Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SlivkaWSDiscoverer	28	75	33	0.00%	Show methods

Class SlivkaWSDiscoverer

Class SlivkaWSDiscoverer	Line # 28	Total Statements 75	Complexity 33	TOTAL Coverage 0.00%
SlivkaWSDiscoverer()   SlivkaWSDiscoverer()	3838	0.00	1.01	-1.0 -1.0 -
getInstance() : SlivkaWSDiscoverer   getInstance() : SlivkaWSDiscoverer	4242	3.03	2.02	0.0 0.00%
addServiceChangeListener(ServiceChangeListener) : void   addServiceChangeListener(ServiceChangeListener) : void	5353	1.01	1.01	0.0 0.00%
removeServiceChangeListener(ServiceChangeListener) : void   removeServiceChangeListener(ServiceChangeListener) : void	5959	1.01	1.01	0.0 0.00%
notifyServiceListeners(List<ServiceWithParameters>) : void   notifyServiceListeners(List<ServiceWithParameters>) : void	6565	2.02	1.01	0.0 0.00%
startDiscoverer() : CompletableFuture<WSDiscovererI>   startDiscoverer() : CompletableFuture<WSDiscovererI>	7878	5.05	1.01	0.0 0.00%
reloadServices() : List<ServiceWithParameters>   reloadServices() : List<ServiceWithParameters>	8989	39.039	12.012	0.0 0.00%
getServices() : List<ServiceWithParameters>   getServices() : List<ServiceWithParameters>	155155	1.01	1.01	0.0 0.00%
hasServices() : boolean   hasServices() : boolean	161161	1.01	1.01	0.0 0.00%
isRunning() : boolean   isRunning() : boolean	167167	1.01	1.01	0.0 0.00%
setServiceUrls(List<String>) : void   setServiceUrls(List<String>) : void	173173	3.03	3.03	0.0 0.00%
getServiceUrls() : List<String>   getServiceUrls() : List<String>	186186	11.011	3.03	0.0 0.00%
testServiceUrl(URL) : boolean   testServiceUrl(URL) : boolean	212212	1.01	1.01	0.0 0.00%
getServerStatusFor(String) : int   getServerStatusFor(String) : int	218218	5.05	3.03	0.0 0.00%
getErrorMessages() : String   getErrorMessages() : String	232232	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws.slivkaws;
2
3		import jalview.bin.Cache;
4		import jalview.bin.Console;
5		import jalview.ws.ServiceChangeListener;
6		import jalview.ws.WSDiscovererI;
7		import jalview.ws.api.ServiceWithParameters;
8		import javajs.http.HttpClientFactory;
9
10		import java.io.IOException;
11		import java.net.MalformedURLException;
12		import java.net.URL;
13		import java.util.ArrayList;
14		import java.util.Collections;
15		import java.util.List;
16		import java.util.Set;
17		import java.util.Vector;
18		import java.util.concurrent.CompletableFuture;
19		import java.util.concurrent.CopyOnWriteArraySet;
20		import java.util.concurrent.ExecutorService;
21		import java.util.concurrent.Executors;
22		import java.util.concurrent.Future;
23
24		import compbio.data.msa.Category;
25		import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
26		import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
27
		0% Uncovered Elements: 104 (104) Complexity: 33 Complexity Density: 0.44
28		public class SlivkaWSDiscoverer implements WSDiscovererI
29		{
30		private static final String SLIVKA_HOST_URLS = "SLIVKAHOSTURLS";
31
32		private static final String COMPBIO_SLIVKA = "https://www.compbio.dundee.ac.uk/slivka/";
33
34		private static SlivkaWSDiscoverer instance = null;
35
36		private List<ServiceWithParameters> services = List.of();
37
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
38	0	private SlivkaWSDiscoverer()...
39		{
40		}
41
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
42	0	public static SlivkaWSDiscoverer getInstance()...
43		{
44	0	if (instance == null)
45		{
46	0	instance = new SlivkaWSDiscoverer();
47		}
48	0	return instance;
49		}
50
51		private Set<ServiceChangeListener> serviceListeners = new CopyOnWriteArraySet<>();
52
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	@Override...
54		public void addServiceChangeListener(ServiceChangeListener l)
55		{
56	0	serviceListeners.add(l);
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public void removeServiceChangeListener(ServiceChangeListener l)
61		{
62	0	serviceListeners.remove(l);
63		}
64
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
65	0	public void notifyServiceListeners(List<ServiceWithParameters> services)...
66		{
67	0	for (var listener : serviceListeners)
68		{
69	0	listener.servicesChanged(this, services);
70		}
71		}
72
73		private final ExecutorService executor = Executors
74		.newSingleThreadExecutor();
75
76		private Vector<Future<?>> discoveryTasks = new Vector<>();
77
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
78	0	public CompletableFuture<WSDiscovererI> startDiscoverer()...
79		{
80	0	CompletableFuture<WSDiscovererI> task = CompletableFuture
81		.supplyAsync(() -> {
82	0	reloadServices();
83	0	return SlivkaWSDiscoverer.this;
84		}, executor);
85	0	discoveryTasks.add(task);
86	0	return task;
87		}
88
		0% Uncovered Elements: 45 (45) Complexity: 12 Complexity Density: 0.31
89	0	private List<ServiceWithParameters> reloadServices()...
90		{
91	0	Console.info("Reloading Slivka services");
92	0	notifyServiceListeners(Collections.emptyList());
93	0	ArrayList<ServiceWithParameters> instances = new ArrayList<>();
94
95	0	for (String url : getServiceUrls())
96		{
97	0	SlivkaClient client = SlivkaClient.newInstance(url);
98
99	0	List<SlivkaService> services;
100	0	try
101		{
102	0	services = client.getServices();
103		} catch (IOException e)
104		{
105	0	e.printStackTrace();
106	0	continue;
107		}
108	0	for (SlivkaService service : services)
109		{
110	0	SlivkaWSInstance newInstance = null;
111	0	for (String classifier : service.classifiers)
112		{
113	0	String[] path = classifier.split("\\s*::\\s*");
114	0	if (path.length >= 3 && path[0].toLowerCase().equals("operation")
115		&& path[1].toLowerCase().equals("analysis"))
116		{
117	0	switch (path[path.length - 1].toLowerCase())
118		{
119	0	case "rna secondary structure prediction":
120	0	newInstance = new RNAalifoldServiceInstance(client,
121		service, "Secondary Structure Prediction");
122	0	break;
123	0	case "sequence alignment analysis (conservation)":
124	0	newInstance = new SlivkaAnnotationServiceInstance(client,
125		service, Category.CATEGORY_CONSERVATION);
126	0	break;
127	0	case "protein sequence analysis":
128	0	newInstance = new SlivkaAnnotationServiceInstance(client,
129		service, Category.CATEGORY_DISORDER);
130	0	break;
131	0	case "protein secondary structure prediction":
132	0	newInstance = new SlivkaAnnotationServiceInstance(client,
133		service, "Secondary Structure Prediction");
134	0	break;
135	0	case "multiple sequence alignment":
136	0	newInstance = new SlivkaMsaServiceInstance(client, service,
137		Category.CATEGORY_ALIGNMENT);
138	0	break;
139		}
140		}
141	0	if (newInstance != null)
142	0	break;
143		}
144	0	if (newInstance != null)
145	0	instances.add(newInstance);
146		}
147		}
148
149	0	services = instances;
150	0	Console.info("Slivka services reloading finished");
151	0	notifyServiceListeners(instances);
152	0	return instances;
153		}
154
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
155	0	@Override...
156		public List<ServiceWithParameters> getServices()
157		{
158	0	return services;
159		}
160
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	@Override...
162		public boolean hasServices()
163		{
164	0	return !isRunning() && services.size() > 0;
165		}
166
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
167	0	@Override...
168		public boolean isRunning()
169		{
170	0	return !discoveryTasks.stream().allMatch(Future::isDone);
171		}
172
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
173	0	@Override...
174		public void setServiceUrls(List<String> wsUrls)
175		{
176	0	if (wsUrls != null && !wsUrls.isEmpty())
177		{
178	0	Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls));
179		}
180		else
181		{
182	0	Cache.removeProperty(SLIVKA_HOST_URLS);
183		}
184		}
185
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.27
186	0	@Override...
187		public List<String> getServiceUrls()
188		{
189	0	String surls = Cache.getDefault(SLIVKA_HOST_URLS, COMPBIO_SLIVKA);
190	0	String[] urls = surls.split(",");
191	0	ArrayList<String> valid = new ArrayList<>(urls.length);
192	0	for (String url : urls)
193		{
194	0	try
195		{
196	0	new URL(url);
197	0	valid.add(url);
198		} catch (MalformedURLException e)
199		{
200	0	Console.warn("Problem whilst trying to make a URL from '"
201	0	+ ((url != null) ? url : "<null>") + "'");
202	0	Console.warn(
203		"This was probably due to a malformed comma separated list"
204		+ " in the " + SLIVKA_HOST_URLS
205		+ " entry of $(HOME)/.jalview_properties)");
206	0	Console.debug("Exception was ", e);
207		}
208		}
209	0	return valid;
210		}
211
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
212	0	@Override...
213		public boolean testServiceUrl(URL url)
214		{
215	0	return getServerStatusFor(url.toString()) == STATUS_OK;
216		}
217
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
218	0	@Override...
219		public int getServerStatusFor(String url)
220		{
221	0	try
222		{
223	0	List<?> services = SlivkaClient.newInstance(url).getServices();
224	0	return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
225		} catch (IOException | org.json.JSONException e)
226		{
227	0	Console.error("Slivka could not retrieve services list", e);
228	0	return STATUS_INVALID;
229		}
230		}
231
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
232	0	@Override...
233		public String getErrorMessages()
234		{
235		// TODO Auto-generated method stub
236	0	return "";
237		}
238		}