X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FInputType.java;h=8741ddc630a714b27947e29cc707adc42a65e5af;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=bc558936a8d2edafacd429a684d68ab2e5f6d49b;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git
diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index bc55893..8741ddc 100644
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.rest;
import jalview.ws.params.ArgumentI;
@@ -6,69 +26,77 @@ import jalview.ws.params.OptionI;
import jalview.ws.params.ParameterI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
-import jalview.ws.rest.params.SeqGroupIndexVector;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
-import java.util.Map;
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
+{
+ private static final Pattern URL_PATTERN = Pattern.compile("^([^=]+)=?'?([^']*)?'?");
+
/**
* not used yet
*/
boolean replaceids;
- public enum molType { NUC, PROT, MIX;
- public static Collection toStringValues()
+ public enum molType
{
- Collection c = new ArrayList();
- for (molType type:values())
+ NUC, PROT, MIX;
+
+ public static Collection toStringValues()
{
- c.add(type.toString());
+ Collection c = new ArrayList();
+ for (molType type : values())
+ {
+ c.add(type.toString());
+ }
+ return c;
}
- return c;
- }}
+ }
+
public String token;
- public int min=1;
- public int max=0; // unbounded
- protected ArrayList inputData=new ArrayList();
+
+ public int min = 1;
+
+ public int max = 0; // unbounded
+
+ protected ArrayList inputData = new ArrayList();
+
/**
- * 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
*/
@@ -76,7 +104,7 @@ public abstract class InputType {
{
if (!validFor(restJob.rsd))
return false;
- for (Class cl:inputData)
+ for (Class cl : inputData)
{
if (!restJob.hasDataOfType(cl))
{
@@ -85,165 +113,221 @@ 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 a url encoded version of this parameter's value, or an empty string
+ * if the parameter has no ='value' content.
+ *
* @return
*/
public abstract List 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
+ * @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);
-
+ 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 type in the string returned from getURLEncodedParameter
+ *
+ * @return the string that prefixes an input parameter of InputType 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
+ * 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 tokenstring, StringBuffer warnings) {
- boolean valid=true;
- for (String tok:tokenstring)
+ public boolean configureFromURLtokenString(List tokenstring,
+ StringBuffer warnings)
+ {
+ boolean valid = true;
+ for (String tok : tokenstring)
+ {
+ Matcher mtch = URL_PATTERN.matcher(tok);
+ if (mtch.find())
{
- 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;
+ 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;
+ }
+ }
+ return valid;
}
+
public void addBaseParams(ArrayList 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+"'");
+ // 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+"'");
+ if (max != 0)
+ {
+ prms.add("max='" + max + "'");
}
}
-
+
public abstract List getOptions();
+
public List getBaseOptions()
{
ArrayList opts = new ArrayList();
- 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));
+ 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();
+ *
+ * @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.
+ *
+ * @param currentSettings
+ * - modified settings originally from getOptions
+ * @throws InvalidArgumentException
+ * thrown if currentSettings contains invalid options for this type.
*/
- public void configureFromArgumentI(List currentSettings) throws InvalidArgumentException
+ public void configureFromArgumentI(List currentSettings)
+ throws InvalidArgumentException
{
ArrayList urltoks = new ArrayList();
String rg;
- for (ArgumentI arg: currentSettings)
+ 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) {
+ 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()))
+ 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);
+ return new Option(name, descr, req, defType == null ? ""
+ : defType.toString(),
+ curType == null ? "" : curType.toString(),
+ molType.toStringValues(), null);
}
-}
\ No newline at end of file
+}