From 1693c01f6cc8a94f3730ae6f27fe7a581a89615a Mon Sep 17 00:00:00 2001
From: anttil <anttil>
Date: Mon, 5 Oct 2015 13:43:00 +0000
Subject: [PATCH] SSDM-2259: Make UniprotQuery to use jetty HTTP client instead
of apache-commons HTTP client
SVN: 34785
---
.../cisd/common/net/uniprot/UniprotQuery.java | 78 +++++++++++--------
1 file changed, 44 insertions(+), 34 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/net/uniprot/UniprotQuery.java b/common/source/java/ch/systemsx/cisd/common/net/uniprot/UniprotQuery.java
index 4265d147583..087b21edffc 100644
--- a/common/source/java/ch/systemsx/cisd/common/net/uniprot/UniprotQuery.java
+++ b/common/source/java/ch/systemsx/cisd/common/net/uniprot/UniprotQuery.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.common.net.uniprot;
import static ch.systemsx.cisd.common.net.uniprot.UniprotColumn.ID;
import java.io.IOException;
+import java.io.InputStream;
import java.util.Arrays;
import java.util.Collections;
import java.util.EnumSet;
@@ -26,12 +27,15 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.concurrent.TimeUnit;
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.methods.GetMethod;
-import org.apache.commons.httpclient.params.HttpMethodParams;
+import org.apache.commons.compress.utils.IOUtils;
+import org.eclipse.jetty.client.HttpClient;
+import org.eclipse.jetty.client.api.Request;
+import org.eclipse.jetty.client.api.Response;
+import org.eclipse.jetty.client.util.InputStreamResponseListener;
+import org.eclipse.jetty.http.HttpMethod;
+import org.eclipse.jetty.http.HttpStatus;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
@@ -48,8 +52,6 @@ import ch.systemsx.cisd.common.parser.TabFileLoader;
*/
public final class UniprotQuery
{
- private static final int RETRY_COUNT = 3;
-
private static final String BASE_URL = "http://www.uniprot.org/uniprot/";
private static final String QUERY_INIT_STR = "query=";
@@ -78,8 +80,8 @@ public final class UniprotQuery
private final String columnsSpecification;
/**
- * Construct a Uniprot query, adding the given database <var>columns</var>. Note that
- * {@link UniprotColumn#ID} will always be added to the set of columns.
+ * Construct a Uniprot query, adding the given database <var>columns</var>. Note that {@link UniprotColumn#ID} will always be added to the set of
+ * columns.
*/
public UniprotQuery(UniprotColumn... columns)
{
@@ -87,8 +89,8 @@ public final class UniprotQuery
}
/**
- * Construct a Uniprot query, adding the given database <var>columns</var>. Note that
- * {@link UniprotColumn#ID} will always be added to the set of columns.
+ * Construct a Uniprot query, adding the given database <var>columns</var>. Note that {@link UniprotColumn#ID} will always be added to the set of
+ * columns.
*/
public UniprotQuery(Set<UniprotColumn> columns)
{
@@ -158,17 +160,29 @@ public final class UniprotQuery
private Iterable<UniprotEntry> runQuery(final String queryURL) throws IOExceptionUnchecked
{
final HttpClient client = new HttpClient();
- final GetMethod method = new GetMethod(queryURL);
- method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(RETRY_COUNT, false));
try
{
- final int statusCode = client.executeMethod(method);
+ client.start();
+ } catch (Exception e)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(e);
+ }
+
+ final InputStreamResponseListener listener = new InputStreamResponseListener();
+
+ Request request = client.newRequest(queryURL).method(HttpMethod.GET);
+
+ final InputStream stream = listener.getInputStream();
+
+ try
+ {
+ request.send(listener);
+ Response response = listener.get(5, TimeUnit.SECONDS);
- if (statusCode != HttpStatus.SC_OK)
+ if (response.getStatus() != HttpStatus.Code.OK.getCode())
{
throw new IOExceptionUnchecked(new IOException("GET failed: "
- + method.getStatusLine()));
+ + response.getStatus() + ": " + response.getReason()));
}
final TabFileLoader<UniprotEntry> parser =
@@ -199,8 +213,7 @@ public final class UniprotQuery
{
Map<String, String> defauts = Collections.emptyMap();
- final Iterator<UniprotEntry> delegate = parser.iterate(
- method.getResponseBodyAsStream(), defauts);
+ final Iterator<UniprotEntry> delegate = parser.iterate(stream, defauts);
@Override
public boolean hasNext()
@@ -208,7 +221,7 @@ public final class UniprotQuery
final boolean hasNext = delegate.hasNext();
if (hasNext == false)
{
- method.releaseConnection();
+ IOUtils.closeQuietly(stream);
}
return hasNext;
}
@@ -221,7 +234,7 @@ public final class UniprotQuery
return delegate.next();
} catch (RuntimeException ex)
{
- method.releaseConnection();
+ IOUtils.closeQuietly(stream);
throw ex;
}
}
@@ -229,20 +242,20 @@ public final class UniprotQuery
@Override
public void remove()
{
- method.releaseConnection();
+ IOUtils.closeQuietly(stream);
throw new UnsupportedOperationException();
}
};
- } catch (IOException ex)
+ } catch (Exception ex)
{
- method.releaseConnection();
+ IOUtils.closeQuietly(stream);
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
};
- } catch (IOException ex)
+ } catch (Exception ex)
{
- method.releaseConnection();
+ IOUtils.closeQuietly(stream);
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
@@ -261,9 +274,8 @@ public final class UniprotQuery
/**
* Runs a query against Uniprot with the given <var>queryExpression</var>.
*
- * @param queryExpression The query expression to use for the query. See <a
- * href="http://www.uniprot.org/help/text-search">Uniprot Online Help</a> for details
- * on the query language.
+ * @param queryExpression The query expression to use for the query. See <a href="http://www.uniprot.org/help/text-search">Uniprot Online Help</a>
+ * for details on the query language.
*/
public Iterable<UniprotEntry> query(String queryExpression) throws IOExceptionUnchecked
{
@@ -274,12 +286,10 @@ public final class UniprotQuery
/**
* Runs a query against Uniprot with the given <var>queryExpression</var>.
*
- * @param queryExpression The query expression to use for the query. See <a
- * href="http://www.uniprot.org/help/text-search">Uniprot Online Help</a> for details
- * on the query language.
+ * @param queryExpression The query expression to use for the query. See <a href="http://www.uniprot.org/help/text-search">Uniprot Online Help</a>
+ * for details on the query language.
* @param limit The maximum number of result entries to return.
- * @param offset The offset, that is the first result entry to return when counting starts with
- * 0.
+ * @param offset The offset, that is the first result entry to return when counting starts with 0.
*/
public Iterable<UniprotEntry> query(String queryExpression, int limit, int offset)
throws IOExceptionUnchecked
--
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