JAL-3829 pull out structure chooser query source tests to new class

[jalview.git] / test / jalview / gui / StructureChooserTest.java

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 91fe602..685e1bc 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
@@ -28,15 +29,28 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser.FilterOption;
-
+import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
+import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
+import jalview.jbgui.FilterOption;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.util.Collection;
 import java.util.Vector;
 
+import org.junit.Assert;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class StructureChooserTest
 {
 
@@ -47,7 +61,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq;
+  Sequence seq,upSeq;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -69,49 +83,47 @@ public class StructureChooserTest
     pdbIds.add(dbRef);
 
     seq.setPDBId(pdbIds);
+    
+    // Uniprot sequence for 3D-Beacons mocks
+    upSeq = new Sequence("P38398", 
+            "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
+            + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+            + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+            + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+            + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+            + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+            + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+            + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+            + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+            + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+            + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+            + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+            + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+            + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+            + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+            + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+            + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+            + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+            + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+            + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+            + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+            + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+            + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+            + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+            + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+            + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+            + "", 1,
+1863);
+    upSeq.createDatasetSequence();
+    upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+    upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
   }
 
   @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;
-  }
-
-  @Test(groups = { "Functional" })
-  public void buildQueryTest()
-  {
-    String query = StructureChooser.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
-    System.out.println("seq >>>> " + seq);
-    seq.getAllPDBEntries().clear();
-    query = StructureChooser.buildQuery(seq);
-    assertEquals(
-            "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
-            query);
-    seq.setDBRefs(null);
-    query = StructureChooser.buildQuery(seq);
-    assertEquals("text:4kqy", query);
-
-    DBRefEntry uniprotDBRef = new DBRefEntry();
-    uniprotDBRef.setAccessionId("P12345");
-    uniprotDBRef.setSource(DBRefSource.UNIPROT);
-    seq.addDBRef(uniprotDBRef);
-
-    DBRefEntry pdbDBRef = new DBRefEntry();
-    pdbDBRef.setAccessionId("1XYZ");
-    pdbDBRef.setSource(DBRefSource.PDB);
-    seq.addDBRef(pdbDBRef);
-
-    for (int x = 1; x < 5; x++)
-    {
-      DBRefEntry dbRef = new DBRefEntry();
-      dbRef.setAccessionId("XYZ_" + x);
-      seq.addDBRef(dbRef);
-    }
-    query = StructureChooser.buildQuery(seq);
-    assertEquals(
-            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-            query);
+    upSeq=null;
   }
 
   @Test(groups = { "Functional" })
@@ -142,26 +154,43 @@ public class StructureChooserTest
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
-    assertTrue(sc.getDiscoveredStructuresSet() != null);
-    assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "discoveredStructuresSet");
+    assertNotNull(ss);
+    assertTrue(ss.size() > 0);
+  }
 
+  @Test(groups = { "Functional" })
+  public void fetchStructuresInfoMockedTest()
+  {
+    Assert.fail("Not yet implemented");
+    TDBeaconsFTSRestClientTest.setMock();
+    
+    // PDBFTSRestClient.setMock();
+    SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
+    StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    sc.fetchStructuresMetaData();
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "discoveredStructuresSet");
+    assertNotNull(ss);
+    assertTrue(ss.size() > 0);
   }
 
   @Test(groups = { "Functional" })
   public void sanitizeSeqNameTest()
   {
     String name = "ab_cdEF|fwxyz012349";
-    assertEquals(name, StructureChooser.sanitizeSeqName(name));
+    assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove a [nn] substring
     name = "abcde12[345]fg";
-    assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove characters other than a-zA-Z0-9 | or _
     name = "ab[cd],.\t£$*!- \\\"@:e";
-    assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     name = "abcde12[345a]fg";
-    assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
   }
 }