From d5d47aa4f5dddde3ec44246ac99180f9e465ce29 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Tue, 22 Sep 2020 14:55:54 -0700 Subject: [PATCH] Add missing dependencies on opencsv and httpmime that used to be leaking out of the labkey-client-api. Since both of these dependencies are included in the api module transitively, we compromise a bit and do not include them in the jars.txt for each individual module. --- GenotypeAssays/build.gradle | 1 + elispot_assay/build.gradle | 2 ++ mGAP/build.gradle | 1 + primeseq/build.gradle | 1 + tcrdb/build.gradle | 1 + variantdb/build.gradle | 1 + 6 files changed, 7 insertions(+) diff --git a/GenotypeAssays/build.gradle b/GenotypeAssays/build.gradle index fe9fbde30..7238668f0 100644 --- a/GenotypeAssays/build.gradle +++ b/GenotypeAssays/build.gradle @@ -3,6 +3,7 @@ import org.labkey.gradle.util.BuildUtils; dependencies { BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile") + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module") BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module") diff --git a/elispot_assay/build.gradle b/elispot_assay/build.gradle index 0f7dcb5ec..c9c62bbda 100644 --- a/elispot_assay/build.gradle +++ b/elispot_assay/build.gradle @@ -2,6 +2,8 @@ import org.labkey.gradle.util.BuildUtils; dependencies { external "org.apache.commons:commons-math3:${commonsMath3Version}" + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" + BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") diff --git a/mGAP/build.gradle b/mGAP/build.gradle index 0b40bcce2..9e73435db 100644 --- a/mGAP/build.gradle +++ b/mGAP/build.gradle @@ -8,6 +8,7 @@ dependencies { BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "apiJarFile") external "com.github.samtools:htsjdk:${htsjdkVersion}" implementation "com.sun.mail:jakarta.mail:${javaMailVersion}" + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "published", depExtension: "module") BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module") diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 718ca7029..014977a2d 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -2,6 +2,7 @@ import org.labkey.gradle.util.BuildUtils; dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiElements") diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index 430731efc..ff76d0e15 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -8,6 +8,7 @@ dependencies { BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "assay"), depProjectConfig: "apiJarFile") external "io.repseq:repseqio:${repseqVersion}" implementation "com.github.samtools:htsjdk:${htsjdkVersion}" + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module") BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module") diff --git a/variantdb/build.gradle b/variantdb/build.gradle index 8d00d81ab..4328d183c 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -4,6 +4,7 @@ dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" external "commons-net:commons-net:${commonsNetVersion}" external "org.apache.commons:commons-math3:${commonsMath3Version}" + implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")