Merge branch 'develop'

julie-sullivan · Jul 28, 2017 · 257851e · 257851e
2 parents fce8432 + aa506bd
commit 257851e
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Showing 7 changed files with 24 additions and 14 deletions.
diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>3.4.2</version>
+        <version>3.5.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>3.4.2</version>
+        <version>3.5.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>3.4.2</version>
+        <version>3.5.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>3.4.2</version>
+        <version>3.5.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-lib/src/main/java/org/opencb/commons/ProgressLogger.java b/commons-lib/src/main/java/org/opencb/commons/ProgressLogger.java
@@ -22,6 +22,7 @@
 import java.text.DecimalFormat;
 import java.util.concurrent.*;
 import java.util.concurrent.atomic.AtomicLong;
+import java.util.concurrent.atomic.AtomicReference;
 import java.util.function.Supplier;
 
 /**
@@ -41,7 +42,7 @@ public class ProgressLogger {
     private final int numLinesLog;
     private long totalCount;
     private boolean isApproximated; // Total count is an approximated value
-    private Future<Long> futureTotalCount;
+    private final AtomicReference<Future<Long>> futureTotalCount = new AtomicReference<>();
     private final AtomicLong count;
 
     private double batchSize;
@@ -86,7 +87,7 @@ private ProgressLogger(String message, long totalCount, Future<Long> futureTotal
         }
         this.numLinesLog = numLinesLog;
         this.totalCount = totalCount;
-        this.futureTotalCount = futureTotalCount;
+        this.futureTotalCount.set(futureTotalCount);
         this.count = new AtomicLong();
         if (totalCount == 0) {
             batchSize = DEFAULT_BATCH_SIZE;
@@ -161,16 +162,17 @@ protected void print(String m) {
     }
 
     private void updateFutureTotalCount() {
-        if (futureTotalCount != null) {
-            if (futureTotalCount.isDone()) {
+        Future<Long> future = futureTotalCount.get();
+        if (future != null) {
+            if (future.isDone()) {
                 try {
-                    totalCount = futureTotalCount.get();
+                    totalCount = future.get();
                     updateBatchSize();
                     isApproximated = false;
                 } catch (InterruptedException | ExecutionException ignore) {
                     logger.warn("There was a problem calculating the total number of elements");
                 } finally {
-                    futureTotalCount = null;
+                    futureTotalCount.set(null);
                 }
             }
         }

diff --git a/commons-lib/src/main/java/org/opencb/commons/utils/CommandLineUtils.java b/commons-lib/src/main/java/org/opencb/commons/utils/CommandLineUtils.java
@@ -52,8 +52,16 @@ public static void printCommandUsage(JCommander commander, PrintStream printStre
             if (parameterDescription.getParameter() != null && !parameterDescription.getParameter().hidden()) {
                 String type = getType(parameterDescription);
                 String defaultValue = "";
-                if (parameterDescription.getDefault() != null && !parameterDescription.isDynamicParameter()) {
-                    defaultValue = ("[" + parameterDescription.getDefault() + "]");
+                if (parameterDescription.getDefault() != null) {
+                    if (parameterDescription.isDynamicParameter()) {
+                        Object def = parameterDescription.getDefault();
+                        if (def instanceof Map && !((Map) def).isEmpty()) {
+                            defaultValue = ("[" + def + "]");
+                        }
+//                        defaultValue = ("[" + parameterDescription.getDefault() + "]");
+                    } else {
+                        defaultValue = ("[" + parameterDescription.getDefault() + "]");
+                    }
                 }
                 String usage = String.format("%5s %-" + paramNameMaxSize + "s %-" + typeMaxSize + "s %s %s\n",
                         (parameterDescription.getParameterized().getParameter() != null

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.commons</groupId>
     <artifactId>commons</artifactId>
-    <version>3.4.2</version>
+    <version>3.5.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>OpenCB commons project</name>
@@ -19,7 +19,7 @@
     </modules>
 
     <properties>
-        <java.commons.version>3.4.2</java.commons.version>
+        <java.commons.version>3.5.0-SNAPSHOT</java.commons.version>
         <compileSource>1.8</compileSource>
         <jackson.version>2.8.4</jackson.version>
         <apache.commons.version>3.5</apache.commons.version>