X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Furls%2FUrlProviderTest.java;h=1b77d4afb2acec59ae6806e9d310542d8920e57e;hb=279c6495df1a0de231600a2d283098c7411c4730;hp=3b52c039a8443725fd3d6dccb729c6e0cc3af88b;hpb=a45bb4b4b3f6ce4067fc94acbfc546637fb30b06;p=jalview.git
diff --git a/test/jalview/urls/UrlProviderTest.java b/test/jalview/urls/UrlProviderTest.java
index 3b52c03..1b77d4a 100644
--- a/test/jalview/urls/UrlProviderTest.java
+++ b/test/jalview/urls/UrlProviderTest.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.urls;
import jalview.urls.api.UrlProviderI;
@@ -9,48 +29,47 @@ import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
-import java.util.Vector;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+public class UrlProviderTest
+{
-public class UrlProviderTest {
-
// Test identifiers.org download file
- private static final String testIdOrgString = "[{\"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 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\"}]}";
private UrlProviderI prov;
@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 UrlProviderTest test: "
- + e.getMessage());
- }
-
- IdOrgSettings.setDownloadLocation(temp.getPath());
+ // 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 UrlProviderTest test: " + e.getMessage());
+ }
+
+ IdOrgSettings.setDownloadLocation(temp.getPath());
String defaultUrlString = "No default";
String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
@@ -60,7 +79,7 @@ public class UrlProviderTest {
DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
defaultUrlString, cachedUrlList, userUrlList);
prov = factory.createUrlProvider();
- }
+ }
@Test(groups = { "Functional" })
public void testInitUrlProvider()
@@ -70,11 +89,11 @@ public class UrlProviderTest {
UrlConstants.DEFAULT_STRING.length());
// chooses EMBL url when default Url id does not exist in provided url lists
- Assert.assertEquals(prov.getDefaultUrlId(), UrlConstants.DEFAULT_LABEL);
- Assert.assertEquals(prov.getDefaultUrl("FER_CAPAN"),
+ Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
+ Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
- Vector menulinks = prov.getLinksForMenu();
+ List menulinks = prov.getLinksForMenu();
List allLinks = prov.getLinksForTable();
// 9 links in provider - 4 from id file, 4 custom links, 1 additional
@@ -84,38 +103,40 @@ public class UrlProviderTest {
// 6 links in menu (cachedUrlList) + new default
Assert.assertEquals(menulinks.size(), 6);
- 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/$DB_ACCESSION$"));
- Assert.assertTrue(menulinks
- .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$"));
- Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
- + UrlConstants.SEP + emblUrl));
+ 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"));
+ Assert.assertTrue(menulinks.contains(
+ UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
}
@Test(groups = { "Functional" })
public void testSetDefaultUrl()
{
// set custom url as default
- Assert.assertTrue(prov.setDefaultUrl("Test1"));
- Assert.assertEquals(prov.getDefaultUrlId(), "Test1");
+ Assert.assertTrue(prov.setPrimaryUrl("Test1"));
+ Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
// set identifiers url as default
- Assert.assertTrue(prov.setDefaultUrl("MIR:00000011"));
- Assert.assertEquals(prov.getDefaultUrlId(), "MIR:00000011");
+ Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
+ Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDefaultUrlWrongly()
{
// don't allow default to be a non-key
- prov.setDefaultUrl("not-a-key");
+ prov.setPrimaryUrl("not-a-key");
}
}