*/
package jalview.io;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" }, enabled = true)
+ public void openCrossrefsForEnsemblTwice()
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/CantShowEnsemblCrossrefsTwice.jvp",
+ DataSourceType.FILE);
+ assertNotNull(af, "Couldn't load test's project.");
+ AlignmentI origAlig = af.getViewport().getAlignment();
+ List<String> source = new CrossRef(origAlig.getSequencesArray(),
+ origAlig.getDataset()).findXrefSourcesForSequences(true);
+ assertEquals(source.size(), 1, "Expected just one crossref to show.");
+ List<AlignmentViewPanel> views;
+ {
+ // try to show once - in a code block so handler is forgotten about
+ CrossRefAction xref1 = CrossRefAction.getHandlerFor(
+ origAlig.getSequencesArray(), true, source.get(0), af);
+ try
+ {
+ xref1.run();
+ views = (List<AlignmentViewPanel>) PA.getValue(xref1, "xrefViews");
+ assertTrue(views.size() > 0,
+ "Couldn't get cross ref on first attempt (SERIOUS FAIL).");
+ } catch (Exception ex)
+ {
+ Assert.fail("Unexpected Exception for first xref action", ex);
+ }
+ }
+
+ views = null;
+ // now just try it again
+ CrossRefAction xref2 = CrossRefAction.getHandlerFor(
+ origAlig.getSequencesArray(), true, source.get(0), af);
+ try
+ {
+ xref2.run();
+ views = (List<AlignmentViewPanel>) PA.getValue(xref2, "xrefViews");
+ assertTrue(views.size() > 0,
+ "Couldn't get cross ref on second attempt (SERIOUS FAIL).");
+ } catch (Exception ex)
+ {
+ Assert.fail("Unexpected Exception for second xref action", ex);
+ }
+ // TODO : check that both views contain the same data
+ }
+
+ @DataProvider(name = "initialAccessions")
+ static Object[][] getAccessions()
+ {
+ return new String[][] { { "UNIPROT", "P00338" },
+ { "UNIPROT", "Q8Z9G6" },
+ { "ENSEMBLGENOMES", "CAD01290" } };
+ }
+
/**
- * test store and recovery of expanded views
+ * test store and recovery of all reachable cross refs from all reachable
+ * crossrefs for one or more fetched db refs. Currently, this test has a known
+ * failure case.
*
* @throws Exception
*/
- @Test(groups = { "Operational" }, enabled = true)
- public void testRetrieveAndShowCrossref() throws Exception
+ @Test(
+ groups =
+ { "Operational" },
+ dataProvider = "initialAccessions",
+ enabled = true)
+ public void testRetrieveAndShowCrossref(String forSource,
+ String forAccession) throws Exception
{
+
+ List<String> failedDBRetr = new ArrayList<>();
+ List<String> failedXrefMenuItems = new ArrayList<>();
+ List<String> failedProjectRecoveries = new ArrayList<>();
+ // only search for ensembl or Uniprot crossrefs
+ List<String> limit=Arrays.asList(new String[] {
+ DBRefUtils.getCanonicalName("ENSEMBL"),
+ DBRefUtils.getCanonicalName("Uniprot")});
// for every set of db queries
// retrieve db query
// verify presence of expected xrefs
// . codonframes
//
//
- HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
- List<String> keyseq = new ArrayList<String>();
- HashMap<String, File> savedProjects = new HashMap<String, File>();
+ Map<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ Map<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
- {
+// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+// {
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
int pass1 = 0, pass2 = 0, pass3 = 0;
// { pass 2 = 0 { pass 3 = 0 } }
do
{
- String first = did[0] + " " + did[1];
+ String first = forSource + " " + forAccession;//did[0] + " " + did[1];
AlignFrame af = null;
+ boolean dna;
+ AlignmentI retral;
+ AlignmentI dataset;
+ SequenceI[] seqs;
+ List<String> ptypes = null;
if (pass1 == 0)
{
// retrieve dbref
+ List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+ forSource, forAccession);
+ // did[0], did[1]);
+ if (afs.size() == 0)
+ {
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
+ }
keyseq.add(first);
-
- af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
- .get(0);
- assertTrue("Didn't retrieve " + first, af != null);
+ af = afs.get(0);
// verify references for retrieved data
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Fetch " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Fetch " + first + ":");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
- // store project to recover on next pass
- stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
}
else
{
Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), FormatAdapter.FILE);
+ .get(first).toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + first + "' from '"
+ + savedProjects.get(first).toString() + "'");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
// verify references for recovered data
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Recover " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Recover " + first + ":");
}
- boolean dna = af.getViewport().getAlignment().isNucleotide();
- AlignmentI retral = af.getViewport().getAlignment();
- AlignmentI dataset = retral.getDataset();
- SequenceI[] seqs = retral.getSequencesArray();
- List<String> ptypes = (seqs == null || seqs.length == 0) ? null
- : new CrossRef(seqs, dataset)
- .findXrefSourcesForSequences(dna);
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
- for (String db : ptypes)
+ ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
+ seqs, dataset).findXrefSourcesForSequences(dna);
+ filterDbRefs(ptypes, limit);
+
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
{
- pass2 = 0;
- do // second cross ref and recover crossref loop
+
+ for (String db : ptypes)
{
// counter for splitframe views retrieved via crossref
- int p = 0;
+ int firstcr_ap = 0;
// build next key so we an retrieve all views
- String nextxref = first + " -> " + db + "{" + p + "}";
+ String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
// perform crossref action, or retrieve stored project
- List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views = new ArrayList<>();
CrossRefAction cra = null;
+
if (pass2 == 0)
{ // retrieve and show cross-refs in this thread
- cra = new CrossRefAction(af, seqs, dna, db);
+ cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs retrieved for " + db);
- cra_views = cra.getXrefViews();
+ cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views.size() == 0)
+ {
+ failedXrefMenuItems.add("No crossrefs retrieved for "
+ + first + " -> " + db);
+ continue;
+ }
+ assertNucleotide(cra_views.get(0),
+ "Nucleotide panel included proteins for " + first
+ + " -> " + db);
+ assertProtein(cra_views.get(1),
+ "Protein panel included nucleotides for " + first
+ + " -> " + db);
}
else
{
Desktop.instance.closeAll_actionPerformed(null);
+ pass3 = 0;
+ // recover stored project
+ File storedProject = savedProjects.get(nextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries.add("Failed to store a view for '"
+ + nextxref + "'");
+ continue;
+ }
+
// recover stored project
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + nextxref
+ + "' from '" + savedProjects.get(nextxref).toString()
+ + "'");
// gymnastics to recover the alignPanel/Complementary alignPanel
if (af2.getViewport().isNucleotide())
{
}
}
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
+ // first save/verify views.
for (AlignmentViewPanel avp : cra_views)
{
- nextxref = first + " -> " + db + "{" + p++ + "}";
-
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
// verify references for this panel
AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
- "" + "Pass (" + pass1 + "," + pass2 + "): For "
- + nextxref + ":");
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+ assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
- stringify(dbtoviewBit, savedProjects, nextxref, avp);
- keyseq.add(nextxref);
-
- List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
+ List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
: new CrossRef(xrseqs, dataset)
.findXrefSourcesForSequences(avp
.getAlignViewport().isNucleotide());
- for (String xrefdb : xrptypes)
+
+ stringify(dbtoviewBit, savedProjects, nextxref, avp);
+ xrptypes.put(nextxref, _xrptypes);
+
+ }
+
+ // now do the second xref pass starting from either saved or just
+ // recovered split pane, in sequence
+ do // retrieve second set of cross refs or recover and verify
+ {
+ firstcr_ap = 0;
+ for (AlignmentViewPanel avp : cra_views)
{
- pass3 = 0;
- do // 3rd cross ref and recover crossref loop
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
{
- List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
int q = 0;
- String nextnextxref = "{" + p + "}" + nextxref + " -> "
- + xrefdb + "{" + q + "}";
+ String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ + q + "}";
- AlignFrame nextaf = Desktop.getAlignFrameFor(avp
- .getAlignViewport());
if (pass3 == 0)
{
+ SequenceI[] xrseqs = avp.getAlignment()
+ .getSequencesArray();
+ AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+ .getAlignViewport());
- cra = new CrossRefAction(nextaf, xrseqs, avp
- .getAlignViewport().isNucleotide(), xrefdb);
+ cra = CrossRefAction.getHandlerFor(xrseqs, avp
+ .getAlignViewport().isNucleotide(), xrefdb,
+ nextaf);
cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs found for '" + nextxref + "' to "
- + xrefdb + " via '" + nextaf.getTitle()
- + "'");
- cra_views2 = cra.getXrefViews();
+ cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
+ cra, "xrefViews");
+ if (cra_views2.size() == 0)
+ {
+ failedXrefMenuItems
+ .add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+ continue;
+ }
+ assertNucleotide(cra_views2.get(0),
+ "Nucleotide panel included proteins for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+ assertProtein(cra_views2.get(1),
+ "Protein panel included nucleotides for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+
}
else
{
Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
+ File storedProject = savedProjects.get(nextnextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries
+ .add("Failed to store a view for '"
+ + nextnextxref + "'");
+ continue;
+ }
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(
savedProjects.get(nextnextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(),
+ DataSourceType.FILE);
+ System.out.println("Recovered view for '"
+ + nextnextxref + "' from '"
+ + savedProjects.get(nextnextxref).toString()
+ + "'");
// gymnastics to recover the alignPanel/Complementary
// alignPanel
if (af2.getViewport().isNucleotide())
for (AlignmentViewPanel nextavp : cra_views2)
{
- nextnextxref = "{" + p + "}" + nextxref + " -> "
- + xrefdb + "{" + q++ + "}";
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
// verify references for this panel
AlignmentTest.assertAlignmentDatasetRefs(
nextavp.getAlignment(), "" + "Pass (" + pass1
+ "," + pass2 + "): For "
+ nextnextxref + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ nextavp.getAlignment(), "" + "Pass (" + pass1
+ + "," + pass2 + "): For "
+ + nextnextxref + ":");
stringify(dbtoviewBit, savedProjects, nextnextxref,
nextavp);
keyseq.add(nextnextxref);
}
- } while (pass3++ < 2 && pass2 < 1);
- }
- }
- } while (pass2++ < 2 && pass1 < 1);
+ } // end of loop around showing all xrefdb for crossrf2
+
+ } // end of loop around all viewpanels from crossrf1
+ } while (pass2 == 2 && pass3++ < 2);
+ // fetchdb->crossref1->crossref-2->verify for xrefs we
+ // either loop twice when pass2=0, or just once when pass2=1
+ // (recovered project from previous crossref)
+
+ } // end of loop over db-xrefs for crossref-2
+
+ // fetchdb-->crossref1
+ // for each xref we try to retrieve xref, store and verify when
+ // pass1=0, or just retrieve and verify when pass1=1
+ } while (pass1 == 1 && pass2++ < 2);
+ // fetchdb
+ // for each ref we
+ // loop twice: first, do the retrieve, second recover from saved project
+
+ // increment pass counters, so we repeat traversal starting from the
+ // oldest saved project first.
+ if (pass1 == 0)
+ {
+ // verify stored projects for first set of cross references
+ pass1 = 1;
+ // and verify cross-references retrieved from stored projects
+ pass2 = 0;
+ pass3 = 0;
+ }
+ else
+ {
+ pass1++;
+ }
+ } while (pass1 < 3);
+
+ if (failedXrefMenuItems.size() > 0)
+ {
+ for (String s : failedXrefMenuItems)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+ + " counts)");
+ }
+ if (failedProjectRecoveries.size() > 0)
+ {
+
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
+ + failedProjectRecoveries.size() + " counts)");
+ }
+ if (failedDBRetr.size() > 0)
+ {
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+ + failedDBRetr.size() + " counts)");
+ }
+ }
+
+ private void filterDbRefs(List<String> ptypes, List<String> limit)
+ {
+ if (limit != null)
+ {
+ int p = 0;
+ while (ptypes.size() > p)
+ {
+ if (!limit.contains(ptypes.get(p)))
+ {
+ ptypes.remove(p);
+ }
+ else
+ {
+ p++;
}
- } while (++pass1 < 2);
+ }
+ }
+ }
+
+ /**
+ * wrapper to trap known defect for AH002001 testcase
+ *
+ * @param alignment
+ * @param string
+ */
+ private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
+ String message)
+ {
+ try
+ {
+ AlignmentTest.assertDatasetIsNormalised(al, message);
+ } catch (AssertionError ae)
+ {
+ if (!ae.getMessage().endsWith("EMBL|AH002001"))
+ {
+ throw ae;
+ }
+ else
+ {
+ System.out
+ .println("Ignored exception for known defect: JAL-2179 : "
+ + message);
+ }
+
+ }
+ }
+
+ private void assertProtein(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(true, alignmentViewPanel, message);
+ }
+
+ private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(false, alignmentViewPanel, message);
+ }
+
+ private void assertType(boolean expectProtein,
+ AlignmentViewPanel alignmentViewPanel, String message)
+ {
+ List<SequenceI> nonType = new ArrayList<>();
+ for (SequenceI sq : alignmentViewPanel.getAlignViewport()
+ .getAlignment().getSequences())
+ {
+ if (sq.isProtein() != expectProtein)
+ {
+ nonType.add(sq);
+ }
+ }
+ if (nonType.size() > 0)
+ {
+ Assert.fail(message + " [ "
+ + (expectProtein ? "nucleotides were " : "proteins were ")
+ + nonType.toString() + " ]");
}
}
* viewpanel needs to be called with a distinct xrefpath to ensure
* each one's strings are compared)
*/
- private void stringify(HashMap<String, String> dbtoviewBit,
- HashMap<String, File> savedProjects, String xrefpath,
+ private void stringify(Map<String, String> dbtoviewBit,
+ Map<String, File> savedProjects, String xrefpath,
AlignmentViewPanel avp)
{
if (savedProjects != null)
{
if (savedProjects.get(xrefpath) == null)
- {
- // write a project file for this view. On the second pass, this will be
- // recovered and cross-references verified
- try
- {
- File prfile = File.createTempFile("crossRefTest", ".jvp");
- AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
- new Jalview2XML(false).saveAlignment(af, prfile.toString(),
- af.getTitle());
- System.out.println("Written view from '" + xrefpath + "' as '"
- + prfile.getAbsolutePath() + "'");
- savedProjects.put(xrefpath, prfile);
- } catch (IOException q)
{
- Assert.fail("Unexpected IO Exception", q);
- }
+ // write a project file for this view. On the second pass, this will be
+ // recovered and cross-references verified
+ try
+ {
+ File prfile = File.createTempFile("crossRefTest", ".jvp");
+ AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
+ new Jalview2XML(false).saveAlignment(af, prfile.toString(),
+ af.getTitle());
+ System.out.println("Written view from '" + xrefpath + "' as '"
+ + prfile.getAbsolutePath() + "'");
+ savedProjects.put(xrefpath, prfile);
+ } catch (IOException q)
+ {
+ Assert.fail("Unexpected IO Exception", q);
+ }
}
else
{