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  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.ws

File SequenceFetcherTest.java

 

Code metrics

52
90
4
1
277
218
35
0.39
22.5
4
8.75

Classes

Class Line # Actions
SequenceFetcherTest 42 90 35
0.095890419.6%
 

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.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 toggle @BeforeClass(alwaysRun = true)
46    public void setUpJvOptionPane()
47    {
48  1 JvOptionPane.setInteractiveMode(false);
49  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50    }
51   
 
52  1 toggle @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 toggle 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 toggle 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    }