Add effect to calculate lab based cvd risk (#5258)

https://app.shortcut.com/simpledotorg/story/14630/calculate-lab-based-cvd-risk-score

---------

Co-authored-by: Siddharth Agarwal <[email protected]>
Co-authored-by: Sasikanth Miriyampalli <[email protected]>

Author: 3 people

CHANGELOG.md

@@ -64,6 +64,7 @@
 - Add `cholesterol_value` to `MedicalHistory` table
 - Bump AGP to v8.8.1
 - Fix JSON variable name in non-lab based statin calculation sheet
+- Add `LabBasedCVDRiskCalculator` and effect to calculate lab based cvd risk.
 
 ### Fixes
 

app/src/main/java/org/simple/clinic/cvdrisk/CVDRiskCalculationSheet.kt

@@ -2,51 +2,54 @@ package org.simple.clinic.cvdrisk
 
 import com.squareup.moshi.Json
 import com.squareup.moshi.JsonClass
+import org.simple.clinic.medicalhistory.Answer
 
 @JsonClass(generateAdapter = true)
 data class LabBasedCVDRiskCalculationSheet(
     val diabetes: DiabetesRisk,
-    @Json(name = "nodiabetes") val noDiabetes: NoDiabetesRisk,
+    @Json(name = "nodiabetes") val noDiabetes: DiabetesRisk,
 ) : CVDRiskCalculationSheet {
 
   @JsonClass(generateAdapter = true)
   data class DiabetesRisk(
       val women: Women<LabBasedRiskEntry>,
       val men: Men<LabBasedRiskEntry>
   )
-
-  @JsonClass(generateAdapter = true)
-  data class NoDiabetesRisk(
-      val women: Women<LabBasedRiskEntry>,
-      val men: Men<LabBasedRiskEntry>
-  )
 }
 
 @JsonClass(generateAdapter = true)
 data class NonLabBasedCVDRiskCalculationSheet(
     val women: Women<NonLabBasedRiskEntry>,
     val men: Men<NonLabBasedRiskEntry>
-): CVDRiskCalculationSheet
+) : CVDRiskCalculationSheet
 
 sealed interface CVDRiskCalculationSheet
 
 @JsonClass(generateAdapter = true)
-data class Women<T: RiskEntry>(
+data class Women<T : RiskEntry>(
     override val smoking: AgeData<T>,
     @Json(name = "nonsmoking")
     override val nonSmoking: AgeData<T>
-): SmokingData<T>
+) : SmokingData<T>
 
 @JsonClass(generateAdapter = true)
-data class Men<T: RiskEntry>(
+data class Men<T : RiskEntry>(
     override val smoking: AgeData<T>,
     @Json(name = "nonsmoking")
     override val nonSmoking: AgeData<T>
-): SmokingData<T>
+) : SmokingData<T>
 
-sealed interface SmokingData<T: RiskEntry> {
+sealed interface SmokingData<T : RiskEntry> {
   val smoking: AgeData<T>
   val nonSmoking: AgeData<T>
+
+  fun ageDataForSmokingStatus(isSmoker: Answer): List<AgeData<T>> {
+    return when (isSmoker) {
+      Answer.Yes -> listOf(smoking)
+      Answer.No -> listOf(nonSmoking)
+      else -> listOf(nonSmoking, smoking)
+    }
+  }
 }
 
 @JsonClass(generateAdapter = true)
@@ -58,20 +61,47 @@ data class AgeData<T : RiskEntry>(
     @Json(name = "60 - 64") val age60to64: List<T>,
     @Json(name = "65 - 69") val age65to69: List<T>,
     @Json(name = "70 - 74") val age70to74: List<T>
-)
+) {
+
+  fun riskForAge(age: Int): List<T> {
+    return when (age) {
+      in 40..44 -> age40to44
+      in 45..49 -> age45to49
+      in 50..54 -> age50to54
+      in 55..59 -> age55to59
+      in 60..64 -> age60to64
+      in 65..69 -> age65to69
+      in 70..74 -> age70to74
+      else -> emptyList()
+    }
+  }
+}
 
 @JsonClass(generateAdapter = true)
 data class LabBasedRiskEntry(
-    @Json(name = "sbp") val systolic: String,
+    @Json(name = "sbp") override val systolic: String,
     @Json(name = "chol") val cholesterol: String,
     val risk: Int
 ) : RiskEntry
 
 @JsonClass(generateAdapter = true)
 data class NonLabBasedRiskEntry(
-    @Json(name = "sbp") val systolic: String,
+    @Json(name = "sbp") override val systolic: String,
     val bmi: String,
     val risk: Int
 ) : RiskEntry
 
-sealed interface RiskEntry
+sealed interface RiskEntry {
+
+  val systolic: String
+
+  fun isInSystolicRange(systolic: Int): Boolean {
+    val systolicRange = when (systolic) {
+      in 0..159 -> "140 - 159"
+      in 160..179 -> "160 - 179"
+      else -> ">= 180"
+    }
+
+    return this.systolic == systolicRange
+  }
+}

app/src/main/java/org/simple/clinic/cvdrisk/CVDRiskCalculator.kt

@@ -37,6 +37,15 @@ data class CVDRiskRange(
   }
 
   companion object {
+
+    fun from(risks: List<Int>): CVDRiskRange? {
+      return when {
+        risks.isEmpty() -> null
+        risks.size == 1 -> CVDRiskRange(min = risks.first(), max = risks.first())
+        else -> CVDRiskRange(risks.min(), risks.max())
+      }
+    }
+
     fun parseRiskRange(risk: String): CVDRiskRange {
       val risks = risk.split("-").map { it.trim() }
       return when (risks.size) {

app/src/main/java/org/simple/clinic/cvdrisk/CVDRiskRange.kt

@@ -0,0 +1,13 @@
+package org.simple.clinic.cvdrisk
+
+import org.simple.clinic.medicalhistory.Answer
+import org.simple.clinic.patient.Gender
+
+data class LabBasedCVDRiskInput(
+    val gender: Gender,
+    val age: Int,
+    val systolic: Int,
+    val isSmoker: Answer = Answer.Unanswered,
+    val diagnosedWithDiabetes: Answer = Answer.Unanswered,
+    val cholesterol: Float? = null,
+)

app/src/main/java/org/simple/clinic/cvdrisk/LabBasedCVDRiskInput.kt

@@ -3,10 +3,11 @@ package org.simple.clinic.cvdrisk
 import org.simple.clinic.medicalhistory.Answer
 import org.simple.clinic.patient.Gender
 
-data class CVDRiskInput(
+data class NonLabBasedCVDRiskInput(
     val gender: Gender,
     val age: Int,
     val systolic: Int,
     val isSmoker: Answer = Answer.Unanswered,
-    val bmi: Float? = null
+    val bmi: Float? = null,
 )
+

…rg/simple/clinic/cvdrisk/CVDRiskInput.kt …linic/cvdrisk/NonLabBasedCVDRiskInput.ktapp/src/main/java/org/simple/clinic/cvdrisk/CVDRiskInput.kt renamed to app/src/main/java/org/simple/clinic/cvdrisk/NonLabBasedCVDRiskInput.kt app/src/main/java/org/simple/clinic/cvdrisk/CVDRiskInput.kt renamed to app/src/main/java/org/simple/clinic/cvdrisk/NonLabBasedCVDRiskInput.kt

@@ -0,0 +1,71 @@
+package org.simple.clinic.cvdrisk.calculator
+
+import dagger.Lazy
+import org.simple.clinic.cvdrisk.CVDRiskRange
+import org.simple.clinic.cvdrisk.LabBasedCVDRiskCalculationSheet
+import org.simple.clinic.cvdrisk.LabBasedCVDRiskInput
+import org.simple.clinic.cvdrisk.LabBasedRiskEntry
+import org.simple.clinic.di.AppScope
+import org.simple.clinic.medicalhistory.Answer
+import org.simple.clinic.patient.Gender
+import javax.inject.Inject
+
+@AppScope
+class LabBasedCVDRiskCalculator @Inject constructor(
+    private val labBasedCVDRiskCalculationSheet: Lazy<LabBasedCVDRiskCalculationSheet?>,
+) {
+
+  fun calculateCvdRisk(cvdRiskInput: LabBasedCVDRiskInput): CVDRiskRange? {
+    with(cvdRiskInput) {
+      val riskEntries = getLabBasedRiskEntries(cvdRiskInput) ?: return null
+      val cholesterolRangeList = getCholesterolRangeList(cholesterol)
+      val risks =
+          riskEntries
+              .filter { it.isInSystolicRange(systolic) && it.cholesterol in cholesterolRangeList }
+              .map { it.risk }
+
+      return CVDRiskRange.from(risks)
+    }
+  }
+
+  private fun getLabBasedRiskEntries(cvdRiskInput: LabBasedCVDRiskInput): List<LabBasedRiskEntry>? {
+    with(cvdRiskInput) {
+      val sheet = labBasedCVDRiskCalculationSheet.get()
+      val diabetesData = sheet?.let { getDiabetesData(it, diagnosedWithDiabetes) }
+      val genderData = diabetesData?.let { getGenderData(it, gender) }
+      val smokingDataList = genderData?.ageDataForSmokingStatus(isSmoker)
+
+      return smokingDataList?.flatMap { it.riskForAge(age) }
+    }
+  }
+
+  private fun getGenderData(genderData: LabBasedCVDRiskCalculationSheet.DiabetesRisk, gender: Gender) = when (gender) {
+    Gender.Female -> genderData.women
+    Gender.Male -> genderData.men
+    else -> null
+  }
+
+  private fun getDiabetesData(diabetesData: LabBasedCVDRiskCalculationSheet, answer: Answer) =
+      when (answer) {
+        Answer.Yes -> diabetesData.diabetes
+        Answer.No -> diabetesData.noDiabetes
+        else -> null
+      }
+
+
+  private fun getCholesterolRangeList(cholesterol: Float?): List<String> {
+    return cholesterol?.let { listOf(getCholesterolRange(it)) }
+        ?: listOf("< 4", "4 - 4.9", "5 - 5.9", "6 - 6.9", ">= 7")
+  }
+
+  private fun getCholesterolRange(cholesterol: Float): String {
+    return when {
+      cholesterol >= 0.0 && cholesterol < 4.0 -> "< 4"
+      cholesterol >= 4.0 && cholesterol < 5.0 -> "4 - 4.9"
+      cholesterol >= 5.0 && cholesterol < 6.0 -> "5 - 5.9"
+      cholesterol >= 6.0 && cholesterol < 7.0 -> "6 - 6.9"
+      else -> ">= 7"
+    }
+  }
+
+}

app/src/main/java/org/simple/clinic/cvdrisk/calculator/LabBasedCVDRiskCalculator.kt

@@ -0,0 +1,58 @@
+package org.simple.clinic.cvdrisk.calculator
+
+import dagger.Lazy
+import org.simple.clinic.cvdrisk.CVDRiskRange
+import org.simple.clinic.cvdrisk.NonLabBasedCVDRiskCalculationSheet
+import org.simple.clinic.cvdrisk.NonLabBasedCVDRiskInput
+import org.simple.clinic.cvdrisk.NonLabBasedRiskEntry
+import org.simple.clinic.di.AppScope
+import org.simple.clinic.patient.Gender
+import javax.inject.Inject
+
+@AppScope
+class NonLabBasedCVDRiskCalculator @Inject constructor(
+    private val nonLabBasedCVDRiskCalculationSheet: Lazy<NonLabBasedCVDRiskCalculationSheet?>,
+) {
+  fun calculateCvdRisk(cvdRiskInput: NonLabBasedCVDRiskInput): CVDRiskRange? {
+    with(cvdRiskInput) {
+      val riskEntries = getNonLabBasedRiskEntries(cvdRiskInput) ?: return null
+      val bmiRangeList = getBMIRangeList(bmi)
+      val risks = riskEntries
+          .filter { it.isInSystolicRange(systolic) && it.bmi in bmiRangeList }
+          .map { it.risk }
+
+      return CVDRiskRange.from(risks)
+    }
+  }
+
+  private fun getNonLabBasedRiskEntries(cvdRiskInput: NonLabBasedCVDRiskInput): List<NonLabBasedRiskEntry>? {
+    with(cvdRiskInput) {
+      val sheet = nonLabBasedCVDRiskCalculationSheet.get()
+      val genderData = sheet?.let { getGenderData(it, gender) }
+      val smokingDataList = genderData?.ageDataForSmokingStatus(isSmoker)
+
+      return smokingDataList?.flatMap { it.riskForAge(age) }
+    }
+  }
+
+  private fun getGenderData(genderData: NonLabBasedCVDRiskCalculationSheet, gender: Gender) = when (gender) {
+    Gender.Female -> genderData.women
+    Gender.Male -> genderData.men
+    else -> null
+  }
+
+  private fun getBMIRangeList(bmi: Float?): List<String> {
+    return bmi?.let { listOf(getBMIRange(it)) }
+        ?: listOf("< 20", "20 - 24", "25 - 29", "30 - 35", "> 35")
+  }
+
+  private fun getBMIRange(bmi: Float): String {
+    return when (bmi) {
+      in 0.0..19.9 -> "< 20"
+      in 20.0..24.9 -> "20 - 24"
+      in 25.0..29.9 -> "25 - 29"
+      in 30.0..34.9 -> "30 - 35"
+      else -> "> 35"
+    }
+  }
+}