X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestServiceDescription.java;h=7ae922c18c4d43914ae81352419c663a893a0260;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=dea7fc9347c2d83f8d56f28da0486d26950d3e94;hpb=9c80addd4e2e5e137e171744be2be1add9f9b483;p=jalview.git

diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index dea7fc9..7ae922c 100644
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -49,6 +49,13 @@ 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 +71,15 @@ 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;
@@ -101,6 +111,36 @@ public class RestServiceDescription
 
   public class UIinfo
   {
+    public String getAction()
+    {
+      return Action;
+    }
+
+    public void setAction(String action)
+    {
+      Action = action;
+    }
+
+    public String getName()
+    {
+      return Name;
+    }
+
+    public void setName(String name)
+    {
+      Name = name;
+    }
+
+    public String getDescription()
+    {
+      return description;
+    }
+
+    public void setDescription(String description)
+    {
+      this.description = description;
+    }
+
     String Action;
 
     String Name;
@@ -110,11 +150,86 @@ public class RestServiceDescription
 
   public UIinfo details = new UIinfo();
 
+  public String getAction()
+  {
+    return details.getAction();
+  }
+
+  public void setAction(String action)
+  {
+    details.setAction(action);
+  }
+
+  public String getName()
+  {
+    return details.getName();
+  }
+
+  public void setName(String name)
+  {
+    details.setName(name);
+  }
+
+  public String getDescription()
+  {
+    return details.getDescription();
+  }
+
+  public void setDescription(String description)
+  {
+    details.setDescription(description);
+  }
+
   /**
    * Service base URL
    */
   String postUrl;
 
+  public String getPostUrl()
+  {
+    return postUrl;
+  }
+
+  public void setPostUrl(String postUrl)
+  {
+    this.postUrl = postUrl;
+  }
+
+  public String getUrlSuffix()
+  {
+    return urlSuffix;
+  }
+
+  public void setUrlSuffix(String urlSuffix)
+  {
+    this.urlSuffix = urlSuffix;
+  }
+
+  public Map<String, InputType> getInputParams()
+  {
+    return inputParams;
+  }
+
+  public void setInputParams(Map<String, InputType> inputParams)
+  {
+    this.inputParams = inputParams;
+  }
+
+  public void setHseparable(boolean hseparable)
+  {
+    this.hseparable = hseparable;
+  }
+
+  public void setVseparable(boolean vseparable)
+  {
+    this.vseparable = vseparable;
+  }
+
+  public void setGapCharacter(char gapCharacter)
+  {
+    this.gapCharacter = gapCharacter;
+  }
+
   /**
    * suffix that should be added to any url used if it does not already end in
    * the suffix.
@@ -124,7 +239,7 @@ public class RestServiceDescription
   /**
    * input info given as key/value pairs - mapped to post arguments
    */
-  Map<String, InputType> inputParams = new HashMap();
+  Map<String, InputType> inputParams = new HashMap<String, InputType>();
 
   /**
    * assigns the given inputType it to its corresponding input parameter token
@@ -213,11 +328,21 @@ public class RestServiceDescription
 
   public RestServiceDescription(RestServiceDescription toedit)
   {
-    if (toedit == null)
-    {
-      return;
-    }
-    // TODO Implement copy constructor NOW
+    // 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());
+     * 
+     * }
+     */
+    // TODO Implement copy constructor NOW*/
   }
 
   /**
@@ -255,12 +380,13 @@ 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)
+    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,
@@ -274,11 +400,20 @@ 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);
@@ -330,7 +465,7 @@ public class RestServiceDescription
       {
         if (list[i] != null)
         {
-          if (i > 0)
+          if (v.length() > 0)
           {
             v.append(separator);
           }
@@ -362,16 +497,18 @@ 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)
     {
@@ -395,8 +532,9 @@ 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 + "'"));
@@ -408,15 +546,17 @@ public class RestServiceDescription
       }
       if (prop.equals("returns"))
       {
-        _configureOurputFormatFrom(val, warnings);
+        _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 "";
     }
@@ -431,9 +571,14 @@ public class RestServiceDescription
     return buff;
   }
 
-  private void _configureOurputFormatFrom(String outstring,
+  private void _configureOutputFormatFrom(String outstring,
           StringBuffer warnings)
   {
+    if (outstring.indexOf(";") == -1)
+    {
+      // we add a token, for simplicity
+      outstring = outstring + ";";
+    }
     StringTokenizer st = new StringTokenizer(outstring, ";");
     String tok = "";
     resultData = new ArrayList<JvDataType>();
@@ -460,18 +605,18 @@ 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);
@@ -495,28 +640,63 @@ 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;
   }
-
+  
   /**
    * @return string representation of the input parameters, their type and
    *         constraints, appended to the service's base submission URL
@@ -612,45 +792,8 @@ public class RestServiceDescription
         iprmparams = iprm.substring(colon + 1);
         iprm = iprm.substring(0, colon);
       }
-      // TODO - find a better way of maintaining this classlist
-      for (Class type : 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 })
-      {
-        try
-        {
-          jinput = (InputType) (type.getConstructor().newInstance(null));
-          if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
-          {
-            ArrayList<String> al = new ArrayList<String>();
-            for (String prprm : separatorListToArray(iprmparams, ","))
-            {
-              al.add(prprm);
-            }
-            if (!jinput.configureFromURLtokenString(al, warnings))
-            {
-              valid = false;
-              warnings.append("Failed to parse '" + prms.group(0)
-                      + "' as a " + jinput.getURLtokenPrefix()
-                      + " input tag.\n");
-            }
-            else
-            {
-              jinput.token = tok;
-              iparams.put(tok, jinput);
-            }
-            break;
-          }
-
-        } catch (Throwable thr)
-        {
-        }
-        ;
-      }
+      valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
+              iparams, warnings);
     }
     if (valid)
     {
@@ -668,8 +811,74 @@ public class RestServiceDescription
     return valid;
   }
 
+  public static Class[] getInputTypes()
+  {
+    // TODO - find a better way of maintaining this classlist
+    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 };
+  }
+
+  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
+      {
+        jinput = (InputType) (type.getConstructor().newInstance(null));
+        if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
+        {
+          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");
+          }
+          else
+          {
+            jinput.token = tok;
+            iparams.put(tok, jinput);
+            valid = true;
+          }
+          break;
+        }
+
+      } catch (Throwable thr)
+      {
+      }
+      ;
+    }
+    return valid;
+  }
+
   public static void main(String argv[])
   {
+    // test separator list
+    try {
+      assert(separatorListToArray("foo=',',min='foo',max='1,2,3',fa=','", ",").length==4);
+      if (separatorListToArray("minsize='2', sep=','", ",").length==2)
+      {
+        assert(false);
+      }
+      
+    } catch (AssertionError x)
+    {
+      System.err.println("separatorListToArray is faulty.");
+    }
     if (argv.length == 0)
     {
       if (!testRsdExchange("Test using default Shmmr service",
@@ -826,7 +1035,7 @@ public class RestServiceDescription
     return jobId + urlSuffix;
   }
 
-  private List<JvDataType> resultData;
+  private List<JvDataType> resultData = new ArrayList<JvDataType>();
 
   /**
    * 
@@ -858,4 +1067,30 @@ 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;
+  }
+
 }