Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblInfo	20	31	19	52	0.00%	Show methods

Class EnsemblInfo

Class EnsemblInfo	Line # 20	Total Statements 31	Complexity 19	Uncovered Elements 52	TOTAL Coverage 0.00%
getDbName() : String   getDbName() : String	4040	1.01	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	4646	1.01	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	5252	1.01	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	5858	1.01	1.01	1.01	0.0 0.00%
getRequestMimeType(boolean) : String   getRequestMimeType(boolean) : String	6464	1.01	1.01	1.01	0.0 0.00%
getResponseMimeType() : String   getResponseMimeType() : String	7070	1.01	1.01	1.01	0.0 0.00%
getDomain(String) : String   getDomain(String) : String	8484	3.03	2.02	5.05	0.0 0.00%
fetchDivisions() : void   fetchDivisions() : void	9797	11.011	5.05	15.015	0.0 0.00%
parseResponse(BufferedReader,String) : void   parseResponse(BufferedReader,String) : void	139139	7.07	3.03	9.09	0.0 0.00%
getDivisionsUrl(String) : URL   getDivisionsUrl(String) : URL	166166	1.01	1.01	1.01	0.0 0.00%
getDivisions() : Set<String>   getDivisions() : Set<String>	177177	3.03	2.02	5.05	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ext.ensembl;
2
3		import jalview.datamodel.AlignmentI;
4		import jalview.datamodel.DBRefSource;
5
6		import java.io.BufferedReader;
7		import java.io.IOException;
8		import java.net.MalformedURLException;
9		import java.net.URL;
10		import java.util.HashMap;
11		import java.util.Iterator;
12		import java.util.List;
13		import java.util.Map;
14		import java.util.Set;
15
16		import org.json.simple.JSONArray;
17		import org.json.simple.parser.JSONParser;
18		import org.json.simple.parser.ParseException;
19
		0% Uncovered Elements: 52 (52) Complexity: 19 Complexity Density: 0.61
20		public class EnsemblInfo extends EnsemblRestClient
21		{
22
23		/*
24		* cached results of REST /info/divisions service, currently
25		* <pre>
26		* {
27		* { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
28		* "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
29		* "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
30		* "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
31		* "ENSEMBLPLANTS", "http://rest.ensemblgenomes.org"},
32		* "ENSEMBL", "http://rest.ensembl.org" }
33		* }
34		* </pre>
35		* The values for EnsemblGenomes are retrieved by a REST call, that for
36		* Ensembl is added programmatically for convenience of lookup
37		*/
38		private static Map<String, String> divisions;
39
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
40	0	@Override...
41		public String getDbName()
42		{
43	0	return "ENSEMBL";
44		}
45
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	@Override...
47		public AlignmentI getSequenceRecords(String queries) throws Exception
48		{
49	0	return null;
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	@Override...
53		protected URL getUrl(List<String> ids) throws MalformedURLException
54		{
55	0	return null;
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	@Override...
59		protected boolean useGetRequest()
60		{
61	0	return true;
62		}
63
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	@Override...
65		protected String getRequestMimeType(boolean multipleIds)
66		{
67	0	return "application/json";
68		}
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	@Override...
71		protected String getResponseMimeType()
72		{
73	0	return "application/json";
74		}
75
76		/**
77		* Answers the domain (http://rest.ensembl.org or
78		* http://rest.ensemblgenomes.org) for the given division, or null if not
79		* recognised by Ensembl.
80		*
81		* @param division
82		* @return
83		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
84	0	public String getDomain(String division)...
85		{
86	0	if (divisions == null)
87		{
88	0	fetchDivisions();
89		}
90	0	return divisions.get(division.toUpperCase());
91		}
92
93		/**
94		* On first request only, populate the lookup map by fetching the list of
95		* divisions known to EnsemblGenomes.
96		*/
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.45
97	0	void fetchDivisions()...
98		{
99	0	divisions = new HashMap<>();
100
101		/*
102		* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
103		*/
104	0	divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
105
106	0	BufferedReader br = null;
107	0	try
108		{
109	0	URL url = getDivisionsUrl(ensemblGenomesDomain);
110	0	if (url != null)
111		{
112	0	br = getHttpResponse(url, null);
113		}
114	0	parseResponse(br, ensemblGenomesDomain);
115		} catch (IOException e)
116		{
117		// ignore
118		} finally
119		{
120	0	if (br != null)
121		{
122	0	try
123		{
124	0	br.close();
125		} catch (IOException e)
126		{
127		// ignore
128		}
129		}
130		}
131		}
132
133		/**
134		* Parses the JSON response to /info/divisions, and add each to the lookup map
135		*
136		* @param br
137		* @param domain
138		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
139	0	void parseResponse(BufferedReader br, String domain)...
140		{
141	0	JSONParser jp = new JSONParser();
142
143	0	try
144		{
145	0	JSONArray parsed = (JSONArray) jp.parse(br);
146
147	0	Iterator rvals = parsed.iterator();
148	0	while (rvals.hasNext())
149		{
150	0	String division = rvals.next().toString();
151	0	divisions.put(division.toUpperCase(), domain);
152		}
153		} catch (IOException | ParseException | NumberFormatException e)
154		{
155		// ignore
156		}
157		}
158
159		/**
160		* Constructs the URL for the EnsemblGenomes /info/divisions REST service
161		* @param domain TODO
162		*
163		* @return
164		* @throws MalformedURLException
165		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
166	0	URL getDivisionsUrl(String domain) throws MalformedURLException...
167		{
168	0	return new URL(domain
169		+ "/info/divisions?content-type=application/json");
170		}
171
172		/**
173		* Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes
174		*
175		* @return
176		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
177	0	public Set<String> getDivisions() {...
178	0	if (divisions == null)
179		{
180	0	fetchDivisions();
181		}
182
183	0	return divisions.keySet();
184		}
185		}