senderTransformErrors: MutableList = mutableListOf(), + open var senderTransformWarnings: MutableList = mutableListOf(), + open var enrichmentSchemaPassed: Boolean = true, + open var enrichmentSchemaErrors: MutableList = mutableListOf(), + open var enrichmentSchemaWarnings: MutableList = mutableListOf(), + open var receiverTransformPassed: Boolean = true, + open var receiverTransformErrors: MutableList = mutableListOf(), + open var receiverTransformWarnings: MutableList = mutableListOf(), + open var filterErrors: MutableList = mutableListOf(), + open var filtersPassed: Boolean = true, + ) + + class MessageOrBundle( + var message: Message? = null, + var bundle: Bundle? = null, + override var senderTransformPassed: Boolean = true, + override var senderTransformErrors: MutableList = mutableListOf(), + override var senderTransformWarnings: MutableList = mutableListOf(), + override var enrichmentSchemaPassed: Boolean = true, + override var enrichmentSchemaErrors: MutableList = mutableListOf(), + override var enrichmentSchemaWarnings: MutableList = mutableListOf(), + override var receiverTransformPassed: Boolean = true, + override var receiverTransformErrors: MutableList = mutableListOf(), + override var receiverTransformWarnings: MutableList = mutableListOf(), + override var filterErrors: MutableList = mutableListOf(), + override var filtersPassed: Boolean = true, + ) : MessageOrBundleParent() + private fun applyConditionFilter(receiver: Receiver, bundle: Bundle): Bundle { val trackingId = if (bundle.id != null) { bundle.id @@ -276,32 +401,41 @@ class ProcessFhirCommands : CliktCommand( } } - private fun getReceiver(): Receiver? { + fun getReceiver( + environment: String?, + receiverName: String?, + orgName: String?, + getMultipleSettings: GetMultipleSettings = GetMultipleSettings(), + isCli: Boolean, + ): Receiver? { if (!environment.isNullOrBlank() && !receiverName.isNullOrBlank() && !orgName.isNullOrBlank()) { - if (!outputFormat.isNullOrBlank()) { + if (isCli && !outputFormat.isNullOrBlank()) { throw CliktError( "Please specify either a receiver OR an output format. Not both." ) } - val foundEnvironment = Environment.get(environment!!) + val foundEnvironment = Environment.get(environment) val accessToken = OktaCommand.fetchAccessToken(foundEnvironment.oktaApp) ?: abort( "Invalid access token. " + "Run ./prime login to fetch/refresh your access " + "token for the $foundEnvironment environment." ) - val organizations = GetMultipleSettings().getAll( + val organizations = getMultipleSettings.getAll( environment = foundEnvironment, accessToken = accessToken, specificOrg = orgName, exactMatch = true ) + if (organizations.isEmpty()) { + return null + } val receivers = organizations[0].receivers.filter { receiver -> receiver.name == receiverName } if (receivers.isNotEmpty()) { return receivers[0] } - } else if (outputFormat.isNullOrBlank()) { + } else if (isCli && outputFormat.isNullOrBlank()) { throw CliktError( "Output format is required if the environment, receiver, and org " + "are not specified. " @@ -327,25 +461,30 @@ class ProcessFhirCommands : CliktCommand( jsonString: String, hl7Configuration: Hl7Configuration = defaultHL7Configuration, receiver: Receiver? = null, - ): Message { - var fhirMessage = FhirTranscoder.decode(jsonString) - fhirMessage = applyEnrichmentSchemas(fhirMessage) + senderSchema: String?, + isCli: Boolean, + ): MessageOrBundle { + val fhirMessage = FhirTranscoder.decode(jsonString) + val enrichmentSchemaMessages = applyEnrichmentSchemas(fhirMessage, isCli) + val errors: MutableList = mutableListOf() + val warnings: MutableList = mutableListOf() return when { - receiverSchema == null && (receiver == null || receiver.schemaName.isBlank()) -> + (isCli && receiverSchema == null) && (receiver == null || (isCli && receiver.schemaName.isBlank())) -> // Receiver schema required because if it's coming out as HL7, it would be getting any transform info // for that from a receiver schema. throw CliktError("You must specify a receiver schema using --receiver-schema.") - receiverSchema != null -> { - var bundle = applySenderTransforms(fhirMessage) + isCli && receiverSchema != null -> { + val senderTransformMessages = applySenderTransforms(enrichmentSchemaMessages.bundle, senderSchema) val stamper = ConditionStamper(LookupTableConditionMapper(Metadata.getInstance())) - bundle.getObservations().forEach { observation -> + senderTransformMessages.bundle.getObservations().forEach { observation -> stamper.stampObservation(observation) } if (receiver != null) { - bundle = applyConditionFilter(receiver, bundle) + senderTransformMessages.bundle = applyConditionFilter(receiver, senderTransformMessages.bundle) } - FhirToHl7Converter( + + val message = FhirToHl7Converter( receiverSchema!!, BlobAccess.BlobContainerMetadata.build("metadata", Environment.get().storageEnvVar), context = FhirToHl7Context( @@ -355,13 +494,24 @@ class ProcessFhirCommands : CliktCommand( receiver ), translationFunctions = CustomTranslationFunctions(), - ) - ).process(bundle) + ), + warnings = warnings, + errors = errors + ).process(senderTransformMessages.bundle) + val messageOrBundle = MessageOrBundle() + messageOrBundle.senderTransformPassed = senderTransformMessages.errors.isEmpty() + messageOrBundle.senderTransformWarnings = senderTransformMessages.warnings + messageOrBundle.senderTransformErrors = senderTransformMessages.errors + messageOrBundle.receiverTransformPassed = errors.isEmpty() + messageOrBundle.receiverTransformErrors = errors + messageOrBundle.receiverTransformWarnings = warnings + messageOrBundle.message = message + messageOrBundle } receiver != null && receiver.schemaName.isNotBlank() -> { - var bundle = applySenderTransforms(fhirMessage) - bundle = applyConditionFilter(receiver, bundle) - FhirToHl7Converter( + val senderTransformMessages = applySenderTransforms(fhirMessage, senderSchema) + val bundle = applyConditionFilter(receiver, senderTransformMessages.bundle) + val message = FhirToHl7Converter( receiver.schemaName, BlobAccess.BlobContainerMetadata.build("metadata", Environment.get().storageEnvVar), context = FhirToHl7Context( @@ -371,11 +521,32 @@ class ProcessFhirCommands : CliktCommand( receiver ), translationFunctions = CustomTranslationFunctions(), - ) + ), + warnings = warnings, + errors = errors ).process(bundle) + val messageOrBundle = MessageOrBundle() + messageOrBundle.senderTransformPassed = senderTransformMessages.errors.isEmpty() + messageOrBundle.senderTransformWarnings = senderTransformMessages.warnings + messageOrBundle.senderTransformErrors = senderTransformMessages.errors + messageOrBundle.receiverTransformPassed = errors.isEmpty() + messageOrBundle.receiverTransformErrors = errors + messageOrBundle.receiverTransformWarnings = warnings + messageOrBundle.message = message + messageOrBundle } else -> { - throw CliktError("Error state reached when trying to apply the transforms.") + if (isCli) { + throw CliktError("Error state reached when trying to apply the transforms.") + } else { + MessageOrBundle( + senderTransformErrors = + mutableListOf("Error state reached when trying to apply the transforms."), + receiverTransformErrors = mutableListOf( + "Error state reached when trying to apply the transforms." + ) + ) + } } } } @@ -383,27 +554,51 @@ class ProcessFhirCommands : CliktCommand( /** * convert an FHIR message to FHIR message */ - private fun convertFhirToFhir(jsonString: String, receiver: Receiver?): Bundle { + private fun convertFhirToFhir( + jsonString: String, + receiver: Receiver?, + senderSchema: String?, + isCli: Boolean, + ): MessageOrBundle { var fhirMessage = FhirTranscoder.decode(jsonString) val stamper = ConditionStamper(LookupTableConditionMapper(Metadata.getInstance())) fhirMessage.getObservations().forEach { observation -> stamper.stampObservation(observation) } + + val messageOrBundle = MessageOrBundle() if (receiver != null) { fhirMessage = applyConditionFilter(receiver, fhirMessage) if (receiver.enrichmentSchemaNames.isNotEmpty()) { receiver.enrichmentSchemaNames.forEach { currentSchema -> - fhirMessage = FhirTransformer(currentSchema).process(fhirMessage) + val transformer = FhirTransformer(currentSchema) + val bundle = transformer.process(fhirMessage) + setEnrichmentSchemaFields( + messageOrBundle, + transformer.warnings, + transformer.errors, + bundle + ) } } } - fhirMessage = applyEnrichmentSchemas(fhirMessage) - if (receiverSchema == null && senderSchema == null) { + setEnrichmentSchemaFields(messageOrBundle, applyEnrichmentSchemas(fhirMessage, isCli)) + if (( + (isCli && receiverSchema == null) || + (!isCli && (receiver == null || receiver.schemaName.isBlank())) + ) && senderSchema == null + ) { // Must have at least one schema or else why are you doing this throw CliktError("You must specify a schema.") } else { - return handleSenderAndReceiverTransforms(fhirMessage) + handleSenderAndReceiverTransforms( + messageOrBundle = messageOrBundle, + senderSchema = senderSchema, + isCli = isCli + ) } + + return messageOrBundle } /** @@ -455,13 +650,15 @@ class ProcessFhirCommands : CliktCommand( * @throws CliktError if senderSchema is present, but unable to be read. * @return If senderSchema is present, apply it, otherwise just return the input bundle. */ - private fun applySenderTransforms(bundle: Bundle): Bundle { + private fun applySenderTransforms(bundle: Bundle, senderSchema: String?): FhirTransformer.BundleWithMessages { return when { senderSchema != null -> { - FhirTransformer(senderSchema!!).process(bundle) + val transformer = FhirTransformer(senderSchema) + val returnedBundle = transformer.process(bundle) + FhirTransformer.BundleWithMessages(returnedBundle, transformer.warnings, transformer.errors) } - else -> bundle + else -> FhirTransformer.BundleWithMessages(bundle = bundle, mutableListOf(), mutableListOf()) } } @@ -470,38 +667,65 @@ class ProcessFhirCommands : CliktCommand( * @throws CliktError if enrichmentSchemaName is present, but unable to be read. * @return If receiverSchema is present, apply it, otherwise just return the input bundle. */ - private fun applyReceiverEnrichmentAndTransforms(bundle: Bundle): Bundle { - val enrichedBundle = applyEnrichmentSchemas(bundle) - - return when { - receiverSchema != null -> { - FhirTransformer( - receiverSchema!! - ).process(enrichedBundle) - } - - else -> enrichedBundle + private fun applyReceiverEnrichmentAndTransforms(bundle: Bundle, isCli: Boolean): MessageOrBundle { + val messageOrBundle = MessageOrBundle() + setEnrichmentSchemaFields(messageOrBundle, applyEnrichmentSchemas(bundle, isCli)) + + if (isCli && receiverSchema != null) { + val transformer = FhirTransformer(receiverSchema!!) + val returnedBundle = transformer.process(messageOrBundle.bundle!!) + messageOrBundle.receiverTransformWarnings.addAll(transformer.warnings) + messageOrBundle.receiverTransformErrors.addAll(transformer.errors) + messageOrBundle.receiverTransformPassed = transformer.errors.isEmpty() + messageOrBundle.bundle = returnedBundle } + + return messageOrBundle } /** * Applies the enrichment schema to the bundle. */ - private fun applyEnrichmentSchemas(bundle: Bundle): Bundle { - if (!enrichmentSchemaNames.isNullOrEmpty()) { + private fun applyEnrichmentSchemas(bundle: Bundle, isCli: Boolean): FhirTransformer.BundleWithMessages { + var enrichedbundle = bundle + val warnings = mutableListOf() + val errors = mutableListOf() + if (isCli && !enrichmentSchemaNames.isNullOrEmpty()) { enrichmentSchemaNames!!.split(",").forEach { currentEnrichmentSchemaName -> - FhirTransformer(currentEnrichmentSchemaName).process(bundle) + val transformer = FhirTransformer(currentEnrichmentSchemaName) + val returnedBundle = transformer.process( + enrichedbundle + ) + errors.addAll(transformer.errors) + warnings.addAll(transformer.warnings) + enrichedbundle = returnedBundle } } - return bundle + return FhirTransformer.BundleWithMessages(enrichedbundle, warnings, errors) } /** * Apply both sender and receiver schemas if present. * @return the FHIR bundle after having sender and/or receiver schemas applied to it. */ - private fun handleSenderAndReceiverTransforms(bundle: Bundle): Bundle { - return applyReceiverEnrichmentAndTransforms(applySenderTransforms(bundle)) + private fun handleSenderAndReceiverTransforms( + messageOrBundle: MessageOrBundle, + senderSchema: String?, + isCli: Boolean, + ): MessageOrBundle { + val senderTransformInfo = applySenderTransforms(messageOrBundle.bundle!!, senderSchema) + val receiverTransformInfo = applyReceiverEnrichmentAndTransforms(senderTransformInfo.bundle, isCli) + messageOrBundle.bundle = receiverTransformInfo.bundle + messageOrBundle.senderTransformWarnings.addAll(senderTransformInfo.warnings) + messageOrBundle.senderTransformErrors.addAll(senderTransformInfo.errors) + messageOrBundle.senderTransformPassed = senderTransformInfo.errors.isEmpty() + messageOrBundle.receiverTransformErrors.addAll(receiverTransformInfo.receiverTransformErrors) + messageOrBundle.receiverTransformWarnings.addAll(receiverTransformInfo.receiverTransformWarnings) + messageOrBundle.receiverTransformPassed = receiverTransformInfo.receiverTransformPassed && + messageOrBundle.receiverTransformPassed + messageOrBundle.enrichmentSchemaPassed + + return messageOrBundle } /** diff --git a/prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt b/prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt index a831daa3b7d..46565172885 100644 --- a/prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt +++ b/prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt @@ -33,7 +33,6 @@ import gov.cdc.prime.router.azure.LookupTableConditionMapper import gov.cdc.prime.router.azure.ProcessEvent import gov.cdc.prime.router.azure.db.Tables import gov.cdc.prime.router.azure.db.enums.TaskAction -import gov.cdc.prime.router.azure.db.tables.pojos.ItemLineage import gov.cdc.prime.router.azure.observability.bundleDigest.BundleDigestExtractor import gov.cdc.prime.router.azure.observability.bundleDigest.FhirPathBundleDigestLabResultExtractorStrategy import gov.cdc.prime.router.azure.observability.context.MDCUtils @@ -277,41 +276,15 @@ class FHIRConverter( }.collect(Collectors.toList()).filterNotNull() } } else { - val nextEvent = ProcessEvent( - Event.EventAction.NONE, - queueMessage.reportId, - Options.None, - emptyMap(), - emptyList() - ) - - // TODO: https://github.com/CDCgov/prime-reportstream/issues/15223 val report = Report( - MimeFormat.FHIR, + format, emptyList(), - 1, + 0, metadata = this.metadata, topic = queueMessage.topic, nextAction = TaskAction.none ) - - // create item lineage - report.itemLineages = listOf( - ItemLineage( - null, - queueMessage.reportId, - 1, - report.id, - 1, - null, - null, - null, - report.getItemHashForRow(1) - ) - ) - - // ensure tracking is set - actionHistory.trackCreatedReport(nextEvent, report) + actionHistory.trackEmptyReport(report) reportEventService.sendReportProcessingError( ReportStreamEventName.REPORT_NOT_PROCESSABLE, report, diff --git a/prime-router/src/main/kotlin/fhirengine/translation/hl7/ConfigSchemaProcessor.kt b/prime-router/src/main/kotlin/fhirengine/translation/hl7/ConfigSchemaProcessor.kt index 0aed4333f42..1d744d91adf 100644 --- a/prime-router/src/main/kotlin/fhirengine/translation/hl7/ConfigSchemaProcessor.kt +++ b/prime-router/src/main/kotlin/fhirengine/translation/hl7/ConfigSchemaProcessor.kt @@ -16,6 +16,8 @@ abstract class ConfigSchemaProcessor< SchemaElement : ConfigSchemaElement, >( val schema: Schema, + val errors: MutableList, + val warnings: MutableList, ) : Logging { @@ -40,7 +42,9 @@ abstract class ConfigSchemaProcessor< * @property input the value to apply the schema to * @return The value after applying the schema to [input] */ - abstract fun process(input: Original): Converted + abstract fun process( + input: Original, + ): Converted /** * Get the first valid value from the list of values specified in the schema for a given [element] using diff --git a/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirToHl7Converter.kt b/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirToHl7Converter.kt index 56c10594e2f..8ddb085e4c5 100644 --- a/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirToHl7Converter.kt +++ b/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirToHl7Converter.kt @@ -38,7 +38,13 @@ class FhirToHl7Converter( // the constant substitutor is not thread safe, so we need one instance per converter instead of using a shared copy private val constantSubstitutor: ConstantSubstitutor = ConstantSubstitutor(), private val context: FhirToHl7Context? = null, -) : ConfigSchemaProcessor(schemaRef), Logging { + warnings: MutableList, + errors: MutableList, +) : ConfigSchemaProcessor( + schemaRef, + warnings, errors +), +Logging { /** * Convert a FHIR bundle to an HL7 message using the [schema] in the [schemaFolder] location to perform the conversion. * The converter will error out if [strict] is set to true and there is an error during the conversion. If [strict] @@ -53,11 +59,15 @@ class FhirToHl7Converter( terser: Terser? = null, context: FhirToHl7Context? = null, blobConnectionInfo: BlobAccess.BlobContainerMetadata, + warnings: MutableList = mutableListOf(), + errors: MutableList = mutableListOf(), ) : this( schemaRef = converterSchemaFromFile(schema, blobConnectionInfo), strict = strict, terser = terser, - context = context + context = context, + warnings = warnings, + errors = errors ) constructor( @@ -66,6 +76,8 @@ class FhirToHl7Converter( strict: Boolean = false, terser: Terser? = null, context: FhirToHl7Context? = null, + warnings: MutableList = mutableListOf(), + errors: MutableList = mutableListOf(), ) : this( ConfigSchemaReader.fromFile( schemaUri, @@ -74,7 +86,10 @@ class FhirToHl7Converter( ), strict = strict, terser = terser, - context = context + context = context, + warnings = warnings, + errors = errors + ) /** @@ -87,7 +102,13 @@ class FhirToHl7Converter( val message = HL7Utils.getMessageInstance(schemaRef.hl7Class!!) terser = Terser(message) - processSchema(schemaRef, input, input) + try { + processSchema(schemaRef, input, input) + } catch (e: Exception) { + if (e.message != null) { + errors.add(e.message!!) + } + } return message } diff --git a/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirTransformer.kt b/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirTransformer.kt index af338c1b338..a206b0262c4 100644 --- a/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirTransformer.kt +++ b/prime-router/src/main/kotlin/fhirengine/translation/hl7/FhirTransformer.kt @@ -24,7 +24,14 @@ import org.hl7.fhir.r4.model.Property */ class FhirTransformer( private val schemaRef: FhirTransformSchema, -) : ConfigSchemaProcessor(schemaRef) { + errors: MutableList = mutableListOf(), + warnings: MutableList = mutableListOf(), +) : ConfigSchemaProcessor< + Bundle, + Bundle, + FhirTransformSchema, + FhirTransformSchemaElement + >(schemaRef, errors, warnings) { private val extensionRegex = """^extension\(["'](?[^'"]+)["']\)""".toRegex() private val valueXRegex = Regex("""value[A-Z][a-z]*""") private val indexRegex = Regex("""(?.*)\[%?(?[0-9A-Za-z]*)\]""") @@ -40,6 +47,8 @@ class FhirTransformer( ), ) : this( schemaRef = fhirTransformSchemaFromFile(schema, blobConnectionInfo), + mutableListOf(), + mutableListOf(), ) /** @@ -51,6 +60,12 @@ class FhirTransformer( return input } + class BundleWithMessages( + var bundle: Bundle, + val warnings: MutableList, + val errors: MutableList, + ) + override fun checkForEquality(converted: Bundle, expectedOutput: Bundle): Boolean { return converted.equalsDeep(expectedOutput) } @@ -107,6 +122,7 @@ class FhirTransformer( debugMsg += "resource: NONE" } + val warnings = mutableListOf() val eligibleFocusResources = focusResources.filter { canEvaluate(element, bundle, it, focusResource, elementContext) } when (element.action) { @@ -141,6 +157,10 @@ class FhirTransformer( "Element ${element.name} is updating a bundle property," + " but did not specify a value or function" ) + warnings.add( + "Element ${element.name} is updating a bundle property, " + + "but did not specify a value" + ) } debugMsg += "condition: true, resourceType: ${singleFocusResource.fhirType()}, " + "value: $value" diff --git a/prime-router/src/main/kotlin/history/DeliveryHistory.kt b/prime-router/src/main/kotlin/history/DeliveryHistory.kt index f5778d5f5b0..d90227fc436 100644 --- a/prime-router/src/main/kotlin/history/DeliveryHistory.kt +++ b/prime-router/src/main/kotlin/history/DeliveryHistory.kt @@ -7,6 +7,8 @@ import com.fasterxml.jackson.annotation.JsonProperty import com.fasterxml.jackson.annotation.JsonPropertyOrder import gov.cdc.prime.router.Receiver import gov.cdc.prime.router.Topic +import gov.cdc.prime.router.azure.db.tables.pojos.Action +import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile import java.time.OffsetDateTime /** @@ -65,6 +67,28 @@ class DeliveryHistory( schema_topic, itemCount ) { + + companion object { + fun createDeliveryHistoryFromReportAndAction( + reportFile: ReportFile, + action: Action, + ): DeliveryHistory { + return DeliveryHistory( + actionId = action.actionId, + createdAt = action.createdAt, + receivingOrg = reportFile.receivingOrg, + receivingOrgSvc = reportFile.receivingOrgSvc, + externalName = action.externalName, + reportId = reportFile.reportId.toString(), + schema_topic = reportFile.schemaTopic, + itemCount = reportFile.itemCount, + bodyUrl = reportFile.bodyUrl, + schemaName = reportFile.schemaName, + bodyFormat = reportFile.bodyFormat + ) + } + } + @JsonIgnore private val DAYS_TO_SHOW = 30L diff --git a/prime-router/src/main/kotlin/history/SubmissionHistory.kt b/prime-router/src/main/kotlin/history/SubmissionHistory.kt index 15f7af3aaee..3b287cb908b 100644 --- a/prime-router/src/main/kotlin/history/SubmissionHistory.kt +++ b/prime-router/src/main/kotlin/history/SubmissionHistory.kt @@ -182,6 +182,12 @@ class DetailedSubmissionHistory( @JsonIgnore var nextActionScheduled = false + /** + * Flag to check if there's a next action for the newest report in this submission + */ + @JsonIgnore + var hasNextAction = false + /** * The step in the delivery process for a submission * Supported values: @@ -297,17 +303,24 @@ class DetailedSubmissionHistory( // if there is ANY action scheduled on this submission history, ensure this flag is true if (report.nextActionAt != null) nextActionScheduled = true } + val sortedReports = reports.sortedBy { it.createdAt } destinations.forEach { destination -> - val reportsForDestination = reports.filter { + val reportsForDestination = sortedReports.filter { destination.organizationId == it.receivingOrg && destination.service == it.receivingOrgSvc - }.sortedBy { it.createdAt } - val latestAction = reportsForDestination.first().nextAction + } + val latestAction = reportsForDestination.last().nextAction val reportsGroupedByLatestAction = reportsForDestination.groupBy { it.nextAction } val mostRecentReportsForDestination = reportsGroupedByLatestAction[latestAction] ?: emptyList() destination.itemCount = mostRecentReportsForDestination.sumOf { it.itemCount } destination.itemCountBeforeQualFilter = mostRecentReportsForDestination.sumOf { it.itemCountBeforeQualFilter ?: 0 } } + if (destinations.isEmpty() && + sortedReports.isNotEmpty() && + sortedReports.last().nextAction != TaskAction.none + ) { + hasNextAction = true + } errors.addAll(consolidateLogs(ActionLogLevel.error)) warnings.addAll(consolidateLogs(ActionLogLevel.warning)) } @@ -384,7 +397,7 @@ class DetailedSubmissionHistory( * the receivers. */ return if ( - reports.size > 1 + reports.size > 1 && !hasNextAction ) { Status.NOT_DELIVERING } else { diff --git a/prime-router/src/main/kotlin/history/azure/DeliveryFacade.kt b/prime-router/src/main/kotlin/history/azure/DeliveryFacade.kt index 3b8e11bbf94..17421529b50 100644 --- a/prime-router/src/main/kotlin/history/azure/DeliveryFacade.kt +++ b/prime-router/src/main/kotlin/history/azure/DeliveryFacade.kt @@ -19,7 +19,7 @@ import java.util.* */ class DeliveryFacade( private val dbDeliveryAccess: DatabaseDeliveryAccess = DatabaseDeliveryAccess(), - dbAccess: DatabaseAccess = BaseEngine.databaseAccessSingleton, + private val dbAccess: DatabaseAccess = BaseEngine.databaseAccessSingleton, val reportService: ReportService = ReportService(), ) : ReportFileFacade( dbAccess @@ -91,17 +91,34 @@ class DeliveryFacade( /** * Get expanded details for a single report * + * @param id either a report id (UUID) or action id (Long) * @param deliveryId id for the delivery being used * @return Report details */ fun findDetailedDeliveryHistory( + id: String, deliveryId: Long, ): DeliveryHistory? { - val deliveryHistory = dbDeliveryAccess.fetchAction( - deliveryId, - orgName = null, - DeliveryHistory::class.java - ) + // This functionality is handling the fact that the calling function supports loading the history either + // by the action id or report id + val reportFileId = try { + UUID.fromString(id) + } catch (ex: IllegalArgumentException) { + null + } + + val deliveryHistory = if (reportFileId != null) { + val action = dbAccess.fetchAction(deliveryId) + val reportFile = dbAccess.fetchReportFile(reportFileId) + DeliveryHistory.createDeliveryHistoryFromReportAndAction(reportFile, action!!) + } else { + dbDeliveryAccess.fetchAction( + deliveryId, + orgName = null, + DeliveryHistory::class.java + ) + } + val reportId = deliveryHistory?.reportId if (reportId != null) { val roots = reportService.getRootReports(UUID.fromString(reportId)) diff --git a/prime-router/src/main/kotlin/history/azure/DeliveryFunction.kt b/prime-router/src/main/kotlin/history/azure/DeliveryFunction.kt index 71fd3deaa46..3a8c9c7065e 100644 --- a/prime-router/src/main/kotlin/history/azure/DeliveryFunction.kt +++ b/prime-router/src/main/kotlin/history/azure/DeliveryFunction.kt @@ -167,7 +167,7 @@ class DeliveryFunction( * @return */ override fun singleDetailedHistory(id: String, txn: DataAccessTransaction, action: Action): DeliveryHistory? { - return deliveryFacade.findDetailedDeliveryHistory(action.actionId) + return deliveryFacade.findDetailedDeliveryHistory(id, action.actionId) } @FunctionName("getDeliveriesV1") 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/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/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/test/kotlin/azure/ReportFunctionTests.kt b/prime-router/src/test/kotlin/azure/ReportFunctionTests.kt index c431198cd5f..68b98a739c9 100644 --- a/prime-router/src/test/kotlin/azure/ReportFunctionTests.kt +++ b/prime-router/src/test/kotlin/azure/ReportFunctionTests.kt @@ -11,6 +11,7 @@ import com.azure.storage.blob.models.BlobItemProperties import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.json.JsonMapper import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule +import com.github.ajalt.clikt.core.CliktError import com.google.common.net.HttpHeaders import com.microsoft.azure.functions.HttpStatus import gov.cdc.prime.router.ActionLog @@ -20,11 +21,14 @@ import gov.cdc.prime.router.CustomerStatus import gov.cdc.prime.router.DeepOrganization import gov.cdc.prime.router.Element import gov.cdc.prime.router.FileSettings +import gov.cdc.prime.router.Hl7Configuration import gov.cdc.prime.router.Metadata import gov.cdc.prime.router.MimeFormat import gov.cdc.prime.router.Organization import gov.cdc.prime.router.Receiver import gov.cdc.prime.router.Report +import gov.cdc.prime.router.ReportStreamFilter +import gov.cdc.prime.router.ReportStreamFilters import gov.cdc.prime.router.Schema import gov.cdc.prime.router.Sender import gov.cdc.prime.router.SettingsProvider @@ -35,7 +39,9 @@ import gov.cdc.prime.router.UniversalPipelineSender import gov.cdc.prime.router.azure.BlobAccess.BlobContainerMetadata import gov.cdc.prime.router.azure.db.enums.TaskAction import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile +import gov.cdc.prime.router.cli.GetMultipleSettings import gov.cdc.prime.router.cli.PIIRemovalCommands +import gov.cdc.prime.router.cli.ProcessFhirCommands import gov.cdc.prime.router.history.DetailedSubmissionHistory import gov.cdc.prime.router.history.azure.SubmissionsFacade import gov.cdc.prime.router.serializers.Hl7Serializer @@ -57,6 +63,7 @@ import org.jooq.tools.jdbc.MockResult import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Test import org.junit.jupiter.api.assertThrows +import java.io.File import java.time.OffsetDateTime import java.util.UUID @@ -979,4 +986,114 @@ class ReportFunctionTests { assert(result.status.equals(HttpStatus.BAD_REQUEST)) } + + @Test + fun `processFhirDataRequest blank file`() { + val file = File("filename.txt") + file.createNewFile() + assertThrows { + ProcessFhirCommands().processFhirDataRequest( + file, + "local", + "full-elr", + "me-phd", + "classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml", + false + ) + } + file.delete() + } + + @Test + fun `processFhirDataRequest no environment, receiver name, or org name and output format blank`() { + val file = File("filename.txt") + file.createNewFile() + assertThrows { + ProcessFhirCommands().processFhirDataRequest( + file, + "", + "", + "", + "classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml", + false + ) + } + file.delete() + } + + @Suppress("ktlint:standard:max-line-length") + val jurisdictionalFilter: ReportStreamFilter = + listOf("(Bundle.entry.resource.ofType(ServiceRequest)[0].requester.resolve().organization.resolve().address.state = 'ME') or (Bundle.entry.resource.ofType(Patient).address.state = 'ME')") + val qualityFilter: ReportStreamFilter = listOf("Bundle.entry.resource.ofType(MessageHeader).id.exists()") + + @Suppress("ktlint:standard:max-line-length") + val conditionFilter: ReportStreamFilter = + listOf("%resource.where(interpretation.coding.code = 'A').code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('840539006'|'895448002')).exists()") + val filters = listOf(jurisdictionalFilter, qualityFilter, conditionFilter) + val organization = Organization( + "me-phd", + "This is my description", + Organization.Jurisdiction.STATE, + "ME", + "Cumberland", + listOf( + ReportStreamFilters( + Topic.FULL_ELR, + jurisdictionalFilter, + qualityFilter, + null, + null, + conditionFilter, + null + ) + ) + ) + val sender = UniversalPipelineSender( + "full-elr", + "me-phd", + MimeFormat.HL7, + CustomerStatus.ACTIVE, + "classpath:/metadata/hl7_mapping/receivers/STLTs/ME/ME-receiver-transform.yml", + Sender.ProcessingType.async, + true, + Sender.SenderType.facility, + Sender.PrimarySubmissionMethod.manual, + Topic.FULL_ELR + ) + val receiver = Receiver( + "full-elr", + "me-phd", + Topic.FULL_ELR, + CustomerStatus.ACTIVE, + Hl7Configuration( + schemaName = "classpath:/metadata/hl7_mapping/receivers/STLTs/ME/ME-receiver-transform.yml", + useTestProcessingMode = true, + useBatchHeaders = true, + messageProfileId = "", + receivingApplicationName = "", + receivingFacilityOID = "", + receivingFacilityName = "", + receivingApplicationOID = "", + receivingOrganization = "" + ), + jurisdictionalFilter, + qualityFilter + ) + + @Test + fun getReceiver() { + val file = File("filename.txt") + file.createNewFile() + val getMultipleSettings = mockkClass(GetMultipleSettings::class) + every { getMultipleSettings.getAll(any(), any(), "me-phd", true) } returns + listOf(DeepOrganization(organization, listOf(sender), listOf(receiver))) + val receiverReturned = ProcessFhirCommands().getReceiver( + "local", + "full-elr", + "me-phd", + getMultipleSettings, + false + ) + assert(receiverReturned!!.name == receiver.name) + } } \ 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/common/ReportNodeBuilder.kt b/prime-router/src/test/kotlin/common/ReportNodeBuilder.kt index 7dfa4555e90..616773f1e6d 100644 --- a/prime-router/src/test/kotlin/common/ReportNodeBuilder.kt +++ b/prime-router/src/test/kotlin/common/ReportNodeBuilder.kt @@ -25,6 +25,7 @@ class ReportGraphBuilder { private lateinit var theTopic: Topic private lateinit var theFormat: MimeFormat private lateinit var theSender: Sender + private var theNextAction: TaskAction? = null fun topic(topic: Topic) { this.theTopic = topic @@ -38,6 +39,10 @@ class ReportGraphBuilder { this.theSender = sender } + fun nextAction(nextAction: TaskAction) { + this.theNextAction = nextAction + } + fun submission(initializer: ReportNodeBuilder.() -> Unit) { this.theSubmission = ReportNodeBuilder().apply(initializer) } @@ -80,7 +85,8 @@ class ReportGraphBuilder { .setItemCount(theSubmission.theItemCount) .setExternalName("test-external-name") .setBodyUrl(theSubmission.theReportBlobUrl) - .setNextAction(theSubmission.reportGraphNodes.firstOrNull()?.theAction) + .setNextAction(theNextAction ?: theSubmission.reportGraphNodes.firstOrNull()?.theAction) + .setCreatedAt(OffsetDateTime.now()) dbAccess.insertReportFile( reportFile, txn, action ) @@ -130,7 +136,8 @@ class ReportGraphBuilder { .setExternalName("test-external-name") .setBodyUrl(node.theReportBlobUrl) .setTransportResult(node.theTransportResult) - .setNextAction(node.reportGraphNodes.firstOrNull()?.theAction) + .setNextAction(node.theNextAction ?: node.reportGraphNodes.firstOrNull()?.theAction) + .setCreatedAt(graph.node.createdAt.plusMinutes(1)) if (node.receiver != null) { childReportFile.setReceivingOrg(node.receiver!!.organizationName) @@ -189,6 +196,7 @@ class ReportNodeBuilder { } } lateinit var theAction: TaskAction + var theNextAction: TaskAction? = null var theReportBlobUrl: String = UUID.randomUUID().toString() var theItemCount: Int = 1 val reportGraphNodes: MutableList = mutableListOf() @@ -204,6 +212,10 @@ class ReportNodeBuilder { this.theAction = action } + fun nextAction(nextAction: TaskAction) { + this.theNextAction = nextAction + } + fun reportBlobUrl(reportBlobUrl: String) { this.theReportBlobUrl = reportBlobUrl } diff --git a/prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt b/prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt index 7a40dd6272b..f158a08993b 100644 --- a/prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt +++ b/prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt @@ -127,6 +127,24 @@ OBX|4|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69||N^No^HL70136| OBX|5|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST SPM|1|0cba76f5-35e0-4a28-803a-2f31308aae9b||258500001^Nasopharyngeal swab^SCT||||71836000^Nasopharyngeal structure (body structure)^SCT^^^^2020-09-01|||||||||202102090000-0600|202102090000-0600""" +// This report is trying to contain two items, but the HL7 is garbled, the first is missing an MSH segment and the second +// has a typo in its MSH segment +@Suppress("ktlint:standard:max-line-length") +const val garbledHL7Record = + """FT|Centers for Disease Control and Prevention|0.1-SNAPSHOT|PRIME ReportStream|0.1-SNAPSHOT||20210210 +PID|1||2a14112c-ece1-4f82-915c-7b3a8d152eda^^^Avante at Ormond Beach^PI||Buckridge^Kareem^Millie^^^^L||19580810|F||2106-3^White^HL70005^^^^2.5.1|688 Leighann Inlet^^South Rodneychester^TX^67071^^^^48077||7275555555:1:^PRN^^roscoe.wilkinson@email.com^1^211^2240784|||||||||U^Unknown^HL70189||||||||N +ORC|RE|73a6e9bd-aaec-418e-813a-0ad33366ca85^6^7^8&F^9|73a6e9bd-aaec-418e-813a-0ad33366ca85|||||||||1629082607^Eddin^Husam^^^^^^CMS&2.16.840.1.113883.3.249&ISO^^^^NPI||^WPN^^^1^386^6825220|20210209||||||Avante at Ormond Beach|170 North King Road^^Ormond Beach^FL^32174^^^^12127|^WPN^^jbrush@avantecenters.com^1^407^7397506|^^^^32174 +OBR|1|73a6e9bd-aaec-418e-813a-0ad33366ca85|0cba76f5-35e0-4a28-803a-2f31308aae9b|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN|||202102090000-0600|202102090000-0600||||||||1629082607^Eddin^Husam^^^^^^CMS&2.16.840.1.113883.3.249&ISO^^^^NPI|^WPN^^^1^386^6825220|||||202102090000-0600|||F +OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN||260415000^Not detected^SCT|||N^Normal (applies to non-numeric results)^HL70078|||F|||202102090000-0600|||CareStart COVID-19 Antigen test_Access Bio, Inc._EUA^^99ELR||202102090000-0600||||Avante at Ormond Beach^^^^^CLIA&2.16.840.1.113883.4.7&ISO^^^^10D0876999^CLIA|170 North King Road^^Ormond Beach^FL^32174^^^^12127 +OBX|2|CWE|95418-0^Whether patient is employed in a healthcare setting^LN^^^^2.69||Y^Yes^HL70136||||||F|||202102090000-0600|||||||||||||||QST +OBX|3|CWE|95417-2^First test for condition of interest^LN^^^^2.69||Y^Yes^HL70136||||||F|||202102090000-0600|||||||||||||||QST +OBX|4|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST +OBX|5|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST +SPM|1|0cba76f5-35e0-4a28-803a-2f31308aae9b||258500001^Nasopharyngeal swab^SCT||||71836000^Nasopharyngeal structure (body structure)^SCT^^^^2020-09-01|||||||||202102090000-0600|202102090000-0600 +SH|^~\&#!|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|Avante at Ormond Beach^10D0876999^CLIA|PRIME_DOH|Prime ReportStream|20210210170737||ORU^R01^ORU_R01|371784|P|2.5.1|||NE|NE|USA||||PHLabReportNoAck^ELR_Receiver^2.16.840.1.113883.9.99^ISO +SFT|Centers for Disease Control and Prevention|0.1-SNAPSHOT|PRIME ReportStream|0.1-SNAPSHOT||20210210 +PID|1||2a14112c-ece1-4f82-915c-7b3a8d152eda^^^Avante at Ormond Beach^PI||Buckridge^Kareem^Millie^^^^L||19580810|F||2106-3^White^HL70005^^^^2.5.1|688 Leighann Inlet^^South Rodneychester^TX^67071^^^^48077||7275555555:1:^PRN^^roscoe.wilkinson@email.com^1^211^2240784|||||||||U^Unknown^HL70189||||||||N""" + @Suppress("ktlint:standard:max-line-length") const val validRadxMarsHL7Message = """MSH|^~\&|MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|CAREEVOLUTION^00Z0000024^CLIA|AIMS.INTEGRATION.PRD^2.16.840.1.114222.4.3.15.1^ISO|AIMS.PLATFORM^2.16.840.1.114222.4.1.217446^ISO|20240403205305+0000||ORU^R01^ORU_R01|20240403205305_dba7572cc6334f1ea0744c5f235c823e|P|2.5.1|||NE|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO @@ -257,12 +275,13 @@ object UniversalPipelineTestUtils { ) /** - * fetch child reports associated with a [parent] report and ensure we find an [expected] number of children + * fetch child reports associated with a [parent] report and ensure we find an [expectedItems] number of children */ fun fetchChildReports( parent: Report, txn: DataAccessTransaction, - expected: Int? = null, + expectedItems: Int? = null, + expectedReports: Int = 1, ): List { val itemLineages = DSL .using(txn) @@ -271,15 +290,15 @@ object UniversalPipelineTestUtils { .where(ItemLineage.ITEM_LINEAGE.PARENT_REPORT_ID.eq(parent.id)) .fetchInto(gov.cdc.prime.router.azure.db.tables.pojos.ItemLineage::class.java) - if (expected != null) { - assertThat(itemLineages).hasSize(expected) - assertThat(itemLineages.map { it.childIndex }).isEqualTo(MutableList(expected) { 1 }) + if (expectedItems != null) { + assertThat(itemLineages).hasSize(expectedItems) + assertThat(itemLineages.map { it.childIndex }).isEqualTo(MutableList(expectedItems) { 1 }) // itemCount is on the report created by the test. It will not be null. if (parent.itemCount > 1) { - assertThat(itemLineages.map { it.parentIndex }).isEqualTo((1..expected).toList()) + assertThat(itemLineages.map { it.parentIndex }).isEqualTo((1..expectedItems).toList()) } else { - assertThat(itemLineages.map { it.parentIndex }).isEqualTo(MutableList(expected) { 1 }) + assertThat(itemLineages.map { it.parentIndex }).isEqualTo(MutableList(expectedItems) { 1 }) } } @@ -290,9 +309,7 @@ object UniversalPipelineTestUtils { .where(ReportLineage.REPORT_LINEAGE.PARENT_REPORT_ID.eq(parent.id)) .fetchInto(gov.cdc.prime.router.azure.db.tables.pojos.ReportLineage::class.java) - if (expected != null) { - assertThat(reportLineages).hasSize(expected) - } + assertThat(reportLineages).hasSize(expectedReports) val childReportIds = reportLineages.map { it.childReportId @@ -307,11 +324,13 @@ object UniversalPipelineTestUtils { ) ) .fetchInto(ReportFile::class.java) - if (expected != null) { - assertThat(reportFiles).hasSize(expected) + + assertThat(reportFiles).hasSize(expectedReports) + + if (expectedItems != 0) { + assertThat(itemLineages).transform { lineages -> lineages.map { it.childReportId }.sorted() } + .isEqualTo(reportFiles.map { it.reportId }.sorted()) } - assertThat(itemLineages).transform { lineages -> lineages.map { it.childReportId }.sorted() } - .isEqualTo(reportFiles.map { it.reportId }.sorted()) return reportFiles } diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt index 69b6dbe7182..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 @@ -49,6 +49,7 @@ import gov.cdc.prime.router.common.cleanHL7Record import gov.cdc.prime.router.common.cleanHL7RecordConverted import gov.cdc.prime.router.common.cleanHL7RecordConvertedAndTransformed import gov.cdc.prime.router.common.conditionCodedValidFHIRRecord1 +import gov.cdc.prime.router.common.garbledHL7Record import gov.cdc.prime.router.common.invalidEmptyFHIRRecord import gov.cdc.prime.router.common.invalidHL7Record import gov.cdc.prime.router.common.invalidHL7RecordConverted @@ -99,7 +100,7 @@ class FHIRConverterIntegrationTests { ) ) - val azureEventService = LocalAzureEventServiceImpl() + val azureEventService = InMemoryAzureEventService() private fun createFHIRFunctionsInstance(): FHIRFunctions { val settings = FileSettings().loadOrganizations(universalPipelineOrganization) @@ -257,7 +258,7 @@ class FHIRConverterIntegrationTests { ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> val (routedReports, unroutedReports) = fetchChildReports( - receiveReport, txn, 4 + receiveReport, txn, 4, 4 ).partition { it.nextAction != TaskAction.none } assertThat(routedReports).hasSize(2) routedReports.forEach { @@ -441,7 +442,7 @@ class FHIRConverterIntegrationTests { ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> val (routedReports, unroutedReports) = fetchChildReports( - receiveReport, txn, 4 + receiveReport, txn, 4, 4 ).partition { it.nextAction != TaskAction.none } assertThat(routedReports).hasSize(2) routedReports.forEach { @@ -584,7 +585,7 @@ class FHIRConverterIntegrationTests { ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> val (routedReports, notRouted) = fetchChildReports( - receiveReport, txn, 2 + receiveReport, txn, 2, 2 ).partition { it.nextAction != TaskAction.none } with(routedReports.single()) { @@ -711,7 +712,7 @@ class FHIRConverterIntegrationTests { fhirFunctions.process(queueMessage, 1, createFHIRConverter(), ActionHistory(TaskAction.convert)) ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> - val routedReports = fetchChildReports(receiveReport, txn, 2) + val routedReports = fetchChildReports(receiveReport, txn, 2, 2) routedReports.forEach { assertThat(it.nextAction).isEqualTo(TaskAction.destination_filter) assertThat(it.receivingOrg).isEqualTo(null) @@ -804,4 +805,62 @@ class FHIRConverterIntegrationTests { assertThat(report.bodyFormat).isEqualTo("FHIR") } } + + @Test + fun `test should gracefully handle a case where number of items is unknown`() { + val receivedReportContents = garbledHL7Record + val receiveBlobUrl = BlobAccess.uploadBlob( + "receive/happy-path.hl7", + receivedReportContents.toByteArray(), + getBlobContainerMetadata() + ) + + val receiveReport = setupConvertStep(MimeFormat.HL7, hl7Sender, receiveBlobUrl, 1) + val queueMessage = generateQueueMessage(receiveReport, receivedReportContents, hl7Sender) + val fhirFunctions = createFHIRFunctionsInstance() + + fhirFunctions.process(queueMessage, 1, createFHIRConverter(), ActionHistory(TaskAction.convert)) + + verify(exactly = 0) { + QueueAccess.sendMessage(any(), any()) + } + ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> + val report = fetchChildReports(receiveReport, txn, 0).single() + assertThat(report.nextAction).isEqualTo(TaskAction.none) + assertThat(report.receivingOrg).isEqualTo(null) + assertThat(report.receivingOrgSvc).isEqualTo(null) + assertThat(report.schemaName).isEqualTo("None") + assertThat(report.schemaTopic).isEqualTo(Topic.FULL_ELR) + assertThat(report.bodyFormat).isEqualTo("HL7") + } + } + + @Test + fun `test should gracefully handle a case with an empty contents`() { + val receivedReportContents = " " + val receiveBlobUrl = BlobAccess.uploadBlob( + "receive/happy-path.hl7", + receivedReportContents.toByteArray(), + getBlobContainerMetadata() + ) + + val receiveReport = setupConvertStep(MimeFormat.HL7, hl7Sender, receiveBlobUrl, 1) + val queueMessage = generateQueueMessage(receiveReport, receivedReportContents, hl7Sender) + val fhirFunctions = createFHIRFunctionsInstance() + + fhirFunctions.process(queueMessage, 1, createFHIRConverter(), ActionHistory(TaskAction.convert)) + + verify(exactly = 0) { + QueueAccess.sendMessage(any(), any()) + } + ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> + val report = fetchChildReports(receiveReport, txn, 0, 1).single() + assertThat(report.nextAction).isEqualTo(TaskAction.none) + assertThat(report.receivingOrg).isEqualTo(null) + assertThat(report.receivingOrgSvc).isEqualTo(null) + assertThat(report.schemaName).isEqualTo("None") + assertThat(report.schemaTopic).isEqualTo(Topic.FULL_ELR) + assertThat(report.bodyFormat).isEqualTo("HL7") + } + } } \ No newline at end of file diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRDestinationFilterIntegrationTests.kt index 76d52f0b353..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() { @@ -194,7 +194,7 @@ class FHIRDestinationFilterIntegrationTests : Logging { // check results ReportStreamTestDatabaseContainer.testDatabaseAccess.transact { txn -> - val routedReports = fetchChildReports(report, txn, 2) + val routedReports = fetchChildReports(report, txn, 2, 2) with(routedReports.first()) { assertThat(this.nextAction).isEqualTo(TaskAction.receiver_filter) assertThat(this.receivingOrg).isEqualTo("phd") diff --git a/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt b/prime-router/src/test/kotlin/fhirengine/azure/FHIRReceiverFilterIntegrationTests.kt index 6092e53516f..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() { @@ -368,6 +368,8 @@ class FHIRReceiverFilterIntegrationTests : Logging { assertThat(routedReport.schemaTopic).isEqualTo(Topic.FULL_ELR) assertThat(routedReport.bodyFormat).isEqualTo("FHIR") assertThat(routedReport.itemCount).isZero() + assertThat(routedReport.receivingOrg).isEqualTo(receiverSetupData.single().orgName) + assertThat(routedReport.receivingOrgSvc).isEqualTo(receiverSetupData.single().name) // check for no queue message verify(exactly = 0) { @@ -543,6 +545,8 @@ class FHIRReceiverFilterIntegrationTests : Logging { assertThat(routedReport.schemaTopic).isEqualTo(Topic.FULL_ELR) assertThat(routedReport.bodyFormat).isEqualTo("FHIR") assertThat(routedReport.itemCount).isZero() + assertThat(routedReport.receivingOrg).isEqualTo(receiverSetupData.single().orgName) + assertThat(routedReport.receivingOrgSvc).isEqualTo(receiverSetupData.single().name) // check for no queue message verify(exactly = 0) { @@ -731,6 +735,8 @@ class FHIRReceiverFilterIntegrationTests : Logging { assertThat(routedReport.schemaTopic).isEqualTo(Topic.FULL_ELR) assertThat(routedReport.bodyFormat).isEqualTo("FHIR") assertThat(routedReport.itemCount).isZero() + assertThat(routedReport.receivingOrg).isEqualTo(receiverSetupData.single().orgName) + assertThat(routedReport.receivingOrgSvc).isEqualTo(receiverSetupData.single().name) // check queue message verify(exactly = 0) { @@ -836,6 +842,8 @@ class FHIRReceiverFilterIntegrationTests : Logging { assertThat(routedReport.schemaTopic).isEqualTo(Topic.FULL_ELR) assertThat(routedReport.bodyFormat).isEqualTo("FHIR") assertThat(routedReport.itemCount).isZero() + assertThat(routedReport.receivingOrg).isEqualTo(receiverSetupData.single().orgName) + assertThat(routedReport.receivingOrgSvc).isEqualTo(receiverSetupData.single().name) // check filter logging val actionLogRecords = DSL.using(txn) @@ -1115,6 +1123,8 @@ class FHIRReceiverFilterIntegrationTests : Logging { assertThat(routedReport.schemaTopic).isEqualTo(Topic.FULL_ELR) assertThat(routedReport.bodyFormat).isEqualTo("FHIR") assertThat(routedReport.itemCount).isZero() + assertThat(routedReport.receivingOrg).isEqualTo(receiverSetupData.single().orgName) + assertThat(routedReport.receivingOrgSvc).isEqualTo(receiverSetupData.single().name) // check filter logging val actionLogRecords = DSL.using(txn) 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/prime-router/src/test/kotlin/fhirengine/engine/LookupTableValueSetTests.kt b/prime-router/src/test/kotlin/fhirengine/engine/LookupTableValueSetTests.kt index a5451867670..0ef5b5c71e4 100644 --- a/prime-router/src/test/kotlin/fhirengine/engine/LookupTableValueSetTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/engine/LookupTableValueSetTests.kt @@ -125,7 +125,7 @@ class LookupTableValueSetTests { val schema = FhirTransformSchema(elements = mutableListOf(elemA)) - FhirTransformer(schema).process(bundle) + FhirTransformer(schema, mutableListOf(), mutableListOf()).process(bundle) assertThat(resource.name[0].text).isEqualTo("ghi789") assertThat(resource.telecom[0].value).isEqualTo("ijk012") diff --git a/prime-router/src/test/kotlin/fhirengine/translation/hl7/FhirToHl7ConverterTests.kt b/prime-router/src/test/kotlin/fhirengine/translation/hl7/FhirToHl7ConverterTests.kt index d435d94b0ce..4700b330438 100644 --- a/prime-router/src/test/kotlin/fhirengine/translation/hl7/FhirToHl7ConverterTests.kt +++ b/prime-router/src/test/kotlin/fhirengine/translation/hl7/FhirToHl7ConverterTests.kt @@ -19,7 +19,6 @@ import fhirengine.engine.CustomTranslationFunctions import gov.cdc.prime.router.Metadata import gov.cdc.prime.router.azure.BlobAccess import gov.cdc.prime.router.fhirengine.config.HL7TranslationConfig -import gov.cdc.prime.router.fhirengine.translation.hl7.schema.ConfigSchemaElementProcessingException import gov.cdc.prime.router.fhirengine.translation.hl7.schema.ConfigSchemaReader import gov.cdc.prime.router.fhirengine.translation.hl7.schema.converter.ConverterSchemaElement import gov.cdc.prime.router.fhirengine.translation.hl7.schema.converter.HL7ConverterSchema @@ -43,7 +42,6 @@ import org.junit.jupiter.api.Nested import java.io.File import kotlin.test.Test import kotlin.test.assertEquals -import kotlin.test.assertFailsWith class FhirToHl7ConverterTests { @Test @@ -54,7 +52,12 @@ class FhirToHl7ConverterTests { bundle.id = "abc123" val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema, terser = mockTerser) + val converter = FhirToHl7Converter( + mockSchema, + terser = mockTerser, + warnings = mutableListOf(), + errors = mutableListOf() + ) var element = ConverterSchemaElement("name") assertThat(converter.canEvaluate(element, bundle, bundle, bundle, customContext)).isTrue() @@ -81,7 +84,7 @@ class FhirToHl7ConverterTests { bundle.addEntry().resource = resource val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema) + val converter = FhirToHl7Converter(mockSchema, warnings = mutableListOf(), errors = mutableListOf()) var element = ConverterSchemaElement("name") var focusResources = converter.getFocusResources(element.resource, bundle, bundle, customContext) @@ -131,7 +134,7 @@ class FhirToHl7ConverterTests { val bundle = Bundle() bundle.id = "abc123" val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema) + val converter = FhirToHl7Converter(mockSchema, warnings = mutableListOf(), errors = mutableListOf()) var element = ConverterSchemaElement("name", value = listOf("Bundle.id", "Bundle.timestamp")) assertThat(converter.getValueAsString(element, bundle, bundle, customContext)).isEqualTo(bundle.id) @@ -149,7 +152,7 @@ class FhirToHl7ConverterTests { val bundle = Bundle() bundle.id = "stagnatious" val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema) + val converter = FhirToHl7Converter(mockSchema, warnings = mutableListOf(), errors = mutableListOf()) val valueSet = InlineValueSet( sortedMapOf( @@ -188,7 +191,7 @@ class FhirToHl7ConverterTests { resource.destination[0].name = "a destination" bundle.addEntry().resource = resource val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema) + val converter = FhirToHl7Converter(mockSchema, warnings = mutableListOf(), errors = mutableListOf()) // Non-primitive values should return an empty string and log an error val element = ConverterSchemaElement("name", value = listOf("Bundle.entry")) @@ -201,7 +204,8 @@ class FhirToHl7ConverterTests { val mockTerser = mockk() val mockSchema = mockk() // Just a dummy schema to pass around var element = ConverterSchemaElement("name", required = true, hl7Spec = listOf("MSH-10")) - var converter = FhirToHl7Converter(mockSchema, terser = mockTerser) + var converter = + FhirToHl7Converter(mockSchema, terser = mockTerser, warnings = mutableListOf(), errors = mutableListOf()) val customContext = CustomContext(Bundle(), Bundle()) // Required element @@ -230,7 +234,13 @@ class FhirToHl7ConverterTests { clearAllMocks() // Strict errors - converter = FhirToHl7Converter(mockSchema, true, mockTerser) + converter = FhirToHl7Converter( + mockSchema, + true, + mockTerser, + warnings = mutableListOf(), + errors = mutableListOf() + ) every { mockTerser.set(element.hl7Spec[0], any()) } throws HL7Exception("some text") assertFailure { converter.setHl7Value(element, fieldValue, customContext) } .hasClass(HL7ConversionException::class.java) @@ -251,7 +261,12 @@ class FhirToHl7ConverterTests { val bundle = Bundle() bundle.id = "abc123" val customContext = CustomContext(bundle, bundle) - val converter = FhirToHl7Converter(mockSchema, terser = mockTerser) + val converter = FhirToHl7Converter( + mockSchema, + terser = mockTerser, + warnings = mutableListOf(), + errors = mutableListOf() + ) val pathWithValue = "Bundle.id" val pathNoValue = "Bundle.timestamp" val conditionTrue = "Bundle.id.exists()" @@ -337,7 +352,8 @@ class FhirToHl7ConverterTests { bundle.addEntry().resource = servRequest1 bundle.addEntry().resource = servRequest2 - val converter = FhirToHl7Converter(mockSchema, terser = mockTerser) + val converter = + FhirToHl7Converter(mockSchema, terser = mockTerser, warnings = mutableListOf(), errors = mutableListOf()) val childElement = ConverterSchemaElement( "childElement", @@ -383,7 +399,7 @@ class FhirToHl7ConverterTests { hl7Class = "ca.uhn.hl7v2.model.v27.message.ORU_R01", elements = listOf(element).toMutableList() ) - val converter = FhirToHl7Converter(schema) + val converter = FhirToHl7Converter(schema, warnings = mutableListOf(), errors = mutableListOf()) val message = converter.process(bundle) assertThat(Terser(message).get("MSH-3-1")).isEqualTo("Epic") } @@ -407,7 +423,7 @@ class FhirToHl7ConverterTests { hl7Class = "ca.uhn.hl7v2.model.v251.message.ORU_R01", elements = mutableListOf(element) ) - val message = FhirToHl7Converter(schema).process(bundle) + val message = FhirToHl7Converter(schema, warnings = mutableListOf(), errors = mutableListOf()).process(bundle) assertThat(message.isEmpty).isFalse() assertThat(Terser(message).get(element.hl7Spec[0])).isEqualTo(bundle.id) @@ -419,16 +435,23 @@ class FhirToHl7ConverterTests { ) schema = HL7ConverterSchema(elements = mutableListOf(element)) - assertFailure { FhirToHl7Converter(schema).process(bundle) } - - // Use a file based schema which will fail as we do not have enough data in the bundle - val missingDataEx = assertFailsWith { + assertFailure { FhirToHl7Converter( - "classpath:/fhirengine/translation/hl7/schema/schema-read-test-01/ORU_R01.yml", - mockk() - ).process(bundle) + schema, + warnings = mutableListOf(), + errors = mutableListOf() + ).process(bundle) } - assertThat(missingDataEx.message).isEqualTo( + + // Use a file based schema which will fail as we do not have enough data in the bundle + val transformer = FhirToHl7Converter( + "classpath:/fhirengine/translation/hl7/schema/schema-read-test-01/ORU_R01.yml", + mockk(), warnings = mutableListOf(), errors = mutableListOf() + ) + + transformer.process(bundle) + + assertThat(transformer.errors[0]).isEqualTo( "Error encountered while applying: message-headers in" + " /fhirengine/translation/hl7/schema/schema-read-test-01/ORU_R01.yml to FHIR bundle. \n" + "Error was: Required element message-headers conditional was false or value was empty." @@ -462,7 +485,8 @@ class FhirToHl7ConverterTests { CustomFhirPathFunctions(), null, CustomTranslationFunctions() - ) + ), + warnings = mutableListOf(), errors = mutableListOf() ).process(bundle) assertThat(message.isEmpty).isFalse() assertThat(Terser(message).get(element.hl7Spec[0])).isEqualTo(loincCode) @@ -491,7 +515,8 @@ class FhirToHl7ConverterTests { val message = FhirToHl7Converter( schema, - context = FhirToHl7Context(CustomFhirPathFunctions(), null, CustomTranslationFunctions()) + context = FhirToHl7Context(CustomFhirPathFunctions(), null, CustomTranslationFunctions()), + warnings = mutableListOf(), errors = mutableListOf() ).process(bundle) assertThat(message.isEmpty).isFalse() assertThat(Terser(message).get(element.hl7Spec[0])).isEqualTo(expectedDate) @@ -513,7 +538,11 @@ class FhirToHl7ConverterTests { elements = mutableListOf(elemA) ) - val message = FhirToHl7Converter(rootSchema).process(bundle) + val message = FhirToHl7Converter( + rootSchema, + warnings = mutableListOf(), + errors = mutableListOf() + ).process(bundle) assertThat(Terser(message).get("MSH-11")).isEqualTo("654321") assertThat(Terser(message).get("MSH-12")).isEqualTo("fedcba") } @@ -540,7 +569,11 @@ class FhirToHl7ConverterTests { val overrideSchema = HL7ConverterSchema(elements = mutableListOf(elemBOverride)) rootSchema.override(overrideSchema) - val message = FhirToHl7Converter(rootSchema).process(bundle) + val message = FhirToHl7Converter( + rootSchema, + warnings = mutableListOf(), + errors = mutableListOf() + ).process(bundle) assertThat(Terser(message).get("MSH-11")).isEqualTo("overrideVal") assertThat(Terser(message).get("MSH-12")).isEqualTo("overrideVal") } @@ -578,7 +611,7 @@ class FhirToHl7ConverterTests { val converter = FhirToHl7Converter( mockSchema, terser = terser, - context = contextWithConfig + context = contextWithConfig, warnings = mutableListOf(), errors = mutableListOf() ) // should truncate to 194 @@ -628,7 +661,7 @@ class FhirToHl7ConverterTests { val converter = FhirToHl7Converter( mockSchema, terser = terser, - context = contextWithConfig + context = contextWithConfig, warnings = mutableListOf(), errors = mutableListOf() ) // should truncate to 199 @@ -690,8 +723,14 @@ class FhirToHl7ConverterTests { val bundle = Bundle() bundle.id = "abc123" - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("MSH-11")).isEqualTo("abc123") // Confirms that we can override an element that exists in the base @@ -702,8 +741,14 @@ class FhirToHl7ConverterTests { fun `test override uses a constant`() { val bundle = Bundle() - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("MSH-10")).isEqualTo("10") // Assert that we can create an override element that uses a constant from the base schema @@ -714,8 +759,14 @@ class FhirToHl7ConverterTests { fun `test override overrides a constant`() { val bundle = Bundle() - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("MSH-8")).isEqualTo("otherValue") // Assert that a constant can get overridden @@ -726,8 +777,14 @@ class FhirToHl7ConverterTests { fun `test the overriding schema takes priority when setting the same HL7 field`() { val bundle = Bundle() - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("MSH-14")).isEqualTo("14") // A new element in the overriding schema sets MSH-14 as well @@ -742,8 +799,14 @@ class FhirToHl7ConverterTests { messageHeader.definition = "definition" bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-2")).isEqualTo("1") // Assert that an element can be overridden in a nested schema @@ -759,8 +822,14 @@ class FhirToHl7ConverterTests { messageHeader.id = "idSft" bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-3")).isEqualTo("definition") @@ -779,8 +848,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "noEvent", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-5")).isEqualTo("idSft") // Asserts that the base extending schema can provide for a nested schema element @@ -797,8 +872,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "code", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-1-1")).isEqualTo("system") // Assert that a deeply nested schema element can be overridden, using a @@ -817,7 +898,12 @@ class FhirToHl7ConverterTests { // Assert that a new element that would be "part" of an existing schema cannot // reference a constant from the nested schema - assertFailure { FhirToHl7Converter(extendedSchema).process(bundle) } + val transformer = FhirToHl7Converter( + extendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ) + transformer.process(bundle) + assertThat(transformer.errors.size > 0) } @Test @@ -829,8 +915,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "xon3", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchemaOverridesSoftware).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchemaOverridesSoftware, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-5")).isEqualTo("idSft") // Assert that the override sets a different schema for software that @@ -847,8 +939,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "aCode", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchemaOverridesXon).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchemaOverridesXon, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-1-1")).isEqualTo("system") // Assert that an extending schema can override the schema for a nested element @@ -864,8 +962,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "aCode", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedSchemaOverridesXon).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedSchemaOverridesXon, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-1-10")).isNull() // Assert that a new element can get added when overriding a nested schema @@ -877,8 +981,14 @@ class FhirToHl7ConverterTests { val bundle = Bundle() bundle.id = "abc123" - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedExtendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedExtendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("MSH-11")).isEqualTo("abc123") // Assert that a schema that extends a schema overriding MSH-11 can further @@ -895,8 +1005,14 @@ class FhirToHl7ConverterTests { messageHeader.event = Coding("system", "aCode", "displayCode") bundle.addEntry().resource = messageHeader - val baseMessage = FhirToHl7Converter(baseSchema).process(bundle) - val message = FhirToHl7Converter(extendedExtendedSchema).process(bundle) + val baseMessage = FhirToHl7Converter( + baseSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) + val message = FhirToHl7Converter( + extendedExtendedSchema, + warnings = mutableListOf(), errors = mutableListOf() + ).process(bundle) assertThat(Terser(baseMessage).get("SFT-1-1")).isEqualTo("system") // Asserts that a nested schema cannot use an extends clause diff --git a/prime-router/src/test/kotlin/history/azure/DeliveryFacadeTests.kt b/prime-router/src/test/kotlin/history/azure/DeliveryFacadeTests.kt index 7e71b827185..1f7b45bd440 100644 --- a/prime-router/src/test/kotlin/history/azure/DeliveryFacadeTests.kt +++ b/prime-router/src/test/kotlin/history/azure/DeliveryFacadeTests.kt @@ -218,6 +218,53 @@ class DeliveryFacadeTests { ) } + @Test + fun `test findDetailedDeliveryHistory with reportId`() { + val mockDeliveryAccess = mockk() + val mockReportService = mockk() + val mockDbAccess = mockk() + val facade = DeliveryFacade(mockDeliveryAccess, mockDbAccess, mockReportService) + + val reportFile = ReportFile() + reportFile.createdAt = OffsetDateTime.parse("2022-04-13T17:06:10.534Z") + reportFile.reportId = UUID.fromString("b3c8e304-8eff-4882-9000-3645054a30b7") + reportFile.sendingOrg = "DogCow Associates" + reportFile.schemaTopic = Topic.FULL_ELR + reportFile.itemCount = 1 + reportFile.bodyUrl = "body-url" + reportFile.schemaName = "" + reportFile.bodyFormat = "HL7" + reportFile.receivingOrg = "ignore" + reportFile.receivingOrgSvc = "FULL-ELR" + + val action = Action() + action.actionId = 1L + action.createdAt = reportFile.createdAt + action.externalName = "external" + + every { mockDbAccess.fetchAction(any()) } returns action + every { mockDbAccess.fetchReportFile(any()) } returns reportFile + + every { + mockReportService.getRootReports( + any(), + ) + } returns listOf(reportFile) + + val result = facade.findDetailedDeliveryHistory( + reportFile.reportId.toString(), + action.actionId, + ) + assertThat(result?.actionId).isEqualTo(1L) + assertThat(result?.topic).isEqualTo(Topic.FULL_ELR) + assertThat(result?.reportId.toString()).isEqualTo(reportFile.reportId.toString()) + assertThat(result?.reportItemCount).isEqualTo(1) + assertThat(result?.fileName).isEqualTo("body-url") + assertThat(result?.originalIngestion?.first()?.get("ingestionTime")).isEqualTo(reportFile.createdAt) + assertThat(result?.originalIngestion?.first()?.get("reportId")).isEqualTo(reportFile.reportId) + assertThat(result?.originalIngestion?.first()?.get("sendingOrg")).isEqualTo(reportFile.sendingOrg) + } + @Test fun `test findDetailedDeliveryHistory`() { val mockDeliveryAccess = mockk() @@ -258,6 +305,7 @@ class DeliveryFacadeTests { } returns listOf(reportFile) val result = facade.findDetailedDeliveryHistory( + delivery.actionId.toString(), delivery.actionId, ) diff --git a/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt b/prime-router/src/test/kotlin/history/azure/DeliveryFunctionTests.kt index bcef66ebe44..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) @@ -497,7 +504,7 @@ class DeliveryFunctionTests : Logging { action.actionName = TaskAction.batch every { mockDeliveryFacade.fetchActionForReportId(any()) } returns action every { mockDeliveryFacade.fetchAction(any()) } returns null // not used for a UUID - every { mockDeliveryFacade.findDetailedDeliveryHistory(any()) } returns returnBody + every { mockDeliveryFacade.findDetailedDeliveryHistory(any(), any()) } returns returnBody every { mockDeliveryFacade.checkAccessAuthorizationForAction(any(), any(), any()) } returns true response = function.getDeliveryDetails(mockRequest, goodUuid) assertThat(response.status).isEqualTo(HttpStatus.OK) @@ -536,7 +543,7 @@ class DeliveryFunctionTests : Logging { // Happy path with a good actionId every { mockDeliveryFacade.fetchActionForReportId(any()) } returns null // not used for an actionId every { mockDeliveryFacade.fetchAction(any()) } returns action - every { mockDeliveryFacade.findDetailedDeliveryHistory(any()) } returns returnBody + every { mockDeliveryFacade.findDetailedDeliveryHistory(any(), any()) } returns returnBody every { mockDeliveryFacade.checkAccessAuthorizationForAction(any(), any(), any()) } returns true response = function.getDeliveryDetails(mockRequest, goodActionId) assertThat(response.status).isEqualTo(HttpStatus.OK) @@ -713,7 +720,7 @@ class DeliveryFunctionTests : Logging { every { mockDeliveryFacade.fetchActionForReportId(any()) } returns action every { mockDeliveryFacade.fetchAction(any()) } returns null // not used for a UUID - every { mockDeliveryFacade.findDetailedDeliveryHistory(any()) } returns returnBody + every { mockDeliveryFacade.findDetailedDeliveryHistory(any(), any()) } returns returnBody every { mockDeliveryFacade.checkAccessAuthorizationForAction(any(), any(), any()) } returns true val restCreds = mockk() @@ -814,7 +821,7 @@ class DeliveryFunctionTests : Logging { every { mockDeliveryFacade.fetchActionForReportId(any()) } returns action every { mockDeliveryFacade.fetchAction(any()) } returns null // not used for a UUID - every { mockDeliveryFacade.findDetailedDeliveryHistory(any()) } returns null + every { mockDeliveryFacade.findDetailedDeliveryHistory(any(), any()) } returns null every { mockDeliveryFacade.checkAccessAuthorizationForAction(any(), any(), any()) } returns true val restCreds = mockk() diff --git a/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt b/prime-router/src/test/kotlin/history/azure/SubmissionFunctionIntegrationTests.kt index 1493ec5daf6..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 @@ -33,13 +36,202 @@ 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) class SubmissionFunctionIntegrationTests { + @Test + fun `it should return a history for a received report`() { + val submittedReport = reportGraph { + topic(Topic.FULL_ELR) + format(MimeFormat.HL7) + sender(UniversalPipelineTestUtils.hl7Sender) + + submission { + action(TaskAction.receive) + reportGraphNode { + action(TaskAction.convert) + } + } + }.generate(ReportStreamTestDatabaseContainer.testDatabaseAccess) + + val httpRequestMessage = MockHttpRequestMessage() + + val func = setupSubmissionFunction() + + val history = func + .getReportDetailedHistory(httpRequestMessage, submittedReport.node.reportId.toString()) + assertThat(history).isNotNull() + val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) + assertThat( + historyNode.get("overallStatus").asText() + ).isEqualTo(DetailedSubmissionHistory.Status.RECEIVED.toString()) + assertThat(historyNode.get("destinations").size()).isEqualTo(0) + assertThat(historyNode.get("errors").size()).isEqualTo(0) + 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 { + topic(Topic.FULL_ELR) + format(MimeFormat.HL7) + sender(UniversalPipelineTestUtils.hl7Sender) + + submission { + action(TaskAction.receive) + reportGraphNode { + action(TaskAction.convert) + log(ActionLog(InvalidParamMessage("log"), type = ActionLogLevel.warning)) + reportGraphNode { + action(TaskAction.destination_filter) + reportGraphNode { + action(TaskAction.none) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[1]) + itemCount(0) + } + } + reportGraphNode { + action(TaskAction.destination_filter) + reportGraphNode { + action(TaskAction.receiver_filter) + reportGraphNode { + action(TaskAction.translate) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[0]) + reportGraphNode { + action(TaskAction.send) + transportResult("Success") + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[0]) + } + } + } + reportGraphNode { + action(TaskAction.receiver_filter) + reportGraphNode { + action(TaskAction.none) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[1]) + itemCount(0) + } + } + } + } + } + }.generate(ReportStreamTestDatabaseContainer.testDatabaseAccess) + + val httpRequestMessage = MockHttpRequestMessage() + + val func = setupSubmissionFunction() + + val history = func + .getReportDetailedHistory(httpRequestMessage, submittedReport.node.reportId.toString()) + assertThat(history).isNotNull() + val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) + assertThat( + historyNode.get("overallStatus").asText() + ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) + assertThat(historyNode.get("destinations").size()).isEqualTo(2) + assertThat(historyNode.get("errors").size()).isEqualTo(0) + assertThat(historyNode.get("warnings").size()).isEqualTo(1) + } + + // this test remains to prevent breaking queries against old submissions that used the legacy route step + @Test + fun `it should return a history for an partially delivered submission (for legacy route step)`() { + val submittedReport = reportGraph { + topic(Topic.FULL_ELR) + format(MimeFormat.HL7) + sender(UniversalPipelineTestUtils.hl7Sender) + + submission { + action(TaskAction.receive) + reportGraphNode { + action(TaskAction.convert) + log(ActionLog(InvalidParamMessage("log"), type = ActionLogLevel.warning)) + reportGraphNode { + action(TaskAction.route) + reportGraphNode { + action(TaskAction.none) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[1]) + itemCount(0) + } + } + reportGraphNode { + action(TaskAction.route) + reportGraphNode { + action(TaskAction.translate) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[0]) + reportGraphNode { + action(TaskAction.send) + transportResult("Success") + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[0]) + } + } + reportGraphNode { + action(TaskAction.none) + receiver(UniversalPipelineTestUtils.universalPipelineOrganization.receivers[1]) + itemCount(0) + } + } + } + } + }.generate(ReportStreamTestDatabaseContainer.testDatabaseAccess) + + val httpRequestMessage = MockHttpRequestMessage() + + val func = setupSubmissionFunction() + + val history = func + .getReportDetailedHistory(httpRequestMessage, submittedReport.node.reportId.toString()) + assertThat(history).isNotNull() + val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) + assertThat( + historyNode.get("overallStatus").asText() + ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) + assertThat(historyNode.get("destinations").size()).isEqualTo(2) + assertThat(historyNode.get("errors").size()).isEqualTo(0) + assertThat(historyNode.get("warnings").size()).isEqualTo(1) + } + + // TODO: https://github.com/CDCgov/prime-reportstream/issues/16054 + @Test + fun `it should return a history for an in-flight submission`() { val submittedReport = reportGraph { topic(Topic.FULL_ELR) format(MimeFormat.HL7) @@ -95,15 +287,16 @@ class SubmissionFunctionIntegrationTests { val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) assertThat( historyNode.get("overallStatus").asText() - ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) + ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) // TODO: should be RECEIVED assertThat(historyNode.get("destinations").size()).isEqualTo(2) assertThat(historyNode.get("errors").size()).isEqualTo(0) assertThat(historyNode.get("warnings").size()).isEqualTo(1) } + // TODO: https://github.com/CDCgov/prime-reportstream/issues/16054 // this test remains to prevent breaking queries against old submissions that used the legacy route step @Test - fun `it should return a history for partially delivered submission (for legacy route step)`() { + fun `it should return a history for an in-flight submission (for legacy route step)`() { val submittedReport = reportGraph { topic(Topic.FULL_ELR) format(MimeFormat.HL7) @@ -153,7 +346,7 @@ class SubmissionFunctionIntegrationTests { val historyNode = JacksonMapperUtilities.defaultMapper.readTree(history.body.toString()) assertThat( historyNode.get("overallStatus").asText() - ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) + ).isEqualTo(DetailedSubmissionHistory.Status.PARTIALLY_DELIVERED.toString()) // TODO: should be RECEIVED assertThat(historyNode.get("destinations").size()).isEqualTo(2) assertThat(historyNode.get("errors").size()).isEqualTo(0) assertThat(historyNode.get("warnings").size()).isEqualTo(1) @@ -201,6 +394,7 @@ class SubmissionFunctionIntegrationTests { log(ActionLog(InvalidParamMessage("log"), type = ActionLogLevel.warning)) reportGraphNode { action(TaskAction.destination_filter) + nextAction(TaskAction.none) } } } @@ -237,6 +431,7 @@ class SubmissionFunctionIntegrationTests { log(ActionLog(InvalidParamMessage("log"), type = ActionLogLevel.warning)) reportGraphNode { action(TaskAction.route) + nextAction(TaskAction.none) } } } 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/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_ME_20240806-0001.hl7 b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_ME_20240806-0001.hl7 index c94288fb486..e3505bb4288 100644 --- a/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_ME_20240806-0001.hl7 +++ b/prime-router/src/testIntegration/resources/datatests/FHIR_to_HL7/sample_ME_20240806-0001.hl7 @@ -1,7 +1 @@ -MSH|^~\&|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|CDC-ReportStream^11D2030855^CLIA|ME-DOH|ME-DOH|20240806184343+0000||ORU^R01^ORU_R01|4168584e-1921-40e7-ba70-76e298ec37be|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||20240805221133+0000 -PID|1||98796b2b-f07e-4750-9141-3007811d2b33^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Test^Patientseven^^^^^L||19880423|M||2028-9^asian^HL70005^^^^2.5.1^^asian|345 Simple St^^Portland^ME^04019^USA^^^Cumberland||(340) 555 5555^PRS^CP^^1^340^5555555^^^^^(340) 555 5555|||||||||N^Not Hispanic or Latino^HL70189^^^^2.9^^Not Hispanic or Latino||||||||N -ORC|RE|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|4168584e-1921-40e7-ba70-76e298ec37be^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|20240806184340+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|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|95941-1^Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection^LN|||20240806182840+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|||||20240806184343+0000|||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|||20240806182840+0000|12D4567890^Testing Lab^CLIA||Xpert Xpress CoV-2/Flu/RSV plus_Cepheid^Xpert Xpress CoV-2/Flu/RSV plus^^^^^^^Xpert Xpress CoV-2/Flu/RSV plus_Cepheid|^^MNI|20240806184340+0000||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA -SPM|1|4168584e-1921-40e7-ba70-76e298ec37be&Testing Lab&12D4567890&CLIA^4168584e-1921-40e7-ba70-76e298ec37be&Testing Lab&12D4567890&CLIA||258500001^Nasopharyngeal swab^SCT^^^^2.67^^Nasopharyngeal swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240806182840+0000|20240806182840+0000 \ No newline at end of file +MSH|^~\&|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|CDC-ReportStream^11D2030855^CLIA|ME-DOH|ME-DOH|20240806184343+0000||ORU^R01^ORU_R01|4168584e-1921-40e7-ba70-76e298ec37be|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||20240805221133+0000 PID|1||98796b2b-f07e-4750-9141-3007811d2b33^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Test^Patientseven^^^^^L||19880423|M||2028-9^asian^HL70005^^^^2.5.1^^asian|345 Simple St^^Portland^ME^04019^USA^^^Cumberland||(340) 555 5555^PRS^CP^^1^340^5555555^^^^^(340) 555 5555|||||||||N^Not Hispanic or Latino^HL70189^^^^2.9^^Not Hispanic or Latino||||||||N ORC|RE|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|4168584e-1921-40e7-ba70-76e298ec37be^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|20240806184340+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|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|4168584e-1921-40e7-ba70-76e298ec37be^Testing Lab^12D4567890^CLIA|95941-1^Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection^LN|||20240806182840+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|||||20240806184343+0000|||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|||20240806182840+0000|12D4567890^Testing Lab^CLIA||Xpert Xpress CoV-2/Flu/RSV plus_Cepheid^Xpert Xpress CoV-2/Flu/RSV plus^^^^^^^Xpert Xpress CoV-2/Flu/RSV plus_Cepheid|^^MNI|20240806184340+0000||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA SPM|1|4168584e-1921-40e7-ba70-76e298ec37be&Testing Lab&12D4567890&CLIA^4168584e-1921-40e7-ba70-76e298ec37be&Testing Lab&12D4567890&CLIA||258500001^Nasopharyngeal swab^SCT^^^^2.67^^Nasopharyngeal swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240806182840+0000|20240806182840+0000 \ No newline at end of file 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": "2024-06-05T18:55:01+00:00", - "specimen": [ + "agent": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/provenance-participant-type", + "code": "assembler" + } + ] + }, + "who": { + "reference": "Organization/1727929833167601000.1f916ddc-b37c-40e4-9f47-5aa6e565bf13" + } + } + ] + } + }, + { + "fullUrl": "Organization/1727929833167601000.1f916ddc-b37c-40e4-9f47-5aa6e565bf13", + "resource": { + "resourceType": "Organization", + "id": "1727929833167601000.1f916ddc-b37c-40e4-9f47-5aa6e565bf13", + "extension": [ { - "reference": "Specimen/dc7af370-fc07-4b00-abc7-9b5dd87cf4d2" + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/xon-organization", + "extension": [ + { + "url": "XON.10", + "valueString": "CDC PRIME - Atlanta" + } + ] } ], - "result": [ + "identifier": [ { - "reference": "Observation/5ab37a34-59f5-421f-92bd-baffaf26bb72" + "value": "CDC PRIME - Atlanta" + }, + { + "type": { + "coding": [ + { + "system": 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"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 +878,17 @@ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/v2-0078", + "extension": [ + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", + "valueString": "coding" + }, + { + "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", + "valueString": "HL70078" + } + ], + "version": "2.7", "code": "A", "display": "Abnormal" } @@ -469,239 +896,3378 @@ } ], "method": { - "extension": [ - { - "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/testkit-name-id", - "valueCoding": { - "code": "CareStart COVID-19 MDx RT-PCR_Access Bio, Inc." - } - } - ], "coding": [ { - "display": "CareStart COVID-19 MDx RT-PCR" + "extension": [ + { + "url": 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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 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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/HL7_to_FHIR/sample_oru_20241015-001.fhir b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR/sample_oru_20241015-001.fhir new file mode 100644 index 00000000000..825d26e4e1f --- /dev/null +++ b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR/sample_oru_20241015-001.fhir @@ -0,0 +1,19530 @@ +{ + "resourceType": "Bundle", + "id": "1729025861300130403.6c12f9f9-a0b0-4163-82eb-07aa9a2fec0c", + "meta": { + "lastUpdated": "2024-10-15T20:57:41.307+00:00" + }, + "identifier": { + "system": "https://reportstream.cdc.gov/prime-router", + "value": "AUTOMATEDTEST-003" + }, + "type": "message", + "timestamp": "2024-10-15T03:43:04.000+00:00", + "entry": [ + { + "fullUrl": "MessageHeader/1729025861342077427.5bddfe2f-0d3f-47d8-a6a6-13eda0a3955f", + "resource": { + "resourceType": "MessageHeader", + "id": "1729025861342077427.5bddfe2f-0d3f-47d8-a6a6-13eda0a3955f", + "meta": { + "tag": [ + { + "system": 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b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR/sample_oru_20241015-001.hl7 new file mode 100644 index 00000000000..58e98348cab --- /dev/null +++ b/prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR/sample_oru_20241015-001.hl7 @@ -0,0 +1,173 @@ +MSH|^~\&|TESTSENDER|TESTSENDER|TESTRECEIVER^123456^L,M,N|^automated-staging-test-receiver-id^L,M,N|20241015034304||ORU^R01^ORU_R01|AUTOMATEDTEST-003|T|2.5.1 +PID|1||12345678^^^&NPI^MR||TESTSIX^BOY MOMSIX^^^^^B|||M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||N|1 +NK1|1|CDPHSIX|MTH^Mother|132 ST^^SAN DIEGO^CA^92126^USA +ORC|RE|55555555^FormNumber||456789123^HospOrdNumber||||||||^TEST^DOCTOR|||||||||TEST HOSPITAL^^^^^^^^^R797| 123 MAIN ST.^^SAN DIEGO^CA^99999-9999 +OBR|1|55555555^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBR|2|55555555^FormNumber||57128-1^Newborn Screening Report summary panel|||202410151535|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|CE|57721-3^Reason for lab test in Dried blood spot^LN|1|LA12421-6^Initial screen^LN|||N|||F|||20241015034304 +OBX|2|CE|57718-9^Sample quality of Dried blood spot^LN|1|LA12432-3^Acceptable^LN|||N|||F|||20241015034304 +OBX|3|CE|57130-7^Newborn screening report - overall interpretation^LN|1|LA18944-1^Screen is out of range for at least one condition^LN|||N|||F|||20241015034304 +OBX|4|CE|57131-5^Newborn conditions with positive markers [Identifier] in Dried blood spot^LN|1|LA22279-6^SMA^LN|||N|||F|||20241015034304 +OBX|5|CE|57720-5^Newborn conditions with equivocal markers [Identifier] in Dried blood spot^LN|1|LA137-2^None^LN|||N|||F|||20241015034304 +OBX|6|TX|57724-7^Newborn screening short narrative summary^LN|1|ACTION REQUIRED\.br\\.br\NBS Testing Lab - TEST REG MEDICAL CENTER LAB \R\M 57752YWKP NAEBC, ETS8021 , FRESNO, CA 99999\.br\\.br\Genetic Disease Laboratory - GDL SAW 19221DVLB NOTGNIH, RICHMOND, CA 99999-9999\.br\\.br\Lab Director - Genetic Disease Laboratory, (510) 231-1790\.br\\.br\Follow-up:\.br\\.br\Amino Acid Panel: There was insufficient data to determine whether or not this newborn was at least 12 hours old when this specimen was collected. Testing of amino acids at less than 12 hours of age is not reliable for detecting certain metabolic disorder. \.br\\.br\Spinal Muscular Atrophy (SMA): An immediate referral to a CCS-approved Neuromuscular Center for evaluation and additional testing is strongly recommended due an apparent SMN1 exon 7 homozygous deletion. \.br\\.br\If you have any questions regarding these screening outcomes, please contact the Newborn Screening Staff at Rady Children's Hospital San Diego at (161) 122-8708. \.br\\.br\Methods and Limitations:\.br\\.br\Assays for ALD Tier-1, BD, CAH, CF, GAL, MS/MS Acylcarnitine and Amino Acid Panels, PCH, hemoglobinopathies, and SCID were performed at the testing laboratory specified on the front of this report. Assays for ALD Tier-2, CAH Tier-2, Pompe Disease Tier-1, MPS I Tier-1, and SMA were developed and/or optimized by the Genetic Disease Laboratory (GDL), and performed at GDL. Performance characteristics of these assays are determined by GDL. The SMA assay is designed to identify 95% of SMA patients who have homozygous deletions of the SMN1 gene on chromosome 5q. These assays have not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. The assays are used for clinical purposes. They should not be regarded as investigational or for research. GDL is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA-88) to perform high complexity genetic disease screening. \.br\Attention Healthcare Provider:\.br\\.br\Due to biological variability of newborns and differences in detection rates for the various disorders in the newborn period, the Newborn Screening Program will not identify all newborns with these conditions. While a positive screening result identifies newborns at an increased risk to justify a diagnostic work-up, a negative screening result does not rule out the possibility of a disorder. Health care providers should remain watchful for any sign or symptoms of these disorders in their patients. A newborn screening result should not be considered diagnostic, and cannot replace the individualized evaluation and diagnosis of an infant by a well-trained, knowledgeable health care provider. \.br\\.br\|||N|||F|||20241015034304 +OBX|7|TX|57129-9^Full newborn screening summary report for display or printing^LN|1||||N|||F|||20241015034304 +OBX|8|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|1|LA22279-6^SMA^LN|||N|||F|||20241015034304 +OBX|9|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|2|LA25796-6^X-ALD^LN|||N|||F|||20241015034304 +OBX|10|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|3|LA14037-8^GAA^LN|||N|||F|||20241015034304 +OBX|11|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|4|LA25797-4^MPS-I^LN|||N|||F|||20241015034304 +OBX|12|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|5|LA12466-1^3-MCC^LN|||N|||F|||20241015034304 +OBX|13|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|6|LA12468-7^3MGA^LN|||N|||F|||20241015034304 +OBX|14|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|7|LA12469-5^5-OXO^LN|||N|||F|||20241015034304 +OBX|15|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|8|LA12470-3^ARG^LN|||N|||F|||20241015034304 +OBX|16|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|9|LA12482-8^CIT-I^LN|||N|||F|||20241015034304 +OBX|17|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|10|LA12483-6^CIT-II^LN|||N|||F|||20241015034304 +OBX|18|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|11|LA12485-1^CPT-Ia^LN|||N|||F|||20241015034304 +OBX|19|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|12|LA12486-9^CPT-II^LN|||N|||F|||20241015034304 +OBX|20|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|13|LA12493-5^GA-1^LN|||N|||F|||20241015034304 +OBX|21|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|14|LA12495-0^GA-2^LN|||N|||F|||20241015034304 +OBX|22|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|15|LA12497-6^HHH^LN|||N|||F|||20241015034304 +OBX|23|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|16|LA12499-2^HMG^LN|||N|||F|||20241015034304 +OBX|24|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|17|LA12505-6^IVA^LN|||N|||F|||20241015034304 +OBX|25|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|18|LA12507-2^LCHAD^LN|||N|||F|||20241015034304 +OBX|26|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|19|LA12508-0^MAL^LN|||N|||F|||20241015034304 +OBX|27|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|20|LA12509-8^MCAD^LN|||N|||F|||20241015034304 +OBX|28|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|21|LA12510-6^MCD^LN|||N|||F|||20241015034304 +OBX|29|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|22|LA12512-2^MET^LN|||N|||F|||20241015034304 +OBX|30|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|23|LA12513-0^MSUD^LN|||N|||F|||20241015034304 +OBX|31|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|24|LA12516-3^NKHG^LN|||N|||F|||20241015034304 +OBX|32|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|25|LA12520-5^PKU^LN|||N|||F|||20241015034304 +OBX|33|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|26|LA12521-3^PRO I^LN|||N|||F|||20241015034304 +OBX|34|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|27|LA12528-8^TYR-1^LN|||N|||F|||20241015034304 +OBX|35|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|28|LA12529-6^TYR-II^LN|||N|||F|||20241015034304 +OBX|36|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|29|LA12531-2^VLCAD^LN|||N|||F|||20241015034304 +OBX|37|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|30|LA12532-0^BIO^LN|||N|||F|||20241015034304 +OBX|38|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|31|LA12533-8^CAH^LN|||N|||F|||20241015034304 +OBX|39|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|32|LA12537-9^CF^LN|||N|||F|||20241015034304 +OBX|40|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|33|LA12543-7^GALT^LN|||N|||F|||20241015034304 +OBX|41|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|34|LA12566-8^SCID^LN|||N|||F|||20241015034304 +OBX|42|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|35|LA12576-7^SCAD or EMA or IBG or GA-2 (MADD)^LN|||N|||F|||20241015034304 +OBX|43|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|36|LA16207-5^Hemoglobinopathies^LN|||N|||F|||20241015034304 +OBX|44|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|37|99717-3^Hypothyroidism^L|||N|||F|||20241015034304 +OBX|45|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|38|LA12487-7^CUD^LN|||N|||F|||20241015034304 +OBX|46|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|39|LA12474-5^BKT^LN|||N|||F|||20241015034304 +OBX|47|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|40|LA12523-9^PA^LN|||N|||F|||20241015034304 +OBX|48|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|41|LA12515-5^MMA^LN|||N|||F|||20241015034304 +OBX|49|CE|57719-7^Conditions tested for in this newborn screening study [Identifier] in Dried blood spot^LN|42|LA12464-6^2M3HBA^LN|||N|||F|||20241015034304 +OBR|3|55555555^FormNumber||57717-1^Newborn screen card data panel|||202410151535|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|ST|57716-3^State printed on filter paper card [Identifier] in NBS card^LN|1|CA|||N|||F|||20241015034304 +OBX|2|NM|8339-4^Birthweight^LN|1|3000|grams||N|||F|||20241015034304 +OBX|3|CE|57722-1^Birth plurality of Pregnancy^LN|1|LA12411-7^Singleton^LN|||N|||F|||20241015034304 +OBX|4|CE|57713-0^Infant NICU factors that affect newborn screening interpretation^LN|1|LA137-2^None^LN|||N|||F|||20241015034304 +OBX|5|CE|67704-7^Feeding types^LN|1|LA16914-6^Breast milk^LN|||N|||F|||20241015034304 +OBX|6|TX|^^^99717-5^Accession Number^L|1|045-89-477/21-2024-21|||N|||F|||20241015034304 +OBX|7|TX|62324-9^Post-discharge provider name^LN|1|TEST DOCTOR|||N|||F|||20241015034304 +OBX|8|TX|62327-2^Post-discharge provider practice address^LN|1|123 MAIN ST SAN DIEGO CA 99999-9999 USA|||N|||F|||20241015034304 +OBR|4|55555555^FormNumber||57794-0^Newborn screening test results panel in Dried blood spot|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBR|5|55555555^FormNumber||53261-4^Amino acid newborn screen panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|47633-3^Glycine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20241015034304 +OBX|2|NM|53150-9^Alanine+Beta Alanine+Sarcosine [Moles/volume] in Dried blood spot^LN|1|500|µmol/L|<1000|N|||F|||20241015034304 +OBX|3|NM|47799-2^Valine [Moles/volume] in Dried blood spot^LN|1|0.5|µmol/L||N|||F|||20241015034304 +OBX|4|NM|53151-7^Valine/Phenylalanine [Molar ratio] in Dried blood spot^LN|1|0.00645|{Ratio}|<4.3|N|||F|||20241015034304 +OBX|5|NM|53152-5^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline^LN|1|125|µmol/L|<230|N|||F|||20241015034304 +OBX|6|NM|53154-1^Alloisoleucine+Isoleucine+Leucine+Hydroxyproline/Alanine [Molar ratio] in Dried blood spot^LN|1|0.65|{Ratio}|<1.35|N|||F|||20241015034304 +OBX|7|NM|29573-3^Phenylalanine [Moles/volume] in Dried blood spot^LN|1|77.5|µmol/L|<175|N|||F|||20241015034304 +OBX|8|NM|35572-7^Phenylalanine/Tyrosine [Molar ratio] in Dried blood spot^LN|1|0.75|{Ratio}|<2.6|N|||F|||20241015034304 +OBX|9|NM|35571-9^Tyrosine [Moles/volume] in Dried blood spot^LN|1|425|µmol/L|<680|N|||F|||20241015034304 +OBX|10|NM|53231-7^Succinylacetone [Moles/volume] in Dried blood spot^LN|1|2.25|µmol/L|<6.1|N|||F|||20241015034304 +OBX|11|NM|47700-0^Methionine [Moles/volume] in Dried blood spot^LN|1|27|µmol/L|6.3-100|N|||F|||20241015034304 +OBX|12|NM|42892-0^Citrulline [Moles/volume] in Dried blood spot^LN|1|16.25|µmol/L|5-49|N|||F|||20241015034304 +OBX|13|NM|54092-2^Citrulline/Arginine [Molar ratio] in Dried blood spot^LN|1|3|{Ratio}|<4.8|N|||F|||20241015034304 +OBX|14|NM|53155-8^Asparagine+Ornithine [Moles/volume] in Dried blood spot^LN|1|400|µmol/L|<800|N|||F|||20241015034304 +OBX|15|NM|75215-4^Ornithine/Citrulline [Molar ratio] in Dried blood spot^LN|1|0.5|{Ratio}||N|||F|||20241015034304 +OBX|16|NM|47562-4^Arginine [Moles/volume] in Dried blood spot^LN|1|25|µmol/L|<63|N|||F|||20241015034304 +OBX|17|NM|75214-7^Arginine/Ornithine [Molar ratio] in Dried blood spot^LN|1|0.7|{Ratio}|<1.9|N|||F|||20241015034304 +OBX|18|NM|47732-3^Proline [Moles/volume] in Dried blood spot^LN|1|750|µmol/L|<1500|N|||F|||20241015034304 +OBX|19|TX|57710-6^Amino acidemias newborn screening comment/discussion^LN|1|Collected Early. No Interpretation.|||A|||F|||20241015034304 +OBR|6|55555555^FormNumber||58092-8^Acylcarnitine newborn screen panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|CE|58088-6^Acylcarnitine newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|2|TX|58093-6^Acylcarnitine newborn screening comment/discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|7|7181233072^FormNumber||57084-6^Fatty acid oxidation newborn screen panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|38481-8^Carnitine.free (C0)^LN|1|33|µmol/L|6.4-125|N|||F|||20241015034304 +OBX|2|NM|53235-8^Carnitine.free (C0)/Palmitoylcarnitine (C16)+Stearoylcarnitine (C18)^LN|1|37.5|{Ratio}|<70|N|||F|||20241015034304 +OBX|3|NM|50157-7^Acetylcarnitine (C2)^LN|1|20.38|µmol/L|10-80|N|||F|||20240226034304 +OBX|4|NM|75212-1^Malonylcarnitine (C3-DC)/Decanoylcarnitine (C10) [Molar ratio] in Dried blood spot^LN|1|0.62500|{Ratio}|<7.6|N|||F|||20241015034304 +OBX|5|NM|45211-0^Hexanoylcarnitine (C6)^LN|1|0.48|µmol/L|<0.95|N|||F|||20241015034304 +OBX|6|NM|53175-6^Octanoylcarnitine (C8)^LN|1|0.3|µmol/L|<0.45|N|||F|||20241015034304 +OBX|7|NM|53177-2^Octanoylcarnitine (C8)/Decanoylcarnitine (C10)^LN|1|0.5|{Ratio}||N|||F|||20241015034304 +OBX|8|NM|53174-9^Octenoylcarnitine (C8:1)^LN|1|0.35|µmol/L|<0.65|N|||F|||20241015034304 +OBX|9|NM|45197-1^Decanoylcarnitine (C10)^LN|1|0.32|µmol/L|<0.65|N|||F|||20241015034304 +OBX|10|NM|45198-9^Decenoylcarnitine (C10:1)^LN|1|0.22|µmol/L|<0.45|N|||F|||20241015034304 +OBX|11|NM|45199-7^Dodecanoylcarnitine (C12)^LN|1|1|µmol/L|<2|N|||F|||20241015034304 +OBX|12|NM|45200-3^Dodecenoylcarnitine (C12:1)^LN|1|0.5|µmol/L||N|||F|||20241015034304 +OBX|13|NM|53192-1^Tetradecanoylcarnitine (C14)^LN|1|0.6|µmol/L|<1.2|N|||F|||20241015034304 +OBX|14|NM|53191-3^Tetradecenoylcarnitine (C14:1)^LN|1|0.4|µmol/L|<0.9|N|||F|||20241015034304 +OBX|15|NM|53194-7^Tetradecenoylcarnitine (C14:1)/Dodecenoylcarnitine (C12:1)^LN|1|0.5|{Ratio}||N|||F|||20241015034304 +OBX|16|NM|53190-5^Tetradecadienoylcarnitine (C14:2)^LN|1|0.5|µmol/L||N|||F|||20241015034304 +OBX|17|NM|50281-5^3-Hydroxytetradecanoylcarnitine (C14-OH)^LN|1|0.1|µmol/L|<0.2|N|||F|||20241015034304 +OBX|18|NM|53199-6^Palmitoylcarnitine (C16)^LN|1|5|µmol/L|<12|N|||F|||20241015034304 +OBX|19|NM|53198-8^Palmitoleylcarnitine (C16:1)^LN|1|0.7|µmol/L|<1.4|N|||F|||20241015034304 +OBX|20|NM|50125-4^3-Hydroxypalmitoylcarnitine (C16-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20241015034304 +OBX|21|NM|53201-0^3-Hydroxypalmitoylcarnitine (C16-OH)/Palmitoylcarnitine (C16)^LN|1|0.01000|{Ratio}|<0.07|N|||F|||20241015034304 +OBX|22|NM|53241-6^Stearoylcarnitine (C18)^LN|1|2|µmol/L|<3.5|N|||F|||20241015034304 +OBX|23|NM|53202-8^Oleoylcarnitine (C18:1)^LN|1|3.5|µmol/L|<7|N|||F|||20241015034304 +OBX|24|NM|45217-7^Linoleoylcarnitine (C18:2)^LN|1|0.5|µmol/L||N|||F|||20241015034304 +OBX|25|NM|50132-0^3-Hydroxystearoylcarnitine (C18-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20241015034304 +OBX|26|NM|50113-0^3-Hydroxyoleoylcarnitine (C18:1-OH)^LN|1|0.05|µmol/L|<0.1|N|||F|||20241015034304 +OBR|8|55555555^FormNumber||57085-3^Organic acid newborn screen panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|53160-8^Propionylcarnitine (C3)^LN|1|3.15|µmol/L|<7.9|N|||F|||20241015034304 +OBX|2|NM|53163-2^Propionylcarnitine (C3)/Acetylcarnitine (C2)^LN|1|0.15|{Ratio}|<0.42|N|||F|||20241015034304 +OBX|3|NM|67708-8^Malonylcarnitine (C3-DC)+3-Hydroxybutyrylcarnitine (C4-OH)^LN|1|0.2|µmol/L|<0.48|N|||F|||20241015034304 +OBX|4|NM|53166-5^Butyrylcarnitine+Isobutyrylcarnitine (C4)^LN|1|0.85|µmol/L|<1.7|N|||F|||20241015034304 +OBX|5|NM|45216-9^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)^LN|1|0.5|µmol/L|<0.95|N|||F|||20241015034304 +OBX|6|NM|53240-8^Isovalerylcarnitine+Methylbutyrylcarnitine (C5)/Propionylcarnitine (C3)^LN|1|0.15873|{Ratio}|<0.38|N|||F|||20241015034304 +OBX|7|NM|53170-7^Tiglylcarnitine (C5:1)^LN|1|0.3|µmol/L|<0.5|N|||F|||20241015034304 +OBX|8|NM|50106-4^3-Hydroxyisovalerylcarnitine (C5-OH)^LN|1|0.45|µmol/L|<1.15|N|||F|||20241015034304 +OBX|9|NM|67710-4^Glutarylcarnitine (C5-DC)+3-Hydroxyhexanoylcarnitine (C6-OH)^LN|1|0.3|µmol/L|<0.38|N|||F|||20241015034304 +OBX|10|NM|75216-2^Glutarylcarnitine (C5-DC)/Malonylcarnitine (C3-DC) [Molar ratio] in Dried blood spot^LN|1|1.50000|{Ratio}|>0.1|N|||F|||20241015034304 +OBR|9|55555555^FormNumber||54078-1^Cystic fibrosis newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|48633-2^Trypsinogen I.free^LN|1|31.00|ng/mL|<71|N|||F|||20241015034304 +OBX|2|CE|46769-6^Cystic fibrosis newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|57707-2^Cystic fibrosis newborn screening comment/discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|10|55555555^FormNumber||57086-1^Congenital adrenal hyperplasia newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|38473-5^17-Hydroxyprogesterone^LN|1|35|nmol/L|<85|N|||F|||20241015034304 +OBX|2|CE|46758-9^Congenital adrenal hyperplasia newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|57706-4^Congenital adrenal hyperplasia newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|11|55555555^FormNumber||54090-6^Thyroid newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|29575-8^Thyrotropin^LN|1|14.50|mIU/L|<29|N|||F|||20241015034304 +OBX|2|CE|46762-1^Congenital hypothyroidism newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|57705-6^Congenital hypothyroidism newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|12|55555555^FormNumber||54079-9^Galactosemia newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|55.00|enzyme units|>50|N|||F|||20241015034304 +OBX|2|CE|46737-3^Galactosemias newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|57704-9^Galactosemias newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|13|55555555^FormNumber||54081-5^Hemoglobinopathies newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|TX|54104-5^Hemoglobin pattern^LN|1|FA||||||F|||20241015034304 +OBX|2|TX|57703-1^Hemoglobin disorders newborn screening comment/discussion^LN|1|Usual hemoglobin pattern.†These results assume no transfusion prior to testing and do not rule out the possibility of a thalassemia trait or rare hemoglobin variants.||||||F|||20241015034304 +OBR|14|55555555^FormNumber||57087-9^Biotinidase newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|75217-0^Biotinidase [Enzymatic activity/volume] in Dried blood spot^LN|1|15.00|ERU|>10|N|||F|||20241015034304 +OBX|2|CE|46761-3^Biotinidase deficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|57699-1^Biotinidase deficiency newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|15|55555555^FormNumber||62333-0^Severe combined immunodeficiency (SCID) newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|62320-7^T-cell receptor excision circle [#/volume] in Dried blood spot by Probe and target amplification method^LN|1|33|copies/µL|>18|N|||F|||20241015034304 +OBX|2|CE|62321-5^Severe combined immunodeficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|62322-3^Severe combined immunodeficiency newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBR|16|55555555^FormNumber||63414-7^Pompe Disease newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|55827-0^Acid alpha glucosidase [Enzymatic activity/volume] in DBS^LN|1|12.923|µmol/L/h|>=2.079|N|||F|||20241015034304 +OBX|2|CE|63415-4^Pompe Disease deficiency newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|63416-2^Pompe Disease deficiency newborn screening comments-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBX|4|TX|63416-2^Pompe Disease deficiency newborn screening comments-discussion^LN|2|Interpretation Comments: The acid alpha-glucosidase Enzyme activity level is above the 18% of the daily patient median and suggests it is screen negative for Pompe disease.|||N|||F|||20241015034304 +OBR|17|55555555^FormNumber||79563-3^Mucopolysaccharidosis type I newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|55909-6^Alpha-L-iduronidase [Enzymatic activity/volume] in DBS^LN|1|3.117|µmol/L/h|>=1.2204|N|||F|||20241015034304 +OBX|2|CE|79564-1^Mucopolysaccharidosis type I newborn screen interpretation^LN|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|3|TX|79565-8^Mucopolysaccharidosis type I newborn screening comment-discussion^LN|1|Negative|||N|||F|||20241015034304 +OBX|4|TX|79565-8^Mucopolysaccharidosis type I newborn screening comment-discussion^LN|2|Interpretation Comments: The alpha-L-iduronidase Enzyme activity is above the 18% of the daily patient median and suggests it is screen negative for Mucopolysaccharidosis I (MPS I) disease.|||N|||F|||20241015034304 +OBR|18|55555555^FormNumber||92005-8^Spinal muscular atrophy newborn screening panel|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|TX|^^^99717-60^SMN1 Homozygous Deletion Analysis^L|1|Exon 7 Absent||Exon 7 Present|A|||F|||20241015034304 +OBX|2|CE|92004-1^Spinal muscular atrophy newborn screen interpretation^LN|1|LA18593-6^Out of range^LN|||A|||F|||20241015034304 +OBX|3|TX|92003-3^Spinal muscular atrophy newborn screening comment-discussion^LN|1|SMA Positive|||A|||F|||20241015034304 +OBX|4|TX|92003-3^Spinal muscular atrophy newborn screening comment-discussion^LN|2|Interpretation Comments: qPCR detected possible homozygoues deletion in exon 7 of the SMN1 gene. Confirmatory test for SMN1 and SMN2 copy determination are required.|||A|||F|||20241015034304 +OBR|19|55555555^FormNumber||^^^99717-28^Adrenoleukodystrophy newborn screening panel^L|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|CE|^^^99717-32^Adrenoleukodystrophy deficiency newborn screening interpretation^L|1|LA18592-8^In range^LN|||N|||F|||20241015034304 +OBX|2|TX|^^^99717-33^Adrenoleukodystrophy deficiency newborn screening comments-discussion^L|1|Negative|||N|||F|||20241015034304 +OBR|20|555555552^FormNumber||^^^99717-29^Adrenoleukodystrophy Tier-1 newborn screening panel^L|||202410150335|||||||||^TEST^DOCTOR||||||20241015034304|||F +OBX|1|NM|79321-6^Lysophosphatidylcholine(26:0) [Moles/volume] in Dried blood spot^LN|1|0.2|µmol/L|<0.49|N|||F|||20241015034304 \ No newline at end of file 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 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 4e0b4b8b346..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" @@ -71,3 +71,4 @@ FHIR_to_HL7/sample_ME_20240806-0001.fhir,,FHIR_to_HL7/sample_ME_20240806-0001.hl FHIR_to_HL7/sample_SR_CSVUPLOADER_20240819-0001.fhir,,FHIR_to_HL7/sample_SR_CSVUPLOADER_20240819-0001.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/MA/MA-receiver-transform.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml","","","" FHIR_to_HL7/mars_unwanted_condition_to_notes.fhir,,FHIR_to_HL7/mars_unwanted_condition_to_notes.hl7,classpath:/metadata/hl7_mapping/receivers/STLTs/Test/test-receiver-transform.yml,HL7,PASS,,,classpath:/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml,,, FHIR_to_HL7/sample_SR_ENTEREDINERROR_20240904-0001.fhir,,FHIR_to_HL7/sample_SR_ENTEREDINERROR_20240904-0001.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","","","" +HL7_to_FHIR/sample_oru_20241015-001.hl7,,HL7_to_FHIR/sample_oru_20241015-001.fhir,,FHIR,PASS,"","","","","","" \ No newline at end of file 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 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..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 @@ -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 ) } }