*/
package jalview.ext.ensembl;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.util.StringUtils;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
-import com.stevesoft.pat.Regex;
-
/**
* Base class for Ensembl REST service clients
*
/*
* update these constants when Jalview has been checked / updated for
- * changes to Ensembl REST API
+ * changes to Ensembl REST API (ref JAL-2105)
* @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 = "4.6";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
- private static final Regex TRANSCRIPT_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)T[0-9]{11}$");
-
- private static final Regex GENE_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)G[0-9]{11}$");
-
static
{
domainData = new HashMap<String, EnsemblInfo>();
- domainData.put(ENSEMBL_REST, new EnsemblInfo(ENSEMBL_REST,
- LATEST_ENSEMBL_REST_VERSION));
+ 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));
}
setDomain(d);
}
- /**
- * Answers true if the query matches the regular expression pattern for an
- * Ensembl transcript stable identifier
- *
- * @param query
- * @return
- */
- public boolean isTranscriptIdentifier(String query)
- {
- return query == null ? false : TRANSCRIPT_REGEX.search(query);
- }
-
- /**
- * Answers true if the query matches the regular expression pattern for an
- * Ensembl gene stable identifier
- *
- * @param query
- * @return
- */
- public boolean isGeneIdentifier(String query)
- {
- return query == null ? false : GENE_REGEX.search(query);
- }
-
@Override
public boolean queryInProgress()
{
{
// 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");
+ URL ping = new URL(
+ getDomain() + "/info/ping?content-type=application/json");
/*
* 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)
+ {
+ // 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("Error connecting to " + PING_URL + ": "
- + t.getMessage());
+ System.err.println(
+ "Error connecting to " + PING_URL + ": " + t.getMessage());
} finally
{
if (br != null)
* @return
* @throws IOException
*/
- protected FileParse getSequenceReader(List<String> ids)
- throws IOException
+ protected FileParse getSequenceReader(List<String> ids) throws IOException
{
URL url = getUrl(ids);
// request failed
return null;
}
- FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+ FileParse fp = new FileParse(reader, url.toString(),
+ DataSourceType.URL);
return fp;
}
* sequence queries, but not for overlap
*/
boolean multipleIds = ids != null && ids.size() > 1;
- connection.setRequestMethod(multipleIds ? HttpMethod.POST
- : HttpMethod.GET);
+ connection.setRequestMethod(
+ multipleIds ? HttpMethod.POST : HttpMethod.GET);
connection.setRequestProperty("Content-Type",
getRequestMimeType(multipleIds));
connection.setRequestProperty("Accept", getResponseMimeType());
void checkRateLimits(HttpURLConnection connection)
{
// number of requests allowed per time interval:
- String limit = connection.getHeaderField("X-RateLimit-Limit");
+ // 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");
+ // String reset = connection.getHeaderField("X-RateLimit-Reset");
// number of requests remaining from quota for current period:
- String remaining = connection.getHeaderField("X-RateLimit-Remaining");
+ // String remaining = connection.getHeaderField("X-RateLimit-Remaining");
// number of seconds to wait before retrying (if remaining == 0)
String retryDelay = connection.getHeaderField("Retry-After");
+ (1000 * Integer.valueOf(retryDelay));
} catch (NumberFormatException e)
{
- System.err.println("Unexpected value for Retry-After: "
- + retryDelay);
+ System.err
+ .println("Unexpected value for Retry-After: " + retryDelay);
}
}
else
/*
* recheck if Ensembl is up if it was down, or the recheck period has elapsed
*/
- boolean retestAvailability = (now - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ boolean retestAvailability = (now
+ - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
if (!info.restAvailable || retestAvailability)
{
info.restAvailable = checkEnsembl();
/*
* refetch Ensembl versions if the recheck period has elapsed
*/
- boolean refetchVersion = (now - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
+ boolean refetchVersion = (now
+ - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
if (refetchVersion)
{
checkEnsemblRestVersion();
byte[] thepostbody = postBody.toString().getBytes();
connection.setRequestProperty("Content-Length",
Integer.toString(thepostbody.length));
- DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
+ DataOutputStream wr = new DataOutputStream(
+ connection.getOutputStream());
wr.write(thepostbody);
wr.flush();
wr.close();
URL url = null;
try
{
- url = new URL(getDomain()
- + "/info/rest?content-type=application/json");
+ url = new URL(
+ getDomain() + "/info/rest?content-type=application/json");
BufferedReader br = getHttpResponse(url, null);
+ if (br == null)
+ {
+ return;
+ }
JSONObject val = (JSONObject) jp.parse(br);
String version = val.get("release").toString();
String majorVersion = version.substring(0, version.indexOf("."));
* if so warn; we don't worry if it is earlier (this indicates Jalview has
* been tested in advance against the next pending REST version)
*/
- boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
+ boolean laterVersion = StringUtils.compareVersions(version,
+ expected) == 1;
if (laterVersion)
{
System.err.println(String.format(
- "Expected %s REST version %s but found %s, see %s",
+ "EnsemblRestClient expected %s REST version %s but found %s, see %s",
getDbSource(), expected, version, REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
{
- System.err.println("Error checking Ensembl REST version: "
- + t.getMessage());
+ System.err.println(
+ "Error checking Ensembl REST version: " + t.getMessage());
}
}
URL url = null;
try
{
- url = new URL(getDomain()
- + "/info/data?content-type=application/json");
+ url = new URL(
+ getDomain() + "/info/data?content-type=application/json");
BufferedReader br = getHttpResponse(url, null);
- JSONObject val = (JSONObject) jp.parse(br);
- JSONArray versions = (JSONArray) val.get("releases");
- domainData.get(getDomain()).dataVersion = versions.get(0).toString();
+ if (br != null)
+ {
+ JSONObject val = (JSONObject) jp.parse(br);
+ JSONArray versions = (JSONArray) val.get("releases");
+ domainData.get(getDomain()).dataVersion = versions.get(0)
+ .toString();
+ }
} catch (Throwable t)
{
- System.err.println("Error checking Ensembl data version: "
- + t.getMessage());
+ System.err.println(
+ "Error checking Ensembl data version: " + t.getMessage());
}
}
git://source.jalview.org / jalview.git / blobdiff