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SequenceFetcherTest | 42 | 90 | 35 |
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.ws; | |
22 | ||
23 | import jalview.analysis.CrossRef; | |
24 | import jalview.datamodel.Alignment; | |
25 | import jalview.datamodel.AlignmentI; | |
26 | import jalview.datamodel.DBRefSource; | |
27 | import jalview.datamodel.SequenceI; | |
28 | import jalview.gui.JvOptionPane; | |
29 | import jalview.ws.seqfetcher.ASequenceFetcher; | |
30 | import jalview.ws.seqfetcher.DbSourceProxy; | |
31 | ||
32 | import java.util.Enumeration; | |
33 | import java.util.HashMap; | |
34 | import java.util.List; | |
35 | import java.util.Map; | |
36 | import java.util.Vector; | |
37 | ||
38 | import org.testng.Assert; | |
39 | import org.testng.annotations.BeforeClass; | |
40 | import org.testng.annotations.Test; | |
41 | ||
42 | public class SequenceFetcherTest | |
43 | { | |
44 | ||
45 | 1 | @BeforeClass(alwaysRun = true) |
46 | public void setUpJvOptionPane() | |
47 | { | |
48 | 1 | JvOptionPane.setInteractiveMode(false); |
49 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
50 | } | |
51 | ||
52 | 1 | @Test(groups = "Functional") |
53 | public void testNoDuplicatesInFetchDbRefs() | |
54 | { | |
55 | 1 | Map<String, List<DbSourceProxy>> seen = new HashMap<>(); |
56 | 1 | jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher(); |
57 | 1 | String dupes = ""; |
58 | // for (String src : sfetcher.getOrderedSupportedSources()) | |
59 | 1 | for (String src : sfetcher.getNonAlignmentSources()) |
60 | { | |
61 | 5 | List<DbSourceProxy> seenitem = seen.get(src); |
62 | 5 | if (seenitem != null) |
63 | { | |
64 | 0 | dupes += (dupes.length() > 0 ? "," : "") + src; |
65 | } | |
66 | else | |
67 | { | |
68 | 5 | seen.put(src, sfetcher.getSourceProxy(src)); |
69 | } | |
70 | } | |
71 | 1 | if (dupes.length() > 0) |
72 | { | |
73 | 0 | Assert.fail("Duplicate sources : " + dupes); |
74 | } | |
75 | } | |
76 | ||
77 | /** | |
78 | * simple run method to test dbsources. | |
79 | * | |
80 | * @param argv | |
81 | * @j2sIgnore | |
82 | */ | |
83 | 0 | public static void main(String[] argv) |
84 | { | |
85 | // TODO: extracted from SequenceFetcher - convert to network dependent | |
86 | // functional integration test with | |
87 | // assertions | |
88 | ||
89 | 0 | String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n" |
90 | + "With no arguments, all DbSources will be queried with their test Accession number.\n" | |
91 | + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n" | |
92 | + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it."; | |
93 | ||
94 | 0 | if (argv != null && argv.length > 0) |
95 | { | |
96 | 0 | String targs[] = new String[argv.length - 1]; |
97 | 0 | System.arraycopy(argv, 1, targs, 0, targs.length); |
98 | 0 | argv = targs; |
99 | } | |
100 | 0 | if (argv != null && argv.length > 0) |
101 | { | |
102 | 0 | List<DbSourceProxy> sps = new SequenceFetcher() |
103 | .getSourceProxy(argv[0]); | |
104 | ||
105 | 0 | if (sps != null) |
106 | { | |
107 | 0 | for (DbSourceProxy sp : sps) |
108 | { | |
109 | 0 | AlignmentI al = null; |
110 | 0 | try |
111 | { | |
112 | 0 | testRetrieval(argv[0], sp, |
113 | 0 | argv.length > 1 ? argv[1] : sp.getTestQuery()); |
114 | } catch (Exception e) | |
115 | { | |
116 | 0 | e.printStackTrace(); |
117 | 0 | System.err.println("Error when retrieving " |
118 | 0 | + (argv.length > 1 ? argv[1] : sp.getTestQuery()) |
119 | + " from " + argv[0] + "\nUsage: " + usage); | |
120 | } | |
121 | } | |
122 | 0 | return; |
123 | } | |
124 | else | |
125 | { | |
126 | 0 | System.err.println("Can't resolve " + argv[0] |
127 | + " as a database name. Allowed values are :\n" | |
128 | + new SequenceFetcher().getSupportedDb()); | |
129 | } | |
130 | 0 | System.out.println(usage); |
131 | 0 | return; |
132 | } | |
133 | 0 | ASequenceFetcher sfetcher = new SequenceFetcher(); |
134 | 0 | String[] dbSources = sfetcher.getSupportedDb(); |
135 | 0 | for (int dbsource = 0; dbsource < dbSources.length; dbsource++) |
136 | { | |
137 | 0 | String db = dbSources[dbsource]; |
138 | // skip me | |
139 | 0 | if (db.equals(DBRefSource.PDB)) |
140 | { | |
141 | 0 | continue; |
142 | } | |
143 | 0 | for (DbSourceProxy sp : sfetcher.getSourceProxy(db)) |
144 | { | |
145 | 0 | testRetrieval(db, sp, sp.getTestQuery()); |
146 | } | |
147 | } | |
148 | ||
149 | } | |
150 | ||
151 | 0 | private static void testRetrieval(String db, DbSourceProxy sp, |
152 | String testQuery) | |
153 | { | |
154 | 0 | AlignmentI ds = null; |
155 | 0 | Vector<Object[]> noProds = new Vector<>(); |
156 | 0 | System.out.println("Source: " + sp.getDbName() + " (" + db |
157 | + "): retrieving test:" + sp.getTestQuery()); | |
158 | { | |
159 | 0 | AlignmentI al = null; |
160 | 0 | try |
161 | { | |
162 | 0 | al = sp.getSequenceRecords(testQuery); |
163 | 0 | if (al != null && al.getHeight() > 0) |
164 | { | |
165 | 0 | boolean dna = sp.isDnaCoding(); |
166 | 0 | al.setDataset(null); |
167 | 0 | AlignmentI alds = al.getDataset(); |
168 | // try and find products | |
169 | 0 | CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds); |
170 | 0 | List<String> types = crossRef.findXrefSourcesForSequences(dna); |
171 | 0 | if (types != null) |
172 | { | |
173 | 0 | System.out.println("Xref Types for: " + (dna ? "dna" : "prot")); |
174 | 0 | for (String source : types) |
175 | { | |
176 | 0 | System.out.println("Type: " + source); |
177 | 0 | SequenceI[] prod = crossRef.findXrefSequences(source, dna) |
178 | .getSequencesArray(); | |
179 | 0 | System.out.println( |
180 | 0 | "Found " + ((prod == null) ? "no" : "" + prod.length) |
181 | + " products"); | |
182 | 0 | if (prod != null) |
183 | { | |
184 | 0 | for (int p = 0; p < prod.length; p++) |
185 | { | |
186 | 0 | System.out.println( |
187 | "Prod " + p + ": " + prod[p].getDisplayId(true)); | |
188 | } | |
189 | } | |
190 | } | |
191 | } | |
192 | else | |
193 | { | |
194 | 0 | noProds.addElement( |
195 | 0 | (dna ? new Object[] |
196 | { al, al } : new Object[] { al })); | |
197 | } | |
198 | ||
199 | } | |
200 | } catch (Exception ex) | |
201 | { | |
202 | 0 | System.out.println("ERROR:Failed to retrieve test query."); |
203 | 0 | ex.printStackTrace(System.out); |
204 | } | |
205 | ||
206 | 0 | if (al == null) |
207 | { | |
208 | 0 | System.out.println("ERROR:No alignment retrieved."); |
209 | 0 | StringBuffer raw = sp.getRawRecords(); |
210 | 0 | if (raw != null) |
211 | { | |
212 | 0 | System.out.println(raw.toString()); |
213 | } | |
214 | else | |
215 | { | |
216 | 0 | System.out.println("ERROR:No Raw results."); |
217 | } | |
218 | } | |
219 | else | |
220 | { | |
221 | 0 | System.out.println("Retrieved " + al.getHeight() + " sequences."); |
222 | 0 | if (ds == null) |
223 | { | |
224 | 0 | ds = al.getDataset(); |
225 | } | |
226 | else | |
227 | { | |
228 | 0 | ds.append(al.getDataset()); |
229 | 0 | al.setDataset(ds); |
230 | } | |
231 | } | |
232 | 0 | System.out.flush(); |
233 | 0 | System.err.flush(); |
234 | } | |
235 | 0 | if (noProds.size() > 0) |
236 | { | |
237 | 0 | Enumeration<Object[]> ts = noProds.elements(); |
238 | 0 | while (ts.hasMoreElements()) |
239 | ||
240 | { | |
241 | 0 | Object[] typeSq = ts.nextElement(); |
242 | 0 | boolean dna = (typeSq.length > 1); |
243 | 0 | AlignmentI al = (AlignmentI) typeSq[0]; |
244 | 0 | System.out.println("Trying getProducts for " |
245 | + al.getSequenceAt(0).getDisplayId(true)); | |
246 | 0 | System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot")); |
247 | // have a bash at finding the products amongst all the retrieved | |
248 | // sequences. | |
249 | 0 | SequenceI[] seqs = al.getSequencesArray(); |
250 | 0 | Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null, |
251 | dna); | |
252 | 0 | System.out.println("Found " |
253 | 0 | + ((prodal == null) ? "no" : "" + prodal.getHeight()) |
254 | + " products"); | |
255 | 0 | if (prodal != null) |
256 | { | |
257 | 0 | SequenceI[] prod = prodal.getSequencesArray(); // note |
258 | // should | |
259 | // test | |
260 | // rather | |
261 | // than | |
262 | // throw | |
263 | // away | |
264 | // codon | |
265 | // mapping | |
266 | // (if | |
267 | // present) | |
268 | 0 | for (int p = 0; p < prod.length; p++) |
269 | { | |
270 | 0 | System.out.println( |
271 | "Prod " + p + ": " + prod[p].getDisplayId(true)); | |
272 | } | |
273 | } | |
274 | } | |
275 | } | |
276 | } | |
277 | } |