+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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
+{
+ private static final Pattern URL_PATTERN = Pattern
+ .compile("^([^=]+)=?'?([^']*)?'?");
+
/**
* 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
*/
{
if (!validFor(restJob.rsd))
return false;
- for (Class cl:inputData)
+ for (Class cl : inputData)
{
if (!restJob.hasDataOfType(cl))
{
}
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<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
+ * @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<T> type in the string returned from getURLEncodedParameter
+ *
+ * @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
+ * 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)
+ public boolean configureFromURLtokenString(List<String> 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");
- }
-
- valid = valid && configureProperty(mtch.group(1), mtch.group(2), warnings);
+ 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<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+"'");
+ // 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);
+ }
}
- if (max!=0) {
- prms.add("min='"+max+"'");
+ StringBuffer warnings;
+ if (!configureFromURLtokenString(urltoks, warnings = new StringBuffer()))
+ {
+ throw new InvalidArgumentException(warnings.toString());
}
}
-}
\ No newline at end of file
+
+ 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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff