From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 23 Aug 2011 12:28:20 +0000 (+0100)
Subject: JAL-715 - allow rest service attributes to be exported and imported as a | separated... 
X-Git-Tag: Release_2_7~90
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=231cba7c0cb9097957cd61ef96aab8e32e2d0337;p=jalview.git

JAL-715 - allow rest service attributes to be exported and imported as a | separated string
---

diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index 9a4f297..28bfda0 100644
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -8,6 +8,9 @@ import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
+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;
@@ -100,4 +103,70 @@ public abstract class InputType {
   {
     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");
+            }
+          
+          valid = valid && configureProperty(mtch.group(1), mtch.group(2), warnings);
+        }
+        }
+      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("min='"+max+"'");
+    }
+  }
 }
\ No newline at end of file
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 0027057..770b564 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -5,6 +5,7 @@ import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
 import jalview.ws.rest.InputType.molType;
+import jalview.ws.rest.RestServiceDescription;
 
 import java.io.BufferedOutputStream;
 import java.io.ByteArrayOutputStream;
@@ -16,6 +17,8 @@ import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.FileBody;
@@ -23,46 +26,143 @@ import org.apache.http.entity.mime.content.StringBody;
 
 /**
  * format an alignment for input to rest service.
+ * 
  * @author JimP
- *
+ * 
  */
-public class Alignment extends InputType {
+public class Alignment extends InputType
+{
   public Alignment()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[]
+    { AlignmentI.class });
   }
 
-  String format="FASTA";
+  String format = "FASTA";
+
   molType type;
-  boolean jvsuffix=false;
+
+  boolean jvsuffix = false;
+
   /**
    * input data as a file upload rather than inline content
    */
   public boolean writeAsFile;
+
   @Override
-  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException
   {
-    AlignmentI alignment = rj.getAlignmentForInput(token,type);
+    AlignmentI alignment = rj.getAlignmentForInput(token, type);
     if (writeAsFile)
     {
-    try {
-      File fa = File.createTempFile("jvmime", ".fa");
-      PrintWriter pw = new PrintWriter(new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(fa)), "UTF-8"));
-      pw.append(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix));
-      pw.close();
-      return new FileBody(fa, "text/plain");
-    } catch (Exception ex)
-    {
-      throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
+      try
+      {
+        File fa = File.createTempFile("jvmime", ".fa");
+        PrintWriter pw = new PrintWriter(
+                new OutputStreamWriter(new BufferedOutputStream(
+                        new FileOutputStream(fa)), "UTF-8"));
+        pw.append(new jalview.io.FormatAdapter().formatSequences(format,
+                alignment, jvsuffix));
+        pw.close();
+        return new FileBody(fa, "text/plain");
+      } catch (Exception ex)
+      {
+        throw new NoValidInputDataException(
+                "Couldn't write out alignment to file.", ex);
+      }
     }
-    } else {
+    else
+    {
       jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
       fa.setNewlineString("\r\n");
-      return new StringBody((fa.formatSequences(format, alignment, jvsuffix)));
-      //,
-      //"text/plain",Charset.forName("UTF-8"));
+      return new StringBody(
+              (fa.formatSequences(format, alignment, jvsuffix)));
+      // ,
+      // "text/plain",Charset.forName("UTF-8"));
       // , "text/plain", Charset.forName("UTF-8"));
-    // sb.getContentTypeParameters().put("filename", "alignment.fa");
+      // sb.getContentTypeParameters().put("filename", "alignment.fa");
+    }
+  }
+
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    prms.add("format='" + format + "'");
+    if (type != null)
+    {
+      prms.add("type='" + type.toString() + "'");
+    }
+    if (jvsuffix)
+    {
+      prms.add("jvsuffix");
+    }
+    ;
+    if (writeAsFile)
+    {
+      prms.add("writeasfile");
+    }
+    ;
+    return prms;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "ALIGNMENT";
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+    if (tok.startsWith("jvsuffix"))
+    {
+      jvsuffix = true;
+      return true;
+    }
+    if (tok.startsWith("writeasfile"))
+    {
+      writeAsFile = true;
+      return true;
+    }
+
+    if (tok.startsWith("format"))
+    {
+      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      {
+        if (val.equalsIgnoreCase(fmt))
+        {
+          format = fmt;
+          return true;
+        }
+      }
+      warnings.append("Invalid alignment format '" + val
+              + "'. Must be one of (");
+      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      {
+        warnings.append(" " + fmt);
+      }
+      warnings.append(")\n");
+    }
+    if (tok.startsWith("type"))
+    {
+      try
+      {
+        type = molType.valueOf(val);
+        return true;
+      } catch (Exception x)
+      {
+        warnings.append("Invalid molecule type '" + val
+                + "'. Must be one of (");
+        for (molType v : molType.values())
+        {
+          warnings.append(" " + v);
+        }
+        warnings.append(")\n");
+      }
     }
+    return false;
   }
 }
\ No newline at end of file
diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index 84dcfb9..5abf0fc 100644
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -4,9 +4,12 @@ import jalview.datamodel.AlignmentI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
 import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
@@ -49,4 +52,42 @@ public class AnnotationFile extends InputType {
         return new StringBody(new jalview.io.AnnotationFile().printCSVAnnotations(al.getAlignmentAnnotation()));
       }
   }
-}
\ No newline at end of file
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    prms.add("format='"+format+"'");
+    return prms;     
+  }
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "ALANNOTATION";
+  }
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+
+    if (tok.startsWith("format"))
+    {
+      for (String fmt : new String[] { CSVANNOT, JVANNOT})
+      {
+        if (val.equalsIgnoreCase(fmt))
+        {
+          format = fmt;
+          return true;
+        }
+      }
+      warnings.append("Invalid annotation file format '" + val
+              + "'. Must be one of (");
+      for (String fmt : new String[] { CSVANNOT, JVANNOT})
+      {
+        warnings.append(" " + fmt);
+      }
+      warnings.append(")\n");
+    }
+    return false;
+  }
+}
diff --git a/src/jalview/ws/rest/params/JobConstant.java b/src/jalview/ws/rest/params/JobConstant.java
index 1ff6964..01b54cb 100644
--- a/src/jalview/ws/rest/params/JobConstant.java
+++ b/src/jalview/ws/rest/params/JobConstant.java
@@ -5,6 +5,8 @@ import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
 
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
@@ -39,4 +41,43 @@ public class JobConstant extends InputType
     return new StringBody(value);
   }
 
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prm = new ArrayList<String>();
+    
+    if (value!=null && value.length()>0)
+    {
+      prm.add(value);
+    }
+    return prm;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "";
+  }
+
+  @Override
+  public boolean configureFromURLtokenString(List<String> tokenstring,
+          StringBuffer warnings)
+  {
+    if (tokenstring.size()>1) {
+      warnings.append("IMPLEMENTATION ERROR: Constant POST parameters cannot have more than one value.");
+      return false;
+    }
+    if (tokenstring.size()==1) {
+      value = tokenstring.get(0);
+    }
+    return true;
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+    warnings.append("IMPLEMENTATION ERROR: No Properties to configure for a Constant parameter.");
+    return false;
+  }
 }
diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 91b1fff..7df7d1c 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -7,10 +7,12 @@ import jalview.ws.rest.AlignmentProcessor;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
 import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -170,4 +172,64 @@ public class SeqGroupIndexVector extends InputType implements
         minsize=1;
       }
   }
-}
\ No newline at end of file
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    prms.add("minsize='"+ minsize+"'");
+    prms.add("sep='"+ sep+"'");
+    if (type!=null)
+    {
+      prms.add("type='"+type+"'");
+    }
+    return prms;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "PARTITION";
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+
+    if (tok.startsWith("sep"))
+    {
+      sep=val;
+      return true;
+    }
+    if (tok.startsWith("minsize"))
+    {
+      try {
+        minsize=Integer.valueOf(val);
+        if (minsize>=0)
+        return true;
+      } catch (Exception x)
+      {
+        
+      }
+      warnings.append("Invalid minsize value '"+val+"'. Must be a positive integer.\n");
+    }
+    if (tok.startsWith("type"))
+    {
+      try {
+        type=molType.valueOf(val);
+        return true;
+      } catch (Exception x)
+      {
+        warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
+        for (molType v:molType.values())
+        {
+          warnings.append(" "+v);
+        }
+        warnings.append(")\n");
+      }
+    }
+    return false;
+  }
+
+}
diff --git a/src/jalview/ws/rest/params/SeqIdVector.java b/src/jalview/ws/rest/params/SeqIdVector.java
index 9bdaed1..5f7c551 100644
--- a/src/jalview/ws/rest/params/SeqIdVector.java
+++ b/src/jalview/ws/rest/params/SeqIdVector.java
@@ -5,9 +5,14 @@ import jalview.datamodel.SequenceI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
 import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+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;
@@ -17,7 +22,7 @@ import org.apache.http.entity.mime.content.StringBody;
  * @author JimP
  *
  */
-class SeqIdVector extends InputType {
+public class SeqIdVector extends InputType {
   public SeqIdVector()
   {
     super(new Class[] { AlignmentI.class} );
@@ -42,5 +47,44 @@ class SeqIdVector extends InputType {
       idvector.append(seq.getName());
     }
     return new StringBody(idvector.toString());
+  }  
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    prms.add("sep='"+ sep+"'");
+    prms.add("type='"+type+"'");
+    return prms;
+  }
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "SEQIDS";
+  }
+  @Override
+  public boolean configureProperty(String tok, String val, StringBuffer warnings)
+  {
+    if (tok.startsWith("sep"))
+    {
+      sep=val;
+      return true;
+    }
+    if (tok.startsWith("type"))
+    {
+      try {
+        type=molType.valueOf(val);
+        return true;
+      } catch (Exception x)
+      {
+        warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
+        for (molType v:molType.values())
+        {
+          warnings.append(" "+v);
+        }
+        warnings.append(")\n");
+      }
+    }
+    return false;
   }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index 9a98f3e..3a5b414 100644
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -5,9 +5,12 @@ import jalview.datamodel.SequenceI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
 import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
@@ -17,7 +20,7 @@ import org.apache.http.entity.mime.content.StringBody;
  * @author JimP
  *
  */
-class SeqVector extends InputType {
+public class SeqVector extends InputType {
   String sep;
   molType type;
   public SeqVector()
@@ -40,4 +43,48 @@ class SeqVector extends InputType {
     }
     return new StringBody(idvector.toString());
   }
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    prms.add("sep='"+ sep+"'");
+    prms.add("type='"+type+"'");
+    return prms;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "SEQS";
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+
+    if (tok.startsWith("sep"))
+    {
+      sep=val;
+      return true;
+    }
+    if (tok.startsWith("type"))
+    {
+      try {
+        type=molType.valueOf(val);
+        return true;
+      } catch (Exception x)
+      {
+        warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
+        for (molType v:molType.values())
+        {
+          warnings.append(" "+v);
+        }
+        warnings.append(")\n");
+      }
+    }
+    return false;
+  }
+
 }
\ No newline at end of file
diff --git a/src/jalview/ws/rest/params/Tree.java b/src/jalview/ws/rest/params/Tree.java
index 91fab40..69d2f58 100644
--- a/src/jalview/ws/rest/params/Tree.java
+++ b/src/jalview/ws/rest/params/Tree.java
@@ -3,8 +3,12 @@ package jalview.ws.rest.params;
 import jalview.datamodel.AlignmentI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.RestJob;
+import jalview.ws.rest.RestServiceDescription;
+import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 
@@ -13,7 +17,7 @@ import org.apache.http.entity.mime.content.ContentBody;
  * @author JimP
  *
  */
-class Tree extends InputType {
+public class Tree extends InputType {
   public Tree()
   {
     super(new Class[] { jalview.analysis.NJTree.class} );
@@ -29,5 +33,24 @@ class Tree extends InputType {
     throw new Error("Tree InputType not yet implemented");
     //return null;
   }
+  public String getURLtokenPrefix()
+  {
+    return "NEWICK"; 
+  }
   
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    return prms;
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+    return true;
+  }
+
 }
\ No newline at end of file