X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=309b5ad38e0a37d5f7a0be3b48cb4b1c25b889ce;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=f69e6b53503dd4163367f9d60ee3c64207ab912c;hpb=d156987a513b1da92fd6fbf7678b4a8e7ffc8d08;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index f69e6b5..309b5ad 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -30,7 +30,13 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
-import jalview.jbgui.GStructureChooser.FilterOption;
+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;
@@ -52,7 +58,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq;
+  Sequence seq,upSeq;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -74,27 +80,67 @@ 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")
   @Test(groups = { "Functional" })
   public void buildQueryTest()
   {
-    String query = StructureChooser.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
     System.out.println("seq >>>> " + seq);
+    
+    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
+    assertTrue(scquery instanceof PDBStructureChooserQuerySource);
+    String query = scquery.buildQuery(seq);
+    assertEquals("pdb_id:1tim", query);
     seq.getAllPDBEntries().clear();
-    query = StructureChooser.buildQuery(seq);
+    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 = StructureChooser.buildQuery(seq);
+    query = scquery.buildQuery(seq);
+    System.out.println(query);
     assertEquals("text:4kqy", query);
 
     DBRefEntry uniprotDBRef = new DBRefEntry();
@@ -113,12 +159,72 @@ public class StructureChooserTest
       dbRef.setAccessionId("XYZ_" + x);
       seq.addDBRef(dbRef);
     }
-    query = StructureChooser.buildQuery(seq);
+    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);
   }
 
+  @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
   {
@@ -158,17 +264,17 @@ public class StructureChooserTest
   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));
   }
 }