JAL-2113 EBIFetchClient refactor / unit tests / remove unused fields and

[jalview.git] / test / jalview / ws / ebi / EBIFetchClientTest.java

diff --git a/test/jalview/ws/ebi/EBIFetchClientTest.java b/test/jalview/ws/ebi/EBIFetchClientTest.java
new file mode 100644 (file)
index 0000000..4eaa5b1
--- /dev/null
+++ b/test/jalview/ws/ebi/EBIFetchClientTest.java
@@ -0,0 +1,113 @@
+package jalview.ws.ebi;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
+import org.testng.annotations.Test;
+
+public class EBIFetchClientTest
+{
+  /**
+   * Test method that constructs URL to fetch from
+   */
+  @Test(groups = "Functional")
+  public void testBuildUrl()
+  {
+    /*
+     * EMBL
+     */
+    assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
+            EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
+
+    /*
+     * EMBLCDS
+     */
+    assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
+            EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
+
+    /*
+     * Uniprot
+     */
+    assertEquals(
+            "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
+            EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
+
+    /*
+     * PDB / pdb
+     */
+    assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
+            EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
+
+    /*
+     * PDB / mmCIF
+     */
+    assertEquals(
+            "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
+            EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
+  }
+
+  /**
+   * Test method that parses db:id;id;id
+   */
+  @Test(groups = "Functional")
+  public void testParseIds()
+  {
+    /*
+     * pdb, two accessions
+     */
+    StringBuilder queries = new StringBuilder();
+    String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
+    assertEquals("pdb", db);
+    assertEquals("3a6s,1A70", queries.toString());
+
+    /*
+     * pdb specified on second accession
+     */
+    queries.setLength(0);
+    queries = new StringBuilder();
+    db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
+    assertEquals("pdb", db);
+    assertEquals("3a6s,1A70", queries.toString());
+
+    /*
+     * uniprot, one accession
+     */
+    queries.setLength(0);
+    db = EBIFetchClient.parseIds("uniprot:P00340", queries);
+    assertEquals("uniprot", db);
+    assertEquals("P00340", queries.toString());
+
+    /*
+     * uniprot, one accession, appending to existing queries
+     */
+    queries.setLength(0);
+    queries.append("P30419");
+    db = EBIFetchClient.parseIds("uniprot:P00340", queries);
+    assertEquals("uniprot", db);
+    assertEquals("P30419,P00340", queries.toString());
+
+    /*
+     * pdb and uniprot mixed - rejected
+     */
+    queries.setLength(0);
+    db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
+    assertNull(db);
+    assertEquals("3a6s,1a70", queries.toString());
+
+    /*
+     * pdb and PDB mixed - ok
+     */
+    queries.setLength(0);
+    db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
+    assertEquals("PDB", db);
+    assertEquals("3a6s,1a70,1QIP", queries.toString());
+
+    /*
+     * no database (improper format)
+     */
+    queries.setLength(0);
+    db = EBIFetchClient.parseIds("P00340", queries);
+    assertNull(db);
+    assertEquals("P00340", queries.toString());
+  }
+}