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20 package org.openi.stat.r.rserve;
21
22 import org.apache.log4j.*;
23 import org.openi.stat.r.RClient;
24 import org.rosuda.JRclient.*;
25 import java.util.*;
26 import java.io.*;
27 import java.io.IOException  ;
28 import org.openi.stat.r.RFunction;
29 import org.openi.stat.r.RFunctionParam;
30
31
38 public class RServeClient implements RClient {
39 private static Logger logger = Logger.getLogger(RServeClient.class);
40 private String serverIP;
41 private int serverPort;
42
44
45
50 public RServeClient(String rServerIP, int serverPort) throws RSrvException {
51 logger.debug("IP:" + rServerIP);
52 this.serverIP = rServerIP;
53 this.serverPort = serverPort;
54
55 }
56
57
63
64 public void execute(RFunction function, String outputPath) throws Exception {
65
66 String script = generateScript(function);
67 logger.debug("Generated Script: " + script);
68 Rconnection rConnection = new Rconnection(serverIP, serverPort);
69 String scriptContent = getContent(function.getFile());
70 logger.debug("Executing R Script file");
71 rConnection.voidEval(scriptContent);
72
73 if (function.getDataSetFile() != null &&
74 !"".equals(function.getDataSetFile())) {
75 logger.debug("Sending dataSet file " + function.getDataSetFile() +
76 " to the R server");
77 sendFileToServer(rConnection, function.getDataSetFile());
78 }
79
80 logger.debug(
81 "Executing generated R Script to call method on uploaded R script");
82 REXP xp = rConnection.eval(script);
83
84 if (function.getDataSetFile() != null &&
85 !"".equals(function.getDataSetFile())) {
86 logger.debug("Removing dataSet file " + function.getDataSetFile() +
87 " from the R server");
88 removeFileFromServer(rConnection, function.getDataSetFile());
89 }
90
91 Vector output = xp.asVector();
92 logger.debug("Saving " + output.size() +
93 " file(s) are generated by the R script to path " +
94 outputPath);
95 Iterator iter = output.iterator();
96
97 while (iter.hasNext()) {
98 REXP xpFile = (REXP) iter.next();
99 String file = xpFile.asString();
100 logger.info("downloading '" + file + "' from r server");
101 saveFileFromServer(rConnection, file, outputPath);
102 removeFileFromServer(rConnection, file);
103 }
104
105 logger.debug("closing R");
106 rConnection.close();
107
108 }
109
110
120 private String generateScript(RFunction function) {
121 StringBuffer generatedScript = new StringBuffer ();
122 String functionName = function.getName();
123 StringBuffer paramString = new StringBuffer ();
124 Iterator iterator = function.getParams().iterator();
125
126 if (function.getDataSetFile() != null &&
127 !"".equals(function.getDataSetFile())) {
128 String dataSetFileName = new File(function.getDataSetFile()).
129 getName();
130 generatedScript.append("data <- read.delim(\"" + dataSetFileName +
131 "\", ");
132 generatedScript.append("header=TRUE, sep=\"\\t\")");
133 paramString.append("dataFrame=data");
134 paramString.append(", ");
135 generatedScript.append("\n");
136
137 } while (iterator.hasNext()) {
138 RFunctionParam param = (RFunctionParam) iterator.next();
139 String paramVal = "String".equals(param.getType()) ?
140 "\"" + param.getValue() + "\"" : param.getValue();
141 String paramWithVal = param.getName() + " = " + paramVal;
142 paramString.append(paramWithVal);
143 paramString.append(",");
144 }
145
146 if (paramString.lastIndexOf(",") != -1) {
147 paramString.deleteCharAt(paramString.lastIndexOf(","));
148 }
149
150 generatedScript.append("filenames <- " + functionName + "(");
151 generatedScript.append(paramString.toString());
152 generatedScript.append(")");
153
154 return generatedScript.toString();
155 }
156
157
163 private String getContent(String file) throws IOException {
164 StringBuffer buffer = new StringBuffer ();
165 BufferedReader input = new BufferedReader(new InputStreamReader(new
166 FileInputStream(file)));
167 while (input.ready()) {
168 buffer.append(input.readLine());
169 buffer.append("\n");
170 }
171 return buffer.toString();
172 }
173
174
180 private void sendFileToServer(Rconnection rConnection, String fileName) throws
181 IOException {
182 File file = new File(fileName);
183 RFileOutputStream ros = rConnection.createFile(file.getName());
184
185 BufferedInputStream bis = new BufferedInputStream(new FileInputStream(
186 file));
187
188 byte[] buf = new byte[512];
189 int n = 0;
190
191 while ((n = bis.read(buf)) != -1) {
192 ros.write(buf, 0, n);
193 }
194
195 ros.flush();
196 ros.close();
197 bis.close();
198
199 }
200
201
208 private void saveFileFromServer(Rconnection rConnection, String fileName,
209 String pathToSave) throws Exception {
210 RFileInputStream ris = rConnection.openFile(fileName);
211 FileOutputStream outs = new FileOutputStream(pathToSave + "/" +
212 new File(fileName).getName());
213 byte[] buf = new byte[512];
214 int n = 0;
215 while ((n = ris.read(buf)) != -1) {
216 outs.write(buf, 0, n);
217 }
218 outs.flush();
219 ris.close();
220 outs.close();
221 }
222
223
229 private void removeFileFromServer(Rconnection rConnection, String file) throws
230 RSrvException {
231 rConnection.removeFile(new File(file).getName());
232 }
233 }
234 |
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