Changeset 4551

Timestamp:

Mar 25, 2014, 11:02:42 AM (9 years ago)

Author:

Fredrik Levander

Message:

Refs #630. Added support for URIs with basic authentication. Refs #823. Added possibilities to specify alternate URIs in connection-properties file. Updated installation scripts for the connection-properties file.

Location:

trunk

Files:

• api/core/src/org/proteios/core/Application.java (modified) (3 diffs)
• api/core/src/org/proteios/core/File.java (modified) (3 diffs)
• client/servlet/conf/connection.properties.in (modified) (1 diff)
• client/servlet/www/WEB-INF/init.sh (modified) (1 diff)
• misc/install/update_proteios-win.bat (modified) (2 diffs)

trunk/api/core/src/org/proteios/core/Application.java

@@ -167 +167 @@
    */
   private static SSLSocketFactory sSLSocketFactory;
-
+  /**
+   * Alternate URIs. Used when fetching remote files in the File class.
+   */
+  private static Map<String,String> alternateURIs;
 
   /**
@@ -876 +879 @@
   }
 
+  public static Map<String,String> getAlternateURIs()
+  {
+    return alternateURIs;
+  }
+  
 
   public static SSLSocketFactory getSSLSocketFactory()
@@ -890 +898 @@
     ConnectionPropertiesFile pf = new ConnectionPropertiesFile();
     boolean replaceEmptyStringWithNull = true;
+    int i=1;
+    alternateURIs = new HashMap<String,String>();
+    String originalURI;
+    while ((originalURI = pf.getProperty("alternate.location.source."+i)) !=null)
+    {
+      String alternateURI = pf.getProperty("alternate.location.target."+i);
+      if (!originalURI.equals("")) alternateURIs.put(originalURI, alternateURI);
+      i++;
+    }
     String keyStoreFileName = fetchProperty(pf, "javax.net.ssl.keyStore", replaceEmptyStringWithNull);
     String keyStorePassword = fetchProperty(pf, "javax.net.ssl.keyStorePassword", replaceEmptyStringWithNull);

trunk/api/core/src/org/proteios/core/File.java

@@ -272 +272 @@
   public String getUniformResourceIdentifier()
   {
-    // Temporary fix for BILS
     String uri = getData().getUniformResourceIdentifier();
-    if (uri != null && uri.startsWith("http://proteomics.bils.se"))
-    {
-      uri = uri.replace("http://proteomics.bils.se",
-        "https://srm.swegrid.se/snic/bils");
-    }
     return uri;
   }
 
-
+  /**
+   * @return the uniform resource identifier of this file if one is set, null
+   *         otherwise
+   */
+  public String getAlternativeUniformResourceIdentifier()
+  {
+    String uri = getData().getUniformResourceIdentifier();
+    for (String original : Application.getAlternateURIs().keySet())
+    {
+      if (uri.startsWith(original)) uri = uri.replace(original, Application.getAlternateURIs().get(original));
+    }
+    return uri;
+  }
+  
   /**
    * Set the URI for this <code>File</code> item. The value may be null but
@@ -1116 +1123 @@
         try
         {
-          int attempts = 3;
+          int attempts = 4;
           HttpURLConnection connection = null;
+          InputStream fis = null;
           while (connection == null && attempts > 0) {
             try {
-              connection = getConnection(getUniformResourceIdentifier());
+              if (attempts==4) connection = getConnection(getAlternativeUniformResourceIdentifier());
+              else connection = getConnection(getUniformResourceIdentifier());
+              fis = connection.getInputStream();
             } catch (Exception e) {
               log.warn(e);
               log.warn("Attempts left:"+attempts);
               --attempts;
+              connection=null;
               if (attempts==0) throw new BaseException(e);
             }
           }
           // HttpURLConnection connection = getConnection(getUniformResourceIdentifier());
-          InputStream fis = connection.getInputStream();
           if (isCompressed())
           {
@@ -1352 +1362 @@
   {
     log.debug("# Enter getConnection()\n#   URL=" + url_str);
+    String basicAuth = "";
+    if (url_str.matches(".*:\\/\\/.*:.*@.*"))
+    {
+      String userAndPw = url_str.substring(url_str.indexOf("://")+3,url_str.indexOf("@"));
+      url_str = url_str.replace("userAndPassword"+"@", "");
+      basicAuth = "Basic " + javax.xml.bind.DatatypeConverter.printBase64Binary(userAndPw.getBytes());
+    }
     URL url = new URL(url_str);
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+    if (!basicAuth.equals("")) connection.setRequestProperty ("Authorization", basicAuth);
     if (connection instanceof HttpsURLConnection)
     {

trunk/client/servlet/conf/connection.properties.in

@@ -51 +51 @@
 # If a file URL starts with a listed 'source' path, the path with the
 # source path exchanged for the corresponding target path is tried first.
+# For URLs requiring authentication it can be written into the URL:
+# https://USERNAME:PASSWORD@www.example.org/
 #
-# Default settings for BILS project:
+# Example settings for BILS project:
 #
 # alternate.location.source.1 = https://srm.swegrid.se/snic/bils/lu_proteomics/external/raw/
-# alternate.location.target.1 = http://synology.immunoprot.lth.se/external/
+# alternate.location.target.1 = http://user:pass@local.storage.lu.se/external/
 # alternate.location.source.2 = https://srm.swegrid.se/snic/bils/lu_proteomics/external/mzml/
 # alternate.location.target.2 = http://synology.immunoprot.lth.se/external/mzml/

trunk/client/servlet/www/WEB-INF/init.sh

@@ -114 +114 @@
 fi
 
+# Create proteios connection.properties file if not existing.
+if [ ! -f connection.properties ]; then
+  cp -p connection.properties.in connection.properties
+fi
+
+
 # Update proteios Proteios FTP Server start script
 java -jar ../lib/Replace.jar \

trunk/misc/install/update_proteios-win.bat

@@ -158 +158 @@
 :step_1c10
 
+set filename=connection.properties
+set rel_path="."
+set next_step=step_1c11
+goto copy_file_from_tomcat_installation
+:step_1c11
+
 rem
 rem Check if necessary configuration files exist.
@@ -244 +250 @@
 goto create_config_file_if_not_existing
 :step_3c7
+
+set filename=connection.properties
+set rel_path="."
+set file_title="Connection"
+set next_step=step_3c8
+goto create_config_file_if_not_existing
+:step_3c8
 
 rem