From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 3 Sep 2021 17:47:53 +0000 (+0100)
Subject: JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
X-Git-Tag: Release_2_11_2_0~39^2~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bed0c230be450b16213e30ee1dcaf3e76ddfc669;p=jalview.git

JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
---

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index f3c5ed8..309b5ad 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -30,6 +30,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
+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;
@@ -56,7 +58,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq;
+  Sequence seq,upSeq;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -78,12 +80,47 @@ 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;
+    upSeq=null;
   }
 
   @SuppressWarnings("deprecation")
@@ -131,6 +168,63 @@ public class StructureChooserTest
             query);
   }
 
+  @SuppressWarnings("deprecation")
+  @Test(groups = { "Functional" })
+  public void buildThreeDBQueryTest()
+  {
+    System.out.println("seq >>>> " + upSeq);
+    TDBeaconsFTSRestClientTest.setMock();
+    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
+    assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
+    String query = scquery.buildQuery(upSeq);
+    assertEquals("P38398", query);
+    
+    // query shouldn't change regardless of additional entries
+    // because 3DBeacons requires canonical entries.
+    upSeq.getAllPDBEntries().clear();
+    query = scquery.buildQuery(upSeq);
+    assertEquals("P38398", query);
+    upSeq.setDBRefs(null);
+    query = scquery.buildQuery(upSeq);
+    /*
+     * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
+     * graceful behaviour would be to
+     *  - pick one ? not possible
+     *  - iterate through all until a 200 is obtained ?
+     *  ---> ideal but could be costly
+     *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
+     *  ----> need a test to check that accessions can be promoted to canonical!
+     */
+    assertEquals(null, query);
+
+    // TODO: 
+//    
+//    DBRefEntry uniprotDBRef = new DBRefEntry();
+//    uniprotDBRef.setAccessionId("P12345");
+//    uniprotDBRef.setSource(DBRefSource.UNIPROT);
+//    upSeq.addDBRef(uniprotDBRef);
+//
+//    DBRefEntry pdbDBRef = new DBRefEntry();
+//    pdbDBRef.setAccessionId("1XYZ");
+//    pdbDBRef.setSource(DBRefSource.PDB);
+//    upSeq.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);
+  }
+  
+
   @Test(groups = { "Functional" })
   public void populateFilterComboBoxTest() throws InterruptedException
   {