feat: add r pbpk ode solver (#117)

ntua-unit-of-control-and-informatics · Nov 19, 2024 · 56fa770 · 56fa770
1 parent b7c8d13
commit 56fa770
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Showing 4 changed files with 16 additions and 0 deletions.
diff --git a/src/main/kotlin/org/jaqpot/api/entity/Model.kt b/src/main/kotlin/org/jaqpot/api/entity/Model.kt
@@ -101,6 +101,8 @@ class Model(
     @SQLRestriction("score_type = 'TRAIN'")
     var trainScores: List<Scores>? = null,
 
+    val rPbpkOdeSolver: String? = null,
+
     @OneToMany(mappedBy = "model", cascade = [CascadeType.ALL], orphanRemoval = true)
     @SQLRestriction("score_type = 'TEST'")
     var testScores: List<Scores>? = null,

diff --git a/src/main/kotlin/org/jaqpot/api/mapper/ModelMapper.kt b/src/main/kotlin/org/jaqpot/api/mapper/ModelMapper.kt
@@ -64,6 +64,7 @@ fun ModelDto.toEntity(creatorId: String): Model {
         trainScores = mutableListOf(),
         testScores = mutableListOf(),
         crossValidationScores = mutableListOf(),
+        rPbpkOdeSolver = this.rPbpkConfig?.odeSolver,
         rawPreprocessor = this.rawPreprocessor,
         rawModel = this.rawModel,
     )
@@ -115,6 +116,7 @@ fun Model.toPredictionModelDto(
         featurizers = this.featurizers.map { it.toDto() },
         preprocessors = this.preprocessors.map { it.toDto() },
         torchConfig = this.torchConfig,
+        rPbpkOdeSolver = this.rPbpkOdeSolver,
         legacyAdditionalInfo = this.legacyAdditionalInfo,
         legacyPredictionService = this.legacyPredictionService
     )

diff --git a/src/main/resources/db/migration/V39__add_r_pbpk_config.sql b/src/main/resources/db/migration/V39__add_r_pbpk_config.sql
@@ -0,0 +1,2 @@
+ALTER TABLE model
+    ADD r_pbpk_ode_solver VARCHAR(255);
diff --git a/src/main/resources/openapi.yaml b/src/main/resources/openapi.yaml
@@ -1253,6 +1253,8 @@ components:
               type: array
               items:
                 $ref: '#/components/schemas/Scores'
+        rPbpkConfig:
+          $ref: '#/components/schemas/RPbpkConfig'
         createdAt:
           type: string
           format: date-time
@@ -1448,6 +1450,12 @@ components:
               format: float
             maxItems: 100
           maxItems: 100
+    RPbpkConfig:
+      type: object
+      description: Configuration for the R PBPK models
+      properties:
+        odeSolver:
+          type: string
     OrganizationSummary:
       type: object
       required:
@@ -2017,6 +2025,8 @@ components:
             $ref: '#/components/schemas/AnyValue'
           description: "Torch configuration settings, optional"
           nullable: true
+        rPbpkOdeSolver:
+          type: string
         legacyAdditionalInfo:
           type: object
           additionalProperties:
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		ALTER TABLE model
		ADD r_pbpk_ode_solver VARCHAR(255);