X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestServiceDescription.java;h=9c39b37483055404c2e664def13cfe7d211d4eb7;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=fe1434c99b582a48f56638b21eaecf0b940ad7d9;hpb=603ec5f3d10d05a8668477ad627ac3010473b579;p=jalview.git

diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index fe1434c..9c39b37 100644
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -1,31 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.rest;
 
 import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider;
-import jalview.io.packed.SimpleDataProvider;
 import jalview.io.packed.DataProvider.JvDataType;
-import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.Platform;
 import jalview.ws.rest.params.Alignment;
 import jalview.ws.rest.params.AnnotationFile;
-import jalview.ws.rest.params.JobConstant;
 import jalview.ws.rest.params.SeqGroupIndexVector;
 
 import java.net.URL;
@@ -36,19 +34,20 @@ import java.util.List;
 import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.StringTokenizer;
-import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.swing.JViewport;
-
-import com.stevesoft.pat.Regex;
-import com.sun.org.apache.xml.internal.serialize.OutputFormat.DTD;
-import com.sun.tools.doclets.internal.toolkit.util.DocFinder.Output;
-
 public class RestServiceDescription
 {
   /**
+   * create a new rest service description ready to be configured
+   */
+  public RestServiceDescription()
+  {
+
+  }
+
+  /**
    * @param details
    * @param postUrl
    * @param urlSuffix
@@ -64,12 +63,15 @@ public class RestServiceDescription
   {
     super();
     this.details = new UIinfo();
-    details.Action = action;
-    details.description = description;
-    details.Name = name;
-    this.postUrl = postUrl;
-    this.urlSuffix = urlSuffix;
-    this.inputParams = inputParams;
+    details.Action = action == null ? "" : action;
+    details.description = description == null ? "" : description;
+    details.Name = name == null ? "" : name;
+    this.postUrl = postUrl == null ? "" : postUrl;
+    this.urlSuffix = urlSuffix == null ? "" : urlSuffix;
+    if (inputParams != null)
+    {
+      this.inputParams = inputParams;
+    }
     this.hseparable = hseparable;
     this.vseparable = vseparable;
     this.gapCharacter = gapCharacter;
@@ -229,7 +231,7 @@ public class RestServiceDescription
   /**
    * input info given as key/value pairs - mapped to post arguments
    */
-  Map<String, InputType> inputParams = new HashMap<String,InputType>();
+  Map<String, InputType> inputParams = new HashMap<String, InputType>();
 
   /**
    * assigns the given inputType it to its corresponding input parameter token
@@ -318,30 +320,20 @@ public class RestServiceDescription
 
   public RestServiceDescription(RestServiceDescription toedit)
   {
-    // Rather then do the above, we cheat and use our human readable serialization code to clone everything
+    // Rather then do the above, we cheat and use our human readable
+    // serialization code to clone everything
     this(toedit.toString());
     /**
-    if (toedit == null)
-    {
-      return;
-    }
-    /**
-    urlSuffix = toedit.urlSuffix;
-    postUrl = toedit.postUrl;
-    hseparable = toedit.hseparable;
-    vseparable = toedit.vseparable;
-    gapCharacter = toedit.gapCharacter;
-    details = new RestServiceDescription.UIinfo();
-    details.Action = toedit.details.Action;
-    details.description = toedit.details.description;
-    details.Name = toedit.details.Name;
-    for (InputType itype: toedit.inputParams.values())
-    {
-      inputParams.put(itype.token, itype.clone());
-      
-    }
-            
-       */
+     * if (toedit == null) { return; } /** urlSuffix = toedit.urlSuffix; postUrl
+     * = toedit.postUrl; hseparable = toedit.hseparable; vseparable =
+     * toedit.vseparable; gapCharacter = toedit.gapCharacter; details = new
+     * RestServiceDescription.UIinfo(); details.Action = toedit.details.Action;
+     * details.description = toedit.details.description; details.Name =
+     * toedit.details.Name; for (InputType itype: toedit.inputParams.values()) {
+     * inputParams.put(itype.token, itype.clone());
+     * 
+     * }
+     */
     // TODO Implement copy constructor NOW*/
   }
 
@@ -380,12 +372,13 @@ public class RestServiceDescription
       return null;
     java.util.ArrayList<String> jv = new ArrayList<String>();
     int cp = 0, pos, escape;
-    boolean wasescaped = false;
+    boolean wasescaped = false, wasquoted = false;
     String lstitem = null;
     while ((pos = list.indexOf(separator, cp)) >= cp)
     {
-      escape = (list.charAt(pos - 1) == '\\') ? -1 : 0;
-      if (wasescaped)
+
+      escape = (pos > 0 && list.charAt(pos - 1) == '\\') ? -1 : 0;
+      if (wasescaped || wasquoted)
       {
         // append to previous pos
         jv.set(jv.size() - 1,
@@ -399,11 +392,20 @@ public class RestServiceDescription
       }
       cp = pos + seplen;
       wasescaped = escape == -1;
+      if (!wasescaped)
+      {
+        // last separator may be in an unmatched quote
+        if (java.util.regex.Pattern.matches("('[^']*')*[^']*'", lstitem))
+        {
+          wasquoted = true;
+        }
+      }
+
     }
     if (cp < list.length())
     {
       String c = list.substring(cp);
-      if (wasescaped)
+      if (wasescaped || wasquoted)
       {
         // append final separator
         jv.set(jv.size() - 1, lstitem + separator + c);
@@ -455,7 +457,7 @@ public class RestServiceDescription
       {
         if (list[i] != null)
         {
-          if (i > 0)
+          if (v.length() > 0)
           {
             v.append(separator);
           }
@@ -487,16 +489,18 @@ public class RestServiceDescription
    *          param warnings a StringBuffer that any warnings about invalid
    *          content will be appended to.
    */
-  private void configureFromServiceInputProperties(String propList,
+  private boolean configureFromServiceInputProperties(String propList,
           StringBuffer warnings)
   {
     String[] props = separatorListToArray(propList, ",");
     if (props == null)
     {
-      return;
+      return true;
     }
     ;
+    boolean valid = true;
     String val = null;
+    int l = warnings.length();
     int i;
     for (String prop : props)
     {
@@ -520,8 +524,9 @@ public class RestServiceDescription
       }
       if (prop.equals("gapCharacter"))
       {
-        if (val == null || val.length() > 1)
+        if (val == null || val.length() == 0 || val.length() > 1)
         {
+          valid = false;
           warnings.append((warnings.length() > 0 ? "\n" : "")
                   + ("Invalid service property: gapCharacter=' ' (single character) - was given '"
                           + val + "'"));
@@ -536,12 +541,14 @@ public class RestServiceDescription
         _configureOutputFormatFrom(val, warnings);
       }
     }
+    // return true if valid is true and warning buffer was not appended to.
+    return valid && (l == warnings.length());
   }
 
   private String _genOutputFormatString()
   {
     String buff = "";
-    if (resultData==null)
+    if (resultData == null)
     {
       return "";
     }
@@ -559,9 +566,10 @@ public class RestServiceDescription
   private void _configureOutputFormatFrom(String outstring,
           StringBuffer warnings)
   {
-    if (outstring.indexOf(";")==-1) {
+    if (outstring.indexOf(";") == -1)
+    {
       // we add a token, for simplicity
-      outstring = outstring+";";
+      outstring = outstring + ";";
     }
     StringTokenizer st = new StringTokenizer(outstring, ";");
     String tok = "";
@@ -589,18 +597,26 @@ public class RestServiceDescription
 
   private String getServiceIOProperties()
   {
-    String[] vls = new String[]
-    { isHseparable() ? "hseparable" : "",
-        isVseparable() ? "vseparable" : "",
-        (new String("gapCharacter='" + gapCharacter + "'")),
-        (new String("returns='" + _genOutputFormatString() + "'")) };
-
-    return arrayToSeparatorList(vls, ",");
+    ArrayList<String> vls = new ArrayList<String>();
+    if (isHseparable())
+    {
+      vls.add("hseparable");
+    }
+    ;
+    if (isVseparable())
+    {
+      vls.add("vseparable");
+    }
+    ;
+    vls.add(new String("gapCharacter='" + gapCharacter + "'"));
+    vls.add(new String("returns='" + _genOutputFormatString() + "'"));
+    return arrayToSeparatorList(vls.toArray(new String[0]), ",");
   }
 
   public String toString()
   {
     StringBuffer result = new StringBuffer();
+    result.append("|");
     result.append(details.Name);
     result.append('|');
     result.append(details.Action);
@@ -624,26 +640,71 @@ public class RestServiceDescription
     return result.toString();
   }
 
+  /**
+   * processes a service encoded as a string (as generated by
+   * RestServiceDescription.toString()) Note - this will only use the first
+   * service definition encountered in the string to configure the service.
+   * 
+   * @param encoding
+   * @param warnings
+   *          - where warning messages are reported.
+   * @return true if configuration was parsed successfully.
+   */
   public boolean configureFromEncodedString(String encoding,
           StringBuffer warnings)
   {
-    boolean valid = false;
     String[] list = separatorListToArray(encoding, "|");
-    details.Name = list[0];
-    details.Action = list[1];
-    details.description = list[2];
-    configureFromServiceInputProperties(list[3], warnings);
-    if (list.length > 5)
+
+    int nextpos = parseServiceList(list, warnings, 0);
+    if (nextpos > 0)
     {
-      urlSuffix = list[4];
-      valid |= configureFromInputParamEncodedUrl(list[5], warnings);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * processes the given list from position p, attempting to configure the
+   * service from it. Service lists are formed by concatenating individual
+   * stringified services. The first character of a stringified service is '|',
+   * enabling this, and the parser will ignore empty fields in a '|' separated
+   * list when they fall outside a service definition.
+   * 
+   * @param list
+   * @param warnings
+   * @param p
+   * @return
+   */
+  protected int parseServiceList(String[] list, StringBuffer warnings, int p)
+  {
+    boolean invalid = false;
+    // look for the first non-empty position - expect it to be service name
+    while (list[p] != null && list[p].trim().length() == 0)
+    {
+      p++;
+    }
+    details.Name = list[p];
+    details.Action = list[p + 1];
+    details.description = list[p + 2];
+    invalid |= !configureFromServiceInputProperties(list[p + 3], warnings);
+    if (list.length - p > 5 && list[p + 5] != null
+            && list[p + 5].trim().length() > 5)
+    {
+      urlSuffix = list[p + 4];
+      invalid |= !configureFromInputParamEncodedUrl(list[p + 5], warnings);
+      p += 6;
     }
     else
     {
-      urlSuffix = null;
-      valid |= configureFromInputParamEncodedUrl(list[4], warnings);
+      if (list.length - p > 4 && list[p + 4] != null
+              && list[p + 4].trim().length() > 5)
+      {
+        urlSuffix = null;
+        invalid |= !configureFromInputParamEncodedUrl(list[p + 4], warnings);
+        p += 5;
+      }
     }
-    return valid;
+    return invalid ? -1 : p;
   }
 
   /**
@@ -741,7 +802,8 @@ public class RestServiceDescription
         iprmparams = iprm.substring(colon + 1);
         iprm = iprm.substring(0, colon);
       }
-      valid = parseTypeString(prms.group(0), tok,  iprm, iprmparams, iparams, warnings);
+      valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
+              iparams, warnings);
     }
     if (valid)
     {
@@ -759,19 +821,25 @@ public class RestServiceDescription
     return valid;
   }
 
-  public static boolean parseTypeString(String fullstring, String tok, String iprm, String iprmparams,
-           Map<String, InputType> iparams, StringBuffer warnings)
+  public static Class[] getInputTypes()
   {
-    boolean valid=true;
-    InputType jinput;
     // TODO - find a better way of maintaining this classlist
-    for (Class type : new Class[]
+    return new Class[]
     { jalview.ws.rest.params.Alignment.class,
         jalview.ws.rest.params.AnnotationFile.class,
         SeqGroupIndexVector.class,
         jalview.ws.rest.params.SeqIdVector.class,
         jalview.ws.rest.params.SeqVector.class,
-        jalview.ws.rest.params.Tree.class })
+        jalview.ws.rest.params.Tree.class };
+  }
+
+  public static boolean parseTypeString(String fullstring, String tok,
+          String iprm, String iprmparams, Map<String, InputType> iparams,
+          StringBuffer warnings)
+  {
+    boolean valid = true;
+    InputType jinput;
+    for (Class type : getInputTypes())
     {
       try
       {
@@ -781,20 +849,21 @@ public class RestServiceDescription
           ArrayList<String> al = new ArrayList<String>();
           for (String prprm : separatorListToArray(iprmparams, ","))
           {
+            // hack to ensure that strings like "sep=','" containing unescaped
+            // commas as values are concatenated
             al.add(prprm.trim());
           }
           if (!jinput.configureFromURLtokenString(al, warnings))
           {
             valid = false;
-            warnings.append("Failed to parse '" + fullstring
-                    + "' as a " + jinput.getURLtokenPrefix()
-                    + " input tag.\n");
+            warnings.append("Failed to parse '" + fullstring + "' as a "
+                    + jinput.getURLtokenPrefix() + " input tag.\n");
           }
           else
           {
             jinput.token = tok;
             iparams.put(tok, jinput);
-            valid=true;
+            valid = true;
           }
           break;
         }
@@ -807,87 +876,6 @@ public class RestServiceDescription
     return valid;
   }
 
-
-  public static void main(String argv[])
-  {
-    if (argv.length == 0)
-    {
-      if (!testRsdExchange("Test using default Shmmr service",
-              RestClient.makeShmmrRestClient().service))
-      {
-        System.err.println("default test failed.");
-      }
-      else
-      {
-        System.err.println("default test passed.");
-      }
-    }
-    else
-    {
-      int i = 0, p = 0;
-      for (String svc : argv)
-      {
-        p += testRsdExchange("Test " + (++i), svc) ? 1 : 0;
-      }
-      System.err.println("" + p + " out of " + i + " tests passed.");
-
-    }
-  }
-
-  private static boolean testRsdExchange(String desc, String servicestring)
-  {
-    try
-    {
-      RestServiceDescription newService = new RestServiceDescription(
-              servicestring);
-      if (!newService.isValid())
-      {
-        throw new Error("Failed to create service from '" + servicestring
-                + "'.\n" + newService.getInvalidMessage());
-      }
-      return testRsdExchange(desc, newService);
-    } catch (Throwable x)
-    {
-      System.err.println("Failed for service (" + desc + "): "
-              + servicestring);
-      x.printStackTrace();
-      return false;
-    }
-  }
-
-  private static boolean testRsdExchange(String desc,
-          RestServiceDescription service)
-  {
-    try
-    {
-      String fromservicetostring = service.toString();
-      RestServiceDescription newService = new RestServiceDescription(
-              fromservicetostring);
-      if (!newService.isValid())
-      {
-        throw new Error("Failed to create service from '"
-                + fromservicetostring + "'.\n"
-                + newService.getInvalidMessage());
-      }
-
-      if (!service.equals(newService))
-      {
-        System.err.println("Failed for service (" + desc + ").");
-        System.err.println("Original service and parsed service differ.");
-        System.err.println("Original: " + fromservicetostring);
-        System.err.println("Parsed  : " + newService.toString());
-        return false;
-      }
-    } catch (Throwable x)
-    {
-      System.err.println("Failed for service (" + desc + "): "
-              + service.toString());
-      x.printStackTrace();
-      return false;
-    }
-    return true;
-  }
-
   /**
    * covenience method to generate the id and sequence string vector from a set
    * of seuqences using each sequence's getName() and getSequenceAsString()
@@ -966,7 +954,7 @@ public class RestServiceDescription
     return jobId + urlSuffix;
   }
 
-  private List<JvDataType> resultData;
+  private List<JvDataType> resultData = new ArrayList<JvDataType>();
 
   /**
    * 
@@ -998,5 +986,41 @@ public class RestServiceDescription
   {
     return resultData;
   }
-  
+
+  /**
+   * parse a concatenated list of rest service descriptions into an array
+   * 
+   * @param services
+   * @return zero or more services.
+   * @throws exceptions
+   *           if the services are improperly encoded.
+   */
+  public static List<RestServiceDescription> parseDescriptions(
+          String services) throws Exception
+  {
+    String[] list = separatorListToArray(services, "|");
+    List<RestServiceDescription> svcparsed = new ArrayList<RestServiceDescription>();
+    int p = 0, lastp = 0;
+    StringBuffer warnings = new StringBuffer();
+    do
+    {
+      RestServiceDescription rsd = new RestServiceDescription();
+      p = rsd.parseServiceList(list, warnings, lastp = p);
+      if (p > lastp && rsd.isValid())
+      {
+        svcparsed.add(rsd);
+      }
+      else
+      {
+        throw new Exception(
+                "Failed to parse user defined RSBS services from :"
+                        + services
+                        + "\nFirst error was encountered at token " + lastp
+                        + " starting " + list[lastp] + ":\n"
+                        + rsd.getInvalidMessage());
+      }
+    } while (p < lastp && p < list.length - 1);
+    return svcparsed;
+  }
+
 }