From 8342e15a7e887adaa59bd369583e3ea79076dbbc Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 7 Sep 2020 12:06:31 -0700 Subject: [PATCH 1/5] commons-net no longer coming out of :server:modules:platform:api --- SequenceAnalysis/build.gradle | 3 ++- SequenceAnalysis/resources/credits/dependencies.txt | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 848009913..dddde74c2 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -31,6 +31,7 @@ dependencies { exclude group: "org.apache.commons", module: "commons-collections4" } + external "commons-net:commons-net:${commonsNetVersion}" BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module") BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module") } @@ -61,4 +62,4 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null & testProject.tasks.named("startTomcat").configure { dependsOn(createPipelineConfigTask) } -} \ No newline at end of file +} diff --git a/SequenceAnalysis/resources/credits/dependencies.txt b/SequenceAnalysis/resources/credits/dependencies.txt index 139ac845b..7cdd58437 100644 --- a/SequenceAnalysis/resources/credits/dependencies.txt +++ b/SequenceAnalysis/resources/credits/dependencies.txt @@ -6,3 +6,4 @@ bzip2-0.9.1.jar sam-1.96.jar commons-math3-3.6.1.jar picard-2.22.4.jar +commons-net-3.5.jar From 87cd443af2cf0004f990d57faa60852829d9dcfb Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 7 Sep 2020 15:17:28 -0700 Subject: [PATCH 2/5] Remove commons-math3 from :server:modules:platform:api --- SequenceAnalysis/build.gradle | 2 ++ 1 file changed, 2 insertions(+) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index dddde74c2..ea5aa5a64 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -32,6 +32,8 @@ dependencies { } external "commons-net:commons-net:${commonsNetVersion}" + apiImplementation "org.apache.commons:commons-math3:${commonsMath3Version}" + external "org.apache.commons:commons-math3:${commonsMath3Version}" 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") } From 7f15a2109f283212ab293993d0ddb8a7dbf52a26 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Sun, 13 Sep 2020 13:46:57 -0700 Subject: [PATCH 3/5] reference commons-math3 locally --- .../src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java index a21f4de14..49525626d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java @@ -359,7 +359,7 @@ private List getBaseParams() throws FileNotFoundException if (!samJar.exists()) throw new RuntimeException("Not found: " + samJar.getPath()); - File commonsMath = new File(apiLibDir, "commons-math3-3.6.1.jar"); + File commonsMath = new File(libDir, "commons-math3-3.6.1.jar"); if (!commonsMath.exists()) { throw new RuntimeException("Not found: " + commonsMath.getPath()); From 3839e2261b2aaaa9bafc041d2127931edbb7f3aa Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Thu, 17 Sep 2020 13:17:34 -0700 Subject: [PATCH 4/5] Align jars.txt with dependency declarations --- SequenceAnalysis/resources/credits/jars.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/resources/credits/jars.txt b/SequenceAnalysis/resources/credits/jars.txt index 89d8766e8..c50ebd98c 100644 --- a/SequenceAnalysis/resources/credits/jars.txt +++ b/SequenceAnalysis/resources/credits/jars.txt @@ -5,6 +5,7 @@ sam-1.96.jar|picard tools|1.96|{link:picard tools|http://sourceforge.net/project biojava3-core-3.0.7.jar|biojava3-core|3.0.7|{link:biojava|http://biojava.org/wiki/Main_Page}|{link:GNU Lesser GPL V2.1|http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}|bbimber|Java framework for processing biological data biojava3-genome-3.0.7.jar|biojava3-genome|3.0.7|{link:biojava|http://biojava.org/wiki/Main_Page}|{link:GNU Lesser GPL V2.1|http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}|bbimber|Java framework for processing biological data commons-math3-3.6.1.jar|commons-math|3-3.6.1|{link:commons-math|http://commons.apache.org/proper/commons-math/}|{link:Apache License, Version 2.0|http://www.apache.org/licenses/LICENSE-2.0.txt}|bbimber|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}|bbimber|FTPClient used to retrieve resources from other servers (e.g., GO annotations) htsjdk-2.21.3.jar|htsjdk|2.21.3|{link:htsjdk|http://samtools.github.io/htsjdk/}|{link:MIT License|http://opensource.org/licenses/MIT}|bbimber|Description A Java API for high-throughput sequencing data (HTS) formats picard-2.22.4.jar|Picard Tools Lib|2.22.4|{link:PicardTools|https://github.com/broadinstitute/picard}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|bbimber|Manipulating Sequence Data -{table} \ No newline at end of file +{table} From f6909cfc054feeed0246766d1f1fd4d6db7f18ef Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Fri, 18 Sep 2020 15:00:54 -0700 Subject: [PATCH 5/5] Get commons-math3 from the core module instead of api --- .../org/labkey/sequenceanalysis/run/util/FastqcRunner.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java index 49525626d..1363365f8 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java @@ -349,7 +349,7 @@ private List getBaseParams() throws FileNotFoundException } File libDir = new File(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.NAME).getExplodedPath(), "lib"); - File apiLibDir = new File(ModuleLoader.getInstance().getModule("api").getExplodedPath(), "lib"); + File coreLibDir = new File(ModuleLoader.getInstance().getModule("core").getExplodedPath(), "lib"); File fastqcDir = new File(libDir.getParentFile(), "external/fastqc"); File bzJar = new File(libDir, "bzip2-0.9.1.jar"); if (!bzJar.exists()) @@ -359,7 +359,7 @@ private List getBaseParams() throws FileNotFoundException if (!samJar.exists()) throw new RuntimeException("Not found: " + samJar.getPath()); - File commonsMath = new File(libDir, "commons-math3-3.6.1.jar"); + File commonsMath = new File(coreLibDir, "commons-math3-3.6.1.jar"); if (!commonsMath.exists()) { throw new RuntimeException("Not found: " + commonsMath.getPath());