feat(snomed): medications dates good pray

Refs: #1442

packages/core/src/external/aws/lambda-logic/bundle-to-html-snomed.ts

@@ -39,6 +39,7 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  patient,
  medications,
  medicationAdministrations,
+ medicationStatements,
  conditions,
  allergies,
  procedures,
@@ -219,7 +220,8 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  ${createMRHeader(patient)}
  <div class="divider"></div>
  <div id="mr-sections">
- ${createConditionLinkedMedicationSection(medications, medicationAdministrations)}
+ ${createDischargeMedicationsSection(medications, medicationAdministrations)}
+ ${createMedicationSection(medications, medicationStatements)}
  ${createConditionSection(conditions, encounters)}
  ${createAllergySection(allergies)}
  ${createProcedureSection(procedures)}
@@ -744,7 +746,7 @@ function createOrganiztionField(
  return organization?.name ? `<p>Facility: ${organization.name}</p>` : "";
 }
 
-function createConditionLinkedMedicationSection(
+function createDischargeMedicationsSection(
  medications: Medication[],
  medicationAdministrations: MedicationAdministration[]
 ) {
@@ -779,17 +781,35 @@ function createConditionLinkedMedicationSection(
  );
  });
 
- const medicationSection = createMedLinkedConditionSectionInMedications(
+ const activeMedications = removeDuplicate.filter(
+ medicationAdministration => medicationAdministration.status !== "stopped"
+ );
+
+ const oneYearAgo = dayjs().subtract(1, "year");
+
+ const activeMedicationsWithinLastYear = activeMedications.filter(medicationAdministration => {
+ const start = medicationAdministration.effectivePeriod?.start;
+ const end = medicationAdministration.effectivePeriod?.end;
+ const medicationStart = start ? dayjs(start) : undefined;
+ const medicationEnd = end ? dayjs(end) : undefined;
+ const isActive = medicationAdministration.status != "stopped";
+ const isWithinLastYear1 = medicationStart && medicationStart.isAfter(oneYearAgo);
+ const isWithinLastYear2 = medicationEnd && medicationEnd.isAfter(oneYearAgo);
+ const isWithinLastYear = isWithinLastYear1 || isWithinLastYear2;
+ return isActive && isWithinLastYear;
+ });
+
+ const medicationSection = createDischargeMedicationSection(
  mappedMedications,
- removeDuplicate,
- "Condition Linked Medications"
+ activeMedicationsWithinLastYear,
+ "Active Medications"
  );
 
  const medicalTableContents = `
  ${medicationSection}
  `;
 
- return createSection("Medications", medicalTableContents);
+ return createSection("Discharge Medications", medicalTableContents);
 }
 
 export function createMedicationSection(
@@ -801,6 +821,7 @@ export function createMedicationSection(
  }
 
  const mappedMedications = mapResourceToId<Medication>(medications);
+ //console.log("mappedMedications", mappedMedications);
 
  const medicationsSortedByDate = medicationStatements.sort((a, b) => {
  return dayjs(a.effectivePeriod?.start).isBefore(dayjs(b.effectivePeriod?.start)) ? 1 : -1;
@@ -813,52 +834,53 @@ export function createMedicationSection(
  return aDate === bDate && a.dosage?.[0]?.text === b.dosage?.[0]?.text;
  });
 
- const otherMedications = removeDuplicate.filter(
- medicationStatement => medicationStatement.status !== ("active" || "unknown")
- );
-
  const activeMedications = removeDuplicate.filter(
  medicationStatement => medicationStatement.status === "active"
  );
 
- const emptyMedications = removeDuplicate.filter(
- medicationStatement => !medicationStatement.status || medicationStatement.status === "unknown"
- );
+ const oneYearAgo = dayjs().subtract(1, "year");
+
+ const activeMedicationsWithinLastYear = activeMedications.filter(medicationStatement => {
+ const start = medicationStatement.effectivePeriod?.start;
+ const end = medicationStatement.effectivePeriod?.end;
+ const medicationStart = start ? dayjs(start) : undefined;
+ const medicationEnd = end ? dayjs(end) : undefined;
+ const isActive = medicationStatement.status === "active";
+ const isWithinLastYear1 = medicationStart && medicationStart.isAfter(oneYearAgo);
+ const isWithinLastYear2 = medicationEnd && medicationEnd.isAfter(oneYearAgo);
+ const isWithinLastYear = isWithinLastYear1 || isWithinLastYear2;
+ return isActive && isWithinLastYear;
+ });
+
+ // console.log("medications", medications);
+ // console.log("activeMedicationsWithinLastYear", activeMedicationsWithinLastYear);
 
  const activeMedicationsSection = createSectionInMedications(
  mappedMedications,
- activeMedications,
+ activeMedicationsWithinLastYear,
  "Active Medications"
  );
 
- const emptyMedicationsSection = createSectionInMedications(
- mappedMedications,
- emptyMedications,
- "Unknown Status Medications"
- );
-
- const completedMedicationsSection = createSectionInMedications(
- mappedMedications,
- otherMedications,
- "Other Status Medications"
- );
-
  const medicalTableContents = `
  ${activeMedicationsSection}
- ${emptyMedicationsSection}
- ${completedMedicationsSection}
  `;
 
  return createSection("Medications", medicalTableContents);
 }
 
-function getDateFromMedicationStatement(v: MedicationStatement): string | undefined {
+function getStartDateFromMedicationStatement(v: MedicationStatement): string | undefined {
  return v.effectivePeriod?.start;
 }
+function getEndDateFromMedicationStatement(v: MedicationStatement): string | undefined {
+ return v.effectivePeriod?.end;
+}
 
-function getDateFromMedicationAdministration(v: MedicationAdministration): string | undefined {
+function getStartDateFromMedicationAdministration(v: MedicationAdministration): string | undefined {
  return v.effectivePeriod?.start;
 }
+function getEndDateFromMedicationAdministration(v: MedicationAdministration): string | undefined {
+ return v.effectivePeriod?.end;
+}
 
 function createSectionInMedications(
  mappedMedications: Record<string, Medication>,
@@ -870,8 +892,8 @@ function createSectionInMedications(
  return ` <h4>${title}</h4><table><tbody><tr><td>${noMedFound}</td></tr></tbody></table>`;
  }
  const medicationStatementsSortedByDate = medicationStatements.sort((a, b) => {
- const aDate = getDateFromMedicationStatement(a);
- const bDate = getDateFromMedicationStatement(b);
+ const aDate = getStartDateFromMedicationStatement(a);
+ const bDate = getStartDateFromMedicationStatement(b);
  if (!aDate && !bDate) return 0;
  if (aDate && !bDate) return -1;
  if (!aDate && bDate) return 1;
@@ -888,7 +910,8 @@ function createSectionInMedications(
  <th>Dosage</th>
  <th>Status</th>
  <th>Code</th>
- <th>Date</th>
+ <th> Start Date</th>
+ <th> End Date</th>
  </div>
  </tr>
  </thead>
@@ -923,7 +946,10 @@ function createSectionInMedications(
  <td>${medicationStatement.status ?? ""}</td>
  <td>${code ?? ""}</td>
  <td>${formatDateForDisplay(
- getDateFromMedicationStatement(medicationStatement)
+ getStartDateFromMedicationStatement(medicationStatement)
+ )}</td>
+ <td>${formatDateForDisplay(
+ getEndDateFromMedicationStatement(medicationStatement)
  )}</td>
  </tr>
  `;
@@ -935,7 +961,7 @@ function createSectionInMedications(
  return medicalTableContents;
 }
 
-function createMedLinkedConditionSectionInMedications(
+function createDischargeMedicationSection(
  mappedMedications: Record<string, Medication>,
  medicationAdministrations: MedicationAdministration[],
  title: string
@@ -945,8 +971,8 @@ function createMedLinkedConditionSectionInMedications(
  return ` <h4>${title}</h4><table><tbody><tr><td>${noMedFound}</td></tr></tbody></table>`;
  }
  const medicationStatementsSortedByDate = medicationAdministrations.sort((a, b) => {
- const aDate = getDateFromMedicationAdministration(a);
- const bDate = getDateFromMedicationAdministration(b);
+ const aDate = getStartDateFromMedicationAdministration(a);
+ const bDate = getStartDateFromMedicationAdministration(b);
  if (!aDate && !bDate) return 0;
  if (aDate && !bDate) return -1;
  if (!aDate && bDate) return 1;
@@ -963,7 +989,8 @@ function createMedLinkedConditionSectionInMedications(
  <th>Dosage</th>
  <th>Status</th>
  <th>Code</th>
- <th>Date</th>
+ <th> Start Date</th>
+ <th> End Date</th>
  </div>
  </tr>
  </thead>
@@ -992,7 +1019,12 @@ function createMedLinkedConditionSectionInMedications(
  }</td>
  <td>${medicationAdministration.status ?? ""}</td>
  <td>${code ?? ""}</td>
- <td>${formatDateForDisplay(medicationAdministration.effectivePeriod?.start)}</td>
+ <td>${formatDateForDisplay(
+ getStartDateFromMedicationAdministration(medicationAdministration)
+ )}</td>
+ <td>${formatDateForDisplay(
+ getEndDateFromMedicationAdministration(medicationAdministration)
+ )}</td>
  </tr>
  `;
  })

packages/fhir-converter/src/templates/cda/Sections/Medication.hbs

@@ -10,50 +10,44 @@
  {{#if medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial}}
  {{>Resources/Medication.hbs medication=medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial ID=(generateUUID (toJsonString medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial))}},
  {{>References/MedicationStatement/medicationReference.hbs ID=(generateUUID (toJsonString medEntry.substanceAdministration)) REF=(concat 'Medication/' (generateUUID (toJsonString medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial)))}},
- {{#each (toArray medEntry.substanceAdministration.entryRelationship) as |medReq|}}
- {{#if medReq.supply}}
- {{>Resources/MedicationRequest.hbs medicationRequest=medReq.supply ID=(generateUUID (toJsonString medReq.supply))}},
+ {{#each (toArray medEntry.substanceAdministration.entryRelationship) as |entryRelationship|}}
+ {{#if entryRelationship.supply}}
+ {{>Resources/MedicationRequest.hbs medicationRequest=entryRelationship.supply ID=(generateUUID (toJsonString entryRelationship.supply))}},
  {{#with (evaluate 'Utils/GeneratePatientId.hbs' obj=@metriportPatientId) as |patientId|}}
- {{>References/MedicationRequest/subject.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Patient/' patientId.Id)}},
+ {{>References/MedicationRequest/subject.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Patient/' patientId.Id)}},
  {{/with}}
- {{>References/MedicationRequest/medicationReference.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Medication/' (generateUUID (toJsonString medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial)))}},
+ {{>References/MedicationRequest/medicationReference.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Medication/' (generateUUID (toJsonString medEntry.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial)))}},
  {{/if}}
  {{!-- I am keeping what was originally here but I have yet to see an author placed here --}}
- {{#if medReq.supply.author.assignedAuthor}}
- {{#with (evaluate 'Utils/GeneratePractitionerId.hbs' obj=medReq.supply.author.assignedAuthor) as |practitionerId|}}
- {{>Resources/Practitioner.hbs practitioner=medReq.supply.author.assignedAuthor ID=practitionerId.Id}},
- {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Practitioner/' practitionerId.Id)}}
+ {{#if entryRelationship.supply.author.assignedAuthor}}
+ {{#with (evaluate 'Utils/GeneratePractitionerId.hbs' obj=entryRelationship.supply.author.assignedAuthor) as |practitionerId|}}
+ {{>Resources/Practitioner.hbs practitioner=entryRelationship.supply.author.assignedAuthor ID=practitionerId.Id}},
+ {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Practitioner/' practitionerId.Id)}}
  {{/with}}
- {{#if medReq.supply.author.assignedAuthor.representedOrganization}}
- {{#with (evaluate 'Utils/GenerateOrganizationId.hbs' obj=medReq.supply.author.assignedAuthor.representedOrganization) as |orgId|}}
- {{>Resources/Organization.hbs org=medReq.supply.author.assignedAuthor.representedOrganization ID=orgId.Id}},
- {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Organization/' orgId.Id)}}
+ {{#if entryRelationship.supply.author.assignedAuthor.representedOrganization}}
+ {{#with (evaluate 'Utils/GenerateOrganizationId.hbs' obj=entryRelationship.supply.author.assignedAuthor.representedOrganization) as |orgId|}}
+ {{>Resources/Organization.hbs org=entryRelationship.supply.author.assignedAuthor.representedOrganization ID=orgId.Id}},
+ {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Organization/' orgId.Id)}}
  {{/with}}
  {{/if}}
- {{else if (and medReq.supply medEntry.substanceAdministration.author.assignedAuthor)}}
+ {{else if (and entryRelationship.supply medEntry.substanceAdministration.author.assignedAuthor)}}
  {{#with (evaluate 'Utils/GeneratePractitionerId.hbs' obj=medEntry.substanceAdministration.author.assignedAuthor) as |practitionerId|}}
  {{>Resources/Practitioner.hbs practitioner=medEntry.substanceAdministration.author.assignedAuthor ID=practitionerId.Id}},
- {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Practitioner/' practitionerId.Id)}}
+ {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Practitioner/' practitionerId.Id)}}
  {{/with}}
  {{#if medEntry.substanceAdministration.author.assignedAuthor.representedOrganization}}
  {{#with (evaluate 'Utils/GenerateOrganizationId.hbs' obj=medEntry.substanceAdministration.author.assignedAuthor.representedOrganization) as |orgId|}}
  {{>Resources/Organization.hbs org=medEntry.substanceAdministration.author.assignedAuthor.representedOrganization ID=orgId.Id}},
- {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString medReq.supply)) REF=(concat 'Organization/' orgId.Id)}}
+ {{>References/MedicationRequest/requester.hbs ID=(generateUUID (toJsonString entryRelationship.supply)) REF=(concat 'Organization/' orgId.Id)}}
  {{/with}}
  {{/if}}
+ {{else if (contains (toJsonString entryRelationship.observation.templateId) '2.16.840.1.113883.10.20.22.4.19')}}
+ {{>Resources/Condition.hbs conditionEntry=entryRelationship.observation ID=(generateUUID (toJsonString entryRelationship.observation))}},
+ {{!-- add condition recorder here --}}
+ {{>References/MedicationStatement/reasonReference.hbs ID=(generateUUID (toJsonString medEntry.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString entryRelationship.observation)))}},
  {{/if}}
-
  {{/each}}
  {{/if}}
- {{#if medEntry.substanceAdministration.precondition}}
- {{#each (toArray medEntry.substanceAdministration.precondition) as |precondition|}}
- {{#if precondition.criterion.value.code}}
- {{>Resources/Condition.hbs conditionEntry=precondition.criterion ID=(generateUUID (toJsonString criterion.value))}},
- {{>References/MedicationStatement/reasonReference.hbs ID=(generateUUID (toJsonString medEntry.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString criterion.value)))}},
- {{/if}}
- {{/each}}
- {{/if}}
-
  {{#if medEntry.substanceAdministration.informant.assignedEntity.representedOrganization.name._}}
  {{>Resources/Organization.hbs org=medEntry.substanceAdministration.informant.assignedEntity.representedOrganization ID=(generateUUID (toJsonString medEntry.substanceAdministration.informant.assignedEntity.representedOrganization))}},
  {{/if}}

packages/utils/src/customer-requests/full-snomed-pipeline.ts

@@ -54,7 +54,7 @@ export async function ensureDirectory(): Promise<void> {
 
 async function fetchAndSavePatientData(patientId: string): Promise<void> {
  try {
- const resources = ["Conditions, Procedures, MedicationAdministration"];
+ const resources = ["Condition, Procedure, MedicationStatement, MedicationAdministration"];
  const data = await metriportApi.getPatientConsolidated(patientId, resources);
  const fhirPatient = await getFhirPatientData(patientId);
  const resourceWrappedFhirPatient = { resource: fhirPatient };

packages/utils/src/fhir-converter/e2e-test.ts

@@ -54,8 +54,8 @@ dayjs.extend(duration);
  * - fhirBaseUrl: the URL of the FHIR server;
  */
 
-const cdaLocation = ``;
-const converterBaseUrl = "http:https://localhost:8777";
+const cdaLocation = `/Users/jonahkaye/Desktop/2024-01-23T08:02:29.892Z/test-patient-sample`;
+const converterBaseUrl = "http:https://localhost:8080";
 const fhirBaseUrl = "http:https://localhost:8889";
 const parallelConversions = 10;
 // Execute 1 batch at a time to avoid concurrency when upserting resources (resulting in 409/Conflict), which