Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblXref	44	26	14	0.763157976.3%	Show methods

Class EnsemblXref

Class EnsemblXref	Line # 44	Total Statements 26	Complexity 14	TOTAL Coverage 0.763157976.3%
EnsemblXref(String,String,String)   EnsemblXref(String,String,String)	5656	3.03	1.01	1.0 1.0100%
getDbName() : String   getDbName() : String	6464	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	7070	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	7676	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	8282	1.01	1.01	0.0 0.00%
getCrossReferences(String) : List<DBRefEntry>   getCrossReferences(String) : List<DBRefEntry>	9999	14.014	6.06	1.0 1.0100%
getXRefVersion() : String   getXRefVersion() : String	154154	1.01	1.01	1.0 1.0100%
getUrl(String) : URL   getUrl(String) : URL	167167	4.04	2.02	0.75 0.7575%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7631579	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 java.io.IOException;
24		import java.net.MalformedURLException;
25		import java.net.URL;
26		import java.util.ArrayList;
27		import java.util.Iterator;
28		import java.util.List;
29		import java.util.Map;
30
31		import org.json.simple.parser.ParseException;
32
33		import jalview.datamodel.AlignmentI;
34		import jalview.datamodel.DBRefEntry;
35		import jalview.util.DBRefUtils;
36
37		/**
38		* A class to fetch cross-references from Ensembl by calling the /xrefs REST
39		* service
40		*
41		* @author gmcarstairs
42		* @see http://rest.ensembl.org/documentation/info/xref_id
43		*/
		76.3% Uncovered Elements: 9 (38) Complexity: 14 Complexity Density: 0.54
44		class EnsemblXref extends EnsemblRestClient
45		{
46
47		private static final String GO_GENE_ONTOLOGY = "GO";
48
49		private String dbName = "ENSEMBL (xref)";
50
51		/**
52		* Constructor given the target domain to fetch data from
53		*
54		* @param d
55		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
56	1	public EnsemblXref(String d, String dbSource, String version)...
57		{
58	1	super(d);
59	1	dbName = dbSource;
60	1	xrefVersion = dbSource + ":" + version;
61
62		}
63
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	@Override...
65		public String getDbName()
66		{
67	0	return dbName;
68		}
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	@Override...
71		public AlignmentI getSequenceRecords(String queries) throws Exception
72		{
73	0	return null;
74		}
75
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	@Override...
77		protected URL getUrl(List<String> ids) throws MalformedURLException
78		{
79	0	return getUrl(ids.get(0));
80		}
81
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		protected boolean useGetRequest()
84		{
85	0	return true;
86		}
87
88		/**
89		* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
90		* ("primary_id") for the given identifier (Ensembl accession id) and database
91		* names. The "dbname" returned by Ensembl is canonicalised to Jalview's
92		* standard version, and a DBRefEntry constructed. Currently takes all
93		* identifiers apart from GO terms and synonyms.
94		*
95		* @param identifier
96		* an Ensembl stable identifier
97		* @return
98		*/
		100% Uncovered Elements: 0 (18) Complexity: 6 Complexity Density: 0.43
99	1	@SuppressWarnings("unchecked")...
100		public List<DBRefEntry> getCrossReferences(String identifier)
101		{
102	1	List<DBRefEntry> result = new ArrayList<>();
103	1	List<String> ids = new ArrayList<>();
104	1	ids.add(identifier);
105
106	1	try
107		{
108	1	Iterator<Object> rvals = (Iterator<Object>) getJSON(
109		getUrl(identifier), ids, -1, MODE_ITERATOR, null);
110	4	while (rvals.hasNext())
111		{
112	3	Map<String, Object> val = (Map<String, Object>) rvals.next();
113	3	String db = val.get("dbname").toString();
114	3	String id = val.get("primary_id").toString();
115	3	if (db != null && id != null && !GO_GENE_ONTOLOGY.equals(db))
116		{
117	2	db = DBRefUtils.getCanonicalName(db);
118	2	DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
119	2	result.add(dbref);
120		}
121		}
122		} catch (ParseException | IOException e)
123		{
124		// ignore
125		}
126	1	return result;
127		}
128
129		// /**
130		// * Parses "primary_id" and "dbname" values from the JSON response and
131		// * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note
132		// we
133		// * don't parse "synonyms" as they appear to be either redirected or obsolete
134		// * in Uniprot.
135		// *
136		// * @param br
137		// * @return
138		// * @throws IOException
139		// */
140		// @SuppressWarnings("unchecked")
141		// protected List<DBRefEntry> parseResponse(BufferedReader br)
142		// throws IOException
143		// {
144		// return result;
145		// }
146		//
147		private String xrefVersion = "ENSEMBL:0";
148
149		/**
150		* version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
151		*
152		* @return
153		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
154	2	public String getXRefVersion()...
155		{
156	2	return xrefVersion;
157		}
158
159		/**
160		* Returns the URL for the REST endpoint to fetch all cross-references for an
161		* identifier. Note this may return protein cross-references for nucleotide.
162		* Filter the returned list as required.
163		*
164		* @param identifier
165		* @return
166		*/
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 0.5
167	1	protected URL getUrl(String identifier)...
168		{
169	1	String url = getDomain() + "/xrefs/id/" + identifier + CONTENT_TYPE_JSON
170		+ "&all_levels=1";
171	1	try
172		{
173	1	return new URL(url);
174		} catch (MalformedURLException e)
175		{
176	0	return null;
177		}
178		}
179
180		}