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Coverage Report

  1. Project Clover database Tue Oct 29 2024 21:36:55 GMT
  2. Package jalview.ext.ensembl

File EnsemblRestClient.java

 

Coverage histogram

../../../img/srcFileCovDistChart1.png
55% of files have more coverage

Code metrics

48
144
20
1
642
357
56
0.39
7.2
20
2.8

Classes

Class Line # Actions
EnsemblRestClient 48 144 56
0.0707547147.1%
 

Contributing tests

This file is covered by 28 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ext.ensembl;
22   
23    import java.io.BufferedReader;
24    import java.io.DataOutputStream;
25    import java.io.IOException;
26    import java.io.InputStream;
27    import java.net.HttpURLConnection;
28    import java.net.MalformedURLException;
29    import java.net.ProtocolException;
30    import java.net.URL;
31    import java.util.HashMap;
32    import java.util.List;
33    import java.util.Map;
34   
35    import javax.ws.rs.HttpMethod;
36   
37    import org.json.simple.parser.ParseException;
38   
39    import jalview.util.HttpUtils;
40    import jalview.util.Platform;
41    import jalview.util.StringUtils;
42   
43    /**
44    * Base class for Ensembl REST service clients
45    *
46    * @author gmcarstairs
47    */
 
48    abstract class EnsemblRestClient extends EnsemblSequenceFetcher
49    {
50   
 
51  7 toggle static
52    {
53  7 Platform.addJ2SDirectDatabaseCall("http://rest.ensembl");
54  7 Platform.addJ2SDirectDatabaseCall("https://rest.ensembl");
55    }
56   
57    private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
58   
59    private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
60   
61    private static final int MAX_RETRIES = 3;
62   
63    private static final int HTTP_OK = 200;
64   
65    private static final int HTTP_OVERLOAD = 429;
66   
67    /*
68    * update these constants when Jalview has been checked / updated for
69    * changes to Ensembl REST API, and updated JAL-3018
70    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
71    * @see http://rest.ensembl.org/info/rest?content-type=application/json
72    */
73    private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.8";
74   
75    private static final String LATEST_ENSEMBL_REST_VERSION = "15.8";
76   
77    private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
78   
79    private static Map<String, EnsemblData> domainData;
80   
81    private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
82   
83    private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
84   
85    protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
86   
 
87  7 toggle static
88    {
89  7 domainData = new HashMap<>();
90  7 domainData.put(DEFAULT_ENSEMBL_BASEURL, new EnsemblData(
91    DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
92  7 domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL,
93    new EnsemblData(DEFAULT_ENSEMBL_GENOMES_BASEURL,
94    LATEST_ENSEMBLGENOMES_REST_VERSION));
95    }
96   
97    protected volatile boolean inProgress = false;
98   
99    /**
100    * Default constructor to use rest.ensembl.org
101    */
 
102  49 toggle public EnsemblRestClient()
103    {
104  49 super();
105   
106    /*
107    * initialise domain info lazily
108    */
109  49 if (!domainData.containsKey(ensemblDomain))
110    {
111  0 domainData.put(ensemblDomain,
112    new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
113    }
114  49 if (!domainData.containsKey(ensemblGenomesDomain))
115    {
116  0 domainData.put(ensemblGenomesDomain, new EnsemblData(
117    ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
118    }
119    }
120   
121    /**
122    * Constructor given the target domain to fetch data from
123    *
124    * @param d
125    */
 
126  1 toggle public EnsemblRestClient(String d)
127    {
128  1 setDomain(d);
129    }
130   
 
131  0 toggle @Override
132    public boolean queryInProgress()
133    {
134  0 return inProgress;
135    }
136   
 
137  0 toggle @Override
138    public StringBuffer getRawRecords()
139    {
140  0 return null;
141    }
142   
143    /**
144    * Returns the URL for the client http request
145    *
146    * @param ids
147    * @return
148    * @throws MalformedURLException
149    */
150    protected abstract URL getUrl(List<String> ids)
151    throws MalformedURLException;
152   
153    /**
154    * Returns true if client uses GET method, false if it uses POST
155    *
156    * @return
157    */
158    protected abstract boolean useGetRequest();
159   
160    /**
161    * Returns the desired value for the Content-Type request header. Default is
162    * application/json, override if required to vary this.
163    *
164    * @return
165    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
166    */
 
167  0 toggle protected String getRequestMimeType()
168    {
169  0 return "application/json";
170    }
171   
172    /**
173    * Return the desired value for the Accept request header. Default is
174    * application/json, override if required to vary this.
175    *
176    * @return
177    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
178    */
 
179  0 toggle protected String getResponseMimeType()
180    {
181  0 return "application/json";
182    }
183   
184    /**
185    * Checks Ensembl's REST 'ping' endpoint, and returns true if response
186    * indicates available, else false
187    *
188    * @see http://rest.ensembl.org/documentation/info/ping
189    * @return
190    */
 
191  0 toggle @SuppressWarnings("unchecked")
192    boolean checkEnsembl()
193    {
194  0 BufferedReader br = null;
195  0 String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
196  0 try
197    {
198    // note this format works for both ensembl and ensemblgenomes
199    // info/ping.json works for ensembl only (March 2016)
200   
201    /*
202    * expect {"ping":1} if ok
203    * if ping takes more than 2 seconds to respond, treat as if unavailable
204    */
205  0 Map<String, Object> val = (Map<String, Object>) getJSON(
206    new URL(pingUrl), null, 2 * 1000, MODE_MAP, null);
207  0 if (val == null)
208    {
209  0 return false;
210    }
211  0 String pingString = val.get("ping").toString();
212  0 return pingString != null;
213    } catch (Throwable t)
214    {
215  0 jalview.bin.Console.errPrintln(
216    "Error connecting to " + pingUrl + ": " + t.getMessage());
217    } finally
218    {
219  0 if (br != null)
220    {
221  0 try
222    {
223  0 br.close();
224    } catch (IOException e)
225    {
226    // ignore
227    }
228    }
229    }
230  0 return false;
231    }
232   
233    protected final static int MODE_ARRAY = 0;
234   
235    protected final static int MODE_MAP = 1;
236   
237    protected final static int MODE_ITERATOR = 2;
238   
239    // /**
240    // * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
241    // * If the request failed the return value may be null.
242    // *
243    // * @param ids
244    // * @return
245    // * @throws IOException
246    // * @throws ParseException
247    // */
248    // protected Object getSequenceJSON(List<String> ids, int mode)
249    // throws IOException, ParseException
250    // {
251    // URL url = getUrl(ids);
252    // return getJSON(url, ids, -1, mode);
253    // }
254    //
255    // /**
256    // * Gets a reader to the HTTP response, using the default read timeout of 5
257    // * minutes
258    // *
259    // * @param url
260    // * @param ids
261    // * @return
262    // * @throws IOException
263    // */
264    // protected BufferedReader getHttpResponse(URL url, List<String> ids)
265    // throws IOException
266    // {
267    // return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
268    // }
269   
270    /**
271    * Sends the HTTP request and gets the response as a reader. Returns null if
272    * the HTTP response code was not 200.
273    *
274    * @param url
275    * @param ids
276    * written as Json POST body if more than one
277    * @param readTimeout
278    * in milliseconds
279    * @return
280    * @throws IOException
281    * @throws ParseException
282    */
 
283  0 toggle private Object getJSON(URL url, List<String> ids, int readTimeout)
284    throws IOException, ParseException
285    {
286   
287  0 if (readTimeout < 0)
288    {
289  0 readTimeout = DEFAULT_READ_TIMEOUT;
290    }
291  0 int retriesLeft = MAX_RETRIES;
292  0 HttpURLConnection connection = null;
293  0 int responseCode = 0;
294   
295  0 Platform.setAjaxJSON(url);
296   
297  0 while (retriesLeft > 0)
298    {
299  0 connection = tryConnection(url, ids, readTimeout);
300  0 responseCode = connection.getResponseCode();
301  0 if (responseCode == HTTP_OVERLOAD) // 429
302    {
303  0 retriesLeft--;
304  0 checkRetryAfter(connection);
305    }
306    else
307    {
308  0 retriesLeft = 0;
309    }
310    }
311  0 if (responseCode != HTTP_OK) // 200
312    {
313    /*
314    * note: a GET request for an invalid id returns an error code e.g. 415
315    * but POST request returns 200 and an empty Fasta response
316    */
317  0 jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for
318    // " +
319    // url);
320  0 return null;
321    }
322   
323  0 InputStream response = connection.getInputStream();
324   
325    // Platform.timeCheck(null, Platform.TIME_MARK);
326  0 Object ret = Platform.parseJSON(response);
327    // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
328    // Platform.TIME_MARK);
329   
330  0 return ret;
331    }
332   
333    /**
334    * @param url
335    * @param ids
336    * @param readTimeout
337    * @return
338    * @throws IOException
339    * @throws ProtocolException
340    */
 
341  0 toggle protected HttpURLConnection tryConnection(URL url, List<String> ids,
342    int readTimeout) throws IOException, ProtocolException
343    {
344    // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
345   
346  0 HttpURLConnection connection = (HttpURLConnection) HttpUtils
347    .openConnection(url);
348   
349    /*
350    * POST method allows multiple queries in one request; it is supported for
351    * sequence queries, but not for overlap
352    */
353  0 boolean multipleIds = ids != null && ids.size() > 1;
354  0 connection.setRequestMethod(
355  0 multipleIds ? HttpMethod.POST : HttpMethod.GET);
356  0 connection.setRequestProperty("Content-Type", getRequestMimeType());
357  0 connection.setRequestProperty("Accept", getResponseMimeType());
358   
359  0 connection.setDoInput(true);
360  0 connection.setDoOutput(multipleIds);
361   
362  0 connection.setUseCaches(false);
363  0 connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
364  0 connection.setReadTimeout(readTimeout);
365   
366  0 if (multipleIds)
367    {
368  0 writePostBody(connection, ids);
369    }
370  0 return connection;
371    }
372   
373    /**
374    * Inspects response headers for a 'retry-after' directive, and waits for the
375    * directed period (if less than 10 seconds)
376    *
377    * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
378    * @param connection
379    */
 
380  0 toggle void checkRetryAfter(HttpURLConnection connection)
381    {
382  0 String retryDelay = connection.getHeaderField("Retry-After");
383   
384    // to test:
385    // retryDelay = "5";
386   
387  0 if (retryDelay != null)
388    {
389  0 try
390    {
391  0 int retrySecs = Integer.valueOf(retryDelay);
392  0 if (retrySecs > 0 && retrySecs < 10)
393    {
394  0 jalview.bin.Console.errPrintln(
395    "Ensembl REST service rate limit exceeded, waiting "
396    + retryDelay + " seconds before retrying");
397  0 Thread.sleep(1000 * retrySecs);
398    }
399    } catch (NumberFormatException | InterruptedException e)
400    {
401  0 jalview.bin.Console.errPrintln(
402    "Error handling Retry-After: " + e.getMessage());
403    }
404    }
405    }
406   
407    /**
408    * Rechecks if Ensembl is responding, unless the last check was successful and
409    * the retest interval has not yet elapsed. Returns true if Ensembl is up,
410    * else false. Also retrieves and saves the current version of Ensembl data
411    * and REST services at intervals.
412    *
413    * @return
414    */
 
415  0 toggle protected boolean isEnsemblAvailable()
416    {
417  0 EnsemblData info = domainData.get(getDomain());
418   
419  0 long now = System.currentTimeMillis();
420   
421    /*
422    * recheck if Ensembl is up if it was down, or the recheck period has elapsed
423    */
424  0 boolean retestAvailability = (now
425    - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
426  0 if (!info.restAvailable || retestAvailability)
427    {
428  0 info.restAvailable = checkEnsembl();
429  0 info.lastAvailableCheckTime = now;
430    }
431   
432    /*
433    * refetch Ensembl versions if the recheck period has elapsed
434    */
435  0 boolean refetchVersion = (now
436    - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
437  0 if (refetchVersion)
438    {
439  0 checkEnsemblRestVersion();
440  0 checkEnsemblDataVersion();
441  0 info.lastVersionCheckTime = now;
442    }
443   
444  0 return info.restAvailable;
445    }
446   
447    /**
448    * Constructs, writes and flushes the POST body of the request, containing the
449    * query ids in JSON format
450    *
451    * @param connection
452    * @param ids
453    * @throws IOException
454    */
 
455  0 toggle protected void writePostBody(HttpURLConnection connection,
456    List<String> ids) throws IOException
457    {
458  0 boolean first;
459  0 StringBuilder postBody = new StringBuilder(64);
460  0 postBody.append("{\"ids\":[");
461  0 first = true;
462  0 for (int i = 0, n = ids.size(); i < n; i++)
463    {
464  0 String id = ids.get(i);
465  0 if (!first)
466    {
467  0 postBody.append(",");
468    }
469  0 first = false;
470  0 postBody.append("\"");
471  0 postBody.append(id.trim());
472  0 postBody.append("\"");
473    }
474  0 postBody.append("]}");
475  0 byte[] thepostbody = postBody.toString().getBytes();
476  0 connection.setRequestProperty("Content-Length",
477    Integer.toString(thepostbody.length));
478  0 DataOutputStream wr = new DataOutputStream(
479    connection.getOutputStream());
480  0 wr.write(thepostbody);
481  0 wr.flush();
482  0 wr.close();
483    }
484   
485    /**
486    * Primary access point to parsed JSON data, including the call to retrieve
487    * and parsing.
488    *
489    * @param url
490    * request url; if null, getUrl(ids) will be used
491    * @param ids
492    * optional; may be null
493    * @param msDelay
494    * -1 for default delay
495    * @param mode
496    * map, array, or array iterator
497    * @param mapKey
498    * an optional key for an outer map
499    * @return a Map, List, Iterator, or null
500    * @throws IOException
501    * @throws ParseException
502    *
503    * @author Bob Hanson 2019
504    */
 
505  0 toggle @SuppressWarnings("unchecked")
506    protected Object getJSON(URL url, List<String> ids, int msDelay, int mode,
507    String mapKey) throws IOException, ParseException
508    {
509  0 if (url == null)
510    {
511  0 url = getUrl(ids);
512    }
513   
514  0 Object json = (url == null ? null : getJSON(url, ids, msDelay));
515   
516  0 if (json != null && mapKey != null)
517    {
518  0 json = ((Map<String, Object>) json).get(mapKey);
519    }
520  0 if (json == null)
521    {
522  0 return null;
523    }
524  0 switch (mode)
525    {
526  0 case MODE_ARRAY:
527  0 case MODE_MAP:
528  0 break;
529  0 case MODE_ITERATOR:
530  0 json = ((List<Object>) json).iterator();
531  0 break;
532    }
533  0 return json;
534    }
535   
536    /**
537    * Fetches and checks Ensembl's REST version number
538    *
539    * @return
540    */
 
541  0 toggle @SuppressWarnings("unchecked")
542    private void checkEnsemblRestVersion()
543    {
544  0 EnsemblData info = domainData.get(getDomain());
545   
546  0 try
547    {
548  0 Map<String, Object> val = (Map<String, Object>) getJSON(
549    new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null,
550    -1, MODE_MAP, null);
551  0 if (val == null)
552    {
553  0 return;
554    }
555  0 String version = val.get("release").toString();
556  0 String majorVersion = version.substring(0, version.indexOf("."));
557  0 String expected = info.expectedRestVersion;
558  0 String expectedMajorVersion = expected.substring(0,
559    expected.indexOf("."));
560  0 info.restMajorVersionMismatch = false;
561  0 try
562    {
563    /*
564    * if actual REST major version is ahead of what we expect,
565    * record this in case we want to warn the user
566    */
567  0 if (Float.valueOf(majorVersion) > Float
568    .valueOf(expectedMajorVersion))
569    {
570  0 info.restMajorVersionMismatch = true;
571    }
572    } catch (NumberFormatException e)
573    {
574  0 jalview.bin.Console
575    .errPrintln("Error in REST version: " + e.toString());
576    }
577   
578    /*
579    * check if REST version is later than what Jalview has tested against,
580    * if so warn; we don't worry if it is earlier (this indicates Jalview has
581    * been tested in advance against the next pending REST version)
582    */
583  0 boolean laterVersion = StringUtils.compareVersions(version,
584    expected) == 1;
585  0 if (laterVersion)
586    {
587  0 jalview.bin.Console.errPrintln(String.format(
588    "EnsemblRestClient expected %s REST version %s but found %s, see %s",
589    getDbSource(), expected, version, REST_CHANGE_LOG));
590    }
591  0 info.restVersion = version;
592    } catch (Throwable t)
593    {
594  0 jalview.bin.Console.errPrintln(
595    "Error checking Ensembl REST version: " + t.getMessage());
596    }
597    }
598   
 
599  0 toggle public boolean isRestMajorVersionMismatch()
600    {
601  0 return domainData.get(getDomain()).restMajorVersionMismatch;
602    }
603   
604    /**
605    * Fetches and checks Ensembl's data version number
606    *
607    * @return
608    */
 
609  0 toggle @SuppressWarnings("unchecked")
610    private void checkEnsemblDataVersion()
611    {
612  0 Map<String, Object> val;
613  0 try
614    {
615  0 val = (Map<String, Object>) getJSON(
616    new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null,
617    -1, MODE_MAP, null);
618  0 if (val == null)
619    {
620  0 return;
621    }
622  0 List<Object> versions = (List<Object>) val.get("releases");
623  0 domainData.get(getDomain()).dataVersion = versions.get(0).toString();
624    } catch (Throwable e)
625    {// could be IOException | ParseException e) {
626  0 jalview.bin.Console.errPrintln(
627    "Error checking Ensembl data version: " + e.getMessage());
628    }
629    }
630   
 
631  0 toggle public String getEnsemblDataVersion()
632    {
633  0 return domainData.get(getDomain()).dataVersion;
634    }
635   
 
636  0 toggle @Override
637    public String getDbVersion()
638    {
639  0 return getEnsemblDataVersion();
640    }
641   
642    }
  • Report generated by OpenClover v 4.4.1 on Tue Oct 29 2024 21:44:08 GMT using coverage data from Tue Oct 29 2024 21:43:45 GMT.
  • OpenClover is free and open-source software.