1
|
package eu.dnetlib.parthenos.workflows.nodes;
|
2
|
|
3
|
import java.net.URI;
|
4
|
import java.net.URISyntaxException;
|
5
|
import java.util.List;
|
6
|
import java.util.Map;
|
7
|
import java.util.NoSuchElementException;
|
8
|
import java.util.concurrent.BlockingQueue;
|
9
|
import java.util.concurrent.ExecutorService;
|
10
|
import java.util.concurrent.Executors;
|
11
|
import java.util.concurrent.TimeUnit;
|
12
|
|
13
|
import com.google.common.collect.Lists;
|
14
|
import com.google.common.collect.Maps;
|
15
|
import com.google.common.collect.Queues;
|
16
|
import eu.dnetlib.data.collector.ThreadSafeIterator;
|
17
|
import eu.dnetlib.rmi.data.CollectorServiceRuntimeException;
|
18
|
import org.apache.commons.lang3.StringEscapeUtils;
|
19
|
import org.apache.commons.lang3.StringUtils;
|
20
|
import org.apache.commons.logging.Log;
|
21
|
import org.apache.commons.logging.LogFactory;
|
22
|
import org.apache.http.client.utils.URIBuilder;
|
23
|
import org.springframework.http.*;
|
24
|
import org.springframework.web.client.ResourceAccessException;
|
25
|
import org.springframework.web.client.RestClientException;
|
26
|
import org.springframework.web.client.RestTemplate;
|
27
|
|
28
|
/**
|
29
|
* Created by Alessia Bardi on 31/01/2018.
|
30
|
*
|
31
|
* @author Alessia Bardi
|
32
|
*/
|
33
|
public class VirtuosoParthenosIterator extends ThreadSafeIterator {
|
34
|
|
35
|
private static final Log log = LogFactory.getLog(VirtuosoParthenosIterator.class);
|
36
|
protected static final int QUEUE_TIMEOUT_SECONDS = 100;
|
37
|
public final static String TERMINATOR = "ARNOLD";
|
38
|
public final static String ERROR_TERMINATOR = "SCHWARZ";
|
39
|
protected final static int SLEEP_MS = 5000;
|
40
|
protected final static int MAX_RETRIES = 3;
|
41
|
protected final static int LIMIT = 100;
|
42
|
|
43
|
private String datasourceName;
|
44
|
private String datasourceInterface;
|
45
|
private String virtuosoReaderAPIUrl;
|
46
|
private boolean started = false;
|
47
|
private Map<String, Integer> errors = Maps.newHashMap();
|
48
|
private List<String> listForClass = Lists.newArrayList();
|
49
|
private BlockingQueue<String> elements = Queues.newArrayBlockingQueue(10);
|
50
|
|
51
|
private String currentElement = null;
|
52
|
private ExecutorService executor = Executors.newSingleThreadExecutor();
|
53
|
|
54
|
private RestTemplate restTemplate;
|
55
|
|
56
|
|
57
|
private synchronized void verifyStarted(){
|
58
|
if (!this.started) {
|
59
|
this.started = true;
|
60
|
fillQueue();
|
61
|
getNextElement(MAX_RETRIES);
|
62
|
}
|
63
|
}
|
64
|
|
65
|
protected void fillQueue(){
|
66
|
log.info("Virtuoso reader at : " + getVirtuosoReaderAPIUrl());
|
67
|
getExecutor().submit(() -> {
|
68
|
try {
|
69
|
int offset = 0;
|
70
|
boolean again = true;
|
71
|
do {
|
72
|
List<String> subjectList = getSubjectList(offset);
|
73
|
for (String subject : subjectList) {
|
74
|
String xmlFile = tryGetRDF(subject, MAX_RETRIES);
|
75
|
if (StringUtils.isBlank(xmlFile)) {
|
76
|
log.warn("Skipping blank RDF for " + subject);
|
77
|
} else {
|
78
|
getElements().offer(xmlFile, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
|
79
|
}
|
80
|
}
|
81
|
again = subjectList.size() == LIMIT;
|
82
|
offset += LIMIT;
|
83
|
} while(again);
|
84
|
log.debug("End of subject list, adding terminator to the queue");
|
85
|
getElements().offer(TERMINATOR, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
|
86
|
} catch (Exception e) {
|
87
|
log.error(e.getMessage());
|
88
|
try {
|
89
|
getElements().offer(ERROR_TERMINATOR, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
|
90
|
} catch (InterruptedException e1) {
|
91
|
log.error(e1.getMessage());
|
92
|
}
|
93
|
}
|
94
|
|
95
|
});
|
96
|
getExecutor().shutdown();
|
97
|
}
|
98
|
|
99
|
|
100
|
protected String tryGetRDF(final String subjectURL, int attempt) throws URISyntaxException, InterruptedException, VirtuosoParthenosException {
|
101
|
log.debug("Quering Api, remaining attempts: "+attempt);
|
102
|
if (attempt <= 0) {
|
103
|
errors.merge("Failed tryGetRDF", 1, Integer::sum);
|
104
|
return null;
|
105
|
}
|
106
|
ResponseEntity<String> response = null;
|
107
|
try {
|
108
|
response = getRDF(subjectURL);
|
109
|
}catch(ResourceAccessException e){
|
110
|
//request timed out --> sleep and try again
|
111
|
log.warn("Request timeout for "+subjectURL+": I'll sleep and then try again");
|
112
|
Thread.sleep(SLEEP_MS);
|
113
|
return tryGetRDF(subjectURL, --attempt);
|
114
|
}
|
115
|
HttpStatus responseStatus = response.getStatusCode();
|
116
|
if (responseStatus.is2xxSuccessful()) {
|
117
|
String rdfFile = response.getBody();
|
118
|
if(StringUtils.isBlank(rdfFile)){
|
119
|
log.warn("Got blank RDF for "+subjectURL+" , let's try again...");
|
120
|
Thread.sleep(SLEEP_MS);
|
121
|
return tryGetRDF(subjectURL, --attempt);
|
122
|
}
|
123
|
else {
|
124
|
final String xmlFile = completeXML(rdfFile, subjectURL);
|
125
|
return xmlFile;
|
126
|
}
|
127
|
} else {
|
128
|
if (responseStatus.is5xxServerError()) {
|
129
|
//sleep for a while and re-try
|
130
|
log.warn("HTTP ERROR: "+responseStatus.value() + ": " + responseStatus.getReasonPhrase()+": I'll sleep and then try again");
|
131
|
Thread.sleep(SLEEP_MS);
|
132
|
return tryGetRDF(subjectURL, --attempt);
|
133
|
} else {
|
134
|
log.error("ERROR: Can't get the RDF for " + subjectURL + " " + responseStatus.value() + ": " + responseStatus.getReasonPhrase());
|
135
|
errors.merge(responseStatus.value() + ": " + responseStatus.getReasonPhrase(), 1, Integer::sum);
|
136
|
}
|
137
|
}
|
138
|
return null;
|
139
|
}
|
140
|
|
141
|
protected URI getURIForSubjectList(final int offset) throws URISyntaxException {
|
142
|
URIBuilder builder = new URIBuilder(getVirtuosoReaderAPIUrl() + "/apiSubjects");
|
143
|
builder.addParameter("api", getDatasourceInterface());
|
144
|
builder.addParameter("limit", Integer.toString(LIMIT));
|
145
|
builder.addParameter("offset", Integer.toString(offset));
|
146
|
return builder.build();
|
147
|
}
|
148
|
|
149
|
protected List<String> getSubjectList(final int offset) throws URISyntaxException, VirtuosoParthenosException {
|
150
|
URI uri = getURIForSubjectList(offset);
|
151
|
log.debug("fillQueue -- Calling for subject list: " + uri.toString());
|
152
|
List<String> subjectList;
|
153
|
try {
|
154
|
subjectList = getRestTemplate().getForObject(uri, getListForClass().getClass());
|
155
|
}catch(RestClientException rce){
|
156
|
throw new VirtuosoParthenosException(rce);
|
157
|
}
|
158
|
return subjectList;
|
159
|
}
|
160
|
|
161
|
protected URI getURIForRDFRequest(final String subjectURL) throws URISyntaxException {
|
162
|
URIBuilder builder = new URIBuilder(getVirtuosoReaderAPIUrl() + "/subject").addParameter("subjectURL", subjectURL);
|
163
|
return builder.build();
|
164
|
}
|
165
|
|
166
|
protected ResponseEntity<String> getRDF(final String subjectURL) throws URISyntaxException {
|
167
|
HttpHeaders headers = new HttpHeaders();
|
168
|
headers.setAccept(Lists.newArrayList(MediaType.APPLICATION_XML));
|
169
|
URI uri = getURIForRDFRequest(subjectURL);
|
170
|
log.debug("fillQueue -- Calling for subject RDF: " + uri.toString());
|
171
|
HttpEntity<String> entity = new HttpEntity<>("parameters", headers);
|
172
|
return restTemplate.exchange(uri, HttpMethod.GET, entity, String.class);
|
173
|
}
|
174
|
|
175
|
|
176
|
public String completeXML(final String rdfFile, final String url) {
|
177
|
String xmlEscapedURL = StringEscapeUtils.escapeXml11(url);
|
178
|
String rdfFileNoXmlDecl = rdfFile.replaceAll("\\<\\?xml(.+?)\\?\\>", "").trim();
|
179
|
return "<?xml version=\"1.0\" encoding=\"UTF-8\"?><record xmlns=\"http://www.openarchives.org/OAI/2.0/\"><header xmlns:dri=\"http://www.driver-repository.eu/namespace/dri\"><dri:objIdentifier>"
|
180
|
+ xmlEscapedURL + "</dri:objIdentifier><dri:datasourceapi>" + datasourceInterface + "</dri:datasourceapi><dri:datasourcename>" + datasourceName
|
181
|
+ "</dri:datasourcename></header><metadata>" + rdfFileNoXmlDecl + "</metadata></record>";
|
182
|
}
|
183
|
|
184
|
@Override
|
185
|
public boolean doHasNext() {
|
186
|
try {
|
187
|
verifyStarted();
|
188
|
} catch (Exception e) {
|
189
|
getExecutor().shutdownNow();
|
190
|
throw new CollectorServiceRuntimeException(e);
|
191
|
}
|
192
|
switch(currentElement){
|
193
|
case TERMINATOR:
|
194
|
if(!executor.isTerminated()) executor.shutdownNow();
|
195
|
return false;
|
196
|
case ERROR_TERMINATOR:
|
197
|
executor.shutdownNow();
|
198
|
throw new CollectorServiceRuntimeException("Error getting elements from virtuoso");
|
199
|
default:
|
200
|
return true;
|
201
|
}
|
202
|
}
|
203
|
|
204
|
@Override
|
205
|
public String doNext() {
|
206
|
if(!hasNext()) {
|
207
|
log.error("Next called but hasNext is false", new NoSuchElementException());
|
208
|
throw new NoSuchElementException();
|
209
|
}
|
210
|
switch(currentElement){
|
211
|
case TERMINATOR:
|
212
|
case ERROR_TERMINATOR:
|
213
|
executor.shutdownNow();
|
214
|
throw new NoSuchElementException();
|
215
|
default:
|
216
|
String res = currentElement;
|
217
|
getNextElement(MAX_RETRIES);
|
218
|
return res;
|
219
|
}
|
220
|
}
|
221
|
|
222
|
private void getNextElement(int attempt){
|
223
|
log.debug("polling from queue, remaining attempts: "+attempt);
|
224
|
if(attempt <= 0) currentElement = ERROR_TERMINATOR;
|
225
|
else{
|
226
|
try {
|
227
|
currentElement = elements.take();
|
228
|
} catch (InterruptedException e) {
|
229
|
//current thread interrupted. Let's end.
|
230
|
currentElement = ERROR_TERMINATOR;
|
231
|
executor.shutdownNow();
|
232
|
}
|
233
|
}
|
234
|
}
|
235
|
|
236
|
@Override
|
237
|
public void remove() {
|
238
|
throw new UnsupportedOperationException();
|
239
|
}
|
240
|
|
241
|
public VirtuosoParthenosIterator datasourceInterface(final String datasourceInterface) {
|
242
|
this.datasourceInterface = datasourceInterface;
|
243
|
return this;
|
244
|
}
|
245
|
|
246
|
public VirtuosoParthenosIterator virtuosoReaderAPIUrl(final String virtuosoReaderAPIUrl) {
|
247
|
this.virtuosoReaderAPIUrl = virtuosoReaderAPIUrl;
|
248
|
return this;
|
249
|
}
|
250
|
|
251
|
public VirtuosoParthenosIterator datasourceName(final String datasourceName) {
|
252
|
this.datasourceName = datasourceName;
|
253
|
return this;
|
254
|
}
|
255
|
|
256
|
public VirtuosoParthenosIterator errors(final Map<String, Integer> errors) {
|
257
|
this.errors = errors;
|
258
|
return this;
|
259
|
}
|
260
|
|
261
|
public String getDatasourceInterface() {
|
262
|
return datasourceInterface;
|
263
|
}
|
264
|
|
265
|
public String getVirtuosoReaderAPIUrl() {
|
266
|
return virtuosoReaderAPIUrl;
|
267
|
}
|
268
|
|
269
|
public Map<String, Integer> getErrors() {
|
270
|
return errors;
|
271
|
}
|
272
|
|
273
|
public BlockingQueue<String> getElements() {
|
274
|
return elements;
|
275
|
}
|
276
|
|
277
|
public RestTemplate getRestTemplate() {
|
278
|
return restTemplate;
|
279
|
}
|
280
|
|
281
|
public VirtuosoParthenosIterator restTemplate(final RestTemplate restTemplate) {
|
282
|
this.restTemplate = restTemplate;
|
283
|
return this;
|
284
|
}
|
285
|
|
286
|
public String getDatasourceName() {
|
287
|
return datasourceName;
|
288
|
}
|
289
|
|
290
|
public boolean isStarted() {
|
291
|
return started;
|
292
|
}
|
293
|
|
294
|
public List<String> getListForClass() {
|
295
|
return listForClass;
|
296
|
}
|
297
|
|
298
|
public String getCurrentElement() {
|
299
|
return currentElement;
|
300
|
}
|
301
|
|
302
|
public ExecutorService getExecutor() {
|
303
|
return executor;
|
304
|
}
|
305
|
|
306
|
public void setDatasourceName(final String datasourceName) {
|
307
|
this.datasourceName = datasourceName;
|
308
|
}
|
309
|
|
310
|
public void setDatasourceInterface(final String datasourceInterface) {
|
311
|
this.datasourceInterface = datasourceInterface;
|
312
|
}
|
313
|
|
314
|
public void setVirtuosoReaderAPIUrl(final String virtuosoReaderAPIUrl) {
|
315
|
this.virtuosoReaderAPIUrl = virtuosoReaderAPIUrl;
|
316
|
}
|
317
|
|
318
|
public void setStarted(final boolean started) {
|
319
|
this.started = started;
|
320
|
}
|
321
|
|
322
|
public void setErrors(final Map<String, Integer> errors) {
|
323
|
this.errors = errors;
|
324
|
}
|
325
|
|
326
|
public void setListForClass(final List<String> listForClass) {
|
327
|
this.listForClass = listForClass;
|
328
|
}
|
329
|
|
330
|
public void setElements(final BlockingQueue<String> elements) {
|
331
|
this.elements = elements;
|
332
|
}
|
333
|
|
334
|
public void setCurrentElement(final String currentElement) {
|
335
|
this.currentElement = currentElement;
|
336
|
}
|
337
|
|
338
|
public void setExecutor(final ExecutorService executor) {
|
339
|
this.executor = executor;
|
340
|
}
|
341
|
|
342
|
public void setRestTemplate(final RestTemplate restTemplate) {
|
343
|
this.restTemplate = restTemplate;
|
344
|
}
|
345
|
}
|