From 20092d3190c578b9990bfde8b015e8666d92e53f Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 21 Apr 2026 16:49:01 -0700 Subject: [PATCH 1/4] Stop copying Graphviz/DOT executables during the build --- build.gradle | 7 ------- gradle.properties | 5 +---- server/build.gradle | 4 ++-- 3 files changed, 3 insertions(+), 13 deletions(-) diff --git a/build.gradle b/build.gradle index ca3fb4df1b..ed890c6e1a 100644 --- a/build.gradle +++ b/build.gradle @@ -79,7 +79,6 @@ allprojects { configurations { driver - utilities } configurations.configureEach { // exclude log4j 1.x, which may come in transitively, from all configurations to avoid its potential vulnerabilities @@ -88,17 +87,11 @@ allprojects { exclude group: "org.springframework.boot", module:"spring-boot-starter-logging" } configurations.driver.setDescription("Dependencies used for Gradle SetUpProperties task") - configurations.utilities.setDescription("Utility binaries for use on Windows platform") dependencies { driver "org.postgresql:postgresql:${postgresqlDriverVersion}" driver "com.microsoft.sqlserver:mssql-jdbc:${mssqlJdbcVersion}" - - if (SystemUtils.IS_OS_WINDOWS) - { - utilities "org.labkey.tools.windows:utils:${windowsUtilsVersion}@zip" - } } // We apply the base module here so we get the configurations (in particular external and modules) diff --git a/gradle.properties b/gradle.properties index ca69307243..f722056374 100644 --- a/gradle.properties +++ b/gradle.properties @@ -47,11 +47,8 @@ buildFromSource=true labkeyVersion=26.5-SNAPSHOT labkeyClientApiVersion=7.2.0 -# Version numbers for the various binary artifacts that are included when -# deploying via deployApp or deployDist and when creating distributions. -windowsUtilsVersion=1.0 # Uncomment the following line to download proteomics binaries -#includeProteomicsBinaries +includeProteomicsBinaries linuxProteomicsBinariesVersion=2.0 osxProteomicsBinariesVersion=1.0 windowsProteomicsBinariesVersion=1.0 diff --git a/server/build.gradle b/server/build.gradle index 02d2316d06..f833e42194 100644 --- a/server/build.gradle +++ b/server/build.gradle @@ -39,9 +39,9 @@ dependencies configurations { - binaries.extendsFrom(utilities) + binaries } -configurations.binaries.setDescription("Utility and proteomics binaries") +configurations.binaries.setDescription("Proteomics binaries") if (project.hasProperty('includeProteomicsBinaries')) { From 8cf9f44d10544df8cd386fa4b542b1ba8de4d3ec Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 21 Apr 2026 17:27:13 -0700 Subject: [PATCH 2/4] Comment out the proteomics property --- gradle.properties | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gradle.properties b/gradle.properties index f722056374..ec8cc83d26 100644 --- a/gradle.properties +++ b/gradle.properties @@ -48,7 +48,7 @@ labkeyVersion=26.5-SNAPSHOT labkeyClientApiVersion=7.2.0 # Uncomment the following line to download proteomics binaries -includeProteomicsBinaries +#includeProteomicsBinaries linuxProteomicsBinariesVersion=2.0 osxProteomicsBinariesVersion=1.0 windowsProteomicsBinariesVersion=1.0 @@ -164,6 +164,7 @@ googleOauthClientVersion=1.39.0 googleProtocolBufVersion=3.25.9 graphSupportVersion=1.5.2 +grpcVersion=1.80.0 # Cloud and SequenceAnalysis bring gson in as a transitive dependency. # We resolve to the later version here to keep things consistent @@ -171,8 +172,6 @@ graphSupportVersion=1.5.2 # "java.lang.NoSuchMethodError: 'void com.google.gson.internal.ConstructorConstructor.(java.util.Map)'" errors gsonVersion=2.8.9 -grpcVersion=1.80.0 - guavaVersion=33.6.0-jre # Note: You won't find usages in the product sources; this property is used by the gradle plugin. From f5e18bfae9261e215d3543493421f3cea885ff46 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Wed, 22 Apr 2026 13:17:00 -0700 Subject: [PATCH 3/4] Test new gradlePlugins version --- gradle.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gradle.properties b/gradle.properties index ec8cc83d26..4ddcde59be 100644 --- a/gradle.properties +++ b/gradle.properties @@ -56,7 +56,7 @@ windowsProteomicsBinariesVersion=1.0 # The current version numbers for the gradle plugins. artifactoryPluginVersion=5.2.5 gradleNodePluginVersion=7.1.0 -gradlePluginsVersion=8.0.0 +gradlePluginsVersion=8.1.0-no_binaries-SNAPSHOT owaspDependencyCheckPluginVersion=12.2.1 # Versions of node and npm to use during the build. If set, these versions From b3ddd0c098e3230ffa198ee73d4760a838cd9ca3 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Wed, 22 Apr 2026 17:36:20 -0700 Subject: [PATCH 4/4] Update gradle plugins version --- gradle.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gradle.properties b/gradle.properties index f2f54560b0..c71e68fe1d 100644 --- a/gradle.properties +++ b/gradle.properties @@ -56,7 +56,7 @@ windowsProteomicsBinariesVersion=1.0 # The current version numbers for the gradle plugins. artifactoryPluginVersion=5.2.5 gradleNodePluginVersion=7.1.0 -gradlePluginsVersion=8.1.0-no_binaries-SNAPSHOT +gradlePluginsVersion=8.1.0 owaspDependencyCheckPluginVersion=12.2.1 # Versions of node and npm to use during the build. If set, these versions