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package jalview.util; |
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import static jalview.util.UrlConstants.DB_ACCESSION; |
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import static jalview.util.UrlConstants.SEQUENCE_ID; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertFalse; |
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import static org.testng.AssertJUnit.assertNull; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.Sequence; |
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import jalview.gui.JvOptionPane; |
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import java.util.ArrayList; |
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import java.util.Comparator; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (233) |
Complexity: 10 |
Complexity Density: 0.04 |
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public class UrlLinkTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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final static String DB = "Test"; |
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final static String URL_PREFIX = "http://www.jalview.org/"; |
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final static String URL_SUFFIX = "/blah"; |
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final static String SEP = "|"; |
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final static String DELIM = "$"; |
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final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/="; |
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final static String REGEX_RUBBISH = "=/[0-9]++/="; |
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68 |
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69 |
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| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testUrlLinkCreationNoRegex() |
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{ |
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UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID |
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+ DELIM + URL_SUFFIX); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX, ul.getUrlPrefix()); |
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assertEquals(URL_SUFFIX, ul.getUrlSuffix()); |
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assertTrue(ul.isDynamic()); |
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assertFalse(ul.usesDBAccession()); |
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assertNull(ul.getRegexReplace()); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM |
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+ URL_SUFFIX); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX, ul.getUrlPrefix()); |
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assertEquals(URL_SUFFIX, ul.getUrlSuffix()); |
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assertTrue(ul.isDynamic()); |
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assertTrue(ul.usesDBAccession()); |
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assertNull(ul.getRegexReplace()); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1)); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix()); |
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assertFalse(ul.isDynamic()); |
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assertFalse(ul.usesDBAccession()); |
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assertNull(ul.getRegexReplace()); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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} |
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| 100% |
Uncovered Elements: 0 (30) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testUrlLinkCreationWithRegex() |
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{ |
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UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID |
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+ REGEX_NESTED + DELIM + URL_SUFFIX); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX, ul.getUrlPrefix()); |
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assertEquals(URL_SUFFIX, ul.getUrlSuffix()); |
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assertTrue(ul.isDynamic()); |
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assertFalse(ul.usesDBAccession()); |
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assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2), |
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ul.getRegexReplace()); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION |
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+ REGEX_NESTED + DELIM + URL_SUFFIX); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX, ul.getUrlPrefix()); |
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assertEquals(URL_SUFFIX, ul.getUrlSuffix()); |
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assertTrue(ul.isDynamic()); |
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assertTrue(ul.usesDBAccession()); |
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assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2), |
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ul.getRegexReplace()); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION |
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+ REGEX_RUBBISH + DELIM + URL_SUFFIX); |
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assertEquals(DB, ul.getTarget()); |
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assertEquals(DB, ul.getLabel()); |
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assertEquals(URL_PREFIX, ul.getUrlPrefix()); |
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assertEquals(URL_SUFFIX, ul.getUrlSuffix()); |
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assertTrue(ul.isDynamic()); |
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assertTrue(ul.usesDBAccession()); |
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assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2), |
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ul.getRegexReplace()); |
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assertFalse(ul.isValid()); |
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assertEquals( |
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"Invalid Regular Expression : '" |
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+ REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2) |
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+ "'\n", |
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ul.getInvalidMessage()); |
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} |
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167 |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
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168 |
1 |
@Test(groups = { "Functional" })... |
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public void testMakeUrlNoRegex() |
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{ |
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UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID |
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+ DELIM + URL_SUFFIX); |
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String idstring = "FER_CAPAA"; |
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String[] urls = ul.makeUrls(idstring, true); |
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assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
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assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
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urls = ul.makeUrls(idstring, false); |
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assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
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assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
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} |
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189 |
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190 |
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191 |
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| 100% |
Uncovered Elements: 0 (49) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
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192 |
1 |
@Test(groups = { "Functional" })... |
193 |
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public void testMakeUrlWithRegex() |
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{ |
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UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION |
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+ REGEX_NESTED + DELIM + URL_SUFFIX); |
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String idstring = "FER_CAPAA"; |
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String[] urls = ul.makeUrls(idstring, true); |
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201 |
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assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
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assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
204 |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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207 |
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urls = ul.makeUrls(idstring, false); |
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209 |
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assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
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assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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idstring = "Label:gi|9234|pdb|102L|A"; |
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urls = ul.makeUrls(idstring, true); |
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assertEquals(2, urls.length); |
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assertEquals("9234", urls[0]); |
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assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]); |
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assertTrue(ul.isValid()); |
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assertNull(ul.getInvalidMessage()); |
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urls = ul.makeUrls(idstring, false); |
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227 |
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assertEquals(2, urls.length); |
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assertEquals("9234", urls[0]); |
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assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]); |
230 |
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assertTrue(ul.isValid()); |
231 |
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assertNull(ul.getInvalidMessage()); |
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233 |
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idstring = "this does not match"; |
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urls = ul.makeUrls(idstring, true); |
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237 |
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assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
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assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
240 |
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assertTrue(ul.isValid()); |
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1 |
assertNull(ul.getInvalidMessage()); |
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243 |
1 |
urls = ul.makeUrls(idstring, false); |
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1 |
assertEquals(2, urls.length); |
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assertEquals(idstring, urls[0]); |
247 |
1 |
assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]); |
248 |
1 |
assertTrue(ul.isValid()); |
249 |
1 |
assertNull(ul.getInvalidMessage()); |
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252 |
1 |
idstring = ""; |
253 |
1 |
urls = ul.makeUrls(idstring, true); |
254 |
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255 |
1 |
assertNull(urls); |
256 |
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257 |
1 |
urls = ul.makeUrls(idstring, false); |
258 |
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259 |
1 |
assertEquals(2, urls.length); |
260 |
1 |
assertEquals("", urls[0]); |
261 |
1 |
assertEquals(URL_PREFIX + URL_SUFFIX, urls[1]); |
262 |
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assertTrue(ul.isValid()); |
263 |
1 |
assertNull(ul.getInvalidMessage()); |
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} |
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266 |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
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269 |
1 |
@Test(groups = { "Functional" })... |
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public void testCreateLinksFromNullSequence() |
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{ |
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UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID |
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+ DELIM + URL_SUFFIX); |
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Map<String, List<String>> linkset = new LinkedHashMap<>(); |
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ul.createLinksFromSeq(null, linkset); |
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String key = DB + SEP + URL_PREFIX; |
279 |
1 |
assertEquals(1, linkset.size()); |
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1 |
assertTrue(linkset.containsKey(key)); |
281 |
1 |
assertEquals(DB, linkset.get(key).get(0)); |
282 |
1 |
assertEquals(DB, linkset.get(key).get(1)); |
283 |
1 |
assertEquals(null, linkset.get(key).get(2)); |
284 |
1 |
assertEquals(URL_PREFIX, linkset.get(key).get(3)); |
285 |
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} |
286 |
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287 |
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288 |
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289 |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
|
|
290 |
1 |
@Test(groups = { "Functional" })... |
291 |
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public void testCreateLinksForNonDynamic() |
292 |
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{ |
293 |
1 |
UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX); |
294 |
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295 |
1 |
Map<String, List<String>> linkset = new LinkedHashMap<>(); |
296 |
1 |
ul.createLinksFromSeq(null, linkset); |
297 |
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298 |
1 |
String key = DB + SEP + URL_PREFIX + URL_SUFFIX; |
299 |
1 |
assertEquals(1, linkset.size()); |
300 |
1 |
assertTrue(linkset.containsKey(key)); |
301 |
1 |
assertEquals(DB, linkset.get(key).get(0)); |
302 |
1 |
assertEquals(DB, linkset.get(key).get(1)); |
303 |
1 |
assertEquals(null, linkset.get(key).get(2)); |
304 |
1 |
assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3)); |
305 |
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} |
306 |
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307 |
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308 |
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309 |
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| 100% |
Uncovered Elements: 0 (61) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
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|
310 |
1 |
@Test(groups = { "Functional" })... |
311 |
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public void testCreateLinksFromSequence() |
312 |
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{ |
313 |
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314 |
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315 |
1 |
List<String> links = new ArrayList<>(); |
316 |
1 |
List<DBRefEntry> refs = new ArrayList<>(); |
317 |
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318 |
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319 |
1 |
links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" |
320 |
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+ SEQUENCE_ID + "$"); |
321 |
1 |
links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION |
322 |
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+ "$"); |
323 |
1 |
links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" |
324 |
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+ DB_ACCESSION + "$"); |
325 |
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326 |
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327 |
1 |
refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); |
328 |
1 |
refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041")); |
329 |
1 |
refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058")); |
330 |
1 |
refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675")); |
331 |
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|
332 |
1 |
Sequence seq0 = new Sequence("FER1", "AKPNGVL"); |
333 |
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334 |
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335 |
1 |
seq0.addDBRef(refs.get(0)); |
336 |
1 |
seq0.addDBRef(refs.get(1)); |
337 |
1 |
seq0.addDBRef(refs.get(2)); |
338 |
1 |
seq0.addDBRef(refs.get(3)); |
339 |
1 |
seq0.createDatasetSequence(); |
340 |
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|
341 |
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|
342 |
1 |
UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID |
343 |
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+ DELIM + URL_SUFFIX); |
344 |
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|
345 |
1 |
Map<String, List<String>> linkset = new LinkedHashMap<>(); |
346 |
1 |
ul.createLinksFromSeq(seq0, linkset); |
347 |
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|
348 |
1 |
String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName() |
349 |
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+ URL_SUFFIX; |
350 |
1 |
assertEquals(1, linkset.size()); |
351 |
1 |
assertTrue(linkset.containsKey(key)); |
352 |
1 |
assertEquals(DB, linkset.get(key).get(0)); |
353 |
1 |
assertEquals(DB, linkset.get(key).get(1)); |
354 |
1 |
assertEquals(seq0.getName(), linkset.get(key).get(2)); |
355 |
1 |
assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, linkset.get(key) |
356 |
|
.get(3)); |
357 |
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|
358 |
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|
359 |
1 |
ul = new UrlLink(links.get(1)); |
360 |
1 |
linkset = new LinkedHashMap<>(); |
361 |
1 |
ul.createLinksFromSeq(seq0, linkset); |
362 |
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|
363 |
1 |
key = "P83527|http://www.uniprot.org/uniprot/P83527"; |
364 |
1 |
assertEquals(linkset.size(), 1); |
365 |
1 |
assertTrue(linkset.containsKey(key)); |
366 |
1 |
assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0)); |
367 |
1 |
assertEquals(DBRefSource.UNIPROT + SEP + "P83527", linkset.get(key) |
368 |
|
.get(1)); |
369 |
1 |
assertEquals("P83527", linkset.get(key).get(2)); |
370 |
1 |
assertEquals("http://www.uniprot.org/uniprot/P83527", linkset.get(key) |
371 |
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.get(3)); |
372 |
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|
373 |
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|
374 |
1 |
ul = new UrlLink(links.get(2)); |
375 |
1 |
linkset = new LinkedHashMap<>(); |
376 |
1 |
ul.createLinksFromSeq(seq0, linkset); |
377 |
1 |
assertEquals(3, linkset.size()); |
378 |
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|
379 |
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|
380 |
1 |
key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041"; |
381 |
1 |
assertTrue(linkset.containsKey(key)); |
382 |
1 |
assertEquals("INTERPRO", linkset.get(key).get(0)); |
383 |
1 |
assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1)); |
384 |
1 |
assertEquals("IPR001041", linkset.get(key).get(2)); |
385 |
1 |
assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", linkset |
386 |
|
.get(key).get(3)); |
387 |
|
|
388 |
1 |
key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058"; |
389 |
1 |
assertTrue(linkset.containsKey(key)); |
390 |
1 |
assertEquals("INTERPRO", linkset.get(key).get(0)); |
391 |
1 |
assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1)); |
392 |
1 |
assertEquals("IPR006058", linkset.get(key).get(2)); |
393 |
1 |
assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", linkset |
394 |
|
.get(key).get(3)); |
395 |
|
|
396 |
1 |
key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675"; |
397 |
1 |
assertTrue(linkset.containsKey(key)); |
398 |
1 |
assertEquals("INTERPRO", linkset.get(key).get(0)); |
399 |
1 |
assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1)); |
400 |
1 |
assertEquals("IPR012675", linkset.get(key).get(2)); |
401 |
1 |
assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", linkset |
402 |
|
.get(key).get(3)); |
403 |
|
|
404 |
|
|
405 |
1 |
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM |
406 |
|
+ URL_SUFFIX); |
407 |
1 |
linkset = new LinkedHashMap<>(); |
408 |
1 |
ul.createLinksFromSeq(seq0, linkset); |
409 |
1 |
assertTrue(linkset.isEmpty()); |
410 |
|
} |
411 |
|
|
412 |
|
|
413 |
|
|
414 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
|
|
415 |
1 |
@Test(groups = { "Functional" })... |
416 |
|
public void testLinksWithTargets() |
417 |
|
{ |
418 |
1 |
UrlLink ul = new UrlLink( |
419 |
|
"Protein Data Bank | http://www.identifiers.org/pdb/$" |
420 |
|
+ DB_ACCESSION + "$" + " | pdb"); |
421 |
|
|
422 |
1 |
assertEquals("Protein Data Bank", ul.getLabel()); |
423 |
1 |
assertEquals("pdb", ul.getTarget()); |
424 |
1 |
assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", |
425 |
|
ul.getUrlWithToken()); |
426 |
|
|
427 |
1 |
assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$" |
428 |
|
+ DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget()); |
429 |
|
|
430 |
1 |
ul = new UrlLink("Protein Data Bank", |
431 |
|
"http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb"); |
432 |
|
|
433 |
1 |
assertEquals("Protein Data Bank", ul.getLabel()); |
434 |
1 |
assertEquals("pdb", ul.getTarget()); |
435 |
1 |
assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", |
436 |
|
ul.getUrlWithToken()); |
437 |
|
|
438 |
1 |
assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$" |
439 |
|
+ DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget()); |
440 |
|
|
441 |
|
} |
442 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
443 |
1 |
@Test(groups = { "Functional" })... |
444 |
|
public void testLinkComparator() |
445 |
|
{ |
446 |
1 |
Comparator<String> c = UrlLink.LINK_COMPARATOR; |
447 |
1 |
assertEquals(0, c.compare(null, null)); |
448 |
1 |
assertEquals(0, c.compare(null, "x")); |
449 |
1 |
assertEquals(0, c.compare("y", null)); |
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
1 |
String dbRefUrl = "Cath|http://www.cathdb.info/version/v4_2_0/superfamily/$DB_ACCESSION$"; |
455 |
1 |
String seqIdUrl = "EBI|https://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"; |
456 |
1 |
assertTrue(c.compare(seqIdUrl, dbRefUrl) < 0); |
457 |
1 |
assertTrue(c.compare(dbRefUrl, seqIdUrl) > 0); |
458 |
|
|
459 |
1 |
String interpro = "Interpro|https://www.ebi.ac.uk/interpro/entry/$DB_ACCESSION$"; |
460 |
1 |
String prosite = "ProSite|https://prosite.expasy.org/PS00197"; |
461 |
1 |
assertTrue(c.compare(interpro, prosite) < 0); |
462 |
1 |
assertTrue(c.compare(prosite, interpro) > 0); |
463 |
|
} |
464 |
|
} |