import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.io.IOException;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
- * 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
{
+
+ List<String> failedDBRetr = new ArrayList<>();
+ List<String> failedXrefMenuItems = new ArrayList<>();
+ List<String> failedProjectRecoveries = new ArrayList<>();
// 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>();
+ HashMap<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ HashMap<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+ for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+ { "UNIPROT", "P01731" } })
{
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
{
// 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);
- Assert.assertTrue(af != null, "Didn't retrieve " + first);
+ 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();
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();
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Recover " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Recover " + first + ":");
}
// build next key so we an retrieve all views
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.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
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()
+ "'");
}
}
- HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
// first save/verify views.
for (AlignmentViewPanel avp : cra_views)
{
"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();
: new CrossRef(xrseqs, dataset)
.findXrefSourcesForSequences(avp
.getAlignViewport().isNucleotide());
-
+
stringify(dbtoviewBit, savedProjects, nextxref, avp);
xrptypes.put(nextxref, _xrptypes);
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 = nextxref
- + " -> " + xrefdb + "{" + q + "}";
+ String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ + q + "}";
if (pass3 == 0)
{
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 '"
{
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()
for (AlignmentViewPanel nextavp : cra_views2)
{
- nextnextxref = 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);
}
else
{
- // verify stored projects for second set of cross references
- pass2 = 1;
- // and verify cross-references retrievable from those stored projects.
- pass3 = 0;
+ pass1++;
}
- } while (pass3 < 2);
+ } 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)");
+ }
+ }
+
+ /**
+ * 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 assertType(boolean expectProtein,
AlignmentViewPanel alignmentViewPanel, String message)
{
- List<SequenceI> nonType = new ArrayList<SequenceI>();
+ List<SequenceI> nonType = new ArrayList<>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
- .getAlignment()
- .getSequences())
+ .getAlignment().getSequences())
{
if (sq.isProtein() != expectProtein)
{
{
Assert.fail(message + " [ "
+ (expectProtein ? "nucleotides were " : "proteins were ")
- + nonType.toString()
- + " ]");
+ + nonType.toString() + " ]");
}
}
git://source.jalview.org / jalview.git / blobdiff