*/
package jalview.ext.ensembl;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.util.StringUtils;
-
-import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.ProtocolException;
import javax.ws.rs.HttpMethod;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+import jalview.bin.Cache;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
/**
* Base class for Ensembl REST service clients
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
- private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
+ private static final int HTTP_OK = 200;
+
+ private static final int HTTP_OVERLOAD = 429;
- private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+ static
+ {
+ Platform.addJ2SDirectDatabaseCall("http://rest.ensembl");
+ Platform.addJ2SDirectDatabaseCall("https://rest.ensembl");
+ }
- private static final int MAX_RETRIES = 3;
+ /*
+ * constants for http retries and timeout;
+ * not final so they can be changed by a Groovy script
+ */
+ private static int PING_TIMEOUT_MS = 2 * 1000;
- private static final int HTTP_OK = 200;
+ private static long PING_RETEST_INTERVAL = 10 * 1000L; // 10 seconds
- private static final int HTTP_OVERLOAD = 429;
+ private static int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
+
+ private static int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+
+ private static int MAX_RETRIES = 3;
/*
* update these constants when Jalview has been checked / updated for
- * changes to Ensembl REST API (ref JAL-2105)
+ * changes to Ensembl REST API, and updated JAL-3018
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.0";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "12.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "6.1";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "12.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map<String, EnsemblData> domainData;
- // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
- private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
-
- private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
-
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
static
{
domainData = new HashMap<>();
- domainData.put(DEFAULT_ENSEMBL_BASEURL,
- new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
- domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
- DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_BASEURL, new EnsemblData(
+ DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL,
+ new EnsemblData(DEFAULT_ENSEMBL_GENOMES_BASEURL,
+ LATEST_ENSEMBLGENOMES_REST_VERSION));
}
protected volatile boolean inProgress = false;
protected abstract boolean useGetRequest();
/**
- * Return the desired value for the Content-Type request header
- *
- * @param multipleIds
+ * Returns the desired value for the Content-Type request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getRequestMimeType(boolean multipleIds);
+ protected String getRequestMimeType()
+ {
+ return "application/json";
+ }
/**
- * Return the desired value for the Accept request header
+ * Return the desired value for the Accept request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getResponseMimeType();
+ protected String getResponseMimeType()
+ {
+ return "application/json";
+ }
/**
* Checks Ensembl's REST 'ping' endpoint, and returns true if response
*/
boolean checkEnsembl()
{
- BufferedReader br = null;
String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
+ for (int i = 0 ; i < MAX_RETRIES ; i++)
+ {
+ if (pingEnsembl(pingUrl))
+ {
+ if (i > 0)
+ {
+ Cache.log.info("Ensembl ping responded on attempt " + (i+1));
+ }
+ return true;
+ }
+ }
+ Cache.log.error("Ensembl ping failed after " + MAX_RETRIES + " retries");
+ return false;
+ }
+
+ /**
+ * Connects to Ensembl REST service's 'ping' URL and answers true if
+ * successful, false if no reply, or no reply within the 2 second timeout
+ *
+ * @param pingUrl
+ * @return
+ */
+ @SuppressWarnings("unchecked")
+ protected boolean pingEnsembl(String pingUrl)
+ {
try
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
- URL ping = new URL(pingUrl);
/*
* expect {"ping":1} if ok
* if ping takes more than 2 seconds to respond, treat as if unavailable
*/
- br = getHttpResponse(ping, null, 2 * 1000);
- if (br == null)
+ Map<String, Object> val = (Map<String, Object>) getJSON(
+ new URL(pingUrl), null, PING_TIMEOUT_MS, MODE_MAP, null);
+ if (val == null)
{
- // error reponse status
return false;
}
- JSONParser jp = new JSONParser();
- JSONObject val = (JSONObject) jp.parse(br);
String pingString = val.get("ping").toString();
return pingString != null;
} catch (Throwable t)
{
- System.err.println(
+ Cache.log.error(
"Error connecting to " + pingUrl + ": " + t.getMessage());
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ return false;
}
- return false;
}
- /**
- * returns a reader to a Fasta response from the Ensembl sequence endpoint
- *
- * @param ids
- * @return
- * @throws IOException
- */
- protected FileParse getSequenceReader(List<String> ids) throws IOException
- {
- URL url = getUrl(ids);
-
- BufferedReader reader = getHttpResponse(url, ids);
- if (reader == null)
- {
- // request failed
- return null;
- }
- FileParse fp = new FileParse(reader, url.toString(),
- DataSourceType.URL);
- return fp;
- }
-
- /**
- * Gets a reader to the HTTP response, using the default read timeout of 5
- * minutes
- *
- * @param url
- * @param ids
- * @return
- * @throws IOException
- */
- protected BufferedReader getHttpResponse(URL url, List<String> ids)
- throws IOException
- {
- return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
- }
+ protected final static int MODE_ARRAY = 0;
+
+ protected final static int MODE_MAP = 1;
+
+ protected final static int MODE_ITERATOR = 2;
+
+ // /**
+ // * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+ // * If the request failed the return value may be null.
+ // *
+ // * @param ids
+ // * @return
+ // * @throws IOException
+ // * @throws ParseException
+ // */
+ // protected Object getSequenceJSON(List<String> ids, int mode)
+ // throws IOException, ParseException
+ // {
+ // URL url = getUrl(ids);
+ // return getJSON(url, ids, -1, mode);
+ // }
+ //
+ // /**
+ // * Gets a reader to the HTTP response, using the default read timeout of 5
+ // * minutes
+ // *
+ // * @param url
+ // * @param ids
+ // * @return
+ // * @throws IOException
+ // */
+ // protected BufferedReader getHttpResponse(URL url, List<String> ids)
+ // throws IOException
+ // {
+ // return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
+ // }
/**
- * Sends the HTTP request and gets the response as a reader
+ * Sends the HTTP request and gets the response as a reader. Returns null if
+ * the HTTP response code was not 200.
*
* @param url
* @param ids
* in milliseconds
* @return
* @throws IOException
- * if response code was not 200, or other I/O error
+ * @throws ParseException
*/
- protected BufferedReader getHttpResponse(URL url, List<String> ids,
- int readTimeout) throws IOException
+ private Object getJSON(URL url, List<String> ids, int readTimeout)
+ throws IOException, ParseException
{
+
+ if (readTimeout < 0)
+ {
+ readTimeout = DEFAULT_READ_TIMEOUT;
+ }
int retriesLeft = MAX_RETRIES;
HttpURLConnection connection = null;
int responseCode = 0;
+ Platform.setAjaxJSON(url);
+
while (retriesLeft > 0)
{
connection = tryConnection(url, ids, readTimeout);
* note: a GET request for an invalid id returns an error code e.g. 415
* but POST request returns 200 and an empty Fasta response
*/
- System.err.println("Response code " + responseCode + " for " + url);
+ Cache.log.error("Response code " + responseCode);// + " for " + url);
return null;
}
InputStream response = connection.getInputStream();
- // System.out.println(getClass().getName() + " took "
- // + (System.currentTimeMillis() - now) + "ms to fetch");
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ Object ret = Platform.parseJSON(response);
+ // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+ // Platform.TIME_MARK);
- BufferedReader reader = null;
- reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
- return reader;
+ return ret;
}
/**
int readTimeout) throws IOException, ProtocolException
{
// System.out.println(System.currentTimeMillis() + " " + url);
+
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
/*
boolean multipleIds = ids != null && ids.size() > 1;
connection.setRequestMethod(
multipleIds ? HttpMethod.POST : HttpMethod.GET);
- connection.setRequestProperty("Content-Type",
- getRequestMimeType(multipleIds));
+ connection.setRequestProperty("Content-Type", getRequestMimeType());
connection.setRequestProperty("Accept", getResponseMimeType());
- connection.setUseCaches(false);
connection.setDoInput(true);
connection.setDoOutput(multipleIds);
+ connection.setUseCaches(false);
connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
connection.setReadTimeout(readTimeout);
int retrySecs = Integer.valueOf(retryDelay);
if (retrySecs > 0 && retrySecs < 10)
{
- System.err
- .println("Ensembl REST service rate limit exceeded, waiting "
+ System.err.println(
+ "Ensembl REST service rate limit exceeded, waiting "
+ retryDelay + " seconds before retrying");
Thread.sleep(1000 * retrySecs);
}
* recheck if Ensembl is up if it was down, or the recheck period has elapsed
*/
boolean retestAvailability = (now
- - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ - info.lastAvailableCheckTime) > PING_RETEST_INTERVAL;
if (!info.restAvailable || retestAvailability)
{
info.restAvailable = checkEnsembl();
StringBuilder postBody = new StringBuilder(64);
postBody.append("{\"ids\":[");
first = true;
- for (String id : ids)
+ for (int i = 0, n = ids.size(); i < n; i++)
{
+ String id = ids.get(i);
if (!first)
{
postBody.append(",");
}
/**
+ * Primary access point to parsed JSON data, including the call to retrieve
+ * and parsing.
+ *
+ * @param url
+ * request url; if null, getUrl(ids) will be used
+ * @param ids
+ * optional; may be null
+ * @param msDelay
+ * -1 for default delay
+ * @param mode
+ * map, array, or array iterator
+ * @param mapKey
+ * an optional key for an outer map
+ * @return a Map, List, Iterator, or null
+ * @throws IOException
+ * @throws ParseException
+ *
+ * @author Bob Hanson 2019
+ */
+ @SuppressWarnings("unchecked")
+ protected Object getJSON(URL url, List<String> ids, int msDelay, int mode,
+ String mapKey) throws IOException, ParseException
+ {
+ if (url == null)
+ {
+ url = getUrl(ids);
+ }
+
+ Object json = (url == null ? null : getJSON(url, ids, msDelay));
+
+ if (json != null && mapKey != null)
+ {
+ json = ((Map<String, Object>) json).get(mapKey);
+ }
+ if (json == null)
+ {
+ return null;
+ }
+ switch (mode)
+ {
+ case MODE_ARRAY:
+ case MODE_MAP:
+ break;
+ case MODE_ITERATOR:
+ json = ((List<Object>) json).iterator();
+ break;
+ }
+ return json;
+ }
+
+ /**
* Fetches and checks Ensembl's REST version number
*
* @return
*/
+ @SuppressWarnings("unchecked")
private void checkEnsemblRestVersion()
{
EnsemblData info = domainData.get(getDomain());
- JSONParser jp = new JSONParser();
- URL url = null;
try
{
- url = new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON);
- BufferedReader br = getHttpResponse(url, null);
- if (br == null)
+ Map<String, Object> val = (Map<String, Object>) getJSON(
+ new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON), null,
+ -1, MODE_MAP, null);
+ if (val == null)
{
return;
}
- JSONObject val = (JSONObject) jp.parse(br);
String version = val.get("release").toString();
String majorVersion = version.substring(0, version.indexOf("."));
String expected = info.expectedRestVersion;
*
* @return
*/
+ @SuppressWarnings("unchecked")
private void checkEnsemblDataVersion()
{
- JSONParser jp = new JSONParser();
- URL url = null;
- BufferedReader br = null;
-
+ Map<String, Object> val;
try
{
- url = new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON);
- br = getHttpResponse(url, null);
- if (br != null)
+ val = (Map<String, Object>) getJSON(
+ new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON), null,
+ -1, MODE_MAP, null);
+ if (val == null)
{
- JSONObject val = (JSONObject) jp.parse(br);
- JSONArray versions = (JSONArray) val.get("releases");
- domainData.get(getDomain()).dataVersion = versions.get(0)
- .toString();
+ return;
}
- } catch (Throwable t)
- {
+ List<Object> versions = (List<Object>) val.get("releases");
+ domainData.get(getDomain()).dataVersion = versions.get(0).toString();
+ } catch (Throwable e)
+ {// could be IOException | ParseException e) {
System.err.println(
- "Error checking Ensembl data version: " + t.getMessage());
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ "Error checking Ensembl data version: " + e.getMessage());
}
}
git://source.jalview.org / jalview.git / blobdiff