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Declare api and implementation dependencies to align with code usages #57

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Merged
labkey-susanh merged 6 commits into from
Sep 22, 2020
Merged

Declare api and implementation dependencies to align with code usages #57

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8342e15
commons-net no longer coming out of :server:modules:platform:api
labkey-susanh Sep 7, 2020
87cd443
Remove commons-math3 from :server:modules:platform:api
labkey-susanh Sep 7, 2020
7f15a21
reference commons-math3 locally
labkey-susanh Sep 13, 2020
50c476a
Merge remote-tracking branch 'origin/develop' into fb_dependencyHealth
labkey-susanh Sep 17, 2020
3839e22
Align jars.txt with dependency declarations
labkey-susanh Sep 17, 2020
f6909cf
Get commons-math3 from the core module instead of api
labkey-susanh Sep 18, 2020
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5 changes: 4 additions & 1 deletion SequenceAnalysis/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@ dependencies {
exclude group: "org.apache.commons", module: "commons-collections4"
}

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")
}
Expand Down Expand Up @@ -61,4 +64,4 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
testProject.tasks.named("startTomcat").configure {
dependsOn(createPipelineConfigTask)
}
}
}
1 change: 1 addition & 0 deletions SequenceAnalysis/resources/credits/dependencies.txt
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Expand Up @@ -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
3 changes: 2 additions & 1 deletion SequenceAnalysis/resources/credits/jars.txt
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Expand Up @@ -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}
{table}
4 changes: 2 additions & 2 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
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Expand Up @@ -349,7 +349,7 @@ private List<String> 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())
Expand All @@ -359,7 +359,7 @@ private List<String> 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(coreLibDir, "commons-math3-3.6.1.jar");
if (!commonsMath.exists())
{
throw new RuntimeException("Not found: " + commonsMath.getPath());
Expand Down