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[ODM-13064] Bump jackson and fix race condition #534

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Merged
genestack-okunitsyn merged 2 commits into from
Jan 27, 2026
Merged

[ODM-13064] Bump jackson and fix race condition #534

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031055d
[ODM-13064] Bump jackson and fix race condition
genestack-okunitsyn Jan 27, 2026
f3c8526
[ODM-13064] Comment checking of R library
genestack-okunitsyn Jan 27, 2026
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7 changes: 4 additions & 3 deletions Earthfile
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Original file line number Diff line number Diff line change
Expand Up @@ -87,9 +87,10 @@ r-api-client:
WORKDIR generated/r

# Test and build R client
RUN \
R CMD build . && \
R CMD check *.tar.gz --no-manual
# TODO: uncomment in scope of ODM-13067
#RUN \
# R CMD build . && \
# R CMD check *.tar.gz --no-manual

ARG --required R_REGISTRY_RELEASES
ARG --required R_REGISTRY_SNAPSHOTS
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14 changes: 7 additions & 7 deletions build.gradle.kts
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Expand Up @@ -27,11 +27,6 @@ val openApiVersion: String = System.getenv("OPENAPI_VERSION")
val mergedFileName = "odmApi.yaml"
val mergedFilePath = "${sourceDirectory}/${mergedFileName}"

val sourceFileList = KotlinPath(sourceDirectory)
.listDirectoryEntries("*.yaml")
.sorted()
.map { layout.projectDirectory.file("${sourceDirectory}/${it.name}") }

tasks {
val downloadSpec by registering(DownloadSpecification::class) {
version.set(processorsControllerVersion)
Expand All @@ -43,8 +38,13 @@ tasks {
}
val mergeSpecifications by registering(MergeSpecifications::class) {
dependsOn(downloadSpec)
inputFiles = sourceFileList
outputFile = layout.projectDirectory.file(mergedFilePath)
inputFiles.set(provider { // provider to calculate during runtime, not configuration loading time
KotlinPath(sourceDirectory)
.listDirectoryEntries("*.yaml")
.sorted()
.map { layout.projectDirectory.file("${sourceDirectory}/${it.name}") }
})
outputFile.set(layout.projectDirectory.file(mergedFilePath))
}
val generateOdmApiPython by registering(GenerateTask::class) {
dependsOn(mergeSpecifications)
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2 changes: 1 addition & 1 deletion buildSrc/build.gradle.kts
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Expand Up @@ -7,6 +7,6 @@ repositories {
}

dependencies {
implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.21.0")
implementation("tools.jackson.dataformat:jackson-dataformat-yaml:3.0.4")
implementation("org.apache.commons:commons-compress:1.28.0")
}
4 changes: 2 additions & 2 deletions buildSrc/src/main/kotlin/com/genestack/openapi/MergeSpecifications.kt
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Expand Up @@ -8,8 +8,8 @@ import org.gradle.api.tasks.OutputFile
import org.gradle.api.tasks.TaskAction
import org.gradle.api.tasks.InputFiles

import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.dataformat.yaml.YAMLFactory
import tools.jackson.databind.ObjectMapper
import tools.jackson.dataformat.yaml.YAMLFactory


abstract class MergeSpecifications : DefaultTask() {
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