test: add junit tests for variant association analysis, #126

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java

@@ -99,6 +99,9 @@ public void execute() throws Exception {
             case "rvtests":
                 rvtests();
                 break;
+            case "association":
+                assoc();
+                break;
             default:
                 logger.error("Variant subcommand '" + subCommandString + "' not valid");
                 break;
@@ -852,4 +855,33 @@ public void rvtests() throws Exception {
 //        rvtests.run(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
         rvtests.run00(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
     }
+
+    public void assoc() throws Exception {
+        File metaFile = new File(variantCommandOptions.associationVariantCommandOptions.input + ".meta.json");
+        if (!metaFile.isFile() || !metaFile.exists() || !metaFile.canRead()) {
+            throw new FileNotFoundException("Check your input metadata file.");
+        }
+
+        SparkConf sparkConf = SparkConfCreator.getConf("variant association", "local", 1, true);
+        logger.debug("sparkConf = {}", sparkConf.toDebugString());
+        SparkSession sparkSession = new SparkSession(new SparkContext(sparkConf));
+
+        VariantDataset vd = new VariantDataset(sparkSession);
+        vd.load(variantCommandOptions.associationVariantCommandOptions.input);
+        vd.createOrReplaceTempView("vcf");
+        vd.show(2);
+
+        VariantMetadataManager variantMetadataManager = new VariantMetadataManager();
+        variantMetadataManager.load(metaFile.getPath());
+        Pedigree pedigree = variantMetadataManager.getPedigree("noname");
+
+        for (String key: pedigree.getIndividuals().keySet()) {
+            System.out.println(key + " = " + pedigree.getIndividuals().get(key));
+        }
+        //PedigreeManager pedigreeManager = new PedigreeManager();
+        //pedigreeManager.
+        //String pheno = variantCommandOptions.associationVariantCommandOptions.pheno;
+
+        sparkSession.stop();
+    }
 }

hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantAssocCLITest.java

@@ -0,0 +1,41 @@
+package org.opencb.hpg.bigdata.app.cli.local;
+
+import org.junit.Test;
+
+import java.net.URISyntaxException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+/**
+ * Created by joaquin on 1/19/17.
+ */
+public class VariantAssocCLITest {
+    Path inPath;
+    Path outPath;
+    Path confPath;
+
+    private void init() throws URISyntaxException {
+        String root = "/home/jtarraga//data150/test/assoc";
+        inPath = Paths.get(root + "/test.vcf.avro");
+        outPath = Paths.get(root + "/assoc.out");
+    }
+
+    @Test
+    public void assoc() {
+        try {
+            init();
+
+            StringBuilder commandLine = new StringBuilder();
+            commandLine.append(" variant association");
+            commandLine.append(" --log-level ERROR");
+            commandLine.append(" -i ").append(inPath);
+            commandLine.append(" -o ").append(outPath);
+            commandLine.append(" --dataset noname");
+
+            VariantQueryCLITest.execute(commandLine.toString());
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+}