platform/dependabot/2024-12-26

auth/build.gradle.kts

@@ -48,7 +48,7 @@ configurations.all {
 
 dependencyManagement {
     imports {
-        mavenBom("com.azure.spring:spring-cloud-azure-dependencies:5.18.0")
+        mavenBom("com.azure.spring:spring-cloud-azure-dependencies:5.19.0")
         mavenBom("org.springframework.cloud:spring-cloud-dependencies:2024.0.0")
     }
 }

frontend-react/src/content/developer-resources/reportstream-api/ReportStreamApi.mdx

@@ -31,9 +31,6 @@ import site from "../../site.json";
         </Card>
     </CardGroup>
 
-
-    <p>Our API guide and documentation is also available as a <A href={site.assets.programmersGuidePdf.path} trackClick={{name: "ReportStream API"}} download>downloadable PDF</A>.</p>
-
     ***
     <br/>
 

frontend-react/src/content/developer-resources/reportstream-api/getting-started/GettingStarted.mdx

@@ -8,10 +8,14 @@ meta:
             altText: "A collection of lines extend out from a central point. Each line ends in a circle of square, some green and some white."
 ---
 
-import Step1 from "./Step1.mdx";
-import Step2 from "./Step2.mdx";
-import Step3 from "./Step3.mdx";
-import Step4 from "./Step4.mdx";
+import Step2_1 from "./Step2_1.mdx";
+import Step2_2 from "./Step2_2.mdx";
+import Step2_3 from "./Step2_3.mdx";
+import Step2_4 from "./Step2_4.mdx";
+import Step3_1 from "./Step3_1.mdx";
+import Step3_2 from "./Step3_2.mdx";
+import Step3_3 from "./Step3_3.mdx";
+import Step3_4 from "./Step3_4.mdx";
 import Sidenav from "../Sidenav.mdx";
 import site from "../../../site.json";
 
@@ -25,7 +29,7 @@ import site from "../../../site.json";
 Examples in this guide use curl commands for simplicity with the assumption you’ll be coding these calls into your sending system.
 You can also use a program like Postman to test submissions.
 
-<p className="text-base">**Last updated:** 11/4/24</p>
+<p className="text-base">**Last updated:** 12/17/24</p>
 
 ***
 
@@ -42,10 +46,41 @@ to review <A href={site.forms.contactUs.url}>upon request</A>.
 
 When you’ve formatted your fake (non-PII) data file, test your data model using the
 <A href={site.external.nistValidationSuite.url}>NIST Electronic Lab Reporting (ELR) Validation Suite</A>. 
-(Note: If you’re testing OTC data, use the <A href={site.external.nistGeneralValidationTool.url}>NIST HL7 General Validation Tool</A> and 
-select “RADx MARS HL7v2” from the tool scope dropdown. Navigate to the “Context-free” tab and select the “Onboarding” profile group).
+Note: If you’re testing OTC data, use the <A href={site.external.nistGeneralValidationTool.url}>NIST HL7 General Validation Tool</A> and 
+select **RADx MARS HL7v2** from the **Tool Scopes** dropdown. Navigate to the **Context-free** tab and select the **Onboarding** profile group.
 Correct any errors you receive.
 
+<h2 className="rs-numbered">Map your codes</h2>
+
+We will ensure that all potential codes you might send to ReportStream are mapped in our system as part of your onboarding. First, format your result and organism codes in a CSV file using our <A href={site.assets.codeMapTemplate.path}>template</A>. Then, send the completed CSV to your onboarding engineer or <A href={site.orgs.RS.email}>[email protected]</A>. We will review your codes and provide next steps to continue your onboarding.
+
+<Accordion bordered multiselectable items={[
+    {
+        headingLevel: "h3",
+        title: "Step 2.1: Set up your file",
+        content: <Step2_1 />,
+        id: "2_1"
+    },
+    {
+        headingLevel: "h3",
+        title: "Step 2.2: Input all result codes",
+        content: <Step2_2 />,
+        id: "2_2"
+    },
+    {
+        headingLevel: "h3",
+        title: "Step 2.3: Input all organism codes (if applicable)",
+        content: <Step2_3 />,
+        id: "2_3"
+    },
+    {
+        headingLevel: "h3",
+        title: "Step 2.4: Upload your file",
+        content: <Step2_4 />,
+        id: "2_4"
+    },
+]} />
+
 <h2 className="rs-numbered">Set up authentication and test your API connection</h2>
 
 After you have finalized the formatting of your data, the ReportStream team will begin onboarding you to our staging environment.
@@ -68,27 +103,27 @@ The data submitted are sent as the payload of the POST, as is, with no changes.
 <Accordion bordered multiselectable items={[
     {
         headingLevel: "h3",
-        title: "Step 1: Prior to submission, send your public key to ReportStream.",
-        content: <Step1 />,
-        id: 1
+        title: "Step 3.1: Prior to submission, send your public key to ReportStream.",
+        content: <Step3_1 />,
+        id: "3_1"
     },
     {
         headingLevel: "h3",
-        title: "Step 2: At the time of submission, generate a signed JWT using your private key",
-        content: <Step2 />,
-        id: 2
+        title: "Step 3.2: At the time of submission, generate a signed JWT using your private key",
+        content: <Step3_2 />,
+        id: "3_2"
     },
     {
         headingLevel: "h3",
-        title: "Step 3: Send the signed JWT to ReportStream to get a temporary bearer token",
-        content: <Step3 />,
-        id: 3
+        title: "Step 3.3: Send the signed JWT to ReportStream to get a temporary bearer token",
+        content: <Step3_3 />,
+        id: "3_3"
     },
     {
         headingLevel: "h3",
-        title: "Step 4: Submit data to ReportStream using the bearer token",
-        content: <Step4 />,
-        id: 4
+        title: "Step 3.4: Submit data to ReportStream using the bearer token",
+        content: <Step3_4 />,
+        id: "3_4"
     },
 ]} />
 

frontend-react/src/content/developer-resources/reportstream-api/getting-started/Step2_1.mdx

@@ -0,0 +1,85 @@
+---
+tableContent: [
+    [
+        {
+            columnKey: "Code",
+            columnHeader: "Code",
+            content: "97099-6",
+        },
+        {
+            columnKey: "Name",
+            columnHeader: "Name",
+            content: "Influenza virus A and B and SARS-CoV-2 (COVID-19) Ag panel - Upper respiratory specimen by Rapid immunoassay",
+        },
+        {
+            columnKey: "CodingSystem",
+            columnHeader: "Coding system",
+            content:
+                "LOINC",
+        },
+    ],
+    [
+        {
+            columnKey: "Code",
+            columnHeader: "Code",
+            content: "123456",
+        },
+        {
+            columnKey: "Name",
+            columnHeader: "Name",
+            content: "LDT Flu Test",
+        },
+        {
+            columnKey: "CodingSystem",
+            columnHeader: "Coding system",
+            content:
+                "LOCAL",
+        },
+    ],
+    [
+        {
+            columnKey: "Code",
+            columnHeader: "Code",
+            content: "47457-7",
+        },
+        {
+            columnKey: "Name",
+            columnHeader: "Name",
+            content: "Influenza virus A H8 Ab [Titer] in Serum",
+        },
+        {
+            columnKey: "CodingSystem",
+            columnHeader: "Coding system",
+            content:
+                "LOINC",
+        },
+    ],
+    [
+        {
+            columnKey: "Code",
+            columnHeader: "Code",
+            content: "115329001",
+        },
+        {
+            columnKey: "Name",
+            columnHeader: "Name",
+            content: "Methicillin resistant Staphylococcus aureus",
+        },
+        {
+            columnKey: "CodingSystem",
+            columnHeader: "Coding system",
+            content: "SNOMEDCT",
+        },
+    ],
+]
+---
+
+import { Table } from "../../../../shared";
+import site from "../../../site.json";
+
+
+Download our <A href={site.assets.codeMapTemplate.path}>template</A> that provides detailed instructions and correctly formatted columns.   
+
+If you do not want to use the template, you can also create your own file. The CSV file should only contain three columns labeled: Code, Name, and Coding system as shown in the example below. 
+
+<Table borderless rowData={frontmatter.tableContent} />

frontend-react/src/content/developer-resources/reportstream-api/getting-started/Step2_2.mdx

@@ -0,0 +1,7 @@
+Enter all result codes your organization will use to send data through ReportStream.   
+
+In column A (**Code**): Enter the coded value for all performed test results. This should be the value sent in `OBX-3.1` in an HL7 Message or `Bundle.entry.resource.ofType(Observation).code.coding.code` of a FHIR Observation resource.   
+
+In column B (**Name**): Enter the textual description of the code in column A. If the value in column A is a LOINC code, use the LOINC Long Common Name. If the value in column A is a local code, use a descriptive result name. 
+
+In column C (**Coding system**): Enter `LOINC` if the value in column A is a LOINC code. Enter `LOCAL` if the value is a local code.  

frontend-react/src/content/developer-resources/reportstream-api/getting-started/Step2_3.mdx

@@ -0,0 +1,7 @@
+Input all codes for organisms that your organization will send through ReportStream. If you are not sending any reportable microbiological culture results, you can move on to Step 2.4.    
+
+In column A (**Code**): Enter the coded value for all potential reportable organisms. This should be the value sent in `OBX-5.1` in an HL7 Message or `Bundle.entry.resource.ofType(Observation).value CodableConcept.cod` of a FHIR Observation resource.   
+
+In column B (**Name**): Enter the textual description of the code in column A. If the value in column A is a SNOMED code, use the SNOMED description. If the value in column A is a local code, use a descriptive result name. 
+
+In column C (**Coding system**):  Enter `SNOMEDCT` if the value in column A is a SNOMED code. Enter `LOCAL` if the value is a local code.   

frontend-react/src/content/developer-resources/reportstream-api/getting-started/Step2_4.mdx

@@ -0,0 +1,3 @@
+import site from "../../../site.json";
+
+After completing the mapping file, export the column headers and filled rows as a CSV file. Send the generated CSV your onboarding engineer or <A href={site.orgs.RS.email}>[email protected]</A>. We will review your codes and provide next steps to continue your onboarding. 

frontend-react/src/content/site.json

@@ -59,6 +59,9 @@
     },
     "onePager": {
       "path": "/assets/pdf/ReportStream_Onepager_20240605.pdf"
+    },
+    "codeMapTemplate": {
+      "path": "/assets/xlsm/20241204_ReportStream-Mapping-Template.xlsm"
     }
   },
   "external": {

frontend-react/src/shared/ReportStreamFooter/ReportStreamFooter.tsx

@@ -68,7 +68,7 @@ export const ReportStreamFooter = () => {
                                 </IdentifierLink>
                             </IdentifierLinkItem>
                             <IdentifierLinkItem>
-                                <IdentifierLink href="https://www.cdc.gov/od/foia">
+                                <IdentifierLink href="https://www.cdc.gov/foia/">
                                     FOIA requests
                                 </IdentifierLink>
                             </IdentifierLinkItem>

prime-router/src/main/resources/metadata/fhir_transforms/senders/MMTC/mmtc-sender-transform.yml

@@ -10,3 +10,37 @@ elements:
     resource: "Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().organization.resolve().address"
     bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/state-from-zip-code").value[x]'
     value: [ '%resource.postalCode.getStateFromZipCode()' ]
+
+  # Ticket 16776
+  # Temporary override for MSH 5 and 6 until original fields are updated
+  # If this override is removed, the associated test files should also be removed: mmtc-msh5-msh6-sender-override.hl7
+  - name: msh-5-1-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.5")'
+    bundleProperty: '%resource.name'
+    value: [ '"CDC PRIME"' ]
+
+  - name: msh-5-2-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.5")'
+    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").value[x]'
+    value: [ '"2.16.840.1.114222.4.1.237821"' ]
+
+  - name: msh-5-3-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.5")'
+    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type").value[x]'
+    value: [ '"ISO"' ]
+
+    # Assume that HL7 messages will have these extension properties...
+  - name: msh-6-1-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.6").identifier.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "HD.1")'
+    bundleProperty: '%resource.value'
+    value: [ '"CDC PRIME"' ]
+
+  - name: msh-6-2-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.6").identifier.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "HD.2,HD.3")'
+    bundleProperty: '%resource.value'
+    value: [ '"2.16.840.1.114222.4.1.237821"' ]
+
+  - name: msh-6-3-override
+    resource: 'Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "MSH.6").identifier.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value = "HD.2,HD.3")'
+    bundleProperty: '%resource.type.coding[0].code'
+    value: [ '"ISO"' ]

prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/mmtc-msh5-msh6-sender-override-expected.hl7

@@ -0,0 +1 @@
+MSH|^~\&|MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|CAREEVOLUTION^00Z0000024^CLIA|CDC PRIME^2.16.840.1.114222.4.1.237821^ISO|CDC PRIME^2.16.840.1.114222.4.1.237821^ISO|20241212005051+0000||ORU^R01^ORU_R01|20241212005051_b1a608d13bee414faf86e1420c41305e|T|2.5.1|||NE|NE||UNICODE UTF-8|ENG^English^ISO||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISOSFT|CAREEVOLUTION|2022|MMTC.STAG|16498||20241203PID|1||a0fbea5818d347b8ba981d90ba48c63c^^^MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO^PI||~^^^^^^S||||||^^^^15206^USA||^^^^^111^1111111ORC|RE||b1a608d13bee414faf86e1420c41305e^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|||||||||^^SA.OTCSelfReport|||||||||SA.OTCSelfReport|^^^^15206|^^^^^111^1111111OBR|1||b1a608d13bee414faf86e1420c41305e^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71|||20241211120000-0500|||||||20241211120000-0500||^^SA.OTCSelfReport||||||20241211120000-0500|||FOBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUA^^99ELR^^^^Vunknown||20241211120000||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake CityNTE|1|L|BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUAOBX|2|NM|35659-2^Age at specimen collection^LN^^^^2.71||33|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|||||QSTSPM|1|^b1a608d13bee414faf86e1420c41305e&MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO||697989009^Anterior nares swab^SCT^^^^20200901|||||||||||||20241211120000-0500|20241211120000-0500

prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR_to_HL7/mmtc-msh5-msh6-sender-override.hl7

@@ -0,0 +1,9 @@
+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|20241212005051+0000||ORU^R01^ORU_R01|20241212005051_b1a608d13bee414faf86e1420c41305e|T|2.5.1|||NE|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO
+SFT|CAREEVOLUTION|2022|MMTC.STAG|16498||20241203
+PID|1||a0fbea5818d347b8ba981d90ba48c63c^^^MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO^PI||~^^^^^^S||||||^^^^15206^USA||^^^^^111^1111111
+ORC|RE||b1a608d13bee414faf86e1420c41305e^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|||||||||^^SA.OTCSelfReport|||||||||SA.OTCSelfReport|^^^^15206|^^^^^111^1111111
+OBR|1||b1a608d13bee414faf86e1420c41305e^MMTC.STAG^2.16.840.1.113883.3.8589.4.2.106.2^ISO|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71|||20241211120000-0500|||||||||^^SA.OTCSelfReport||||||20241211120000-0500|||F
+OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUA^^99ELR^^^^Vunknown||20241211120000||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|14 Fake AtHome Test Street^^Fake City
+NTE|1|L|BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUA
+OBX|2|NM|35659-2^Age at specimen collection^LN^^^^2.71||33|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
+SPM|1|^b1a608d13bee414faf86e1420c41305e&MMTC.STAG&2.16.840.1.113883.3.8589.4.2.106.2&ISO||697989009^Anterior nares swab^SCT^^^^20200901|||||||||||||20241211120000-0500|20241211120000-0500

prime-router/src/testIntegration/resources/datatests/translation-test-config.csv

@@ -70,4 +70,5 @@ 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,"","","","","",""
+HL7_to_FHIR/sample_oru_20241015-001.hl7,,HL7_to_FHIR/sample_oru_20241015-001.fhir,,FHIR,PASS,"","","","","",""
+HL7_to_FHIR_to_HL7/mmtc-msh5-msh6-sender-override.hl7,,HL7_to_FHIR_to_HL7/mmtc-msh5-msh6-sender-override-expected.hl7,classpath:/metadata/hl7_mapping/ORU_R01/ORU_R01-base.yml,HL7,PASS,"","","classpath:/metadata/fhir_transforms/senders/MMTC/mmtc-sender-transform.yml","","",""