X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FUrlLinkTest.java;h=cea1bf2a973cd4b7b0d80eb7be2d63096e08e4f0;hb=b7e9e2edf0c1557089eff0e4b5c17c0b31e698c2;hp=45ef6affd15d21e25cab7cd32b021051e5622906;hpb=f7061cf12f703969bf3e22fc7e37f5712b9df10a;p=jalview.git diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java index 45ef6af..cea1bf2 100644 --- a/test/jalview/util/UrlLinkTest.java +++ b/test/jalview/util/UrlLinkTest.java @@ -20,18 +20,37 @@ */ package jalview.util; +import static jalview.util.UrlConstants.DB_ACCESSION; import static jalview.util.UrlConstants.SEQUENCE_ID; -import static jalview.util.UrlConstants.SEQUENCE_NAME; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.Sequence; +import jalview.gui.JvOptionPane; + +import java.util.ArrayList; +import java.util.Comparator; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class UrlLinkTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + final static String DB = "Test"; final static String URL_PREFIX = "http://www.jalview.org/"; @@ -43,7 +62,7 @@ public class UrlLinkTest final static String DELIM = "$"; final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/="; - + final static String REGEX_RUBBISH = "=/[0-9]++/="; /** @@ -52,39 +71,39 @@ public class UrlLinkTest @Test(groups = { "Functional" }) public void testUrlLinkCreationNoRegex() { - // SEQUENCE_NAME - UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME + // SEQUENCE_ID + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM + URL_SUFFIX); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX, ul.getUrl_prefix()); - assertEquals(URL_SUFFIX, ul.getUrl_suffix()); + assertEquals(URL_PREFIX, ul.getUrlPrefix()); + assertEquals(URL_SUFFIX, ul.getUrlSuffix()); assertTrue(ul.isDynamic()); - assertFalse(ul.usesSeqId()); + assertFalse(ul.usesDBAccession()); assertNull(ul.getRegexReplace()); assertTrue(ul.isValid()); assertNull(ul.getInvalidMessage()); - // SEQUENCE_ID - ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM + // DB_ACCESSION + ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM + URL_SUFFIX); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX, ul.getUrl_prefix()); - assertEquals(URL_SUFFIX, ul.getUrl_suffix()); + assertEquals(URL_PREFIX, ul.getUrlPrefix()); + assertEquals(URL_SUFFIX, ul.getUrlSuffix()); assertTrue(ul.isDynamic()); - assertTrue(ul.usesSeqId()); + assertTrue(ul.usesDBAccession()); assertNull(ul.getRegexReplace()); assertTrue(ul.isValid()); assertNull(ul.getInvalidMessage()); // Not dynamic ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1)); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix()); + assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix()); assertFalse(ul.isDynamic()); - assertFalse(ul.usesSeqId()); + assertFalse(ul.usesDBAccession()); assertNull(ul.getRegexReplace()); assertTrue(ul.isValid()); assertNull(ul.getInvalidMessage()); @@ -96,51 +115,49 @@ public class UrlLinkTest @Test(groups = { "Functional" }) public void testUrlLinkCreationWithRegex() { - // SEQUENCE_NAME - UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME + // SEQUENCE_ID + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + REGEX_NESTED + DELIM + URL_SUFFIX); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX, ul.getUrl_prefix()); - assertEquals(URL_SUFFIX, ul.getUrl_suffix()); + assertEquals(URL_PREFIX, ul.getUrlPrefix()); + assertEquals(URL_SUFFIX, ul.getUrlSuffix()); assertTrue(ul.isDynamic()); - assertFalse(ul.usesSeqId()); + assertFalse(ul.usesDBAccession()); assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2), ul.getRegexReplace()); assertTrue(ul.isValid()); assertNull(ul.getInvalidMessage()); - // SEQUENCE_ID - ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + // DB_ACCESSION + ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + REGEX_NESTED + DELIM + URL_SUFFIX); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX, ul.getUrl_prefix()); - assertEquals(URL_SUFFIX, ul.getUrl_suffix()); + assertEquals(URL_PREFIX, ul.getUrlPrefix()); + assertEquals(URL_SUFFIX, ul.getUrlSuffix()); assertTrue(ul.isDynamic()); - assertTrue(ul.usesSeqId()); + assertTrue(ul.usesDBAccession()); assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2), ul.getRegexReplace()); assertTrue(ul.isValid()); assertNull(ul.getInvalidMessage()); // invalid regex - ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + REGEX_RUBBISH + DELIM + URL_SUFFIX); - assertEquals(DB.toUpperCase(), ul.getTarget()); + assertEquals(DB, ul.getTarget()); assertEquals(DB, ul.getLabel()); - assertEquals(URL_PREFIX, ul.getUrl_prefix()); - assertEquals(URL_SUFFIX, ul.getUrl_suffix()); + assertEquals(URL_PREFIX, ul.getUrlPrefix()); + assertEquals(URL_SUFFIX, ul.getUrlSuffix()); assertTrue(ul.isDynamic()); - assertTrue(ul.usesSeqId()); + assertTrue(ul.usesDBAccession()); assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2), ul.getRegexReplace()); assertFalse(ul.isValid()); - assertEquals( - "Invalid Regular Expression : '" - + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2) - + "'\n", - ul.getInvalidMessage()); + assertEquals("Invalid Regular Expression : '" + + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2) + + "'\n", ul.getInvalidMessage()); } /** @@ -150,7 +167,7 @@ public class UrlLinkTest public void testMakeUrlNoRegex() { // Single non-regex - UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM + URL_SUFFIX); String idstring = "FER_CAPAA"; String[] urls = ul.makeUrls(idstring, true); @@ -167,13 +184,14 @@ public class UrlLinkTest } /** - * Test construction of link by substituting sequence id or name + * Test construction of link by substituting sequence id or name using regular + * expression */ @Test(groups = { "Functional" }) public void testMakeUrlWithRegex() { // Unused regex - UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + REGEX_NESTED + DELIM + URL_SUFFIX); String idstring = "FER_CAPAA"; String[] urls = ul.makeUrls(idstring, true); @@ -243,4 +261,203 @@ public class UrlLinkTest assertNull(ul.getInvalidMessage()); } + /** + * Test creating links with null sequence + */ + @Test(groups = { "Functional" }) + public void testCreateLinksFromNullSequence() + { + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + + DELIM + URL_SUFFIX); + + Map> linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(null, linkset); + + String key = DB + SEP + URL_PREFIX; + assertEquals(1, linkset.size()); + assertTrue(linkset.containsKey(key)); + assertEquals(DB, linkset.get(key).get(0)); + assertEquals(DB, linkset.get(key).get(1)); + assertEquals(null, linkset.get(key).get(2)); + assertEquals(URL_PREFIX, linkset.get(key).get(3)); + } + + /** + * Test creating links with non-dynamic urlLink + */ + @Test(groups = { "Functional" }) + public void testCreateLinksForNonDynamic() + { + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX); + + Map> linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(null, linkset); + + String key = DB + SEP + URL_PREFIX + URL_SUFFIX; + assertEquals(1, linkset.size()); + assertTrue(linkset.containsKey(key)); + assertEquals(DB, linkset.get(key).get(0)); + assertEquals(DB, linkset.get(key).get(1)); + assertEquals(null, linkset.get(key).get(2)); + assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3)); + } + + /** + * Test creating links + */ + @Test(groups = { "Functional" }) + public void testCreateLinksFromSequence() + { + + // create list of links and list of DBRefs + List links = new ArrayList<>(); + List refs = new ArrayList<>(); + + // links as might be added into Preferences | Connections dialog + links.add( + "EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" + + SEQUENCE_ID + "$"); + links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + + "$"); + links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" + + DB_ACCESSION + "$"); + + // make seq0 dbrefs + refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); + refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041")); + refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058")); + refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675")); + + Sequence seq0 = new Sequence("FER1", "AKPNGVL"); + + // add all the dbrefs to the sequence + seq0.addDBRef(refs.get(0)); + seq0.addDBRef(refs.get(1)); + seq0.addDBRef(refs.get(2)); + seq0.addDBRef(refs.get(3)); + seq0.createDatasetSequence(); + + // Test where link takes a sequence id as replacement + UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + + DELIM + URL_SUFFIX); + + Map> linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(seq0, linkset); + + String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName() + + URL_SUFFIX; + assertEquals(1, linkset.size()); + assertTrue(linkset.containsKey(key)); + assertEquals(DB, linkset.get(key).get(0)); + assertEquals(DB, linkset.get(key).get(1)); + assertEquals(seq0.getName(), linkset.get(key).get(2)); + assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, + linkset.get(key).get(3)); + + // Test where link takes a db annotation id and only has one dbref + ul = new UrlLink(links.get(1)); + linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(seq0, linkset); + + key = "P83527|http://www.uniprot.org/uniprot/P83527"; + assertEquals(linkset.size(), 1); + assertTrue(linkset.containsKey(key)); + assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0)); + assertEquals(DBRefSource.UNIPROT + SEP + "P83527", + linkset.get(key).get(1)); + assertEquals("P83527", linkset.get(key).get(2)); + assertEquals("http://www.uniprot.org/uniprot/P83527", + linkset.get(key).get(3)); + + // Test where link takes a db annotation id and has multiple dbrefs + ul = new UrlLink(links.get(2)); + linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(seq0, linkset); + assertEquals(3, linkset.size()); + + // check each link made it in correctly + key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041"; + assertTrue(linkset.containsKey(key)); + assertEquals("INTERPRO", linkset.get(key).get(0)); + assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1)); + assertEquals("IPR001041", linkset.get(key).get(2)); + assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", + linkset.get(key).get(3)); + + key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058"; + assertTrue(linkset.containsKey(key)); + assertEquals("INTERPRO", linkset.get(key).get(0)); + assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1)); + assertEquals("IPR006058", linkset.get(key).get(2)); + assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", + linkset.get(key).get(3)); + + key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675"; + assertTrue(linkset.containsKey(key)); + assertEquals("INTERPRO", linkset.get(key).get(0)); + assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1)); + assertEquals("IPR012675", linkset.get(key).get(2)); + assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", + linkset.get(key).get(3)); + + // Test where there are no matching dbrefs for the link + ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM + + URL_SUFFIX); + linkset = new LinkedHashMap<>(); + ul.createLinksFromSeq(seq0, linkset); + assertTrue(linkset.isEmpty()); + } + + /** + * Test links where label and target are both included + */ + @Test(groups = { "Functional" }) + public void testLinksWithTargets() + { + UrlLink ul = new UrlLink( + "Protein Data Bank | http://www.identifiers.org/pdb/$" + + DB_ACCESSION + "$" + " | pdb"); + + assertEquals("Protein Data Bank", ul.getLabel()); + assertEquals("pdb", ul.getTarget()); + assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", + ul.getUrlWithToken()); + + assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$" + + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget()); + + ul = new UrlLink("Protein Data Bank", + "http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb"); + + assertEquals("Protein Data Bank", ul.getLabel()); + assertEquals("pdb", ul.getTarget()); + assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", + ul.getUrlWithToken()); + + assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$" + + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget()); + + } + + @Test(groups = { "Functional" }) + public void testLinkComparator() + { + Comparator c = UrlLink.LINK_COMPARATOR; + assertEquals(0, c.compare(null, null)); + assertEquals(0, c.compare(null, "x")); + assertEquals(0, c.compare("y", null)); + + /* + * SEQUENCE_ID templates should come before DB_ACCESSION templates + */ + String dbRefUrl = "Cath|http://www.cathdb.info/version/v4_2_0/superfamily/$DB_ACCESSION$"; + String seqIdUrl = "EBI|https://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"; + assertTrue(c.compare(seqIdUrl, dbRefUrl) < 0); + assertTrue(c.compare(dbRefUrl, seqIdUrl) > 0); + + String interpro = "Interpro|https://www.ebi.ac.uk/interpro/entry/$DB_ACCESSION$"; + String prosite = "ProSite|https://prosite.expasy.org/PS00197"; + assertTrue(c.compare(interpro, prosite) < 0); + assertTrue(c.compare(prosite, interpro) > 0); + } }