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josemduartejosemduarte
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Fixing the sifts test to not use external resources, biojava#606 
1 parent 65326fa commit cd99d0e

3 files changed

Lines changed: 59 additions & 4 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@
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* SiftsChainEntry entry2 = sifts.getByChainId("1hiv", "A");
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* System.out.println(entry1.equals(entry2)); // true
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* </pre>
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*
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* See SIFTS project documentation: https://www.ebi.ac.uk/pdbe/docs/sifts/
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* @author dmyersturnbull
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* @see SiftsChainEntry
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* @since 3.0.7
@@ -59,7 +59,7 @@ public class SiftsChainToUniprotMapping {
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private final static Logger logger = LoggerFactory.getLogger(SiftsChainToUniprotMapping.class);
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private static File DEFAULT_FILE;
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public static File DEFAULT_FILE;
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private static final String DEFAULT_FILENAME = "pdb_chain_uniprot.tsv";
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private static final URL DEFAULT_URL;
@@ -113,7 +113,12 @@ public static SiftsChainToUniprotMapping load(boolean useOnlyLocal) throws IOExc
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}
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}
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private static SiftsChainToUniprotMapping build() throws IOException {
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/**
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* Builds the mapping by reading SIFTS the tsv file set in {@link #DEFAULT_FILE} variable.
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* @return
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* @throws IOException
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*/
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public static SiftsChainToUniprotMapping build() throws IOException {
117122
SiftsChainToUniprotMapping sifts = new SiftsChainToUniprotMapping();
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BufferedReader br = new BufferedReader(new FileReader(DEFAULT_FILE));
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String line = "";

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMappingTest.java‎

Lines changed: 18 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,20 +25,37 @@
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import org.junit.Test;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.PrintWriter;
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import static org.junit.Assert.assertEquals;
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/**
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* Tests {@link SiftsChainToUniprotMapping}.
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* @author dmyersturnbull
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* @author Jose Duarte
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* @since 3.0.7
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* @since 5.0.0 uses mock SIFTS data to avoid download of full file
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*/
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public class SiftsChainToUniprotMappingTest {
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@Test
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public void test() throws IOException {
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SiftsChainToUniprotMapping sifts = SiftsChainToUniprotMapping.load();
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SiftsChainToUniprotMapping.DEFAULT_FILE = File.createTempFile("biojavaSiftsTest-", "");
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SiftsChainToUniprotMapping.DEFAULT_FILE.deleteOnExit();
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BufferedReader br = new BufferedReader(new InputStreamReader(getClass().getResourceAsStream("mock_sifts.tsv")));
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PrintWriter pw = new PrintWriter(SiftsChainToUniprotMapping.DEFAULT_FILE);
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String line;
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while ( (line = br.readLine())!=null)
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pw.println(line);
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pw.close();
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br.close();
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SiftsChainToUniprotMapping sifts = SiftsChainToUniprotMapping.build();
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SiftsChainEntry entry = sifts.getByChainId("1hiv", "A");
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assertEquals("1hiv", entry.getPdbId());
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assertEquals("A", entry.getChainId());

‎biojava-structure/src/test/resources/org/biojava/nbio/structure/io/sifts/mock_sifts.tsv‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
# Mock SIFTS file for test SiftsChainToUniprotMappingTest
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# A few lines from beginning of file plus 1hiv entry needed for test.
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PDB CHAIN SP_PRIMARY RES_BEG RES_END PDB_BEG PDB_END SP_BEG SP_END
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101m A P02185 1 154 0 153 1 154
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102l A P00720 1 40 1 40 1 40
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102l A P00720 42 165 41 None 41 164
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102m A P02185 1 154 0 153 1 154
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103l A P00720 1 40 1 None 1 40
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103l A P00720 44 167 41 None 41 164
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103m A P02185 1 154 0 153 1 154
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104l A P00720 1 44 1 44 1 44
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104l A P00720 47 166 45 None 45 164
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104l B P00720 1 44 1 44 1 44
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104l B P00720 47 166 45 None 45 164
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104m A P02185 1 153 1 153 2 154
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105m A P02185 1 153 1 153 2 154
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106m A P02185 1 154 0 153 1 154
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107l A P00720 1 164 1 None 1 164
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107m A P02185 1 154 0 153 1 154
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108l A P00720 1 164 1 None 1 164
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108m A P02185 1 154 0 153 1 154
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109l A P00720 1 164 1 None 1 164
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109m A P02185 1 154 0 153 1 154
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10gs A P09211 1 209 None 209 2 210
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10gs B P09211 1 209 None 209 2 210
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10mh A P05102 1 327 1 327 1 327
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110l A P00720 1 164 1 None 1 164
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110m A P02185 1 154 0 153 1 154
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111l A P00720 1 164 1 None 1 164
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111m A P02185 1 154 0 153 1 154
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112l A P00720 1 164 1 None 1 164
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1hiv A P04585 1 99 1 99 489 587
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1hiv B P04585 1 99 1 99 489 587

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