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

Author: labkey-susanh

SequenceAnalysis/build.gradle

@@ -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")
 }
@@ -61,4 +64,4 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
    testProject.tasks.named("startTomcat").configure {
       dependsOn(createPipelineConfigTask)
    }
-}
+}

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

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}
+{table}

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -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())
@@ -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());