*/
package jalview.gui;
-import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.Assert.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+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 jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
-import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestClient;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
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;
+@Test(singleThreaded = true)
public class StructureChooserTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq;
+ Sequence seq, upSeq, upSeq_nocanonical;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
-
+
// Uniprot sequence for 3D-Beacons mocks
- upSeq = new Sequence("P38398",
+ 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();
+ + "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.setDescription("Breast cancer type 1 susceptibility protein");
- upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+ upSeq_nocanonical = new Sequence(upSeq);
+ upSeq.createDatasetSequence();
+ upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
+ upSeq_nocanonical.createDatasetSequence();
+ // not a canonical reference
+ upSeq_nocanonical.addDBRef(
+ new DBRefEntry("UNIPROT", "0", "P38398", null, false));
+
}
@AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
- upSeq=null;
+ upSeq = null;
+ upSeq_nocanonical = null;
}
@Test(groups = { "Functional" })
public void populateFilterComboBoxTest() throws InterruptedException
{
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ ThreadwaitFor(200, sc);
+
+ // if structures are not discovered then don't
+ // populate filter options
sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
- assertEquals(2, optionsSize); // if structures are not discovered then don't
- // populate filter options
+ System.out.println("Items (no data, no cache): ");
+ StringBuilder items = new StringBuilder();
+ for (int p = 0; p < optionsSize; p++)
+ {
+ items.append("- ")
+ .append(sc.getCmbFilterOption().getItemAt(p).getName())
+ .append("\n");
+
+ }
+ // report items when this fails - seems to be a race condition
+ Assert.assertEquals(items.toString(), optionsSize, 2);
sc.populateFilterComboBox(true, false);
optionsSize = sc.getCmbFilterOption().getItemCount();
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
assertEquals("Cached Structures", filterOpt.getName());
+ FTSRestClient
+ .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void displayTDBQueryTest() throws InterruptedException
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
+ SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
+ StructureChooser sc = new StructureChooser(selectedSeqs,
+ upSeq_nocanonical, null);
+ // mock so should be quick. Exceptions from mocked PDBFTS are expected too
+ ThreadwaitFor(500, sc);
+
+ assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
}
@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);
+ // not mocked, wait for 2s
+ ThreadwaitFor(2000, sc);
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
@Test(groups = { "Functional" })
public void fetchStructuresInfoMockedTest()
{
- Assert.fail("Not yet implemented");
TDBeaconsFTSRestClientTest.setMock();
-
- // PDBFTSRestClient.setMock();
+ PDBFTSRestClientTest.setMock();
SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ ThreadwaitFor(500, sc);
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
assertTrue(ss.size() > 0);
}
+ private void ThreadwaitFor(int i, StructureChooser sc)
+ {
+ long timeout = i + System.currentTimeMillis();
+ while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+
+ }
+
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals(name,
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12345afg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
git://source.jalview.org / jalview.git / blobdiff