*/
package jalview.io;
-import static org.testng.AssertJUnit.assertTrue;
-
import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignedCodonFrame;
@Test(groups = { "Operational" }, enabled = true)
public void testRetrieveAndShowCrossref() throws Exception
{
+
+ List<String> failedDBRetr = new ArrayList<String>();
+ List<String> failedXrefMenuItems = new ArrayList<String>();
+ List<String> failedProjectRecoveries = new ArrayList<String>();
+
// for every set of db queries
// retrieve db query
// verify presence of expected xrefs
{
// retrieve dbref
+ List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+ 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()
// start of pass2: retrieve each cross-ref for fetched or restored
// project.
- pass2 = 0;
- do // second cross ref and recover crossref loop
+ do // first cross ref and recover crossref loop
{
for (String db : ptypes)
// perform crossref action, or retrieve stored project
List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
CrossRefAction cra = null;
+
if (pass2 == 0)
{ // retrieve and show cross-refs in this thread
cra = new CrossRefAction(af, seqs, dna, db);
cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs retrieved for " + db);
+ if (cra.getXrefViews().size() == 0)
+ {
+ failedXrefMenuItems.add("No crossrefs retrieved for "
+ + first + " -> " + db);
+ continue;
+ }
cra_views = cra.getXrefViews();
+ 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)
xrptypes.put(nextxref, _xrptypes);
}
- // now do the next xref pass starting from either saved or just
+
+ // now do the second xref pass starting from either saved or just
// recovered split pane, in sequence
- pass3 = 0;
- do // 3rd cross ref and recover crossref loop, for each view from
- // second xref view set or recover viewset
+ do // retrieve second set of cross refs or recover and verify
{
firstcr_ap = 0;
for (AlignmentViewPanel avp : cra_views)
cra = new CrossRefAction(nextaf, xrseqs, avp
.getAlignViewport().isNucleotide(), xrefdb);
cra.run();
- Assert.assertTrue(
- cra.getXrefViews().size() > 0,
- "No crossrefs found for '" + nextnextxref
- + "' to " + xrefdb + " via '"
- + nextaf.getTitle() + "'");
+ if (cra.getXrefViews().size() == 0)
+ {
+ failedXrefMenuItems
+ .add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ continue;
+ }
cra_views2 = cra.getXrefViews();
+ 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)
} // end of loop around showing all xrefdb for crossrf2
} // end of loop around all viewpanels from crossrf1
- } while (pass3++ < 2 && pass2 < 1);
+ } 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 (pass2++ < 2 && pass1 < 1);
+ } while (pass1 == 1 && pass2++ < 2);
// fetchdb
// for each ref we
// loop twice: first, do the retrieve, second recover from saved project
- } while (pass1++ < 2);
+
+ // 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++;
+ if (pass1 < 2)
+ {
+ // verify stored projects for second set of cross references
+ pass2 = 1;
+ // and verify cross-references retrievable from those stored projects.
+ pass3 = 0;
+ }
+ }
+ } while (pass3 < 2);
+ }
+ 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 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<SequenceI>();
+ 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()
+ + " ]");
}
}
git://source.jalview.org / jalview.git / blobdiff