--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.urls.api.UrlProviderI;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class IdentifiersUrlProviderTest
+{
+ private static final String testIdOrgFile = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
+ + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
+ + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
+ + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
+ + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
+ + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
+ + "\"url\":\"http://identifiers.org/interpro\"},"
+ + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+ + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
+
+ private static final String[] dlinks = {
+ "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot",
+ "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
+ "ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$|ena.embl" };
+
+ private static final String[] dlinks1 = {
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
+
+ private static final String[] dlinks2 = {
+ "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
+
+ private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
+ + "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
+ + "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
+
+ private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
+
+ private static final Vector<String> displayLinks = new Vector<String>(
+ Arrays.asList(dlinks));
+
+ private static final Vector<String> unselDisplayLinks = new Vector<String>(
+ Arrays.asList(unselDlinks));
+
+ private static final Vector<String> displayLinks1 = new Vector<String>(
+ Arrays.asList(dlinks1));
+
+ private static final Vector<String> displayLinks2 = new Vector<String>(
+ Arrays.asList(dlinks2));
+
+ private static final HashMap<String, String> urlMap = new HashMap<String, String>()
+ {
+ {
+ put("MIR:00000005", "http://identifiers.org/uniprot/$DB_ACCESSION$");
+ put("MIR:00000011", "http://identifiers.org/interpro/$DB_ACCESSION$");
+ put("MIR:00000372", "http://identifiers.org/ena.embl/$DB_ACCESSION$");
+ }
+ };
+
+ private String testfile = "";
+
+
+ @BeforeClass(alwaysRun = true)
+ public void setup()
+ {
+ // setup test ids in a file
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("testidsfile", "txt");
+ outFile.deleteOnExit();
+
+ FileWriter fw = new FileWriter(outFile);
+ fw.write(testIdOrgFile);
+ fw.close();
+
+ testfile = outFile.getAbsolutePath();
+
+ } catch (Exception ex)
+ {
+ System.err.println(ex);
+ }
+
+ IdOrgSettings.setDownloadLocation(testfile);
+ }
+
+ /*
+ * Test urls are set and returned correctly
+ */
+ @Test(groups = { "Functional" })
+ public void testUrlLinks()
+ {
+ // creation from cached id list
+ String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
+ UrlProviderI idProv = new IdentifiersUrlProvider(idList);
+
+ assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
+
+ // because UrlProvider does not guarantee order of links, we can't just
+ // compare the output of writeUrlsAsString to a string, hence the hoops here
+ String result = idProv.writeUrlsAsString(true);
+ UrlProviderI up = new IdentifiersUrlProvider(result);
+ assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
+
+ result = idProv.writeUrlsAsString(false);
+ up = new IdentifiersUrlProvider(result);
+ assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
+
+ }
+
+ /*
+ * Test default is set and returned correctly
+ */
+ @Test(groups = { "Functional" })
+ public void testDefaultUrl()
+ {
+ // creation from cached id list
+ String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
+ UrlProviderI idProv = new IdentifiersUrlProvider(idList);
+
+ // initially no default
+ assertEquals(null, idProv.getPrimaryUrl("seqid"));
+
+ // set and then retrieve default
+ assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
+ assertEquals("http://identifiers.org/uniprot/seqid",
+ idProv.getPrimaryUrl("seqid"));
+
+ // ids less than length 4 return null
+ assertEquals(null,
+ idProv.getPrimaryUrl("123"));
+
+ // attempt to set bad default
+ assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
+ // default set to null (as default should have been set elsewhere)
+ assertEquals(null, idProv.getPrimaryUrl("seqid"));
+
+ // chooseDefaultUrl not implemented for IdentifiersUrlProvider
+ assertEquals(null, idProv.choosePrimaryUrl());
+ }
+}
git://source.jalview.org / jalview.git / blobdiff