X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FInputType.java;h=20476328ef1bf7cbf0d43ff4d718bfd4edf31b50;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=9a4f2976cdcfa6c4ffeb51ecfe738c9e507c3e9d;hpb=f5d48464f668eb2ffd8f6cdcd0d04ff5658c54fc;p=jalview.git

diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index 9a4f297..2047632 100644
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -1,51 +1,98 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.rest;
 
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.io.StringWriter;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.Option;
+
 import java.io.UnsupportedEncodingException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
-import sun.io.CharacterEncoding;
-import sun.misc.CharacterEncoder;
-
 /***
- * InputType is the abstract model of each input parameter that a rest service might take.
- * It enables the engine to validate input by providing 
- * { formatter for type, parser for type }
- *  
+ * InputType is the abstract model of each input parameter that a rest service
+ * might take. It enables the engine to validate input by providing { formatter
+ * for type, parser for type }
+ * 
  */
-public abstract class InputType {
+public abstract class InputType
+{
   /**
    * not used yet
    */
   boolean replaceids;
-  public enum molType { NUC, PROT, MIX}
+
+  public enum molType
+  {
+    NUC, PROT, MIX;
+
+    public static Collection<String> toStringValues()
+    {
+      Collection<String> c = new ArrayList<String>();
+      for (molType type : values())
+      {
+        c.add(type.toString());
+      }
+      return c;
+    }
+  }
+
   public String token;
-  public int min=1;
-  public int max=0; // unbounded
-  protected ArrayList<Class> inputData=new ArrayList<Class>();
+
+  public int min = 1;
+
+  public int max = 0; // unbounded
+
+  protected ArrayList<Class> inputData = new ArrayList<Class>();
+
   /**
-   * initialise the InputType with a list of jalview data classes that the RestJob needs to be able to provide to it. 
+   * initialise the InputType with a list of jalview data classes that the
+   * RestJob needs to be able to provide to it.
+   * 
    * @param types
    */
   protected InputType(Class[] types)
   {
-    if(types!=null)
-      {for (Class t:types)
+    if (types != null)
     {
-      inputData.add(t);
-    }
+      for (Class t : types)
+      {
+        inputData.add(t);
       }
+    }
   }
+
   /**
-   * do basic tests to ensure the job's service takes this parameter, and the job's input data can be used to generate the input data 
+   * do basic tests to ensure the job's service takes this parameter, and the
+   * job's input data can be used to generate the input data
+   * 
    * @param restJob
    * @return
    */
@@ -53,7 +100,7 @@ public abstract class InputType {
   {
     if (!validFor(restJob.rsd))
       return false;
-    for (Class cl:inputData)
+    for (Class cl : inputData)
     {
       if (!restJob.hasDataOfType(cl))
       {
@@ -62,42 +109,221 @@ public abstract class InputType {
     }
     return true;
   }
-  
+
   public boolean validFor(RestServiceDescription restServiceDescription)
   {
     if (!restServiceDescription.inputParams.values().contains(this))
       return false;
-    
+
     return true;
   }
+
   protected ContentBody utf8StringBody(String content, String type)
   {
     Charset utf8 = Charset.forName("UTF-8");
-    try {
-    if (type==null ) {
-      return new StringBody(utf8.encode(content).asCharBuffer().toString());
-    } else {
-      return new StringBody(utf8.encode(content).asCharBuffer().toString(), type, utf8);
-    }
+    try
+    {
+      if (type == null)
+      {
+        return new StringBody(utf8.encode(content).asCharBuffer()
+                .toString());
+      }
+      else
+      {
+        return new StringBody(utf8.encode(content).asCharBuffer()
+                .toString(), type, utf8);
+      }
     } catch (Exception ex)
     {
-      System.err.println("Couldn't transform string\n"+content+"\nException was :");
+      System.err.println("Couldn't transform string\n" + content
+              + "\nException was :");
       ex.printStackTrace(System.err);
     }
     return null;
   }
+
   /**
    * 
-   * @param rj data from which input is to be extracted and formatted
+   * @param rj
+   *          data from which input is to be extracted and formatted
    * @return StringBody or FileBody ready for posting
    */
-  abstract public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException,NoValidInputDataException;
+  abstract public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException;
+
   /**
    * 
    * @return true if no input data needs to be provided for this parameter
    */
   public boolean isConstant()
   {
-    return (inputData==null || inputData.size()==0);
+    return (inputData == null || inputData.size() == 0);
+  }
+
+  /**
+   * return a url encoded version of this parameter's value, or an empty string
+   * if the parameter has no ='value' content.
+   * 
+   * @return
+   */
+  public abstract List<String> getURLEncodedParameter();
+
+  /**
+   * set the property known as tok, possibly by assigning it with a given val
+   * 
+   * @param tok
+   * @param val
+   *          (may be empty or null)
+   * @param warnings
+   *          place where parse warnings are reported
+   * @return true if property was set
+   */
+  public abstract boolean configureProperty(String tok, String val,
+          StringBuffer warnings);
+
+  /**
+   * Get unique key for this type of parameter in a URL encoding.
+   * 
+   * @return the string that prefixes an input parameter of InputType<T> type in
+   *         the string returned from getURLEncodedParameter
+   */
+  public abstract String getURLtokenPrefix();
+
+  /**
+   * parse the given token String and set InputParameter properties
+   * appropriately
+   * 
+   * @param tokenstring
+   *          - urlencoded parameter string as returned from
+   *          getURLEncodedParameter
+   * @param warnings
+   *          - place where any warning messages about bad property values are
+   *          written
+   * @return true if configuration succeeded, false otherwise.
+   */
+  public boolean configureFromURLtokenString(List<String> tokenstring,
+          StringBuffer warnings)
+  {
+    boolean valid = true;
+    for (String tok : tokenstring)
+    {
+      Matcher mtch = Pattern.compile("^([^=]+)=?'?([^']*)?'?").matcher(tok);
+      if (mtch.find())
+      {
+        try
+        {
+          if (mtch.group(1).equals("min"))
+          {
+            min = Integer.parseInt(mtch.group(2));
+            continue;
+
+          }
+          else if (mtch.group(1).equals("max"))
+          {
+            max = Integer.parseInt(mtch.group(2));
+            continue;
+          }
+        } catch (NumberFormatException x)
+        {
+          valid = false;
+          warnings.append("Invalid value for parameter "
+                  + mtch.group(1).toLowerCase() + " '" + mtch.group(2)
+                  + "' (expected an integer)\n");
+        }
+
+        if (!configureProperty(mtch.group(1), mtch.group(2), warnings))
+        {
+          if (warnings.length() == 0)
+          {
+            warnings.append("Failed to configure InputType :"
+                    + getURLtokenPrefix() + " with property string: '"
+                    + mtch.group(0) + "'\n (token is '" + mtch.group(1)
+                    + "' and value is '" + mtch.group(2) + "')\n");
+          }
+          valid = false;
+        }
+      }
+    }
+    return valid;
+  }
+
+  public void addBaseParams(ArrayList<String> prms)
+  {
+    // todo : check if replaceids should be a global for the service, rather
+    // than for a specific parameter.
+    if (min != 1)
+    {
+      prms.add("min='" + min + "'");
+    }
+    if (max != 0)
+    {
+      prms.add("max='" + max + "'");
+    }
+  }
+
+  public abstract List<OptionI> getOptions();
+
+  public List<OptionI> getBaseOptions()
+  {
+    ArrayList<OptionI> opts = new ArrayList<OptionI>();
+    opts.add(new IntegerParameter("min",
+            "Minimum number of data of this type", true, 1, min, 0, -1));
+    opts.add(new IntegerParameter("max",
+            "Maximum number of data of this type", false, 0, max, 0, -1));
+    return opts;
+  }
+
+  /**
+   * make a copy of this InputType
+   * 
+   * @return may not be needed public abstract InputType copy();
+   */
+
+  /**
+   * parse a set of configuration options
+   * 
+   * @param currentSettings
+   *          - modified settings originally from getOptions
+   * @throws InvalidArgumentException
+   *           thrown if currentSettings contains invalid options for this type.
+   */
+  public void configureFromArgumentI(List<ArgumentI> currentSettings)
+          throws InvalidArgumentException
+  {
+    ArrayList<String> urltoks = new ArrayList<String>();
+    String rg;
+    for (ArgumentI arg : currentSettings)
+    {
+      if (arg instanceof ParameterI)
+      {
+        rg = arg.getName() + "='" + arg.getValue() + "'";
+      }
+      else
+      {
+        // TODO: revise architecture - this is counter intuitive - options with
+        // different values to their names are actually parameters
+        rg = (arg.getValue().length() > 0) ? (arg.getValue().equals(
+                arg.getName()) ? arg.getName() : arg.getName() + "='"
+                + arg.getValue() + "'") : arg.getName();
+      }
+      if (rg.length() > 0)
+      {
+        urltoks.add(rg);
+      }
+    }
+    StringBuffer warnings;
+    if (!configureFromURLtokenString(urltoks, warnings = new StringBuffer()))
+    {
+      throw new InvalidArgumentException(warnings.toString());
+    }
+  }
+
+  protected OptionI createMolTypeOption(String name, String descr,
+          boolean req, molType curType, molType defType)
+  {
+    return new Option(name, descr, req, defType == null ? ""
+            : defType.toString(),
+            curType == null ? "" : curType.toString(),
+            molType.toStringValues(), null);
   }
-}
\ No newline at end of file
+}