X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Fdbsources%2FRemoteFormatTest.java;h=d48ff918c5928b48d5872aa58a62cb5841dbad8e;hb=b4f40b3f92e17f4373ecf047b393f579bc88164d;hp=90d4472246f64bd27e65346ae9cfa2d5336cf455;hpb=7451c6419c9c94627f79d044228db55b90e9b4cf;p=jalview.git
diff --git a/test/jalview/ws/dbsources/RemoteFormatTest.java b/test/jalview/ws/dbsources/RemoteFormatTest.java
index 90d4472..d48ff91 100644
--- a/test/jalview/ws/dbsources/RemoteFormatTest.java
+++ b/test/jalview/ws/dbsources/RemoteFormatTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.dbsources;
import static org.testng.Assert.assertEquals;
@@ -51,14 +71,15 @@ public class RemoteFormatTest
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
- sf = new SequenceFetcher(false);
+ sf = new SequenceFetcher();
}
@DataProvider(name = "AccessionData")
protected Object[][] getAccessions()
{
return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
- { DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
+ { DBRefSource.PDB, "1QIP" },
+ { DBRefSource.EMBL, "X53828" },
{ DBRefSource.EMBLCDS, "CAA37824" },
{ DBRefSource.ENSEMBL, "ENSG00000157764" },
{ new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
@@ -80,7 +101,7 @@ public class RemoteFormatTest
SequenceI sq = al.getSequenceAt(0);
// suppress this check as only Uniprot and PDB acquire PDB refs
// assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
- assertTrue(sq.getDBRefs().length > 0, "No DBRef on sequence.");
+ assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
// suppress this test as only certain databases provide 'primary' dbrefs
// assertFalse(sq.getPrimaryDBRefs().isEmpty());
int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
@@ -92,21 +113,21 @@ public class RemoteFormatTest
@Test(groups = { "Network" })
public void testUniprotFreeTextSearch() throws Exception
{
- List wantedFields = new ArrayList();
+ List wantedFields = new ArrayList<>();
FTSRestClientI client = UniProtFTSRestClient.getInstance();
wantedFields.add(client.getDataColumnByNameOrCode("id"));
wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
wantedFields.add(client.getDataColumnByNameOrCode("organism"));
wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
wantedFields.add(client.getDataColumnByNameOrCode("length"));
-
+
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
request.setFieldToSearchBy("Search All");
request.setSearchTerm("metanephrops"); // lobster!
request.setWantedFields(wantedFields);
-
+
FTSRestResponse response;
response = client.executeRequest(request);
assertTrue(response.getNumberOfItemsFound() > 20);