Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JobDispatcherWSDiscoverer	18	35	14	0.00%	Show methods

Class JobDispatcherWSDiscoverer

Class JobDispatcherWSDiscoverer	Line # 18	Total Statements 35	Complexity 14	TOTAL Coverage 0.00%
<clinit>, line 22()   <clinit>, line 22()	2222	3.03	2.02	0.0 0.00%
JobDispatcherWSDiscoverer()   JobDispatcherWSDiscoverer()	3636	0.00	1.01	-1.0 -1.0 -
getInstance() : JobDispatcherWSDiscoverer   getInstance() : JobDispatcherWSDiscoverer	3838	3.03	2.02	0.0 0.00%
setParamManager(ParamManager) : void   setParamManager(ParamManager) : void	4444	1.01	1.01	0.0 0.00%
getStatusForUrl(URL) : int   getStatusForUrl(URL) : int	4949	4.04	3.03	0.0 0.00%
getUrlsPropertyKey() : String   getUrlsPropertyKey() : String	6262	1.01	1.01	0.0 0.00%
getDefaultUrl() : URL   getDefaultUrl() : URL	6868	1.01	1.01	0.0 0.00%
fetchServices(URL) : List<WebService<?>>   fetchServices(URL) : List<WebService<?>>	7474	22.022	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.client.ebi;
2
3		import java.io.IOException;
4		import java.net.MalformedURLException;
5		import java.net.URISyntaxException;
6		import java.net.URL;
7		import java.util.List;
8
9		import jalview.bin.Console;
10		import jalview.ws.params.ParamManager;
11		import jalview.ws2.actions.NullAction;
12		import jalview.ws2.actions.api.ActionI;
13		import jalview.ws2.actions.hmmer.PhmmerAction;
14		import jalview.ws2.api.WebService;
15		import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
16		import uk.ac.dundee.compbio.hmmerclient.PhmmerClient;
17
		0% Uncovered Elements: 49 (49) Complexity: 14 Complexity Density: 0.4
18		public final class JobDispatcherWSDiscoverer extends AbstractWebServiceDiscoverer
19		{
20
21		private static final URL DEFAULT_URL;
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
22	0	static...
23		{
24	0	try
25		{
26	0	DEFAULT_URL = new URL("https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
27		} catch (MalformedURLException e)
28		{
29	0	throw new ExceptionInInitializerError(e);
30		}
31		}
32
33		private static JobDispatcherWSDiscoverer instance = null;
34		private static ParamManager paramManager = null;
35
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
36	0	private JobDispatcherWSDiscoverer() {}...
37
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
38	0	public static JobDispatcherWSDiscoverer getInstance() {...
39	0	if (instance == null)
40	0	instance = new JobDispatcherWSDiscoverer();
41	0	return instance;
42		}
43
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
44	0	public static void setParamManager(ParamManager manager)...
45		{
46	0	paramManager = manager;
47		}
48
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
49	0	@Override...
50		public int getStatusForUrl(URL url)
51		{
52	0	try
53		{
54	0	return new PhmmerClient(url).testEndpoint() ? STATUS_OK : STATUS_INVALID;
55		} catch (URISyntaxException e)
56		{
57	0	Console.error(e.getMessage());
58	0	return STATUS_INVALID;
59		}
60		}
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	@Override...
63		protected String getUrlsPropertyKey()
64		{
65	0	return null;
66		}
67
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
68	0	@Override...
69		protected URL getDefaultUrl()
70		{
71	0	return DEFAULT_URL;
72		}
73
		0% Uncovered Elements: 24 (24) Complexity: 3 Complexity Density: 0.14
74	0	@Override...
75		protected List<WebService<?>> fetchServices(URL url) throws IOException
76		{
77	0	PhmmerClient phmmerClient;
78	0	try {
79	0	phmmerClient = new PhmmerClient(url);
80		}
81		catch (URISyntaxException e) {
82	0	throw new MalformedURLException(e.getMessage());
83		}
84	0	if (!phmmerClient.testEndpoint())
85	0	throw new IOException(
86		"unable to reach dispatcher server at " + url);
87	0	var wsBuilder = WebService.<PhmmerAction> newBuilder();
88	0	wsBuilder.url(url);
89	0	wsBuilder.clientName("job dispatcher");
90	0	wsBuilder.category("Database search");
91	0	wsBuilder.name("pHMMER");
92	0	wsBuilder.description("Hmmer3 phmmer is used to search one or more query sequences against a sequence database.");
93	0	wsBuilder.interactive(false);
94	0	wsBuilder.paramDatastore(ParamStores.newPhmmerDatastore(url, paramManager));
95	0	wsBuilder.actionClass(PhmmerAction.class);
96	0	var webService = wsBuilder.build();
97
98	0	var client = new PhmmerWSClient(phmmerClient);
99	0	var actionBuilder = PhmmerAction.newBuilder(client);
100	0	actionBuilder.webService(webService);
101	0	actionBuilder.name("");
102	0	webService.addAction(actionBuilder.build());
103
104	0	return List.of(webService);
105		}
106
107		}