Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
WsParamSetManager	58	112	37	0.00%	Show methods

Class WsParamSetManager

Class WsParamSetManager	Line # 58	Total Statements 112	Complexity 37	TOTAL Coverage 0.00%
getParameterSet(String,String,boolean,boolean) : WsParamSetI[]   getParameterSet(String,String,boolean,boolean) : WsParamSetI[]	6262	23.023	7.07	0.0 0.00%
parseParamFile(String) : WsParamSetI[]   parseParamFile(String) : WsParamSetI[]	118118	22.022	6.06	0.0 0.00%
storeParameterSet(WsParamSetI) : void   storeParameterSet(WsParamSetI) : void	166166	48.048	13.013	0.0 0.00%
deleteParameterSet(WsParamSetI) : void   deleteParameterSet(WsParamSetI) : void	285285	18.018	10.010	0.0 0.00%
registerParser(String,ParamDatastoreI) : void   registerParser(String,ParamDatastoreI) : void	329329	1.01	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package jalview.gui;
22
23		import jalview.bin.Cache;
24		import jalview.bin.Console;
25		import jalview.io.JalviewFileChooser;
26		import jalview.io.JalviewFileView;
27		import jalview.util.MessageManager;
28		import jalview.ws.params.ParamDatastoreI;
29		import jalview.ws.params.ParamManager;
30		import jalview.ws.params.WsParamSetI;
31		import jalview.xml.binding.jalview.ObjectFactory;
32		import jalview.xml.binding.jalview.WebServiceParameterSet;
33
34		import java.io.File;
35		import java.io.FileInputStream;
36		import java.io.FileOutputStream;
37		import java.io.IOException;
38		import java.io.InputStreamReader;
39		import java.io.OutputStreamWriter;
40		import java.io.PrintWriter;
41		import java.util.ArrayList;
42		import java.util.Hashtable;
43		import java.util.List;
44		import java.util.StringTokenizer;
45
46		import javax.xml.bind.JAXBContext;
47		import javax.xml.bind.JAXBElement;
48		import javax.xml.bind.Marshaller;
49		import javax.xml.stream.XMLInputFactory;
50		import javax.xml.stream.XMLStreamReader;
51
52		/**
53		* store and retrieve web service parameter sets.
54		*
55		* @author JimP
56		*
57		*/
		0% Uncovered Elements: 163 (163) Complexity: 37 Complexity Density: 0.33
58		public class WsParamSetManager implements ParamManager
59		{
60		Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
61
		0% Uncovered Elements: 33 (33) Complexity: 7 Complexity Density: 0.3
62	0	@Override...
63		public WsParamSetI[] getParameterSet(String name, String serviceUrl,
64		boolean modifiable, boolean unmodifiable)
65		{
66	0	String files = Cache.getProperty("WS_PARAM_FILES");
67	0	if (files == null)
68		{
69	0	return null;
70		}
71	0	StringTokenizer st = new StringTokenizer(files, "|");
72	0	String pfile = null;
73	0	List<WsParamSetI> params = new ArrayList<>();
74	0	while (st.hasMoreTokens())
75		{
76	0	pfile = st.nextToken();
77	0	try
78		{
79	0	WsParamSetI[] pset = parseParamFile(pfile);
80	0	for (WsParamSetI p : pset)
81		{
82	0	boolean add = false;
83	0	if (serviceUrl != null)
84		{
85	0	for (String url : p.getApplicableUrls())
86		{
87	0	if (url.equals(serviceUrl))
88		{
89	0	add = true;
90		}
91		}
92		}
93		else
94		{
95	0	add = true;
96		}
97	0	add &= (modifiable == p.isModifiable()
98		|| unmodifiable == !p.isModifiable());
99	0	add &= name == null || p.getName().equals(name);
100
101	0	if (add)
102		{
103
104	0	params.add(p);
105		}
106
107		}
108		} catch (IOException e)
109		{
110	0	Console.info("Failed to parse parameter file " + pfile
111		+ " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
112		e);
113		}
114		}
115	0	return params.toArray(new WsParamSetI[0]);
116		}
117
		0% Uncovered Elements: 28 (28) Complexity: 6 Complexity Density: 0.27
118	0	private WsParamSetI[] parseParamFile(String filename) throws IOException...
119		{
120	0	List<WsParamSetI> psets = new ArrayList<>();
121	0	InputStreamReader is = new InputStreamReader(
122		new FileInputStream(new File(filename)), "UTF-8");
123
124	0	WebServiceParameterSet wspset = null;
125	0	try
126		{
127	0	JAXBContext jc = JAXBContext
128		.newInstance("jalview.xml.binding.jalview");
129	0	javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
130	0	XMLStreamReader streamReader = XMLInputFactory.newInstance()
131		.createXMLStreamReader(is);
132	0	JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader,
133		WebServiceParameterSet.class);
134	0	wspset = jbe.getValue();
135		} catch (Exception ex)
136		{
137	0	throw new IOException(ex);
138		}
139
140	0	if (wspset != null && wspset.getParameters().length() > 0)
141		{
142	0	List<String> urls = wspset.getServiceURL();
143	0	final String[] urlArray = urls.toArray(new String[urls.size()]);
144
145	0	for (String url : urls)
146		{
147	0	ParamDatastoreI parser = paramparsers.get(url);
148	0	if (parser != null)
149		{
150	0	WsParamSetI pset = parser.parseServiceParameterFile(
151		wspset.getName(), wspset.getDescription(), urlArray,
152		wspset.getParameters());
153	0	if (pset != null)
154		{
155	0	pset.setSourceFile(filename);
156	0	psets.add(pset);
157	0	break;
158		}
159		}
160		}
161		}
162
163	0	return psets.toArray(new WsParamSetI[0]);
164		}
165
		0% Uncovered Elements: 66 (66) Complexity: 13 Complexity Density: 0.27
166	0	@Override...
167		public void storeParameterSet(WsParamSetI parameterSet)
168		{
169	0	String filename = parameterSet.getSourceFile();
170	0	File outfile = null;
171	0	try
172		{
173	0	if (filename != null && !((outfile = new File(filename)).canWrite()))
174		{
175	0	Console.warn("Can't write to " + filename
176		+ " - Prompting for new file to write to.");
177	0	filename = null;
178		}
179		} catch (Exception e)
180		{
181	0	filename = null;
182		}
183
184	0	ParamDatastoreI parser = null;
185	0	for (String urls : parameterSet.getApplicableUrls())
186		{
187	0	if (parser == null)
188		{
189	0	parser = paramparsers.get(urls);
190		}
191		}
192	0	if (parser == null)
193		{
194	0	throw new Error(MessageManager.getString(
195		"error.implementation_error_cannot_find_marshaller_for_param_set"));
196		}
197	0	if (filename == null)
198		{
199		// TODO: JAL-3048 webservice - not required for Jalview-JS
200
201	0	JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
202		"Web Service Parameter File");
203	0	chooser.setFileView(new JalviewFileView());
204	0	chooser.setDialogTitle(MessageManager
205		.getString("label.choose_filename_for_param_file"));
206	0	chooser.setToolTipText(MessageManager.getString("action.save"));
207	0	int value = chooser.showSaveDialog(Desktop.instance);
208	0	if (value == JalviewFileChooser.APPROVE_OPTION)
209		{
210	0	outfile = chooser.getSelectedFile();
211	0	Cache.setProperty("LAST_DIRECTORY", outfile.getParent());
212	0	filename = outfile.getAbsolutePath();
213	0	if (!filename.endsWith(".wsparams"))
214		{
215	0	filename = filename.concat(".wsparams");
216	0	outfile = new File(filename);
217		}
218		}
219		}
220	0	if (outfile != null)
221		{
222	0	String paramFiles = Cache.getDefault("WS_PARAM_FILES", filename);
223	0	if (paramFiles.indexOf(filename) == -1)
224		{
225	0	if (paramFiles.length() > 0)
226		{
227	0	paramFiles = paramFiles.concat("|");
228		}
229	0	paramFiles = paramFiles.concat(filename);
230		}
231	0	Cache.setProperty("WS_PARAM_FILES", paramFiles);
232
233	0	WebServiceParameterSet paramxml = new WebServiceParameterSet();
234
235	0	paramxml.setName(parameterSet.getName());
236	0	paramxml.setDescription(parameterSet.getDescription());
237	0	for (String url : parameterSet.getApplicableUrls())
238		{
239	0	paramxml.getServiceURL().add(url);
240		}
241	0	paramxml.setVersion("1.0");
242	0	try
243		{
244	0	paramxml.setParameters(
245		parser.generateServiceParameterFile(parameterSet));
246	0	PrintWriter out = new PrintWriter(new OutputStreamWriter(
247		new FileOutputStream(outfile), "UTF-8"));
248	0	JAXBContext jaxbContext = JAXBContext
249		.newInstance(WebServiceParameterSet.class);
250	0	Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
251	0	jaxbMarshaller.marshal(
252		new ObjectFactory().createWebServiceParameterSet(paramxml),
253		out);
254	0	out.close();
255	0	parameterSet.setSourceFile(filename);
256		} catch (Exception e)
257		{
258	0	Console.error("Couldn't write parameter file to " + outfile, e);
259		}
260		}
261		}
262
263		/*
264		*
265		* JalviewFileChooser chooser = new JalviewFileChooser(Cache
266		* .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
267		* "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
268		* jalview.io.JalviewFileView());
269		* chooser.setDialogTitle("Load colour scheme");
270		* chooser.setToolTipText("Load");
271		*
272		* int value = chooser.showOpenDialog(this);
273		*
274		* if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
275		* chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY",
276		* choice.getParent()); String defaultColours = Cache.getDefault(
277		* "USER_DEFINED_COLOURS", choice.getPath()); if
278		* (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
279		* defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
280		*
281		* @see
282		* jalview.ws.params.ParamManager#deleteParameterSet(jalview.ws.params.WsParamSetI
283		* )
284		*/
		0% Uncovered Elements: 30 (30) Complexity: 10 Complexity Density: 0.56
285	0	@Override...
286		public void deleteParameterSet(WsParamSetI parameterSet)
287		{
288	0	String filename = parameterSet.getSourceFile();
289	0	if (filename == null || filename.trim().length() < 1)
290		{
291	0	return;
292		}
293	0	String paramFiles = Cache.getDefault("WS_PARAM_FILES", "");
294	0	if (paramFiles.indexOf(filename) > -1)
295		{
296	0	String nparamFiles = new String();
297	0	StringTokenizer st = new StringTokenizer(paramFiles, "|");
298	0	while (st.hasMoreElements())
299		{
300	0	String fl = st.nextToken();
301	0	if (!fl.equals(filename))
302		{
303	0	nparamFiles = nparamFiles.concat("|").concat(fl);
304		}
305		}
306	0	Cache.setProperty("WS_PARAM_FILES", nparamFiles);
307		}
308
309	0	try
310		{
311	0	File pfile = new File(filename);
312	0	if (pfile.exists() && pfile.canWrite())
313		{
314	0	if (JvOptionPane.showConfirmDialog(Desktop.instance,
315		"Delete the preset's file, too ?", "Delete User Preset ?",
316		JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
317		{
318	0	pfile.delete();
319		}
320		}
321		} catch (Exception e)
322		{
323	0	Console.error(
324		"Exception when trying to delete webservice user preset: ",
325		e);
326		}
327		}
328
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
329	0	@Override...
330		public void registerParser(String hosturl, ParamDatastoreI paramdataStore)
331		{
332	0	paramparsers.put(hosturl, paramdataStore);
333		}
334
335		}