import javax.ws.rs.HttpMethod;
+import com.stevesoft.pat.Regex;
+
/**
* Base class for Ensembl REST service clients
*
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
- protected final static String ENSEMBL_REST = "http://rest.ensembl.org";
+ private final static String ENSEMBL_REST = "http://rest.ensembl.org";
- protected static final String SEQUENCE_ID_URL = ENSEMBL_REST
- + "/sequence/id";
+ protected final static String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
// @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 RETEST_INTERVAL = 10000L; // 10 seconds
+ private static final Regex TRANSCRIPT_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+
+ private static final Regex GENE_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+
+ private String domain = ENSEMBL_REST;
+
private static boolean ensemblRestAvailable = false;
private static long lastCheck = -1;
+ /*
+ * absolute time to wait till if we overloaded the REST service
+ */
+ private static long retryAfter;
+
protected volatile boolean inProgress = false;
+ /**
+ * Default constructor to use rest.ensembl.org
+ */
+ public EnsemblRestClient()
+ {
+ this(ENSEMBL_REST);
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblRestClient(String d)
+ {
+ domain = d;
+ }
+
+ String getDomain()
+ {
+ return domain;
+ }
+
+ void setDomain(String d)
+ {
+ domain = d;
+ }
+
+ public boolean isTranscriptIdentifier(String query)
+ {
+ return query == null ? false : TRANSCRIPT_REGEX.search(query);
+ }
+
+ public boolean isGeneIdentifier(String query)
+ {
+ return query == null ? false : GENE_REGEX.search(query);
+ }
+
@Override
public boolean queryInProgress()
{
/**
* Return the desired value for the Content-Type request header
*
+ * @param multipleIds
+ *
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getRequestMimeType();
+ protected abstract String getRequestMimeType(boolean multipleIds);
/**
* Return the desired value for the Accept request header
{
try
{
- URL ping = new URL(PING_URL);
+ // note this format works for both ensembl and ensemblgenomes
+ // info/ping.json works for ensembl only (March 2016)
+ URL ping = new URL(getDomain()
+ + "/info/ping?content-type=application/json");
HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
int rc = conn.getResponseCode();
conn.disconnect();
{
URL url = getUrl(ids);
+ BufferedReader reader = getHttpResponse(url, ids);
+ FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+ return fp;
+ }
+
+ /**
+ * Writes the HTTP request and gets the response as a reader.
+ *
+ * @param url
+ * @param ids
+ * written as Json POST body if more than one
+ * @return
+ * @throws IOException
+ * if response code was not 200, or other I/O error
+ */
+ protected BufferedReader getHttpResponse(URL url, List<String> ids)
+ throws IOException
+ {
+ // long now = System.currentTimeMillis();
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
/*
* POST method allows multiple queries in one request; it is supported for
* sequence queries, but not for overlap
*/
- connection.setRequestMethod(useGetRequest() ? HttpMethod.GET
- : HttpMethod.POST);
- connection.setRequestProperty("Content-Type", getRequestMimeType());
+ boolean multipleIds = ids.size() > 1;// useGetRequest();
+ connection.setRequestMethod(multipleIds ? HttpMethod.POST
+ : HttpMethod.GET);
+ connection.setRequestProperty("Content-Type",
+ getRequestMimeType(multipleIds));
connection.setRequestProperty("Accept", getResponseMimeType());
connection.setUseCaches(false);
connection.setDoInput(true);
- connection.setDoOutput(true);
+ connection.setDoOutput(multipleIds);
- if (!useGetRequest())
+ if (multipleIds)
{
writePostBody(connection, ids);
}
if (responseCode != 200)
{
- throw new RuntimeException(
+ /*
+ * 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
+ */
+ throw new IOException(
"Response code was not 200. Detected response was "
+ responseCode);
}
+ // System.out.println(getClass().getName() + " took "
+ // + (System.currentTimeMillis() - now) + "ms to fetch");
+
+ checkRateLimits(connection);
BufferedReader reader = null;
reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
- FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
- return fp;
+ return reader;
}
/**
+ * Inspect response headers for any sign of server overload and respect any
+ * 'retry-after' directive
+ *
+ * @see https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits
+ * @param connection
+ */
+ void checkRateLimits(HttpURLConnection connection)
+ {
+ // number of requests allowed per time interval:
+ String limit = connection.getHeaderField("X-RateLimit-Limit");
+ // length of quota time interval in seconds:
+ // String period = connection.getHeaderField("X-RateLimit-Period");
+ // seconds remaining until usage quota is reset:
+ String reset = connection.getHeaderField("X-RateLimit-Reset");
+ // number of requests remaining from quota for current period:
+ String remaining = connection.getHeaderField("X-RateLimit-Remaining");
+ // number of seconds to wait before retrying (if remaining == 0)
+ String retryDelay = connection.getHeaderField("Retry-After");
+
+ // to test:
+ // retryDelay = "5";
+
+ if (retryDelay != null)
+ {
+ System.err.println("Ensembl REST service rate limit exceeded, wait "
+ + retryDelay + " seconds before retrying");
+ try
+ {
+ retryAfter = System.currentTimeMillis()
+ + (1000 * Integer.valueOf(retryDelay));
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Unexpected value for Retry-After: "
+ + retryDelay);
+ }
+ }
+ else
+ {
+ retryAfter = 0;
+ // debug:
+ // System.out.println(String.format(
+ // "%s Ensembl requests remaining of %s (reset in %ss)",
+ // remaining, limit, reset));
+ }
+ }
+ /**
* Rechecks if Ensembl is responding, unless the last check was successful and
* the retest interval has not yet elapsed. Returns true if Ensembl is up,
* else false.
protected boolean isEnsemblAvailable()
{
long now = System.currentTimeMillis();
+
+ /*
+ * check if we are waiting for 'Retry-After' to expire
+ */
+ if (retryAfter > now)
+ {
+ System.err.println("Still " + (1 + (retryAfter - now) / 1000)
+ + " secs to wait before retrying Ensembl");
+ return false;
+ }
+ else
+ {
+ retryAfter = 0;
+ }
+
boolean retest = now - lastCheck > RETEST_INTERVAL;
if (ensemblRestAvailable && !retest)
{
git://source.jalview.org / jalview.git / blobdiff