Switch to maven for jhdf5 JAR (#231)

* Switch to maven for jhdf5 JAR

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/HasJobParams.java

@@ -2,6 +2,7 @@
 
 import org.json.JSONObject;
 
+import java.io.File;
 import java.util.Map;
 
 /**
@@ -12,4 +13,6 @@ public interface HasJobParams
     Map<String, String> getJobParams();
 
     JSONObject getParameterJson();
+
+    File getParametersFile();
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -144,4 +144,6 @@ static public void setInstance(SequencePipelineService instance)
 
     // Note: this primarily exists for testing. The returned TaskFileManager does not have key values set: SequenceJob, WorkingDir (File) and WorkDirectory
     abstract public TaskFileManager getTaskFileManager();
+
+    abstract public Set<JobResourceSettings> getResourceSettings();
 }

SequenceAnalysis/build.gradle

@@ -11,9 +11,9 @@ import java.util.regex.Matcher
 repositories {
    mavenCentral()
    // Added for jhdf5 from FASTQC / sequence analysis module
-//   maven {
-//      url "https://maven.scijava.org/content/groups/public/"
-//   }
+   maven {
+      url "https://maven.scijava.org/content/groups/public/"
+   }
 }
 
 configurations.all {
@@ -92,19 +92,18 @@ dependencies {
             )
     )
 
-    // NOTE: this maven repo has been unreliable
-//    BuildUtils.addExternalDependency(
-//            project,
-//            new ExternalDependency(
-//                    'cisd:jhdf5:19.04.1',
-//                    'JHDF5',
-//                    'JHDF5',
-//                    'https://unlimited.ethz.ch/display/JHDF/',
-//                    ExternalDependency.BSD_LICENSE_NAME,
-//                    ExternalDependency.BSD_LICENSE_URL,
-//                    'JHDF5 is a Java binding for HDF5. Used by FastQC'
-//            )
-//    )
+    BuildUtils.addExternalDependency(
+            project,
+            new ExternalDependency(
+                    'cisd:jhdf5:19.04.1',
+                    'JHDF5',
+                    'JHDF5',
+                    'https://unlimited.ethz.ch/display/JHDF/',
+                    ExternalDependency.BSD_LICENSE_NAME,
+                    ExternalDependency.BSD_LICENSE_URL,
+                    'JHDF5 is a Java binding for HDF5. Used by FastQC'
+            )
+    )
 
     BuildUtils.addExternalDependency(
             project,

SequenceAnalysis/resources/external/cisd-jhdf5.jar

@@ -523,6 +523,7 @@ public void registerResourceSettings(JobResourceSettings settings)
         _resourceSettings.add(settings);
     }
 
+    @Override
     public Set<JobResourceSettings> getResourceSettings()
     {
         return _resourceSettings;

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java

@@ -385,9 +385,7 @@ private List<String> getBaseParams() throws FileNotFoundException
             throw new RuntimeException("Not found: " + commonsMath.getPath());
         }
 
-        // NOTE: the maven repo has been unreliable, but we could ultimately switch to use that:
-        //File jhdf5 = new File(libDir, "cisd-jhdf5-14.12.6.jar");
-        File jhdf5 = new File(libDir.getParentFile(), "external/cisd-jhdf5.jar");
+        File jhdf5 = new File(libDir, "jhdf5-19.04.1.jar");
         if (!jhdf5.exists())
         {
             throw new RuntimeException("Not found: " + jhdf5.getPath());