JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response

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

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index c187c60..23b572f 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -30,14 +30,21 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestClient;
+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;
@@ -55,7 +62,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq;
+  Sequence seq,upSeq;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -77,60 +84,55 @@ 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;
-  }
-
-  @SuppressWarnings("deprecation")
-  @Test(groups = { "Functional" })
-  public void buildQueryTest()
-  {
-    System.out.println("seq >>>> " + seq);
-    StructureChooserQuerySource scquery = StructureChooserQuerySource.getPDBfts();
-    String query = scquery.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
-    seq.getAllPDBEntries().clear();
-    query = scquery.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 = scquery.buildQuery(seq);
-    System.out.println(query);
-    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);
-    }
-    System.out.println("");
-    System.out.println(seq.getDBRefs());
-    System.out.println(query);
-    query = scquery.buildQuery(seq);
-    assertEquals(
-            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-            query);
+    upSeq=null;
   }
 
   @Test(groups = { "Functional" })
   public void populateFilterComboBoxTest() throws InterruptedException
   {
+    TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClient.setMock();
+
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.populateFilterComboBox(false, false);
@@ -153,6 +155,8 @@ public class StructureChooserTest
   @Test(groups = { "Network" })
   public void fetchStructuresInfoTest()
   {
+    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
@@ -160,7 +164,20 @@ public class StructureChooserTest
             "discoveredStructuresSet");
     assertNotNull(ss);
     assertTrue(ss.size() > 0);
+  }
 
+  @Test(groups = { "Functional" })
+  public void fetchStructuresInfoMockedTest()
+  {
+    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" })