/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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 .
*******************************************************************************/
package jalview.ws.rest;
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 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 }
*
*/
public abstract class InputType {
/**
* not used yet
*/
boolean replaceids;
public enum molType { NUC, PROT, MIX;
public static Collection toStringValues()
{
Collection c = new ArrayList();
for (molType type:values())
{
c.add(type.toString());
}
return c;
}}
public String token;
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.
* @param types
*/
protected InputType(Class[] types)
{
if(types!=null)
{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
* @param restJob
* @return
*/
public boolean validFor(RestJob restJob)
{
if (!validFor(restJob.rsd))
return false;
for (Class cl:inputData)
{
if (!restJob.hasDataOfType(cl))
{
return false;
}
}
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);
}
} catch (Exception ex)
{
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
* @return StringBody or FileBody ready for posting
*/
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 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
* @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 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 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 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 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));
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 currentSettings) throws InvalidArgumentException
{
ArrayList urltoks = new ArrayList();
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);
}
}