Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblXref	47	42	22	16	0.7460317674.6%	Show methods

Class EnsemblXref

Class EnsemblXref	Line # 47	Total Statements 42	Complexity 22	Uncovered Elements 16	TOTAL Coverage 0.7460317674.6%
EnsemblXref(String,String,String)   EnsemblXref(String,String,String)	5959	3.03	1.01	0.00	1.0 1.0100%
getDbName() : String   getDbName() : String	6767	1.01	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	7373	1.01	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	7979	1.01	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	8585	1.01	1.01	1.01	0.0 0.00%
getRequestMimeType(boolean) : String   getRequestMimeType(boolean) : String	9191	1.01	1.01	1.01	0.0 0.00%
getResponseMimeType() : String   getResponseMimeType() : String	9797	1.01	1.01	1.01	0.0 0.00%
getCrossReferences(String) : List<DBRefEntry>   getCrossReferences(String) : List<DBRefEntry>	114114	14.014	6.06	3.03	0.85 0.8585%
parseResponse(BufferedReader) : List<DBRefEntry>   parseResponse(BufferedReader) : List<DBRefEntry>	162162	14.014	6.06	0.00	1.0 1.0100%
getXRefVersion() : String   getXRefVersion() : String	198198	1.01	1.01	0.00	1.0 1.0100%
getUrl(String) : URL   getUrl(String) : URL	211211	4.04	2.02	1.01	0.75 0.7575%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.74603176	jalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferencesjalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferences	1PASS

 

Source view

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.ext.ensembl;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.DBRefEntry;
25		import jalview.util.DBRefUtils;
26
27		import java.io.BufferedReader;
28		import java.io.IOException;
29		import java.net.MalformedURLException;
30		import java.net.URL;
31		import java.util.ArrayList;
32		import java.util.Iterator;
33		import java.util.List;
34
35		import org.json.simple.JSONArray;
36		import org.json.simple.JSONObject;
37		import org.json.simple.parser.JSONParser;
38		import org.json.simple.parser.ParseException;
39
40		/**
41		* A class to fetch cross-references from Ensembl by calling the /xrefs REST
42		* service
43		*
44		* @author gmcarstairs
45		* @see http://rest.ensembl.org/documentation/info/xref_id
46		*/
		74.6% Uncovered Elements: 16 (63) Complexity: 22 Complexity Density: 0.52
47		class EnsemblXref extends EnsemblRestClient
48		{
49
50		private static final String GO_GENE_ONTOLOGY = "GO";
51
52		private String dbName = "ENSEMBL (xref)";
53
54		/**
55		* Constructor given the target domain to fetch data from
56		*
57		* @param d
58		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
59	1	public EnsemblXref(String d, String dbSource, String version)...
60		{
61	1	super(d);
62	1	dbName = dbSource;
63	1	xrefVersion = dbSource + ":" + version;
64
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public String getDbName()
69		{
70	0	return dbName;
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		public AlignmentI getSequenceRecords(String queries) throws Exception
75		{
76	0	return null;
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	@Override...
80		protected URL getUrl(List<String> ids) throws MalformedURLException
81		{
82	0	return getUrl(ids.get(0));
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	@Override...
86		protected boolean useGetRequest()
87		{
88	0	return true;
89		}
90
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		protected String getRequestMimeType(boolean multipleIds)
93		{
94	0	return "application/json";
95		}
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	@Override...
98		protected String getResponseMimeType()
99		{
100	0	return "application/json";
101		}
102
103		/**
104		* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
105		* ("primary_id") for the given identifier (Ensembl accession id) and database
106		* names. The "dbname" returned by Ensembl is canonicalised to Jalview's
107		* standard version, and a DBRefEntry constructed. Currently takes all
108		* identifiers apart from GO terms and synonyms.
109		*
110		* @param identifier
111		* an Ensembl stable identifier
112		* @return
113		*/
		85% Uncovered Elements: 3 (20) Complexity: 6 Complexity Density: 0.43
114	1	public List<DBRefEntry> getCrossReferences(String identifier)...
115		{
116	1	List<DBRefEntry> result = new ArrayList<DBRefEntry>();
117	1	List<String> ids = new ArrayList<String>();
118	1	ids.add(identifier);
119
120	1	BufferedReader br = null;
121	1	try
122		{
123	1	URL url = getUrl(identifier);
124	1	if (url != null)
125		{
126	1	br = getHttpResponse(url, ids);
127	1	if (br != null)
128		{
129	1	result = parseResponse(br);
130		}
131		}
132		} catch (IOException e)
133		{
134		// ignore
135		} finally
136		{
137	1	if (br != null)
138		{
139	1	try
140		{
141	1	br.close();
142		} catch (IOException e)
143		{
144		// ignore
145		}
146		}
147		}
148
149	1	return result;
150		}
151
152		/**
153		* Parses "primary_id" and "dbname" values from the JSON response and
154		* constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
155		* don't parse "synonyms" as they appear to be either redirected or obsolete
156		* in Uniprot.
157		*
158		* @param br
159		* @return
160		* @throws IOException
161		*/
		100% Uncovered Elements: 0 (18) Complexity: 6 Complexity Density: 0.43
162	1	protected List<DBRefEntry> parseResponse(BufferedReader br)...
163		throws IOException
164		{
165	1	JSONParser jp = new JSONParser();
166	1	List<DBRefEntry> result = new ArrayList<DBRefEntry>();
167	1	try
168		{
169	1	JSONArray responses = (JSONArray) jp.parse(br);
170	1	Iterator rvals = responses.iterator();
171	4	while (rvals.hasNext())
172		{
173	3	JSONObject val = (JSONObject) rvals.next();
174	3	String db = val.get("dbname").toString();
175	3	String id = val.get("primary_id").toString();
176	3	if (db != null && id != null
177		&& !GO_GENE_ONTOLOGY.equals(db))
178		{
179	2	db = DBRefUtils.getCanonicalName(db);
180	2	DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
181	2	result.add(dbref);
182		}
183		}
184		} catch (ParseException e)
185		{
186		// ignore
187		}
188	1	return result;
189		}
190
191		private String xrefVersion = "ENSEMBL:0";
192
193		/**
194		* version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
195		*
196		* @return
197		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
198	2	public String getXRefVersion()...
199		{
200	2	return xrefVersion;
201		}
202
203		/**
204		* Returns the URL for the REST endpoint to fetch all cross-references for an
205		* identifier. Note this may return protein cross-references for nucleotide.
206		* Filter the returned list as required.
207		*
208		* @param identifier
209		* @return
210		*/
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 0.5
211	1	protected URL getUrl(String identifier)...
212		{
213	1	String url = getDomain() + "/xrefs/id/" + identifier
214		+ CONTENT_TYPE_JSON + "&all_levels=1";
215	1	try
216		{
217	1	return new URL(url);
218		} catch (MalformedURLException e)
219		{
220	0	return null;
221		}
222		}
223
224		}