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

[jalview.git] / src / jalview / ws / rest / params / Alignment.java

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 0027057..770b564 100644 (file)
--- 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;
   }
 }
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