Fixing phosphosite urls and changing default url timeout to 30s

josemduarte · josemduarte · commit 67ca7f20f22c · 2017-09-07T19:39:08.000-07:00
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
@@ -26,7 +26,6 @@
 
 import java.io.*;
 import java.net.URL;
-import java.nio.channels.FileChannel;
 import java.nio.file.Files;
 import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
@@ -49,19 +48,19 @@ public class Dataset {
 
 	private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
 
-	public static final String ACETYLATION = "http://www.phosphosite.org/downloads/Acetylation_site_dataset.gz";
+	public static final String ACETYLATION = "https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz";
 
-	public static final String DISEASE_ASSOC = "http://www.phosphosite.org/downloads/Disease-associated_sites.gz";
+	public static final String DISEASE_ASSOC = "https://www.phosphosite.org/downloads/Disease-associated_sites.gz";
 
-	public static final String METHYLATION = "http://www.phosphosite.org/downloads/Methylation_site_dataset.gz";
+	public static final String METHYLATION = "https://www.phosphosite.org/downloads/Methylation_site_dataset.gz";
 
-	public static final String PHOSPHORYLATION = "http://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz";
+	public static final String PHOSPHORYLATION = "https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz";
 
-	public static final String REGULATORY = "http://www.phosphosite.org/downloads/Regulatory_sites.gz";
+	public static final String REGULATORY = "https://www.phosphosite.org/downloads/Regulatory_sites.gz";
 
-	public static final String SUMOYLATION = "http://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz";
+	public static final String SUMOYLATION = "https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz";
 
-	public static final String UBIQUITINATION = "http://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz";
+	public static final String UBIQUITINATION = "https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz";
 
 
 	public Dataset(){
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
@@ -15,15 +15,17 @@
 import static org.junit.Assert.fail;
 
 
-/** Makes sure there is a local installation of the Acetylation site file from Phosphosite and
+/** 
+ * Makes sure there is a local installation of the Acetylation site file from Phosphosite and
  * tests if it can get parsed by the parser.
  *
  * Created by andreas on 11/29/16.
  */
 public class TestAcetylation  {
 
 
-    /** Make sure an Acetylation file is available locally.
+    /** 
+     * Make sure an Acetylation file is available locally.
      * Downloads from Phosphosite if needed.
      *
      */
@@ -42,7 +44,8 @@ public void setUp() throws IOException{
 
     }
 
-    /** returns the local file name where the Acetylation file will get cached locally.
+    /** 
+     * Returns the local file name where the Acetylation file will get cached locally.
      *
      * @param phosphoSiteFileLocation location of file at PhosphoSitePlus.
      * @return a File pointing to the location of the locally cached file.
@@ -64,7 +67,8 @@ private File getLocalFileName(String phosphoSiteFileLocation){
         return new File(localDir + "/" + fileName);
     }
 
-    /** Tests that the acetylation file can get parsed without problems.
+    /** 
+     * Tests that the acetylation file can get parsed without problems.
      *
      */
     @Test
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/URLConnectionTools.java
@@ -45,7 +45,7 @@
 public class URLConnectionTools {
 
 	/** The default connection timeout in ms - 15 seconds*/
-	public static final int    DEFAULT_CONNECTION_TIMEOUT = 15000;
+	public static final int    DEFAULT_CONNECTION_TIMEOUT = 30000;
 
 	/**
 	 * Open HttpURLConnection. Recommended way to open URL connections in Java 1.7 and 1.8.

Original file line number	Diff line number	Diff line change
`@@ -15,15 +15,17 @@`
`15`	`15`	`import static org.junit.Assert.fail;`
`16`	`16`
`17`	`17`
`18`		`-/** Makes sure there is a local installation of the Acetylation site file from Phosphosite and`
	`18`	`+/**`
	`19`	`+ * Makes sure there is a local installation of the Acetylation site file from Phosphosite and`
`19`	`20`	`* tests if it can get parsed by the parser.`
`20`	`21`	`*`
`21`	`22`	`* Created by andreas on 11/29/16.`
`22`	`23`	`*/`
`23`	`24`	`public class TestAcetylation {`
`24`	`25`
`25`	`26`
`26`		`- /** Make sure an Acetylation file is available locally.`
	`27`	`+ /**`
	`28`	`+ * Make sure an Acetylation file is available locally.`
`27`	`29`	`* Downloads from Phosphosite if needed.`
`28`	`30`	`*`
`29`	`31`	`*/`
`@@ -42,7 +44,8 @@ public void setUp() throws IOException{`
`42`	`44`
`43`	`45`	`}`
`44`	`46`
`45`		`- /** returns the local file name where the Acetylation file will get cached locally.`
	`47`	`+ /**`
	`48`	`+ * Returns the local file name where the Acetylation file will get cached locally.`
`46`	`49`	`*`
`47`	`50`	`* @param phosphoSiteFileLocation location of file at PhosphoSitePlus.`
`48`	`51`	`* @return a File pointing to the location of the locally cached file.`
`@@ -64,7 +67,8 @@ private File getLocalFileName(String phosphoSiteFileLocation){`
`64`	`67`	`return new File(localDir + "/" + fileName);`
`65`	`68`	`}`
`66`	`69`
`67`		`- /** Tests that the acetylation file can get parsed without problems.`
	`70`	`+ /**`
	`71`	`+ * Tests that the acetylation file can get parsed without problems.`
`68`	`72`	`*`
`69`	`73`	`*/`
`70`	`74`	`@Test`