From a70944838432d3052d6b8b3b47ce3d95b41a9ac6 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 7 Sep 2020 15:17:28 -0700 Subject: [PATCH 1/3] Remove commons-math3 from :server:modules:platform:api --- elispot_assay/build.gradle | 1 + 1 file changed, 1 insertion(+) diff --git a/elispot_assay/build.gradle b/elispot_assay/build.gradle index 4ade1fd73..0f7dcb5ec 100644 --- a/elispot_assay/build.gradle +++ b/elispot_assay/build.gradle @@ -1,6 +1,7 @@ import org.labkey.gradle.util.BuildUtils; dependencies { + external "org.apache.commons:commons-math3:${commonsMath3Version}" BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") From 7e767aa2efda10d2ea9e1ba68a815d347dfde536 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 7 Sep 2020 16:21:38 -0700 Subject: [PATCH 2/3] Add external dependencies that had been leaking out of other dependencies --- variantdb/build.gradle | 2 ++ 1 file changed, 2 insertions(+) diff --git a/variantdb/build.gradle b/variantdb/build.gradle index 2ef9d9995..8d00d81ab 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -2,6 +2,8 @@ import org.labkey.gradle.util.BuildUtils; dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" + external "commons-net:commons-net:${commonsNetVersion}" + external "org.apache.commons:commons-math3:${commonsMath3Version}" 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") From d5dd5882f384bc33193b54bc6cd015fdbaad4fc3 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Thu, 17 Sep 2020 13:17:33 -0700 Subject: [PATCH 3/3] Align jars.txt with dependency declarations --- elispot_assay/resources/credits/jars.txt | 4 ++++ variantdb/resources/credits/jars.txt | 5 +++++ 2 files changed, 9 insertions(+) create mode 100644 elispot_assay/resources/credits/jars.txt create mode 100644 variantdb/resources/credits/jars.txt diff --git a/elispot_assay/resources/credits/jars.txt b/elispot_assay/resources/credits/jars.txt new file mode 100644 index 000000000..ca5998602 --- /dev/null +++ b/elispot_assay/resources/credits/jars.txt @@ -0,0 +1,4 @@ +{table} +Filename|Component|Version|Source|License|LabKey Dev|Purpose +commons-math3-3.6.1.jar|Commons Math|3.6.1|{link:Apache|http://commons.apache.org/math/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}||Lightweight, self-contained mathematics and statistics components +{table} diff --git a/variantdb/resources/credits/jars.txt b/variantdb/resources/credits/jars.txt new file mode 100644 index 000000000..74496f3a9 --- /dev/null +++ b/variantdb/resources/credits/jars.txt @@ -0,0 +1,5 @@ +{table} +Filename|Component|Version|Source|License|Purpose +commons-math3-3.6.1.jar|Commons Math|3.6.1|{link:Apache|http://commons.apache.org/math/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|Lightweight, self-contained mathematics and statistics components +commons-net-3.5.jar|Commons Net|3.3|{link:Apache|http://jakarta.apache.org/commons/net/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|FTPClient used to retrieve resources from other servers (e.g., GO annotations) +{table}