JAL-1054 Change the rest of the url.openConnection() calls to use the HttpUtils.openC...

diff --git a/src/jalview/analytics/Plausible.java b/src/jalview/analytics/Plausible.java
index 544fb05..2852734 100644 (file)
--- a/src/jalview/analytics/Plausible.java
+++ b/src/jalview/analytics/Plausible.java
@@ -29,7 +29,6 @@ import java.lang.invoke.MethodHandles;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.net.URLConnection;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 import java.util.AbstractMap;
@@ -44,6 +43,7 @@ import java.util.Random;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.util.ChannelProperties;
+import jalview.util.HttpUtils;
 import jalview.util.UserAgent;
 
 public class Plausible
@@ -213,8 +213,7 @@ public class Plausible
     try
     {
       URL url = new URL(urlSb.toString());
-      URLConnection urlConnection = url.openConnection();
-      HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection;
+      HttpURLConnection httpURLConnection = HttpUtils.openConnection(url);
       httpURLConnection.setRequestMethod("POST");
       httpURLConnection.setDoOutput(true);
 
@@ -553,8 +552,7 @@ public class Plausible
     try
     {
       URL url = new URL(CONFIG_API_BASE_URL);
-      URLConnection urlConnection = url.openConnection();
-      HttpURLConnection httpURLConnection = (HttpURLConnection) urlConnection;
+      HttpURLConnection httpURLConnection = HttpUtils.openConnection(url);
       httpURLConnection.setRequestMethod("GET");
       httpURLConnection.setRequestProperty("User-Agent", USER_AGENT);
       httpURLConnection.setConnectTimeout(5000);

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 709136c..f7651be 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -36,6 +36,7 @@ import javax.ws.rs.HttpMethod;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.util.HttpUtils;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
 
@@ -342,7 +343,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
 
-    HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+    HttpURLConnection connection = HttpUtils.openConnection(url);
 
     /*
      * POST method allows multiple queries in one request; it is supported for

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index ddc8d84..05c5053 100644 (file)
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -38,6 +38,7 @@ import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.gui.Preferences;
 import jalview.structure.StructureCommandI;
+import jalview.util.HttpUtils;
 import jalview.util.Platform;
 
 public class PymolManager
@@ -167,7 +168,7 @@ public class PymolManager
     try
     {
       URL realUrl = new URL(rpcUrl);
-      HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
+      HttpURLConnection conn = HttpUtils.openConnection(realUrl);
       conn.setRequestProperty("accept", "*/*");
       conn.setRequestProperty("content-type", "text/xml");
       conn.setDoOutput(true);

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index fd12dc6..57b2ce5 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -316,7 +316,7 @@ public class FileParse
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(urlStr);
-    URLConnection _conn = url.openConnection();
+    URLConnection _conn = HttpUtils.openConnection(url);
     if (_conn instanceof HttpURLConnection)
     {
       HttpURLConnection conn = HttpUtils

diff --git a/src/jalview/ws/dbsources/TDBeacons.java b/src/jalview/ws/dbsources/TDBeacons.java
index 7326c6e..8a27ad9 100644 (file)
--- a/src/jalview/ws/dbsources/TDBeacons.java
+++ b/src/jalview/ws/dbsources/TDBeacons.java
@@ -20,7 +20,23 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Locale;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
 
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -32,9 +48,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.HttpUtils;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.uniprot.DbReferenceType;
 import jalview.xml.binding.uniprot.Entry;
 import jalview.xml.binding.uniprot.FeatureType;
@@ -42,23 +58,6 @@ import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * This class queries the Uniprot database for sequence data, unmarshals the
  * returned XML, and converts it to Jalview Sequence records (including attached
@@ -152,7 +151,7 @@ public class TDBeacons extends DbSourceProxyImpl
       // String downloadstring = getDomain() + queries + ".json";
 
       URL url = new URL(downloadstring);
-      URLConnection urlconn = url.openConnection();
+      URLConnection urlconn = HttpUtils.openConnection(url);
       InputStream istr = urlconn.getInputStream();
       List<Entry> entries = getUniprotEntries(istr);
       if (entries != null)

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 299224d..b493611 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -49,6 +49,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.HttpUtils;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 import jalview.xml.binding.uniprot.DbReferenceType;
@@ -144,10 +145,11 @@ public class Uniprot extends DbSourceProxyImpl
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
-      String downloadstring = getDomain() + "/uniprotkb/" + queries + ".xml";
+      String downloadstring = getDomain() + "/uniprotkb/" + queries
+              + ".xml";
 
       URL url = new URL(downloadstring);
-      HttpURLConnection urlconn = (HttpURLConnection) url.openConnection();
+      HttpURLConnection urlconn = HttpUtils.openConnection(url);
       // anything other than 200 means we don't have data
       // TODO: JAL-3882 reuse the EnsemblRestClient's fair
       // use/backoff logic to retry when the server tells us to go away

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 8aca9a2..87526a1 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,12 +20,6 @@
  */
 package jalview.ws.ebi;
 
-import java.util.Locale;
-
-import jalview.datamodel.DBRefSource;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
@@ -35,8 +29,14 @@ import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
+import jalview.datamodel.DBRefSource;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * DOCUMENT ME!
  * 
@@ -210,7 +210,7 @@ public class EBIFetchClient
     try
     {
       URL rcall = new URL(url);
-      HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+      HttpURLConnection conn = HttpUtils.openConnection(rcall);
       int responseCode = conn.getResponseCode();
       if (responseCode == 200)
       {

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 58e0b29..cb61ca1 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -20,8 +20,6 @@
  */
 package jalview.ws.sifts;
 
-import java.util.Locale;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -41,6 +39,7 @@ import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
@@ -68,6 +67,7 @@ import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
+import jalview.util.HttpUtils;
 import jalview.util.Platform;
 import jalview.xml.binding.sifts.Entry;
 import jalview.xml.binding.sifts.Entry.Entity;
@@ -335,7 +335,7 @@ public class SiftsClient implements SiftsClientI
     // siftsFileFTPURL);
     // long now = System.currentTimeMillis();
     URL url = new URL(siftsFileFTPURL);
-    URLConnection conn = url.openConnection();
+    URLConnection conn = HttpUtils.openConnection(url);
     InputStream inputStream = conn.getInputStream();
     FileOutputStream outputStream = new FileOutputStream(downloadTo);
     byte[] buffer = new byte[BUFFER_SIZE];