2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.rest;
23 import java.util.Locale;
25 import jalview.ws.params.ArgumentI;
26 import jalview.ws.params.InvalidArgumentException;
27 import jalview.ws.params.OptionI;
28 import jalview.ws.params.ParameterI;
29 import jalview.ws.params.simple.IntegerParameter;
30 import jalview.ws.params.simple.Option;
32 import java.io.UnsupportedEncodingException;
33 import java.nio.charset.Charset;
34 import java.util.ArrayList;
35 import java.util.Collection;
36 import java.util.List;
37 import java.util.regex.Matcher;
38 import java.util.regex.Pattern;
40 import org.apache.http.entity.mime.content.ContentBody;
41 import org.apache.http.entity.mime.content.StringBody;
44 * InputType is the abstract model of each input parameter that a rest service
45 * might take. It enables the engine to validate input by providing { formatter
46 * for type, parser for type }
49 public abstract class InputType
51 private static final Pattern URL_PATTERN = Pattern
52 .compile("^([^=]+)=?'?([^']*)?'?");
63 public static Collection<String> toStringValues()
65 Collection<String> c = new ArrayList<String>();
66 for (molType type : values())
68 c.add(type.toString());
78 public int max = 0; // unbounded
80 protected ArrayList<Class> inputData = new ArrayList<Class>();
83 * initialise the InputType with a list of jalview data classes that the
84 * RestJob needs to be able to provide to it.
88 protected InputType(Class[] types)
100 * do basic tests to ensure the job's service takes this parameter, and the
101 * job's input data can be used to generate the input data
106 public boolean validFor(RestJob restJob)
108 if (!validFor(restJob.rsd))
110 for (Class cl : inputData)
112 if (!restJob.hasDataOfType(cl))
120 public boolean validFor(RestServiceDescription restServiceDescription)
122 if (!restServiceDescription.inputParams.values().contains(this))
128 protected ContentBody utf8StringBody(String content, String type)
130 Charset utf8 = Charset.forName("UTF-8");
135 return new StringBody(
136 utf8.encode(content).asCharBuffer().toString());
140 return new StringBody(
141 utf8.encode(content).asCharBuffer().toString(), type, utf8);
143 } catch (Exception ex)
145 System.err.println("Couldn't transform string\n" + content
146 + "\nException was :");
147 ex.printStackTrace(System.err);
155 * data from which input is to be extracted and formatted
156 * @return StringBody or FileBody ready for posting
158 abstract public ContentBody formatForInput(RestJob rj)
159 throws UnsupportedEncodingException, NoValidInputDataException;
163 * @return true if no input data needs to be provided for this parameter
165 public boolean isConstant()
167 return (inputData == null || inputData.size() == 0);
171 * return a url encoded version of this parameter's value, or an empty string
172 * if the parameter has no ='value' content.
176 public abstract List<String> getURLEncodedParameter();
179 * set the property known as tok, possibly by assigning it with a given val
183 * (may be empty or null)
185 * place where parse warnings are reported
186 * @return true if property was set
188 public abstract boolean configureProperty(String tok, String val,
189 StringBuffer warnings);
192 * Get unique key for this type of parameter in a URL encoding.
194 * @return the string that prefixes an input parameter of InputType<T> type in
195 * the string returned from getURLEncodedParameter
197 public abstract String getURLtokenPrefix();
200 * parse the given token String and set InputParameter properties
204 * - urlencoded parameter string as returned from
205 * getURLEncodedParameter
207 * - place where any warning messages about bad property values are
209 * @return true if configuration succeeded, false otherwise.
211 public boolean configureFromURLtokenString(List<String> tokenstring,
212 StringBuffer warnings)
214 boolean valid = true;
215 for (String tok : tokenstring)
217 Matcher mtch = URL_PATTERN.matcher(tok);
222 if (mtch.group(1).equals("min"))
224 min = Integer.parseInt(mtch.group(2));
228 else if (mtch.group(1).equals("max"))
230 max = Integer.parseInt(mtch.group(2));
233 } catch (NumberFormatException x)
236 warnings.append("Invalid value for parameter "
237 + mtch.group(1).toLowerCase(Locale.ROOT) + " '" + mtch.group(2)
238 + "' (expected an integer)\n");
241 if (!configureProperty(mtch.group(1), mtch.group(2), warnings))
243 if (warnings.length() == 0)
245 warnings.append("Failed to configure InputType :"
246 + getURLtokenPrefix() + " with property string: '"
247 + mtch.group(0) + "'\n (token is '" + mtch.group(1)
248 + "' and value is '" + mtch.group(2) + "')\n");
257 public void addBaseParams(ArrayList<String> prms)
259 // todo : check if replaceids should be a global for the service, rather
260 // than for a specific parameter.
263 prms.add("min='" + min + "'");
267 prms.add("max='" + max + "'");
271 public abstract List<OptionI> getOptions();
273 public List<OptionI> getBaseOptions()
275 ArrayList<OptionI> opts = new ArrayList<OptionI>();
276 opts.add(new IntegerParameter("min",
277 "Minimum number of data of this type", true, 1, min, 0, -1));
278 opts.add(new IntegerParameter("max",
279 "Maximum number of data of this type", false, 0, max, 0, -1));
284 * make a copy of this InputType
286 * @return may not be needed public abstract InputType copy();
290 * parse a set of configuration options
292 * @param currentSettings
293 * - modified settings originally from getOptions
294 * @throws InvalidArgumentException
295 * thrown if currentSettings contains invalid options for this type.
297 public void configureFromArgumentI(List<ArgumentI> currentSettings)
298 throws InvalidArgumentException
300 ArrayList<String> urltoks = new ArrayList<String>();
302 for (ArgumentI arg : currentSettings)
304 if (arg instanceof ParameterI)
306 rg = arg.getName() + "='" + arg.getValue() + "'";
310 // TODO: revise architecture - this is counter intuitive - options with
311 // different values to their names are actually parameters
312 rg = (arg.getValue().length() > 0)
313 ? (arg.getValue().equals(arg.getName()) ? arg.getName()
314 : arg.getName() + "='" + arg.getValue() + "'")
322 StringBuffer warnings;
323 if (!configureFromURLtokenString(urltoks,
324 warnings = new StringBuffer()))
326 throw new InvalidArgumentException(warnings.toString());
330 protected OptionI createMolTypeOption(String name, String descr,
331 boolean req, molType curType, molType defType)
333 return new Option(name, descr, req,
334 defType == null ? "" : defType.toString(),
335 curType == null ? "" : curType.toString(),
336 molType.toStringValues(), null);