Solved merge conflict

CDCgov · Oct 12, 2023 · e8161d5 · e8161d5
2 parents 394f8e3 + 1d35920
commit e8161d5
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Showing 57 changed files with 4,185 additions and 2,992 deletions.
diff --git a/.github/workflows/testingWorkflow.yml b/.github/workflows/testingWorkflow.yml
@@ -71,7 +71,7 @@ jobs:
     outputs:
       version: ${{ steps.set_backend_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Backend Image
         id: set_backend_version
         uses: ./.github/actions/docker-buildx
@@ -96,7 +96,7 @@ jobs:
     outputs:
       version: ${{ steps.set_cypress_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Cypress Image
         id: set_cypress_version
         uses: ./.github/actions/docker-buildx
@@ -121,7 +121,7 @@ jobs:
     outputs:
       version: ${{ steps.set_database_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Database Image
         id: set_database_version
         uses: ./.github/actions/docker-buildx
@@ -146,7 +146,7 @@ jobs:
     outputs:
       version: ${{ steps.set_frontend_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Frontend Image
         id: set_frontend_version
         uses: ./.github/actions/docker-buildx
@@ -179,7 +179,7 @@ jobs:
     outputs:
       version: ${{ steps.set_frontend_lighthouse_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Frontend Lighthouse Image
         id: set_frontend_lighthouse_version
         uses: ./.github/actions/docker-buildx
@@ -210,7 +210,7 @@ jobs:
     outputs:
       version: ${{ steps.set_nginx_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build Nginx Image
         id: set_nginx_version
         uses: ./.github/actions/docker-buildx

diff --git a/.../cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToDiagnosticReportProps.java b/.../cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToDiagnosticReportProps.java
@@ -0,0 +1,15 @@
+package gov.cdc.usds.simplereport.api.converter;
+
+import lombok.Builder;
+import lombok.Getter;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+
+@Builder
+@Getter
+public class ConditionAgnosticConvertToDiagnosticReportProps {
+  private String testPerformedCode;
+  private Patient patient;
+  private Observation observation;
+  private String testEffectiveDate;
+}
diff --git a/...a/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToObservationProps.java b/...a/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToObservationProps.java
@@ -0,0 +1,15 @@
+package gov.cdc.usds.simplereport.api.converter;
+
+import gov.cdc.usds.simplereport.db.model.auxiliary.TestCorrectionStatus;
+import lombok.Builder;
+import lombok.Getter;
+import org.hl7.fhir.r4.model.Patient;
+
+@Builder
+@Getter
+public class ConditionAgnosticConvertToObservationProps {
+  private TestCorrectionStatus correctionStatus;
+  private String testPerformedCode;
+  private Patient patient;
+  private String resultValue;
+}
diff --git a/.../java/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToPatientProps.java b/.../java/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticConvertToPatientProps.java
@@ -0,0 +1,14 @@
+package gov.cdc.usds.simplereport.api.converter;
+
+import lombok.Builder;
+import lombok.Getter;
+
+@Builder
+@Getter
+public class ConditionAgnosticConvertToPatientProps {
+  private String id;
+  private String firstName;
+  private String lastName;
+  private String nameAbsentReason;
+  private String gender;
+}
diff --git a/.../java/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticCreateFhirBundleProps.java b/.../java/gov/cdc/usds/simplereport/api/converter/ConditionAgnosticCreateFhirBundleProps.java
@@ -0,0 +1,19 @@
+package gov.cdc.usds.simplereport.api.converter;
+
+import java.util.List;
+import lombok.Builder;
+import lombok.Getter;
+import org.hl7.fhir.r4.model.DiagnosticReport;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Patient;
+import org.springframework.boot.info.GitProperties;
+
+@Builder
+@Getter
+public class ConditionAgnosticCreateFhirBundleProps {
+  private Patient patient;
+  private List<Observation> resultObservations;
+  private DiagnosticReport diagnosticReport;
+  private GitProperties gitProperties;
+  private String processingId;
+}
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java
@@ -88,4 +88,16 @@ private FhirConstants() {
 
   public static final String ORDER_EFFECTIVE_DATE_EXTENSION_URL =
       "https://reportstream.cdc.gov/fhir/StructureDefinition/order-effective-date";
+
+  public static final String OBSERVATION_CATEGORY_CODE_SYSTEM =
+      "https://terminology.hl7.org/5.2.0/CodeSystem-observation-category.html";
+  public static final String DATA_ABSENT_REASON_EXTENSION_URL =
+      "http://hl7.org/fhir/StructureDefinition/data-absent-reason";
+
+  public static final String DIAGNOSTIC_CODE_SYSTEM =
+      "https://terminology.hl7.org/5.2.0/CodeSystem-v2-0074.html";
+
+  //  Hardcoded category values for our initial condition agnostic spec
+  public static final String LAB_STRING_LITERAL = "LAB";
+  public static final String LABORATORY_STRING_LITERAL = "laboratory";
 }
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java
@@ -46,6 +46,7 @@
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.UNIVERSAL_ID_SYSTEM;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.YESNO_CODE_SYSTEM;
 import static gov.cdc.usds.simplereport.api.model.TestEventExport.FALLBACK_DEFAULT_TEST_MINUTES;
+import static gov.cdc.usds.simplereport.api.model.TestEventExport.UNKNOWN_ADDRESS_INDICATOR;
 import static gov.cdc.usds.simplereport.db.model.PersonUtils.getResidenceTypeMap;
 import static gov.cdc.usds.simplereport.db.model.PersonUtils.pregnancyStatusDisplayMap;
 import static gov.cdc.usds.simplereport.db.model.PersonUtils.pregnancyStatusSnomedMap;
@@ -454,16 +455,35 @@ public Organization convertToOrganization(
     return org;
   }
 
-  public Patient convertToPatient(Person person) {
+  public StreetAddress getPatientAddress(Person person, Facility facility) {
+    var personAddress = person.getAddress();
+    if (UNKNOWN_ADDRESS_INDICATOR.equalsIgnoreCase(person.getStreet()) && facility != null) {
+      var facilityAddress = facility.getAddress();
+      personAddress.setCity(facilityAddress.getCity());
+      personAddress.setState(facilityAddress.getState());
+      personAddress.setPostalCode(facilityAddress.getPostalCode());
+      personAddress.setCounty(facilityAddress.getCounty());
+    }
+    return personAddress;
+  }
+
+  public List<PhoneNumber> getPatientPhoneNumbers(Person person, Facility facility) {
+    if (person.getPhoneNumbers() == null || person.getPhoneNumbers().isEmpty()) {
+      return List.of(new PhoneNumber(PhoneType.LANDLINE, facility.getTelephone()));
+    }
+    return person.getPhoneNumbers();
+  }
+
+  public Patient convertToPatient(Person person, Facility facility) {
     return convertToPatient(
         ConvertToPatientProps.builder()
             .id(person.getInternalId().toString())
             .name(person.getNameInfo())
-            .phoneNumbers(person.getPhoneNumbers())
+            .phoneNumbers(getPatientPhoneNumbers(person, facility))
             .emails(person.getEmails())
             .gender(person.getGender())
             .dob(person.getBirthDate())
-            .address(person.getAddress())
+            .address(getPatientAddress(person, facility))
             .country(person.getCountry())
             .race(person.getRace())
             .ethnicity(person.getEthnicity())
@@ -1081,7 +1101,7 @@ public Bundle createFhirBundle(
 
     return createFhirBundle(
         CreateFhirBundleProps.builder()
-            .patient(convertToPatient(testEvent.getPatient()))
+            .patient(convertToPatient(testEvent.getPatient(), testEvent.getFacility()))
             .testingLab(convertToOrganization(testEvent.getFacility()))
             .orderingFacility(null)
             .practitioner(convertToPractitioner(testEvent.getProviderData()))

diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/model/TestEventExport.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/model/TestEventExport.java
@@ -46,6 +46,7 @@
 public class TestEventExport {
   public static final int FALLBACK_DEFAULT_TEST_MINUTES = 15;
   public static final String USA = "USA";
+  public static final String UNKNOWN_ADDRESS_INDICATOR = "** Unknown / Not Given **";
   private String processingModeCode = "P";
   private final TestEvent testEvent;
   private final Optional<Person> patient;
@@ -293,21 +294,37 @@ public String getPatientStreetTwo() {
 
   @JsonProperty("Patient_city")
   public String getPatientCity() {
+    var street = patient.map(Person::getStreet).orElse(null);
+    if (UNKNOWN_ADDRESS_INDICATOR.equalsIgnoreCase(street)) {
+      return getOrderingFacilityCity();
+    }
     return patient.map(Person::getCity).orElse(null);
   }
 
   @JsonProperty("Patient_county")
   public String getPatientCounty() {
+    var street = patient.map(Person::getStreet).orElse(null);
+    if (UNKNOWN_ADDRESS_INDICATOR.equalsIgnoreCase(street)) {
+      return getOrderingFacilityCounty();
+    }
     return patient.map(Person::getCounty).orElse(null);
   }
 
   @JsonProperty("Patient_state")
   public String getPatientState() {
+    var street = patient.map(Person::getStreet).orElse(null);
+    if (UNKNOWN_ADDRESS_INDICATOR.equalsIgnoreCase(street)) {
+      return getOrderingFacilityState();
+    }
     return patient.map(Person::getState).orElse(null);
   }
 
   @JsonProperty("Patient_zip_code")
   public String getPatientZipCode() {
+    var street = patient.map(Person::getStreet).orElse(null);
+    if (UNKNOWN_ADDRESS_INDICATOR.equalsIgnoreCase(street)) {
+      return getOrderingFacilityZipCode();
+    }
     return patient.map(Person::getZipCode).orElse(null);
   }
 
@@ -318,7 +335,11 @@ public String getPatientCountry() {
 
   @JsonProperty("Patient_phone_number")
   public String getPatientPhoneNumber() {
-    return patient.map(Person::getTelephone).orElse(null);
+    var phone = patient.map(Person::getTelephone).orElse(null);
+    if (phone == null || phone.isBlank()) {
+      return getOrderingFacilityPhoneNumber();
+    }
+    return phone;
   }
 
   @JsonProperty("Patient_email")

diff --git a/...src/main/java/gov/cdc/usds/simplereport/api/model/filerow/ConditionAgnosticResultRow.java b/...src/main/java/gov/cdc/usds/simplereport/api/model/filerow/ConditionAgnosticResultRow.java
@@ -0,0 +1,117 @@
+package gov.cdc.usds.simplereport.api.model.filerow;
+
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.getValue;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateBiologicalSex;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateDataAbsentReason;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateDateTime;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateTestPerformedCode;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateTestResult;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.validateTestResultStatus;
+
+import gov.cdc.usds.simplereport.service.model.reportstream.FeedbackMessage;
+import gov.cdc.usds.simplereport.validators.CsvValidatorUtils.ValueOrError;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import lombok.Getter;
+import org.apache.commons.lang3.StringUtils;
+
+@Getter
+public class ConditionAgnosticResultRow implements FileRow {
+  final ValueOrError testResultStatus;
+  final ValueOrError testResultEffectiveDate;
+  final ValueOrError testPerformedCode;
+  final ValueOrError testResultValue;
+  final ValueOrError patientId;
+  final ValueOrError patientFirstName;
+  final ValueOrError patientLastName;
+  final ValueOrError patientNameAbsentReason;
+  final ValueOrError patientAdminGender;
+
+  public static final String TEST_RESULT_STATUS = "test_result_status";
+  public static final String TEST_RESULT_EFFECTIVE_DATE = "test_result_effective_date";
+  public static final String TEST_PERFORMED_CODE = "test_performed_code";
+  public static final String TEST_RESULT_VALUE = "test_result_value";
+  public static final String PATIENT_ID = "patient_id";
+  public static final String PATIENT_LAST_NAME = "patient_last_name";
+  public static final String PATIENT_FIRST_NAME = "patient_first_name";
+  public static final String PATIENT_NAME_ABSENT_REASON = "patient_name_absent_reason";
+  public static final String PATIENT_ADMIN_GENDER = "patient_admin_gender";
+
+  private static List<String> initialRequiredFields =
+      List.of(
+          TEST_RESULT_STATUS,
+          TEST_RESULT_EFFECTIVE_DATE,
+          TEST_PERFORMED_CODE,
+          TEST_RESULT_VALUE,
+          PATIENT_ID,
+          PATIENT_ADMIN_GENDER);
+
+  private List<String> requiredFields;
+
+  public ConditionAgnosticResultRow(Map<String, String> rawRow) {
+    this.requiredFields = generateRequiredFields(rawRow);
+    testResultStatus = getValue(rawRow, TEST_RESULT_STATUS, isRequired(TEST_RESULT_STATUS));
+    testResultEffectiveDate =
+        getValue(rawRow, TEST_RESULT_EFFECTIVE_DATE, isRequired(TEST_RESULT_EFFECTIVE_DATE));
+    testPerformedCode = getValue(rawRow, TEST_PERFORMED_CODE, isRequired(TEST_PERFORMED_CODE));
+    testResultValue = getValue(rawRow, TEST_RESULT_VALUE, isRequired(TEST_RESULT_VALUE));
+    patientId = getValue(rawRow, PATIENT_ID, isRequired(PATIENT_ID));
+    patientNameAbsentReason =
+        getValue(rawRow, PATIENT_NAME_ABSENT_REASON, isRequired(PATIENT_NAME_ABSENT_REASON));
+    patientFirstName = getValue(rawRow, PATIENT_FIRST_NAME, isRequired(PATIENT_FIRST_NAME));
+    patientLastName = getValue(rawRow, PATIENT_LAST_NAME, isRequired(PATIENT_LAST_NAME));
+    patientAdminGender = getValue(rawRow, PATIENT_ADMIN_GENDER, isRequired(PATIENT_ADMIN_GENDER));
+  }
+
+  // The schema expects that (first_name || last_name) XOR name_absent_reason be present, so add the
+  // name-related fields to the required fields list accordingly
+  private static List<String> generateRequiredFields(Map<String, String> rawRow) {
+    String firstNameVal = getValue(rawRow, PATIENT_FIRST_NAME, false).getValue();
+    String lastNameVal = getValue(rawRow, PATIENT_LAST_NAME, false).getValue();
+
+    boolean firstNameAbsent = StringUtils.isBlank(firstNameVal);
+    boolean lastNameAbsent = StringUtils.isBlank(lastNameVal);
+
+    List<String> requiredFields = new ArrayList<>(initialRequiredFields);
+
+    if (firstNameAbsent ^ lastNameAbsent) {
+      if (firstNameAbsent) requiredFields.add(PATIENT_LAST_NAME);
+      else requiredFields.add(PATIENT_FIRST_NAME);
+    } else if (firstNameAbsent && lastNameAbsent) {
+      requiredFields.add(PATIENT_NAME_ABSENT_REASON);
+    } else {
+      requiredFields.add(PATIENT_LAST_NAME);
+      requiredFields.add(PATIENT_FIRST_NAME);
+    }
+
+    return requiredFields;
+  }
+
+  @Override
+  public Boolean isRequired(String rowName) {
+    return requiredFields.contains(rowName);
+  }
+
+  @Override
+  public List<FeedbackMessage> validateRequiredFields() {
+    return getPossibleErrorsFromFields();
+  }
+
+  @Override
+  public List<String> getRequiredFields() {
+    return requiredFields;
+  }
+
+  @Override
+  public List<FeedbackMessage> validateIndividualValues() {
+    var errors = new ArrayList<FeedbackMessage>();
+    errors.addAll(validateBiologicalSex(patientAdminGender));
+    errors.addAll(validateDataAbsentReason(patientNameAbsentReason));
+    errors.addAll(validateTestResultStatus(testResultStatus));
+    errors.addAll(validateDateTime(testResultEffectiveDate));
+    errors.addAll(validateTestPerformedCode(testPerformedCode));
+    errors.addAll(validateTestResult(testResultValue));
+    return errors;
+  }
+}