X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Furls%2FUrlProviderTest.java;h=1b77d4afb2acec59ae6806e9d310542d8920e57e;hb=f41806761ec9086c852941a7f91c890190fb522a;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"); } }