JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / test / jalview / urls / DesktopUrlProviderFactoryTest.java

diff --git a/test/jalview/urls/DesktopUrlProviderFactoryTest.java b/test/jalview/urls/DesktopUrlProviderFactoryTest.java
deleted file mode 100644 (file)
index cc55034..0000000
--- a/test/jalview/urls/DesktopUrlProviderFactoryTest.java
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * 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 jalview.urls.api.UrlProviderI;
-import jalview.urls.desktop.DesktopUrlProviderFactory;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-public class DesktopUrlProviderFactoryTest
-{
-  private static final String testIdOrgString = "{\"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\"}]}";
-
-  @BeforeMethod(alwaysRun = true)
-  public void setup()
-  {
-    // make a dummy identifiers.org download file
-    File temp = null;
-
-    try
-    {
-      temp = File.createTempFile("tempfile", ".tmp");
-      temp.deleteOnExit();
-      BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
-      bw.write(testIdOrgString);
-      bw.close();
-    } catch (IOException e)
-    {
-      System.out
-              .println("Error initialising DesktopUrlProviderFactoryTest test: "
-                      + e.getMessage());
-    }
-
-    IdOrgSettings.setDownloadLocation(temp.getPath());
-  }
-
-  @Test(groups = { "Functional" })
-  public void testCreateUrlProvider()
-  {
-    String defaultUrlString = "Test1";
-    String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
-    String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
-            + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
-    String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
-
-    DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
-            defaultUrlString, cachedUrlList, userUrlList);
-    UrlProviderI prov = factory.createUrlProvider();
-
-    // default url correctly set
-    Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
-    Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
-            defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
-
-    List<String> menulinks = prov.getLinksForMenu();
-    List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
-
-    // 8 links in provider - 4 from id file, 4 custom links
-    Assert.assertEquals(allLinks.size(), 8);
-
-    // 5 links in menu (cachedUrlList)
-    Assert.assertEquals(menulinks.size(), 5);
-
-    Assert.assertTrue(menulinks
-            .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
-    Assert.assertTrue(menulinks
-            .contains("Test2|http://test2/$DB_ACCESSION$"));
-    Assert.assertTrue(menulinks
-            .contains("Test3|http://test3/$SEQUENCE_ID$"));
-    Assert.assertTrue(menulinks
-            .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
-    Assert.assertTrue(menulinks
-            .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
-  }
-}