X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FSequenceFetcherTest.java;h=0b501ee841f35a44dc3283c02f4c05ef893a9040;hb=60134d1200ccd43a13205159cc10bb3695a55499;hp=7a9b5532ac96e1cbb7d2d14de407971acabfbab3;hpb=409fd993c6e32e999b24082aae107a043a590f8f;p=jalview.git
diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 7a9b553..0b501ee 100644
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -1,9 +1,31 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws;
+import jalview.analysis.CrossRef;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
@@ -11,9 +33,18 @@ import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
+
public class SequenceFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* simple run method to test dbsources.
*
@@ -21,30 +52,26 @@ public class SequenceFetcherTest
*/
public static void main(String[] argv)
{
- // TODO: extracted from SequenceFetcher - convert to proper unit test with
+ // TODO: extracted from SequenceFetcher - convert to network dependent
+ // functional integration test with
// assertions
- AlignmentI ds = null;
- Vector noProds = new Vector();
String usage = "SequenceFetcher.main [-nodas] [ []]\n"
+ "With no arguments, all DbSources will be queried with their test Accession number.\n"
+ "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"
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.\n"
- + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
- boolean withDas = true;
- if (argv != null && argv.length > 0
- && argv[0].toLowerCase().startsWith("-nodas"))
+ + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.";
+
+ if (argv != null && argv.length > 0)
{
- withDas = false;
String targs[] = new String[argv.length - 1];
System.arraycopy(argv, 1, targs, 0, targs.length);
argv = targs;
}
if (argv != null && argv.length > 0)
{
- List sps = new SequenceFetcher(withDas)
+ List sps = new SequenceFetcher()
.getSourceProxy(argv[0]);
-
+
if (sps != null)
{
for (DbSourceProxy sp : sps)
@@ -52,8 +79,8 @@ public class SequenceFetcherTest
AlignmentI al = null;
try
{
- al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
- .getTestQuery());
+ testRetrieval(argv[0], sp,
+ argv.length > 1 ? argv[1] : sp.getTestQuery());
} catch (Exception e)
{
e.printStackTrace();
@@ -61,16 +88,6 @@ public class SequenceFetcherTest
+ (argv.length > 1 ? argv[1] : sp.getTestQuery())
+ " from " + argv[0] + "\nUsage: " + usage);
}
- SequenceI[] prod = al.getSequencesArray();
- if (al != null)
- {
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true) + " : "
- + prod[p].getDescription());
- }
- }
}
return;
}
@@ -83,7 +100,7 @@ public class SequenceFetcherTest
System.out.println(usage);
return;
}
- ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
+ ASequenceFetcher sfetcher = new SequenceFetcher();
String[] dbSources = sfetcher.getSupportedDb();
for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
{
@@ -95,138 +112,135 @@ public class SequenceFetcherTest
}
for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
{
- System.out.println("Source: " + sp.getDbName() + " (" + db
- + "): retrieving test:" + sp.getTestQuery());
- AlignmentI al = null;
- try
+ testRetrieval(db, sp, sp.getTestQuery());
+ }
+ }
+
+ }
+
+ private static void testRetrieval(String db, DbSourceProxy sp,
+ String testQuery)
+ {
+ AlignmentI ds = null;
+ Vector noProds = new Vector<>();
+ System.out.println("Source: " + sp.getDbName() + " (" + db
+ + "): retrieving test:" + sp.getTestQuery());
+ {
+ AlignmentI al = null;
+ try
+ {
+ al = sp.getSequenceRecords(testQuery);
+ if (al != null && al.getHeight() > 0)
{
- al = sp.getSequenceRecords(sp.getTestQuery());
- if (al != null && al.getHeight() > 0)
+ boolean dna = sp.isDnaCoding();
+ al.setDataset(null);
+ AlignmentI alds = al.getDataset();
+ // try and find products
+ CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds);
+ List types = crossRef.findXrefSourcesForSequences(dna);
+ if (types != null)
{
- boolean dna = sp.isDnaCoding();
- // try and find products
- String types[] = jalview.analysis.CrossRef
- .findSequenceXrefTypes(dna, al.getSequencesArray());
- if (types != null)
+ System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
+ for (String source : types)
{
- System.out.println("Xref Types for: "
- + (dna ? "dna" : "prot"));
- for (int t = 0; t < types.length; t++)
+ System.out.println("Type: " + source);
+ SequenceI[] prod = crossRef.findXrefSequences(source, dna)
+ .getSequencesArray();
+ System.out.println("Found "
+ + ((prod == null) ? "no" : "" + prod.length)
+ + " products");
+ if (prod != null)
{
- System.out.println("Type: " + types[t]);
- SequenceI[] prod = jalview.analysis.CrossRef
- .findXrefSequences(al.getSequencesArray(), dna,
- types[t]).getSequencesArray();
- System.out.println("Found "
- + ((prod == null) ? "no" : "" + prod.length)
- + " products");
- if (prod != null)
+ for (int p = 0; p < prod.length; p++)
{
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
+ System.out.println("Prod " + p + ": "
+ + prod[p].getDisplayId(true));
}
}
}
- else
- {
- noProds.addElement((dna ? new Object[] { al, al }
- : new Object[] { al }));
- }
-
- }
- } catch (Exception ex)
- {
- System.out.println("ERROR:Failed to retrieve test query.");
- ex.printStackTrace(System.out);
- }
-
- if (al == null)
- {
- System.out.println("ERROR:No alignment retrieved.");
- StringBuffer raw = sp.getRawRecords();
- if (raw != null)
- {
- System.out.println(raw.toString());
}
else
{
- System.out.println("ERROR:No Raw results.");
+ noProds.addElement((dna ? new Object[] { al, al }
+ : new Object[] { al }));
}
+
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("ERROR:Failed to retrieve test query.");
+ ex.printStackTrace(System.out);
+ }
+
+ if (al == null)
+ {
+ System.out.println("ERROR:No alignment retrieved.");
+ StringBuffer raw = sp.getRawRecords();
+ if (raw != null)
+ {
+ System.out.println(raw.toString());
}
else
{
- System.out.println("Retrieved " + al.getHeight() + " sequences.");
- for (int s = 0; s < al.getHeight(); s++)
- {
- SequenceI sq = al.getSequenceAt(s);
- while (sq.getDatasetSequence() != null)
- {
- sq = sq.getDatasetSequence();
-
- }
- if (ds == null)
- {
- ds = new Alignment(new SequenceI[] { sq });
-
- }
- else
- {
- ds.addSequence(sq);
- }
- }
+ System.out.println("ERROR:No Raw results.");
}
- System.out.flush();
- System.err.flush();
-
}
- if (noProds.size() > 0)
+ else
+ {
+ System.out.println("Retrieved " + al.getHeight() + " sequences.");
+ if (ds == null)
+ {
+ ds = al.getDataset();
+ }
+ else
+ {
+ ds.append(al.getDataset());
+ al.setDataset(ds);
+ }
+ }
+ System.out.flush();
+ System.err.flush();
+ }
+ if (noProds.size() > 0)
+ {
+ Enumeration ts = noProds.elements();
+ while (ts.hasMoreElements())
+
{
- Enumeration ts = noProds.elements();
- while (ts.hasMoreElements())
-
+ Object[] typeSq = ts.nextElement();
+ boolean dna = (typeSq.length > 1);
+ AlignmentI al = (AlignmentI) typeSq[0];
+ System.out.println("Trying getProducts for "
+ + al.getSequenceAt(0).getDisplayId(true));
+ System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));
+ // have a bash at finding the products amongst all the retrieved
+ // sequences.
+ SequenceI[] seqs = al.getSequencesArray();
+ Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
+ dna);
+ System.out.println("Found "
+ + ((prodal == null) ? "no" : "" + prodal.getHeight())
+ + " products");
+ if (prodal != null)
{
- Object[] typeSq = (Object[]) ts.nextElement();
- boolean dna = (typeSq.length > 1);
- AlignmentI al = (AlignmentI) typeSq[0];
- System.out.println("Trying getProducts for "
- + al.getSequenceAt(0).getDisplayId(true));
- System.out.println("Search DS Xref for: "
- + (dna ? "dna" : "prot"));
- // have a bash at finding the products amongst all the retrieved
- // sequences.
- SequenceI[] seqs = al.getSequencesArray();
- Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
- seqs, dna, null, ds);
- System.out.println("Found "
- + ((prodal == null) ? "no" : "" + prodal.getHeight())
- + " products");
- if (prodal != null)
+ SequenceI[] prod = prodal.getSequencesArray(); // note
+ // should
+ // test
+ // rather
+ // than
+ // throw
+ // away
+ // codon
+ // mapping
+ // (if
+ // present)
+ for (int p = 0; p < prod.length; p++)
{
- SequenceI[] prod = prodal.getSequencesArray(); // note
- // should
- // test
- // rather
- // than
- // throw
- // away
- // codon
- // mapping
- // (if
- // present)
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
+ System.out.println("Prod " + p + ": "
+ + prod[p].getDisplayId(true));
}
}
-
}
-
}
}
-
}