Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SimpleParamDatastore	31	97	32	0.00%	Show methods

Class SimpleParamDatastore

Class SimpleParamDatastore	Line # 31	Total Statements 97	Complexity 32	TOTAL Coverage 0.00%
SimpleParamDatastore(URL,List<ArgumentI>,List<? extends WsParamSetI>,ParamManager)   SimpleParamDatastore(URL,List<ArgumentI>,List<? extends WsParamSetI>,ParamManager)	5050	11.011	3.03	0.0 0.00%
_initManager(ParamManager) : void   _initManager(ParamManager) : void	6969	8.08	3.03	0.0 0.00%
getPresets() : List<WsParamSetI>   getPresets() : List<WsParamSetI>	9292	4.04	1.01	0.0 0.00%
getPreset(String) : SimpleParamSet   getPreset(String) : SimpleParamSet	101101	8.08	3.03	0.0 0.00%
getUserPreset(String) : SimpleParamSet   getUserPreset(String) : SimpleParamSet	114114	4.04	2.02	0.0 0.00%
getServicePreset(String) : SimpleParamSet   getServicePreset(String) : SimpleParamSet	124124	4.04	2.02	0.0 0.00%
getServiceParameters() : List<ArgumentI>   getServiceParameters() : List<ArgumentI>	134134	1.01	1.01	0.0 0.00%
presetExists(String) : boolean   presetExists(String) : boolean	140140	1.01	1.01	0.0 0.00%
deletePreset(String) : void   deletePreset(String) : void	146146	8.08	4.04	0.0 0.00%
storePreset(String,String,List<ArgumentI>) : void   storePreset(String,String,List<ArgumentI>) : void	169169	10.010	2.02	0.0 0.00%
updatePreset(String,String,String,List<ArgumentI>) : void   updatePreset(String,String,String,List<ArgumentI>) : void	184184	9.09	4.04	0.0 0.00%
parseServiceParameterFile(String,String,String[],String) : WsParamSetI   parseServiceParameterFile(String,String,String[],String) : WsParamSetI	200200	16.016	3.03	0.0 0.00%
generateServiceParameterFile(WsParamSetI) : String   generateServiceParameterFile(WsParamSetI) : String	231231	13.013	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.params;
2
3		import java.io.ByteArrayOutputStream;
4		import java.io.IOException;
5		import java.io.StringReader;
6		import java.net.URL;
7		import java.util.ArrayList;
8		import java.util.Collections;
9		import java.util.List;
10
11		import javax.xml.bind.JAXBContext;
12		import javax.xml.bind.JAXBException;
13		import javax.xml.bind.Marshaller;
14		import javax.xml.bind.Unmarshaller;
15
16		import jalview.bin.Cache;
17		import jalview.bin.Console;
18		import jalview.util.MessageManager;
19		import jalview.ws.params.ArgumentI;
20		import jalview.ws.params.ParamDatastoreI;
21		import jalview.ws.params.ParamManager;
22		import jalview.ws.params.WsParamSetI;
23
24		/**
25		* A web client agnostic parameters datastore that provides view of the
26		* parameters and delegates parameters storage to {@link ParamManager}
27		* if given. Parameter datastore maintains the applicable service url
28		* the list of service parameters and both presets and user defined
29		* parameter sets
30		*/
		0% Uncovered Elements: 140 (140) Complexity: 32 Complexity Density: 0.33
31		public class SimpleParamDatastore implements ParamDatastoreI
32		{
33		protected URL serviceUrl;
34		protected List<ArgumentI> parameters;
35		protected List<SimpleParamSet> servicePresets;
36		protected List<SimpleParamSet> userPresets = new ArrayList<>();
37		protected ParamManager manager;
38
39		/**
40		* Create new parameter datastore bound to the specified url with
41		* given service parameters and presets. Additionally, a parameters
42		* manager may be provided that will be used to load and store
43		* user parameter sets.
44		*
45		* @param serviceUrl applicable url
46		* @param parameters service parameters
47		* @param presets unmodifiable service presets
48		* @param manager parameter manager used to load and store user presets
49		*/
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27
50	0	public SimpleParamDatastore(URL serviceUrl, List<ArgumentI> parameters,...
51		List<? extends WsParamSetI> presets, ParamManager manager)
52		{
53	0	this.serviceUrl = serviceUrl;
54	0	this.parameters = Collections.unmodifiableList(new ArrayList<>(parameters));
55	0	this.servicePresets = new ArrayList<>(presets.size());
56	0	for (var preset : presets)
57		{
58	0	if (preset instanceof SimpleParamSet)
59	0	servicePresets.add((SimpleParamSet) preset);
60		else
61	0	servicePresets.add(new SimpleParamSet(preset));
62		}
63	0	this.servicePresets = Collections.unmodifiableList(this.servicePresets);
64	0	this.manager = manager;
65	0	if (manager != null)
66	0	_initManager(manager);
67		}
68
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
69	0	private void _initManager(ParamManager manager)...
70		{
71	0	manager.registerParser(serviceUrl.toString(), this);
72	0	WsParamSetI[] paramSets = manager.getParameterSet(null, serviceUrl.toString(),
73		true, false);
74	0	if (paramSets != null)
75		{
76	0	for (WsParamSetI paramSet : paramSets)
77		{
78		// TODO: handle mismatch between preset and current parameters
79	0	if (paramSet instanceof SimpleParamSet)
80	0	userPresets.add((SimpleParamSet) paramSet);
81		else
82		{
83	0	userPresets.add(new SimpleParamSet(paramSet));
84	0	Console.warn(String.format(
85		"Parameter set instance type %s is not applicable to service"
86		+ "at %s.", paramSet.getClass(), serviceUrl));
87		}
88		}
89		}
90		}
91
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
92	0	@Override...
93		public List<WsParamSetI> getPresets()
94		{
95	0	List<WsParamSetI> presets = new ArrayList<>();
96	0	presets.addAll(servicePresets);
97	0	presets.addAll(userPresets);
98	0	return presets;
99		}
100
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
101	0	@Override...
102		public SimpleParamSet getPreset(String name)
103		{
104	0	SimpleParamSet preset = null;
105	0	preset = getUserPreset(name);
106	0	if (preset != null)
107	0	return preset;
108	0	preset = getServicePreset(name);
109	0	if (preset != null)
110	0	return preset;
111	0	return null;
112		}
113
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
114	0	public SimpleParamSet getUserPreset(String name)...
115		{
116	0	for (SimpleParamSet preset : userPresets)
117		{
118	0	if (name.equals(preset.getName()))
119	0	return preset;
120		}
121	0	return null;
122		}
123
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
124	0	public SimpleParamSet getServicePreset(String name)...
125		{
126	0	for (SimpleParamSet preset : servicePresets)
127		{
128	0	if (name.equals(preset.getName()))
129	0	return preset;
130		}
131	0	return null;
132		}
133
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	@Override...
135		public List<ArgumentI> getServiceParameters()
136		{
137	0	return parameters;
138		}
139
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	@Override...
141		public boolean presetExists(String name)
142		{
143	0	return getPreset(name) != null;
144		}
145
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.5
146	0	@Override...
147		public void deletePreset(String name)
148		{
149	0	var userPreset = getUserPreset(name);
150	0	if (userPreset != null)
151		{
152	0	userPresets.remove(userPreset);
153	0	if (manager != null)
154		{
155	0	manager.deleteParameterSet(userPreset);
156		}
157		}
158	0	else if (getServicePreset(name) != null)
159		{
160	0	throw new RuntimeException(MessageManager.getString(
161		"error.implementation_error_attempt_to_delete_service_preset"));
162		}
163		else
164		{
165	0	Console.warn("Implementation error: no preset to delete");
166		}
167		}
168
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
169	0	@Override...
170		public void storePreset(String presetName, String text, List<ArgumentI> jobParams)
171		{
172	0	var builder = SimpleParamSet.newBuilder();
173	0	builder.name(presetName);
174	0	builder.description(text);
175	0	builder.arguments(jobParams);
176	0	builder.url(serviceUrl.toString());
177	0	builder.modifiable(true);
178	0	var preset = builder.build();
179	0	userPresets.add(preset);
180	0	if (manager != null)
181	0	manager.storeParameterSet(preset);
182		}
183
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.44
184	0	@Override...
185		public void updatePreset(String oldName, String newName, String text, List<ArgumentI> jobParams)
186		{
187	0	var preset = getPreset(oldName != null ? oldName : newName);
188	0	if (preset == null)
189	0	throw new RuntimeException(MessageManager.formatMessage(
190		"error.implementation_error_cannot_locate_oldname_presetname",
191		oldName, newName));
192	0	preset.setName(newName);
193	0	preset.setDescription(text);
194	0	preset.setArguments(jobParams);
195	0	preset.setApplicableUrls(new String[] { serviceUrl.toString() });
196	0	if (manager != null)
197	0	manager.storeParameterSet(preset);
198		}
199
		0% Uncovered Elements: 16 (16) Complexity: 3 Complexity Density: 0.19
200	0	@Override...
201		public WsParamSetI parseServiceParameterFile(String name, String description,
202		String[] serviceURL, String parameters)
203		throws IOException
204		{
205	0	var builder = SimpleParamSet.newBuilder();
206	0	builder.name(name);
207	0	builder.description(description);
208	0	builder.urls(serviceURL);
209	0	builder.modifiable(true);
210	0	Unmarshaller unmarshaller;
211	0	try
212		{
213	0	var ctx = JAXBContext.newInstance(ArgumentBeanList.class);
214	0	unmarshaller = ctx.createUnmarshaller();
215		} catch (JAXBException e)
216		{
217	0	throw new RuntimeException(e);
218		}
219	0	ArgumentBeanList argList;
220	0	try
221		{
222	0	argList = (ArgumentBeanList) unmarshaller.unmarshal(new StringReader(parameters));
223		} catch (JAXBException | ClassCastException e)
224		{
225	0	throw new IOException("Unable to load parameters from file", e);
226		}
227	0	builder.arguments(argList.arguments);
228	0	return builder.build();
229		}
230
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.23
231	0	@Override...
232		public String generateServiceParameterFile(WsParamSetI pset) throws IOException
233		{
234	0	Marshaller marshaller;
235	0	try
236		{
237	0	var ctx = JAXBContext.newInstance(ArgumentBeanList.class);
238	0	marshaller = ctx.createMarshaller();
239	0	marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
240	0	marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
241		} catch (JAXBException e)
242		{
243	0	throw new RuntimeException(e);
244		}
245	0	ArgumentBeanList argList = ArgumentBeanList.fromList(pset.getArguments());
246	0	var out = new ByteArrayOutputStream();
247	0	try
248		{
249	0	marshaller.marshal(argList, out);
250		} catch (JAXBException e)
251		{
252	0	throw new IOException("Unable to generate parameters file", e);
253		}
254	0	return out.toString();
255		}
256
257		}