X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=9e01cc4e04af66e195acb0a95a3c157b54a7534e;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=b1bc8e5edb4abb24fd3d10fbab66f4ecd37878ec;hpb=d943fcd0dc04fd4974344eddd13902c89fb595b2;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index b1bc8e5..9e01cc4 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,8 +20,6 @@ */ package jalview.ext.ensembl; -import jalview.io.DataSourceType; -import jalview.io.FileParse; import jalview.util.StringUtils; import java.io.BufferedReader; @@ -66,16 +64,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @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 = "7.0"; - private static final String LATEST_ENSEMBL_REST_VERSION = "6.1"; + private static final String LATEST_ENSEMBL_REST_VERSION = "7.0"; private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; - private static Map 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 static Map domainData; private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds @@ -86,10 +81,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher static { domainData = new HashMap<>(); - domainData.put(ENSEMBL_REST, - new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION)); - domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo( - ENSEMBL_GENOMES_REST, 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; @@ -99,7 +94,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ public EnsemblRestClient() { - this(ENSEMBL_REST); + super(); + + /* + * initialise domain info lazily + */ + if (!domainData.containsKey(ensemblDomain)) + { + domainData.put(ensemblDomain, + new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION)); + } + if (!domainData.containsKey(ensemblGenomesDomain)) + { + domainData.put(ensemblGenomesDomain, new EnsemblData( + ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION)); + } } /** @@ -142,22 +151,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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 @@ -169,11 +184,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher boolean checkEnsembl() { BufferedReader br = null; + String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON; try { // 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_JSON); + URL ping = new URL(pingUrl); /* * expect {"ping":1} if ok @@ -192,7 +208,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } catch (Throwable t) { System.err.println( - "Error connecting to " + PING_URL + ": " + t.getMessage()); + "Error connecting to " + pingUrl + ": " + t.getMessage()); } finally { if (br != null) @@ -210,25 +226,20 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } /** - * returns a reader to a Fasta response from the Ensembl sequence endpoint + * 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 */ - protected FileParse getSequenceReader(List ids) throws IOException + protected BufferedReader getSequenceReader(List 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; + return reader; } /** @@ -247,7 +258,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher } /** - * 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 @@ -256,7 +268,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * in milliseconds * @return * @throws IOException - * if response code was not 200, or other I/O error */ protected BufferedReader getHttpResponse(URL url, List ids, int readTimeout) throws IOException @@ -320,8 +331,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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); @@ -381,7 +391,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ protected boolean isEnsemblAvailable() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); long now = System.currentTimeMillis(); @@ -455,7 +465,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher */ private void checkEnsemblRestVersion() { - EnsemblInfo info = domainData.get(getDomain()); + EnsemblData info = domainData.get(getDomain()); JSONParser jp = new JSONParser(); URL url = null;