| 10 |
10 |
*
|
| 11 |
11 |
* Version: '$Id$'
|
| 12 |
12 |
*/
|
|
13 |
/**************************************************************************
|
|
14 |
Copyright ^?? General Atomics, 1995-1999
|
|
15 |
All Rights Reserved
|
|
16 |
|
|
17 |
This file contains Original Code and/or Modifications of Original Code as
|
|
18 |
defined in and that are subject to the General Atomics Storage Resource
|
|
19 |
Broker Academic and Research Use License (the 'License'). This license is
|
|
20 |
for academic and research use only. You may not use, copy, modify or
|
|
21 |
distribute SRB for commercial purposes, nor incorporate the SRB into
|
|
22 |
commercial products without the express written permission of General
|
|
23 |
Atomics nor may you distribute SRB to any third party.
|
|
24 |
|
|
25 |
You may not use this software except in compliance with the License. Please
|
|
26 |
obtain a copy of the License at http://www.npaci.edu/DICE/SRB/License and
|
|
27 |
read it before using this file.
|
|
28 |
|
|
29 |
The Original Code and all software distributed under the License are
|
|
30 |
distributed on an 'AS IS' basis, WITHOUT WARRANTY OF ANY KIND, EITHER
|
|
31 |
EXPRESS OR IMPLIED, AND GENERAL ATOMICS AND THE SAN DIEGO SUPERCOMPUTER
|
|
32 |
CENTER HEREBY DISCLAIM ALL SUCH WARRANTIES, INCLUDING WITHOUT LIMITATION,
|
|
33 |
ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR
|
|
34 |
NON-INFRINGEMENT OF ANY COPYRIGHT, PATENT , TRADEMARK OR OTHER RIGHTS.
|
|
35 |
GENERAL ATOMICS AND THE SAN DIEGO SUPERCOMPUTER CENTER FURTHER HAVE NO
|
|
36 |
OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCMENTS OR
|
|
37 |
MODIFICATIONS.. Please see the License for the specific language governing
|
|
38 |
rights and limitations under the License."
|
|
39 |
|
|
40 |
Please read the terms of this license carefully. By using the SRB software,
|
|
41 |
you are accepting and agreeing to the terms of this license with General
|
|
42 |
Atomics. If you are agreeing to this license on behalf of a company, or
|
|
43 |
other institution, you represent that you are authorized to bind the
|
|
44 |
company/institution to such a license. If you do not meet this criterion or
|
|
45 |
you do not agree to any of the terms of this license, you are not
|
|
46 |
authorized to use the software.
|
|
47 |
**************************************************************************/
|
| 13 |
48 |
|
| 14 |
49 |
/* Note: Based on Java code originally produced at SDSC
|
| 15 |
50 |
* Copyright 1999 The Regents of the University of California
|
| ... | ... | |
| 23 |
58 |
*
|
| 24 |
59 |
* @version 1.1 6/8/00
|
| 25 |
60 |
* @author Dan Higgins - NCEAS
|
|
61 |
* @version 1.0 10/23/97
|
|
62 |
* @author John Moreland
|
| 26 |
63 |
*/
|
| 27 |
64 |
|
| 28 |
65 |
import java.rmi.*;
|
| ... | ... | |
| 31 |
68 |
|
| 32 |
69 |
|
| 33 |
70 |
public class SrbJavaGlue extends UnicastRemoteObject implements SrbJavaGlueInterface
|
|
71 |
|
| 34 |
72 |
{
|
| 35 |
73 |
byte[] ByteData;
|
| 36 |
74 |
String FileName;
|
| 37 |
|
boolean previouslyConnected = false;
|
| 38 |
75 |
|
| 39 |
76 |
// JNI (Java Native Interface) Glue Routines for the SRB client library.
|
| 40 |
77 |
|
| ... | ... | |
| 42 |
79 |
super();
|
| 43 |
80 |
}
|
| 44 |
81 |
|
| 45 |
|
public synchronized native int clConnectJ( String host, String port, String auth );
|
| 46 |
|
|
| 47 |
|
public synchronized int rmiConnectJ(String host, String port, String auth, String user ) {
|
| 48 |
|
if (previouslyConnected) {
|
| 49 |
|
return -1;
|
| 50 |
|
}
|
| 51 |
|
else {
|
| 52 |
|
writeMdasEnv(user);
|
| 53 |
|
int res = clConnectJ(host, port, auth );
|
| 54 |
|
if (res>0) {previouslyConnected = true;}
|
| 55 |
|
return res;
|
| 56 |
|
|
| 57 |
|
}
|
| 58 |
|
}
|
|
82 |
public native int clConnectJ( String host, String port, String auth,
|
|
83 |
String user, String domain );
|
| 59 |
84 |
|
| 60 |
|
public synchronized native int srbListCollectJ( int conn, int catType,
|
|
85 |
public native int srbListCollectJ( int conn, int catType,
|
| 61 |
86 |
String collectionName, String flag, int types[] );
|
| 62 |
87 |
|
| 63 |
|
public synchronized native String getFileListItem( int index );
|
|
88 |
public native String getFileListItem( int index );
|
| 64 |
89 |
|
| 65 |
|
public synchronized native int clFinishJ( int conn );
|
| 66 |
|
|
| 67 |
|
public synchronized int rmiFinishJ(int conn) {
|
| 68 |
|
Reset();
|
| 69 |
|
return clFinishJ(conn);
|
| 70 |
|
}
|
|
90 |
public native int clFinishJ( int conn );
|
| 71 |
91 |
|
| 72 |
|
public synchronized native int srbObjCopyNewJ( String srcDir, String srcFile,
|
|
92 |
public native int srbObjCopyNewJ( String srcDir, String srcFile,
|
| 73 |
93 |
String dstDir, String dstFile, String dstRes );
|
| 74 |
94 |
|
| 75 |
|
public synchronized native int srbListResourceJ( int bs );
|
|
95 |
public native int srbListResourceJ( int bs );
|
| 76 |
96 |
|
| 77 |
|
public synchronized native String getResListItem( int index );
|
|
97 |
public native String getResListItem( int index );
|
| 78 |
98 |
|
| 79 |
|
public synchronized native String getDefCollection();
|
|
99 |
public native String getDefCollection();
|
| 80 |
100 |
|
| 81 |
|
public synchronized native String getDefResource();
|
|
101 |
public native String getDefResource();
|
| 82 |
102 |
|
| 83 |
|
public synchronized native String getUser();
|
|
103 |
public native String getUser();
|
| 84 |
104 |
|
| 85 |
|
public synchronized native String getDomain();
|
|
105 |
public native String getDomain();
|
| 86 |
106 |
|
| 87 |
|
public synchronized native String getLocalCacheDir();
|
|
107 |
public native String getLocalCacheDir();
|
| 88 |
108 |
|
| 89 |
|
public synchronized native int srbObjReplicateJ(int conn, int catType,
|
|
109 |
public native int srbObjReplicateJ(int conn, int catType,
|
| 90 |
110 |
String objID, String replNum, String collection, String resource);
|
| 91 |
111 |
|
| 92 |
|
public synchronized native int srbCollReplicateJ(int conn, int catType,
|
|
112 |
public native int srbCollReplicateJ(int conn, int catType,
|
| 93 |
113 |
String collection, String resource);
|
| 94 |
114 |
|
| 95 |
|
public synchronized native int queryDataInCollJ (int conn, int catType,
|
|
115 |
public native int queryDataInCollJ (int conn, int catType,
|
| 96 |
116 |
String parColl);
|
| 97 |
117 |
|
| 98 |
|
public synchronized native int queryDataJ (int conn, int catType, String objID,
|
|
118 |
public native int queryDataJ (int conn, int catType, String objID,
|
| 99 |
119 |
String parColl);
|
| 100 |
120 |
|
| 101 |
|
public synchronized native int querySubCollInCollJ (int conn, int catType,
|
|
121 |
public native int querySubCollInCollJ (int conn, int catType,
|
| 102 |
122 |
String parColl);
|
| 103 |
123 |
|
| 104 |
|
public synchronized native String getDataResultJ( int metaIndex, int rowIndex );
|
|
124 |
public native String getDataResultJ( int metaIndex, int rowIndex );
|
| 105 |
125 |
|
| 106 |
|
public synchronized native String getCollResultJ( int metaIndex, int rowIndex );
|
|
126 |
public native String getCollResultJ( int metaIndex, int rowIndex );
|
| 107 |
127 |
|
| 108 |
|
public synchronized native String getGenQueResultJ( int metaIndex, int rowIndex );
|
|
128 |
public native String getGenQueResultJ( int metaIndex, int rowIndex );
|
| 109 |
129 |
|
| 110 |
|
public synchronized native int getNCollAttriJ ();
|
|
130 |
public native int getNCollAttriJ ();
|
| 111 |
131 |
|
| 112 |
|
public synchronized native int getNDataAttriJ ();
|
|
132 |
public native int getNDataAttriJ ();
|
| 113 |
133 |
|
| 114 |
|
public synchronized native int srbObjUnlinkJ (int conn, int catType,
|
|
134 |
public native int srbObjUnlinkJ (int conn, int catType,
|
| 115 |
135 |
String objID, String replNum, String parColl);
|
| 116 |
136 |
|
| 117 |
|
public synchronized native int srbCreateCollectJ (int conn, int catType,
|
|
137 |
public native int srbCreateCollectJ (int conn, int catType,
|
| 118 |
138 |
String parColl, String newColl);
|
| 119 |
139 |
|
| 120 |
|
public synchronized native int srbModifyDatasetMetaDJ (int conn, int catType,
|
|
140 |
public native int srbModifyDatasetMetaDJ (int conn, int catType,
|
| 121 |
141 |
String objID, String collection,
|
| 122 |
142 |
String newValue1, String newValue2, int retractionType);
|
| 123 |
|
|
| 124 |
|
public synchronized native int srbModifyCollectMetaDJ (int conn, int catType,
|
|
143 |
public native int srbModifyCollectMetaDJ (int conn, int catType,
|
| 125 |
144 |
String collection, String newValue1, String newValue2,
|
| 126 |
145 |
String newValue3, int retractionType);
|
| 127 |
|
|
| 128 |
|
public synchronized native int importToOldObjJ (int conn, int catType,
|
|
146 |
public native int importToOldObjJ (int conn, int catType,
|
| 129 |
147 |
String objID, String replNum, String parColl, String resource,
|
| 130 |
148 |
String localFile, String container);
|
| 131 |
149 |
|
| 132 |
|
public synchronized native int importToNewObjJ (int conn, int catType,
|
|
150 |
public native int importToNewObjJ (int conn, int catType,
|
| 133 |
151 |
String objID, String parColl, String resource, String localFile,
|
| 134 |
152 |
String container);
|
| 135 |
153 |
|
| 136 |
|
public synchronized native int importDirJ (int conn, int catType,
|
|
154 |
public native int importDirJ (int conn, int catType,
|
| 137 |
155 |
String parColl, String resource, String localDir, String container);
|
| 138 |
156 |
|
| 139 |
|
public synchronized native int srbRmCollJ (int conn, int catType, String parColl);
|
|
157 |
public native int srbRmCollJ (int conn, int catType, String parColl);
|
| 140 |
158 |
|
| 141 |
|
public synchronized native int srbUnregCollJ (int conn, int catType, String parColl);
|
|
159 |
public native int srbUnregCollJ (int conn, int catType, String parColl);
|
| 142 |
160 |
|
| 143 |
|
public synchronized native int copyToOldObjJ (int conn, int catType,
|
|
161 |
public native int copyToOldObjJ (int conn, int catType,
|
| 144 |
162 |
String objID, String replNum, String srcColl, String targObj,
|
| 145 |
163 |
String targReplNum, String targColl, String targResource,
|
| 146 |
164 |
String container);
|
| 147 |
165 |
|
| 148 |
|
public synchronized native int copyDataToCollJ (int conn, int catType,
|
|
166 |
public native int copyDataToCollJ (int conn, int catType,
|
| 149 |
167 |
String objID, String replNum, String srcColl,
|
| 150 |
168 |
String dataType, String size, String targColl, String targResource,
|
| 151 |
169 |
String container);
|
| 152 |
170 |
|
| 153 |
|
public synchronized native int copyCollToCollJ (int conn, int catType,
|
|
171 |
public native int copyCollToCollJ (int conn, int catType,
|
| 154 |
172 |
String srcColl, String targColl, String targResource,
|
| 155 |
173 |
String container);
|
| 156 |
174 |
|
| 157 |
|
public synchronized native int exportToFileJ(int conn, int catType,
|
|
175 |
public native int exportToFileJ(int conn, int catType,
|
| 158 |
176 |
String objID, String replNum, String srcColl,
|
| 159 |
177 |
String targFile, int forceFlag);
|
| 160 |
178 |
|
| 161 |
|
public synchronized native int exportToDirJ(int conn, int catType,
|
|
179 |
public native int exportToDirJ(int conn, int catType,
|
| 162 |
180 |
String objID, String replNum, String srcColl,
|
| 163 |
181 |
String targDir);
|
| 164 |
182 |
|
| 165 |
|
public synchronized native int exportCollToDirJ(int conn, int catType,
|
|
183 |
public native int exportCollToDirJ(int conn, int catType,
|
| 166 |
184 |
String srcColl, String targDir);
|
| 167 |
185 |
|
| 168 |
|
public synchronized native int srbGenQuery (int conn, int catType,
|
|
186 |
public native int srbGenQuery (int conn, int catType,
|
| 169 |
187 |
String[] qval, int qvalInx[], int selVal[]);
|
| 170 |
188 |
|
| 171 |
|
public synchronized native int srbRegisterDatasetJ(int conn, int catType,
|
|
189 |
public native int srbRegisterDatasetJ(int conn, int catType,
|
| 172 |
190 |
String objID, String dataType, String resource, String collection,
|
| 173 |
191 |
String pathName, int dataSize);
|
| 174 |
192 |
|
| 175 |
|
public synchronized native int srbUnregisterDatasetJ (int conn, int catType,
|
|
193 |
public native int srbUnregisterDatasetJ (int conn, int catType,
|
| 176 |
194 |
String objID, String replNum, String collection);
|
| 177 |
195 |
|
| 178 |
|
public synchronized native int srbRegisterDirJ (int conn, int catType,
|
|
196 |
public native int srbRegisterDirJ (int conn, int catType,
|
| 179 |
197 |
String srcDirPath, String targColl, String resource);
|
| 180 |
198 |
|
| 181 |
|
public synchronized native int getMoreDataRowsJ (int conn, int catType);
|
|
199 |
public native int getMoreDataRowsJ (int conn, int catType);
|
| 182 |
200 |
|
| 183 |
|
public synchronized native int getMoreCollRowsJ (int conn, int catType);
|
|
201 |
public native int getMoreCollRowsJ (int conn, int catType);
|
| 184 |
202 |
|
| 185 |
|
public synchronized native int getMoreGenQueRowsJ (int conn, int catType);
|
|
203 |
public native int getMoreGenQueRowsJ (int conn, int catType);
|
| 186 |
204 |
|
| 187 |
|
public synchronized native int chmodInCollJ (int conn, int catType,
|
|
205 |
public native int chmodInCollJ (int conn, int catType,
|
| 188 |
206 |
String collection, String user, String domain, String mode);
|
| 189 |
207 |
|
| 190 |
|
public synchronized native int ingestUserJ (int conn, int catType,
|
|
208 |
public native int ingestUserJ (int conn, int catType,
|
| 191 |
209 |
String userName, String passwd, String domain,
|
| 192 |
210 |
String userType, String userAddr, String userPhone, String userEmail,
|
| 193 |
211 |
String parentColl);
|
| 194 |
212 |
|
| 195 |
|
public synchronized native int ingestGroupJ (int conn, int catType,
|
|
213 |
public native int ingestGroupJ (int conn, int catType,
|
| 196 |
214 |
String groupName, String passwd,
|
| 197 |
215 |
String groupAddr, String groupPhone, String groupEMail);
|
| 198 |
216 |
|
| 199 |
|
public synchronized native int ingestLocJ (int conn, int catType,
|
| 200 |
|
String locName, String fullAddr, String parentLoc);
|
|
217 |
public native int ingestLocJ (int conn, int catType,
|
|
218 |
String locName, String fullAddr, String parentLoc,
|
|
219 |
String serverUser, String serverUserDomain);
|
| 201 |
220 |
|
| 202 |
|
public synchronized native int ingestResourceJ (int conn, int catType,
|
| 203 |
|
String rescName, String rescType, String location, String phyPath);
|
|
221 |
public native int ingestResourceJ (int conn, int catType,
|
|
222 |
String rescName, String rescType, String location, String phyPath,
|
|
223 |
String rscClass, int size);
|
| 204 |
224 |
|
| 205 |
|
public synchronized native int ingestLogRescJ (int conn, int catType,
|
|
225 |
public native int ingestLogRescJ (int conn, int catType,
|
| 206 |
226 |
String logRescName, String phyResc, String phyPath);
|
| 207 |
227 |
|
| 208 |
|
public synchronized native int addLogRescJ (int conn, int catType,
|
|
228 |
public native int addLogRescJ (int conn, int catType,
|
| 209 |
229 |
String logResc, String phyResc, String phyPath);
|
| 210 |
230 |
|
| 211 |
|
public synchronized native int modifyUserJ (int conn, int catType,
|
|
231 |
public native int modifyUserJ (int conn, int catType,
|
| 212 |
232 |
int modOpr, String userName, String domain, String modValue);
|
| 213 |
233 |
|
| 214 |
|
public synchronized native int containerCreateJ (int conn, int catType,
|
|
234 |
public native int containerCreateJ (int conn, int catType,
|
| 215 |
235 |
String contName, String dataType, String logResc, int size);
|
| 216 |
236 |
|
| 217 |
|
public synchronized native int containerDeleteJ (int conn, int catType,
|
|
237 |
public native int containerDeleteJ (int conn, int catType,
|
| 218 |
238 |
String contName, int forceFlag);
|
| 219 |
239 |
|
| 220 |
240 |
public native int containerSyncJ (int conn, int catType,
|
| 221 |
241 |
String contName, int purgeFlag);
|
| 222 |
242 |
|
| 223 |
243 |
//DFH 6/8/00
|
| 224 |
|
public synchronized byte[] getByteData(String name) {
|
|
244 |
public byte[] getByteData(String name) {
|
| 225 |
245 |
File tmp = new File("./tmp/");
|
| 226 |
246 |
if (!tmp.exists()) { tmp.mkdir();}
|
| 227 |
247 |
|
| ... | ... | |
| 242 |
262 |
return ByteData;
|
| 243 |
263 |
}
|
| 244 |
264 |
|
| 245 |
|
public synchronized void setByteData(String name, byte[] in) {
|
|
265 |
public void setByteData(String name, byte[] in) {
|
| 246 |
266 |
ByteData = in;
|
| 247 |
267 |
FileName = name;
|
| 248 |
268 |
File tmp = new File("./tmp/");
|
| ... | ... | |
| 257 |
277 |
catch (Exception e) {;}
|
| 258 |
278 |
}
|
| 259 |
279 |
|
| 260 |
|
public synchronized void clearTmpFiles() {
|
|
280 |
public void clearTmpFiles() {
|
| 261 |
281 |
File temp = new File("./tmp/"+FileName);
|
| 262 |
282 |
if (temp.exists()) { temp.delete(); }
|
| 263 |
283 |
}
|
| 264 |
284 |
|
| 265 |
|
public synchronized void Reset() {
|
| 266 |
|
try{
|
| 267 |
|
String[] cmdarray = {"java", "-Djava.security.policy=mypolicy", "SrbJavaGlue"};
|
| 268 |
|
Runtime.getRuntime().exec(cmdarray);
|
| 269 |
|
Runtime.getRuntime().exit(0);
|
| 270 |
|
}
|
| 271 |
|
catch (Exception e) {System.out.println("Could not run exec and exit"); }
|
| 272 |
|
}
|
| 273 |
|
|
| 274 |
|
public synchronized void writeMdasEnv(String username) {
|
| 275 |
|
try{
|
| 276 |
|
String userhome = System.getProperty("user.home");
|
| 277 |
|
File file = new File(userhome+"/.srb/.MdasEnv");
|
| 278 |
|
FileWriter fw = new FileWriter(file);
|
| 279 |
|
StringBuffer env = new StringBuffer();
|
| 280 |
|
env.append("mdasCollectionHome '/home/higgins.bioinfo'\n");
|
| 281 |
|
env.append("mdasDomainHome 'bioinfo'\n");
|
| 282 |
|
env.append("srbUser '"+username+"'\n");
|
| 283 |
|
env.append("srbHost 'penelope.nceas.ucsb.edu'\n");
|
| 284 |
|
env.append("defaultResource 'test-unix-nceas'\n");
|
| 285 |
|
env.append("SEA_OPT '0'");
|
| 286 |
|
StringReader sr = new StringReader(env.toString());
|
| 287 |
|
int c;
|
| 288 |
|
while ((c = sr.read()) != -1)
|
| 289 |
|
{
|
| 290 |
|
fw.write(c);
|
| 291 |
|
}
|
| 292 |
|
fw.close();
|
| 293 |
|
sr.close();
|
| 294 |
|
}
|
| 295 |
|
catch (Exception e) {}
|
| 296 |
|
}
|
| 297 |
|
|
| 298 |
285 |
// --
|
| 299 |
286 |
|
| 300 |
287 |
static
|
| 301 |
288 |
{
|
| 302 |
289 |
System.loadLibrary( "SrbJavaGlue" );
|
|
290 |
|
| 303 |
291 |
}
|
| 304 |
292 |
|
| 305 |
293 |
public static void main(String[] args) {
|
SRB v1.1.8