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EnsemblInfo | 41 | 20 | 13 |
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.util.Locale; | |
24 | ||
25 | import jalview.datamodel.AlignmentI; | |
26 | import jalview.datamodel.DBRefSource; | |
27 | import jalview.util.JSONUtils; | |
28 | ||
29 | import java.io.BufferedReader; | |
30 | import java.io.IOException; | |
31 | import java.net.MalformedURLException; | |
32 | import java.net.URL; | |
33 | import java.util.HashMap; | |
34 | import java.util.Iterator; | |
35 | import java.util.List; | |
36 | import java.util.Map; | |
37 | import java.util.Set; | |
38 | ||
39 | import org.json.simple.parser.ParseException; | |
40 | ||
41 | public class EnsemblInfo extends EnsemblRestClient | |
42 | { | |
43 | ||
44 | /* | |
45 | * cached results of REST /info/divisions service, currently | |
46 | * <pre> | |
47 | * { | |
48 | * { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"}, | |
49 | * "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"}, | |
50 | * "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"}, | |
51 | * "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"}, | |
52 | * "ENSEMBLPLANTS", "http://rest.ensemblgenomes.org"}, | |
53 | * "ENSEMBL", "http://rest.ensembl.org" } | |
54 | * } | |
55 | * </pre> | |
56 | * The values for EnsemblGenomes are retrieved by a REST call, that for | |
57 | * Ensembl is added programmatically for convenience of lookup | |
58 | */ | |
59 | private static Map<String, String> divisions; | |
60 | ||
61 | 0 | @Override |
62 | public String getDbName() | |
63 | { | |
64 | 0 | return "ENSEMBL"; |
65 | } | |
66 | ||
67 | 0 | @Override |
68 | public AlignmentI getSequenceRecords(String queries) throws Exception | |
69 | { | |
70 | 0 | return null; |
71 | } | |
72 | ||
73 | 0 | @Override |
74 | protected URL getUrl(List<String> ids) throws MalformedURLException | |
75 | { | |
76 | 0 | return null; |
77 | } | |
78 | ||
79 | 0 | @Override |
80 | protected boolean useGetRequest() | |
81 | { | |
82 | 0 | return true; |
83 | } | |
84 | ||
85 | /** | |
86 | * Answers the domain (http://rest.ensembl.org or | |
87 | * http://rest.ensemblgenomes.org) for the given division, or null if not | |
88 | * recognised by Ensembl. | |
89 | * | |
90 | * @param division | |
91 | * @return | |
92 | */ | |
93 | 0 | public String getDomain(String division) |
94 | { | |
95 | 0 | if (divisions == null) |
96 | { | |
97 | 0 | fetchDivisions(); |
98 | } | |
99 | 0 | return divisions.get(division.toUpperCase(Locale.ROOT)); |
100 | } | |
101 | ||
102 | /** | |
103 | * On first request only, populate the lookup map by fetching the list of | |
104 | * divisions known to EnsemblGenomes. | |
105 | */ | |
106 | 0 | void fetchDivisions() |
107 | { | |
108 | 0 | divisions = new HashMap<>(); |
109 | ||
110 | /* | |
111 | * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL" | |
112 | */ | |
113 | 0 | divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), |
114 | ensemblDomain); | |
115 | 0 | try |
116 | { | |
117 | 0 | @SuppressWarnings("unchecked") |
118 | Iterator<Object> rvals = (Iterator<Object>) getJSON( | |
119 | getDivisionsUrl(ensemblGenomesDomain), null, -1, | |
120 | MODE_ITERATOR, null); | |
121 | 0 | if (rvals == null) |
122 | 0 | return; |
123 | 0 | while (rvals.hasNext()) |
124 | { | |
125 | 0 | String division = rvals.next().toString(); |
126 | 0 | divisions.put(division.toUpperCase(Locale.ROOT), |
127 | ensemblGenomesDomain); | |
128 | } | |
129 | } catch (IOException | ParseException | NumberFormatException e) | |
130 | { | |
131 | // ignore | |
132 | } | |
133 | } | |
134 | ||
135 | /** | |
136 | * Constructs the URL for the EnsemblGenomes /info/divisions REST service | |
137 | * | |
138 | * @param domain | |
139 | * TODO | |
140 | * | |
141 | * @return | |
142 | * @throws MalformedURLException | |
143 | */ | |
144 | 0 | URL getDivisionsUrl(String domain) throws MalformedURLException |
145 | { | |
146 | 0 | return new URL( |
147 | domain + "/info/divisions?content-type=application/json"); | |
148 | } | |
149 | ||
150 | /** | |
151 | * Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes | |
152 | * | |
153 | * @return | |
154 | */ | |
155 | 0 | public Set<String> getDivisions() |
156 | { | |
157 | 0 | if (divisions == null) |
158 | { | |
159 | 0 | fetchDivisions(); |
160 | } | |
161 | ||
162 | 0 | return divisions.keySet(); |
163 | } | |
164 | } |