mv all *.java to java package

piflow-bundle/src/main/java/cn/piflow/bundle/microorganism/util/PDB.java

@@ -1,6 +1,7 @@
 package cn.piflow.bundle.microorganism.util;
 
 import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.log4j.Logger;
 import org.biojava.nbio.structure.*;
@@ -8,13 +9,14 @@ import org.biojava.nbio.structure.io.PDBFileReader;
 import org.json.JSONArray;
 import org.json.JSONObject;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import java.text.DateFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.*;
-import java.util.zip.GZIPInputStream;
-import org.apache.hadoop.fs.FileSystem;
 
 public class PDB {
 

piflow-bundle/src/main/java/cn/piflow/bundle/microorganism/util/Pfam.java

@@ -4,8 +4,13 @@ package cn.piflow.bundle.microorganism.util;
 import org.biojava.bio.seq.io.ParseException;
 import org.json.JSONArray;
 import org.json.JSONObject;
-import java.io.*;
+
-import java.util.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 

piflow-bundle/src/main/java/cn/piflow/bundle/util/ExcelToJson.java

@@ -7,7 +7,6 @@ import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.poi.hssf.usermodel.HSSFDateUtil;
 import org.apache.poi.hssf.usermodel.HSSFWorkbook;
-import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
 import org.apache.poi.poifs.filesystem.POIFSFileSystem;
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;
@@ -15,9 +14,6 @@ import org.apache.poi.ss.usermodel.Sheet;
 import org.apache.poi.ss.usermodel.Workbook;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;

piflow-bundle/src/main/java/cn/piflow/bundle/util/JedisClusterImplSer.java

@@ -8,7 +8,7 @@ import java.io.IOException;
 import java.io.ObjectStreamException;
 import java.io.Serializable;
 
-public class JedisClusterImplSer  implements Serializable {
+public class JedisClusterImplSer implements Serializable {
 
     private static final long serialVersionUID = -51L;
 

piflow-bundle/src/main/scala/cn/piflow/bundle/hdfs/PutHdfs.scala

@@ -29,14 +29,14 @@ class PutHdfs extends ConfigurableStop{
     config.set("fs.defaultFS",hdfsUrl)
     val fs = FileSystem.get(config)
 
-      if (types=="json"){
+    if (types=="json"){
-        inDF.repartition(partition).write.json(hdfsUrl+hdfsPath)
+      inDF.repartition(partition).write.json(hdfsUrl+hdfsPath)
-      } else if (types=="csv"){
+    } else if (types=="csv"){
-        inDF.repartition(partition).write.csv(hdfsUrl+hdfsPath)
+      inDF.repartition(partition).write.csv(hdfsUrl+hdfsPath)
-      } else {
+    } else {
-        //parquet
+      //parquet
-        inDF.repartition(partition).write.save(hdfsUrl+hdfsPath)
+      inDF.repartition(partition).write.save(hdfsUrl+hdfsPath)
-      }
+    }
 
   }
   override def setProperties(map: Map[String, Any]): Unit = {
@@ -50,8 +50,10 @@ class PutHdfs extends ConfigurableStop{
     var descriptor : List[PropertyDescriptor] = List()
     val hdfsPath = new PropertyDescriptor().name("hdfsPath").displayName("hdfsPath").defaultValue("").required(true)
     val hdfsUrl = new PropertyDescriptor().name("hdfsUrl").displayName("hdfsUrl").defaultValue("").required(true)
-    val types = new PropertyDescriptor().name("types").displayName("json,csv,parquet").defaultValue("").required(true)
+    val types = new PropertyDescriptor().name("types").displayName("json,csv,parquet").description("json,csv,parquet")
-    val partition = new PropertyDescriptor().name("partition").displayName("repartition").defaultValue("").required(true)
+      .defaultValue("csv").allowableValues(Set("json","csv","parquet")).required(true)
+
+    val partition = new PropertyDescriptor().name("partition").displayName("repartition").description("partition").defaultValue("").required(true)
     descriptor = partition :: descriptor
     descriptor = types :: descriptor
     descriptor = hdfsPath :: descriptor