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SW-4375 Calculate germination and loss rates (#1453)
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Use the quantity history of a batch to determine its germination and loss
rates, if eligible.

The rates are already included in the batch details API payload and are already
available via the search API; they were just always null previously.
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@sgrimm
sgrimm authored Nov 3, 2023
1 parent ff621ff commit eded5a5
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Showing 6 changed files with 402 additions and 2 deletions.
149 changes: 147 additions & 2 deletions src/main/kotlin/com/terraformation/backend/nursery/db/BatchStore.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ import com.terraformation.backend.db.nursery.tables.pojos.InventoriesRow
import com.terraformation.backend.db.nursery.tables.pojos.WithdrawalsRow
import com.terraformation.backend.db.nursery.tables.records.BatchesRecord
import com.terraformation.backend.db.nursery.tables.references.BATCHES
import com.terraformation.backend.db.nursery.tables.references.BATCH_QUANTITY_HISTORY
import com.terraformation.backend.db.nursery.tables.references.BATCH_SUB_LOCATIONS
import com.terraformation.backend.db.nursery.tables.references.BATCH_WITHDRAWALS
import com.terraformation.backend.db.nursery.tables.references.INVENTORIES
Expand All @@ -62,6 +63,7 @@ import com.terraformation.backend.seedbank.event.AccessionSpeciesChangedEvent
import jakarta.inject.Named
import java.time.Clock
import java.time.LocalDate
import kotlin.math.roundToInt
import org.jooq.DSLContext
import org.jooq.UpdateSetFirstStep
import org.jooq.UpdateSetMoreStep
Expand Down Expand Up @@ -178,6 +180,8 @@ class BatchStore(
createdBy = userId,
createdTime = now,
latestObservedTime = now,
lossRate =
if (newModel.notReadyQuantity > 0 || newModel.readyQuantity > 0) 0 else null,
modifiedBy = userId,
modifiedTime = now,
organizationId = organizationId,
Expand Down Expand Up @@ -400,6 +404,7 @@ class BatchStore(
val successFunc = { newVersion: Int ->
insertQuantityHistoryRow(
batchId, germinating, notReady, ready, historyType, newVersion, withdrawalId)
updateRates(batchId)
}

updateVersionedBatch(batchId, version, successFunc) { update ->
Expand Down Expand Up @@ -626,6 +631,8 @@ class BatchStore(
readyQuantityWithdrawn = batchWithdrawal.readyQuantityWithdrawn)
val nurseryTimeZone = parentStore.getEffectiveTimeZone(batchId)

batchWithdrawalsDao.insert(batchWithdrawalsRow)

retryVersionedBatchUpdate(batchId) { batch ->
// Usually we want to subtract the withdrawal amounts from the batch's
// available quantities. However, if the user is entering data about an older
Expand Down Expand Up @@ -674,8 +681,6 @@ class BatchStore(
it.set(emptyMap<Any, Any>())
}
}

batchWithdrawalsDao.insert(batchWithdrawalsRow)
}

batchWithdrawalsRow
Expand Down Expand Up @@ -987,4 +992,144 @@ class BatchStore(
.execute()
}
}

/**
* Updates the germination and loss rates for a batch. This does not count as a new version of the
* batch. When this is called as part of a quantity update, the quantity history row for the new
* update should be inserted before this is called.
*/
private fun updateRates(batchId: BatchId) {
val quantityHistory =
dslContext
.select(
BATCH_QUANTITY_HISTORY.HISTORY_TYPE_ID,
BATCH_QUANTITY_HISTORY.GERMINATING_QUANTITY,
BATCH_QUANTITY_HISTORY.NOT_READY_QUANTITY,
BATCH_QUANTITY_HISTORY.READY_QUANTITY,
BATCH_WITHDRAWALS.BATCH_ID,
BATCH_WITHDRAWALS.GERMINATING_QUANTITY_WITHDRAWN,
BATCH_WITHDRAWALS.NOT_READY_QUANTITY_WITHDRAWN,
BATCH_WITHDRAWALS.READY_QUANTITY_WITHDRAWN,
WITHDRAWALS.PURPOSE_ID,
)
.from(BATCH_QUANTITY_HISTORY)
.leftJoin(BATCH_WITHDRAWALS)
.on(BATCH_QUANTITY_HISTORY.BATCH_ID.eq(BATCH_WITHDRAWALS.BATCH_ID))
.and(BATCH_QUANTITY_HISTORY.WITHDRAWAL_ID.eq(BATCH_WITHDRAWALS.WITHDRAWAL_ID))
.leftJoin(WITHDRAWALS)
.on(BATCH_QUANTITY_HISTORY.WITHDRAWAL_ID.eq(WITHDRAWALS.ID))
.where(BATCH_QUANTITY_HISTORY.BATCH_ID.eq(batchId))
.orderBy(BATCH_QUANTITY_HISTORY.VERSION)
.fetch()

if (quantityHistory.isEmpty()) {
log.error("BUG! UpdateRates for batch $batchId called with no quantity history rows")
return
}

val initialEvent = quantityHistory.first()
val latestEvent = quantityHistory.last()

var hasManualGerminatingEdit = false
var hasManualNotReadyEdit = false
var hasManualReadyEdit = false
var hasAdditionalIncomingTransfers = false
var totalWithdrawnNotReadyAndReady = 0
var totalNonDeadGerminating = 0
var totalDeadNotReadyAndReady = 0
var totalOutplantAndDeadNotReadyAndReady = 0

// Walk through history starting at the second event, comparing each event to the previous one
// to detect which values were edited and to tally up total withdrawals matching various
// criteria as needed by the rate calculations.
quantityHistory.reduce { previous, current ->
val germinatingQuantityWithdrawn =
current[BATCH_WITHDRAWALS.GERMINATING_QUANTITY_WITHDRAWN] ?: 0
val notReadyQuantityWithdrawn = (current[BATCH_WITHDRAWALS.NOT_READY_QUANTITY_WITHDRAWN] ?: 0)
val readyQuantityWithdrawn = current[BATCH_WITHDRAWALS.READY_QUANTITY_WITHDRAWN] ?: 0

if (current[BATCH_QUANTITY_HISTORY.HISTORY_TYPE_ID] == BatchQuantityHistoryType.Observed) {
// A manual edit, but we care about which of the specific quantities actually changed.
hasManualGerminatingEdit =
hasManualGerminatingEdit ||
(current[BATCH_QUANTITY_HISTORY.GERMINATING_QUANTITY] !=
previous[BATCH_QUANTITY_HISTORY.GERMINATING_QUANTITY])
hasManualNotReadyEdit =
hasManualNotReadyEdit ||
(current[BATCH_QUANTITY_HISTORY.NOT_READY_QUANTITY] !=
previous[BATCH_QUANTITY_HISTORY.NOT_READY_QUANTITY])
hasManualReadyEdit =
hasManualReadyEdit ||
(current[BATCH_QUANTITY_HISTORY.READY_QUANTITY] !=
previous[BATCH_QUANTITY_HISTORY.READY_QUANTITY])
}

if (current[WITHDRAWALS.PURPOSE_ID] == WithdrawalPurpose.NurseryTransfer &&
current[BATCH_WITHDRAWALS.BATCH_ID] != batchId) {
hasAdditionalIncomingTransfers = true
}

if (current[WITHDRAWALS.PURPOSE_ID] == WithdrawalPurpose.OutPlant ||
current[WITHDRAWALS.PURPOSE_ID] == WithdrawalPurpose.Dead) {
totalOutplantAndDeadNotReadyAndReady += notReadyQuantityWithdrawn + readyQuantityWithdrawn
}

if (current[WITHDRAWALS.PURPOSE_ID] == WithdrawalPurpose.Dead) {
totalDeadNotReadyAndReady += notReadyQuantityWithdrawn + readyQuantityWithdrawn
}

if (current[WITHDRAWALS.PURPOSE_ID] != null &&
current[WITHDRAWALS.PURPOSE_ID] != WithdrawalPurpose.Dead) {
totalNonDeadGerminating += germinatingQuantityWithdrawn
}

totalWithdrawnNotReadyAndReady += notReadyQuantityWithdrawn + readyQuantityWithdrawn

current
}

val initialGerminating = initialEvent[BATCH_QUANTITY_HISTORY.GERMINATING_QUANTITY]!!
val initialNotReady = initialEvent[BATCH_QUANTITY_HISTORY.NOT_READY_QUANTITY]!!
val initialReady = initialEvent[BATCH_QUANTITY_HISTORY.READY_QUANTITY]!!
val currentGerminating = latestEvent[BATCH_QUANTITY_HISTORY.GERMINATING_QUANTITY]!!
val currentNotReadyAndReady =
latestEvent[BATCH_QUANTITY_HISTORY.NOT_READY_QUANTITY]!! +
latestEvent[BATCH_QUANTITY_HISTORY.READY_QUANTITY]!!

val germinationRate: Int? =
if (initialGerminating > 0 &&
currentGerminating == 0 &&
!hasManualGerminatingEdit &&
!hasManualNotReadyEdit &&
!hasManualReadyEdit &&
!hasAdditionalIncomingTransfers) {
val numerator =
currentNotReadyAndReady + totalWithdrawnNotReadyAndReady -
initialNotReady -
initialReady
val denominator = initialGerminating - totalNonDeadGerminating

(100.0 * numerator / denominator).roundToInt()
} else {
null
}

val lossRateDenominator = totalOutplantAndDeadNotReadyAndReady + currentNotReadyAndReady
val lossRate: Int? =
if (lossRateDenominator > 0 &&
!hasManualNotReadyEdit &&
!hasManualReadyEdit &&
!hasAdditionalIncomingTransfers) {
(100.0 * totalDeadNotReadyAndReady / lossRateDenominator).roundToInt()
} else {
null
}

dslContext
.update(BATCHES)
.set(BATCHES.GERMINATION_RATE, germinationRate)
.set(BATCHES.LOSS_RATE, lossRate)
.where(BATCHES.ID.eq(batchId))
.execute()
}
}
4 changes: 4 additions & 0 deletions src/test/kotlin/com/terraformation/backend/db/DatabaseTest.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -831,6 +831,8 @@ abstract class DatabaseTest {
speciesId: Any = row.speciesId ?: inserted.speciesId,
version: Int = row.version ?: 1,
batchNumber: String = row.batchNumber ?: id?.toString() ?: "${nextBatchNuber++}",
germinationRate: Int? = row.germinationRate,
lossRate: Int? = row.lossRate ?: if (notReadyQuantity > 0 || readyQuantity > 0) 0 else null,
): BatchId {
val rowWithDefaults =
row.copy(
Expand All @@ -840,11 +842,13 @@ abstract class DatabaseTest {
createdTime = createdTime,
facilityId = facilityId.toIdWrapper { FacilityId(it) },
germinatingQuantity = germinatingQuantity,
germinationRate = germinationRate,
id = id?.toIdWrapper { BatchId(it) },
latestObservedGerminatingQuantity = germinatingQuantity,
latestObservedNotReadyQuantity = notReadyQuantity,
latestObservedReadyQuantity = readyQuantity,
latestObservedTime = createdTime,
lossRate = lossRate,
modifiedBy = createdBy,
modifiedTime = createdTime,
notReadyQuantity = notReadyQuantity,
Expand Down
2 changes: 2 additions & 0 deletions src/test/kotlin/com/terraformation/backend/nursery/db/BatchImporterTest.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -162,6 +162,7 @@ internal class BatchImporterTest : DatabaseTest(), RunsAsUser {
latestObservedNotReadyQuantity = 2,
latestObservedReadyQuantity = 0,
latestObservedTime = Instant.EPOCH,
lossRate = 0,
modifiedBy = user.userId,
modifiedTime = Instant.EPOCH,
notReadyQuantity = 2,
Expand Down Expand Up @@ -245,6 +246,7 @@ internal class BatchImporterTest : DatabaseTest(), RunsAsUser {
latestObservedNotReadyQuantity = 2,
latestObservedReadyQuantity = 0,
latestObservedTime = Instant.EPOCH,
lossRate = 0,
modifiedBy = user.userId,
modifiedTime = Instant.EPOCH,
notReadyQuantity = 2,
Expand Down
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