Merge branch 'main' into feat/1268-add-backup-routine-for-pg

.github/workflows/.deploy.yml

@@ -147,7 +147,6 @@ jobs:
           oc_namespace: ${{ vars.OC_NAMESPACE }}
           oc_server: ${{ vars.OC_SERVER }}
           oc_token: ${{ secrets.OC_TOKEN }}
-          oc_version: ${{ matrix.oc_version }}
           overwrite: ${{ matrix.overwrite }}
           parameters:
             -p TAG=${{ inputs.tag }}
@@ -174,7 +173,6 @@ jobs:
           oc_namespace: ${{ vars.OC_NAMESPACE }}
           oc_server: ${{ vars.OC_SERVER }}
           oc_token: ${{ secrets.OC_TOKEN }}
-          oc_version: "4.13"
           overwrite: true
           parameters:
             -p TAG=${{ inputs.tag }}

backend/src/main/java/ca/bc/gov/backendstartapi/dto/OrchardParentTreeValsDto.java

@@ -31,11 +31,18 @@ public record OrchardParentTreeValsDto(
         BigDecimal pollenCount,
     @Schema(
             description =
-                "A float number representing the value for the SMP success on parent percentage",
+                "A number representing the value for the SMP success on parent percentage",
             example = "5",
             type = "number",
             format = "int")
         Integer smpSuccessPerc,
+      @Schema(
+        description =
+            "A number representing the non-orchard pollen contamination (%) of the parent tree.",
+        example = "15",
+        type = "number",
+        format = "int")
+        Integer nonOrchardPollenContamPct,
     @Schema(
             description =
                 """

backend/src/main/java/ca/bc/gov/backendstartapi/dto/PtCalculationResDto.java

@@ -1,6 +1,7 @@
 package ca.bc.gov.backendstartapi.dto;
 
 import io.swagger.v3.oas.annotations.media.Schema;
+import java.math.BigDecimal;
 import java.util.List;
 
 /** This class represents the JSON that will be returned by the GW calculations. */
@@ -16,4 +17,7 @@ public record PtCalculationResDto(
     @Schema(description = "Various calculated value for the orchard parent trees.")
         CalculatedParentTreeValsDto calculatedPtVals,
     @Schema(description = "The calculated mean geospatial values for SMP mix.")
-        GeospatialRespondDto smpMixMeanGeoData) {}
+        GeospatialRespondDto smpMixMeanGeoData,
+    @Schema(description = "The calculated SMP Success percentage") BigDecimal smpSuccessPct,
+    @Schema(description = "The calculated Orchard Contamination percentage")
+        BigDecimal orchardContaminationPct) {}

backend/src/main/java/ca/bc/gov/backendstartapi/dto/PtValsCalReqDto.java

@@ -2,6 +2,7 @@
 
 import io.swagger.v3.oas.annotations.media.Schema;
 import jakarta.validation.constraints.NotNull;
+import java.math.BigDecimal;
 import java.util.List;
 
 /** This class represents the JSON request body when doing parent tree and SMP calculations. */
@@ -11,4 +12,5 @@
 public record PtValsCalReqDto(
     @NotNull List<OrchardParentTreeValsDto> orchardPtVals,
     @NotNull List<GeospatialRequestDto> smpMixIdAndProps,
-    @NotNull Integer smpParentsOutside) {}
+    @NotNull Integer smpParentsOutside,
+    @NotNull BigDecimal contaminantPollenBv) {}

backend/src/main/java/ca/bc/gov/backendstartapi/dto/SeedlotFormSmpParentOutsideDto.java

@@ -0,0 +1,7 @@
+package ca.bc.gov.backendstartapi.dto;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+
+/** This record represents the seedlot SMP Parents from outside number. */
+@Schema(description = "The seedlot SMP Parents from outside number.")
+public record SeedlotFormSmpParentOutsideDto(Integer smpParentsOutside) {}

backend/src/main/java/ca/bc/gov/backendstartapi/dto/SeedlotFormSubmissionDto.java

@@ -12,6 +12,7 @@ public record SeedlotFormSubmissionDto(
     SeedlotFormOrchardDto seedlotFormOrchardDto,
     List<SeedlotFormParentTreeSmpDto> seedlotFormParentTreeDtoList,
     List<SeedlotFormParentTreeSmpDto> seedlotFormParentTreeSmpDtoList,
+    SeedlotFormSmpParentOutsideDto seedlotFormSmpParentOutsideDto,
     SeedlotFormExtractionDto seedlotFormExtractionDto,
     List<SeedlotReviewSeedPlanZoneDto> seedlotReviewSeedPlanZones,
     SeedlotReviewElevationLatLongDto seedlotReviewElevationLatLong,

backend/src/main/java/ca/bc/gov/backendstartapi/service/GeneticWorthService.java

@@ -3,17 +3,13 @@
 import ca.bc.gov.backendstartapi.config.SparLog;
 import ca.bc.gov.backendstartapi.dto.CodeDescriptionDto;
 import ca.bc.gov.backendstartapi.dto.GeneticWorthDto;
-import ca.bc.gov.backendstartapi.dto.GeneticWorthTraitsDto;
-import ca.bc.gov.backendstartapi.dto.OrchardParentTreeValsDto;
-import ca.bc.gov.backendstartapi.dto.PtCalculationResDto;
 import ca.bc.gov.backendstartapi.entity.GeneticWorthEntity;
 import ca.bc.gov.backendstartapi.exception.NoGeneticWorthException;
 import ca.bc.gov.backendstartapi.repository.GeneticWorthRepository;
 import java.math.BigDecimal;
 import java.math.RoundingMode;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Objects;
 import java.util.Optional;
 import org.springframework.lang.NonNull;
 import org.springframework.stereotype.Service;
@@ -59,44 +55,6 @@ public CodeDescriptionDto getGeneticWorthByCode(@NonNull String code) {
         .orElseThrow(NoGeneticWorthException::new);
   }
 
-  /**
-   * Does the calculation for each genetic trait. PS: if the threshold of 70% of contribution from
-   * the parent tree is not met, the trait value will not be shown.
-   *
-   * @param traitsDto A {@link List} of {@link OrchardParentTreeValsDto} with the traits and values
-   *     to be calculated.
-   * @return A {@link PtCalculationResDto} containing all calculated values
-   */
-  public List<GeneticWorthTraitsDto> calculateGeneticWorth(
-      List<OrchardParentTreeValsDto> traitsDto) {
-    SparLog.info("Starting Genetic Worth calculations");
-    BigDecimal minimumThreshold = new BigDecimal("0.7");
-
-    List<GeneticWorthTraitsDto> calculated = new ArrayList<>();
-
-    // Iterate over all traits
-    List<GeneticWorthDto> geneticWorthList = getAllGeneticWorth();
-
-    for (GeneticWorthDto trait : geneticWorthList) {
-      BigDecimal calculatedValue = null;
-      BigDecimal percentage = calcGeneticTraitThreshold(traitsDto, trait);
-
-      if (percentage.compareTo(minimumThreshold) >= 0) {
-        SparLog.info("Calculating Genetic Worth for {} trait", trait.getCode());
-        calculatedValue = calculateTraitGeneticWorth(traitsDto, trait);
-      } else {
-        SparLog.info(
-            "No Genetic Worth calculations for trait {}, threshold not met.", trait.getCode());
-      }
-
-      GeneticWorthTraitsDto traitResponse =
-          new GeneticWorthTraitsDto(trait.getCode(), null, calculatedValue, percentage);
-      calculated.add(traitResponse);
-    }
-
-    return calculated;
-  }
-
   /**
    * Does the Ne calculation (effective population size).
    *
@@ -156,127 +114,4 @@ public BigDecimal calculateNe(
 
     return varEffectivePopSize.setScale(1, halfUp);
   }
-
-  /**
-   * Do the calculations for each Genetic Worth trait. Note that in the case the parent tree does
-   * not attend the 70% threshold weight, the value for this trait will be zero.
-   *
-   * @param traitsDto A {@link List} of {@link OrchardParentTreeValsDto} with the traits and values.
-   * @return A {@link BigDecimal} representing the value.
-   */
-  private BigDecimal calculateTraitGeneticWorth(
-      List<OrchardParentTreeValsDto> traitsDto, CodeDescriptionDto trait) {
-    BigDecimal malePollenSum = reducePollenCount(traitsDto);
-    BigDecimal femaleConeSum = reduceConeCount(traitsDto);
-    BigDecimal sumGw = BigDecimal.ZERO;
-
-    for (OrchardParentTreeValsDto dto : traitsDto) {
-      BigDecimal traitBreedingValue = getTraitValue(dto, trait);
-      if (!Objects.isNull(traitBreedingValue) && traitBreedingValue.floatValue() != 0) {
-        BigDecimal pi =
-            calculatePi(dto.pollenCount(), dto.coneCount(), malePollenSum, femaleConeSum);
-        BigDecimal gwValue = traitBreedingValue.multiply(pi);
-        sumGw = sumGw.add(gwValue);
-      }
-    }
-
-    return sumGw;
-  }
-
-  /**
-   * Calculate the threshold of a genetic trait. To be used to check if a given trait met the
-   * minimum of 70% of parent tree contribution.
-   *
-   * @param traitsDto A {@link List} of {@link OrchardParentTreeValsDto} with the traits and values
-   *     to be calculated.
-   * @param trait A {@link GeneticWorth} with the trait that should be considered.
-   * @return A BigDecimal representing the trait threshold.
-   */
-  private BigDecimal calcGeneticTraitThreshold(
-      List<OrchardParentTreeValsDto> traitsDto, CodeDescriptionDto trait) {
-    SparLog.debug("Checking genetic trait threshold for {} trait", trait);
-
-    BigDecimal malePollenSum = reducePollenCount(traitsDto);
-    BigDecimal femaleConeSum = reduceConeCount(traitsDto);
-    BigDecimal sumPi = BigDecimal.ZERO;
-
-    SparLog.debug("femaleConeSum {}", femaleConeSum);
-    SparLog.debug("malePollenSum {}", malePollenSum);
-
-    for (OrchardParentTreeValsDto traitFor : traitsDto) {
-      BigDecimal traitBreedingValue = getTraitValue(traitFor, trait);
-      if (!Objects.isNull(traitBreedingValue) && traitBreedingValue.floatValue() != 0) {
-        BigDecimal pi =
-            calculatePi(traitFor.pollenCount(), traitFor.coneCount(), malePollenSum, femaleConeSum);
-        sumPi = sumPi.add(pi);
-      }
-    }
-
-    SparLog.debug("Finished checking Genetic Trait threshold for {} trait with: {}%", trait, sumPi);
-
-    return sumPi;
-  }
-
-  /**
-   * Finds the genetic trait value given the request dto and the trait that should be found.
-   *
-   * @param dto A {@link OrchardParentTreeValsDto} instance with the traits value.
-   * @param trait A {@link GeneticWorth} with the trait that should be considered.
-   * @return a BigDecimal representing the trait value or BigDecimal.ZERO otherwise.
-   */
-  private BigDecimal getTraitValue(OrchardParentTreeValsDto traitDto, CodeDescriptionDto trait) {
-    List<GeneticWorthTraitsDto> geneticTraits = traitDto.geneticTraits();
-    Optional<GeneticWorthTraitsDto> traitOptional =
-        geneticTraits.stream()
-            .filter(x -> x.traitCode().equalsIgnoreCase(trait.getCode()))
-            .findFirst();
-    return traitOptional.isEmpty() ? BigDecimal.ZERO : traitOptional.get().traitValue();
-  }
-
-  /**
-   * Calculate the pi. The P represents the percentage of contribution for a parent tree, the sum of
-   * male and female contribution divided by two.
-   *
-   * @param pollenCount The amount of pollen for this parent tree (clone).
-   * @param coneCount The amount of cone for this parent tree (clone).
-   * @param pollenSum The sum of all pollen count for this calculation.
-   * @param coneSum The sum of all cone count for this calculation.
-   * @return A BigDecimal representing the value.
-   */
-  private BigDecimal calculatePi(
-      BigDecimal pollenCount, BigDecimal coneCount, BigDecimal pollenSum, BigDecimal coneSum) {
-    BigDecimal bigZero = BigDecimal.ZERO;
-    BigDecimal mi =
-        pollenSum.compareTo(bigZero) == 0
-            ? bigZero
-            : pollenCount.divide(pollenSum, 10, RoundingMode.HALF_UP);
-    BigDecimal fi =
-        coneSum.compareTo(bigZero) == 0
-            ? bigZero
-            : coneCount.divide(coneSum, 10, RoundingMode.HALF_UP);
-
-    BigDecimal calculatedPi = mi.add(fi).divide(new BigDecimal("2"), 10, RoundingMode.HALF_UP);
-
-    return calculatedPi;
-  }
-
-  /**
-   * Sums all the pollen count.
-   *
-   * @param traitsDto A {@link List} of {@link OrchardParentTreeValsDto} with the traits and values
-   * @return A BigDecimal representing the value
-   */
-  private BigDecimal reducePollenCount(List<OrchardParentTreeValsDto> traitsDto) {
-    return traitsDto.stream().map(x -> x.pollenCount()).reduce(BigDecimal.ZERO, BigDecimal::add);
-  }
-
-  /**
-   * Sums all the cone count.
-   *
-   * @param traitsDto A {@link List} of {@link OrchardParentTreeValsDto} with the traits and values
-   * @return A BigDecimal representing the value
-   */
-  private BigDecimal reduceConeCount(List<OrchardParentTreeValsDto> traitsDto) {
-    return traitsDto.stream().map(x -> x.coneCount()).reduce(BigDecimal.ZERO, BigDecimal::add);
-  }
 }