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Coverage Report

  1. Project Clover database Wed Nov 13 2024 18:27:33 GMT
  2. Package jalview.ext.ensembl

File EnsemblXref.java

 

Coverage histogram

../../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

4
26
8
1
182
89
14
0.54
3.25
8
1.75

Classes

Class Line # Actions
EnsemblXref 46 26 14
0.763157976.3%
 

Contributing tests

This file is covered by 1 test. .

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