*/
package jalview.io;
-import static org.testng.AssertJUnit.assertTrue;
-
import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
-import java.util.IdentityHashMap;
+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);
+ }
+
+ @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
//
//
- for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+ Map<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ Map<String, File> savedProjects = new HashMap<>();
+
+ // 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;
+ // each do loop performs two iterations in the first outer loop pass, but
+ // only performs one iteration on the second outer loop
+ // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
+ // { pass 2 = 0 { pass 3 = 0 } }
+ do
{
- AlignFrame af = jalview.gui.SequenceFetcher.fetchAndShow(did[0],
- did[1]).get(0);
- assertTrue("Didn't read in the example file correctly.", af != null);
- 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
+ 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
+
+ SequenceFetcher sf = new SequenceFetcher(Desktop.getInstance(),
+ forSource, forAccession);
+ sf.run();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ if (afs.length == 0)
+ {
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
+ }
+ keyseq.add(first);
+ af = afs[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();
+
+ }
+ else
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ // recover stored project
+ af = new FileLoader(false).LoadFileWaitTillLoaded(
+ savedProjects.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 + ":");
+
+ }
+
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+
+ ptypes = (seqs == null || seqs.length == 0) ? null
: new CrossRef(seqs, dataset)
.findXrefSourcesForSequences(dna);
- /*
- * map between a view, and views generated after retrieving xrefs
- */
- IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
- /*
- * map between a particular view and it's originating dbref path
- */
- IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();
-
- String first = did[0] + " " + did[1];
- viewsourcedb.put(af.alignPanel, first);
- for (String db : ptypes)
+ filterDbRefs(ptypes, limit);
+
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
{
- // retrieve and show cross-refs in this thread
- CrossRefAction cra = new CrossRefAction(af, seqs, dna, db);
- cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs retrieved for " + db);
- viewxrefview.put(af.alignPanel, cra.getXrefViews());
-
- for (AlignmentViewPanel avp : cra.getXrefViews())
+
+ for (String db : ptypes)
{
+ // counter for splitframe views retrieved via crossref
+ int firstcr_ap = 0;
+ // 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<>();
+ CrossRefAction cra = null;
- SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
- String nextxref = first + " -> " + db;
- viewsourcedb.put(avp, nextxref);
- List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
- : new CrossRef(xrseqs, dataset)
- .findXrefSourcesForSequences(avp
- .getAlignViewport().isNucleotide());
- for (String xrefdb : xrptypes)
- {
- AlignFrame nextaf = Desktop.getAlignFrameFor(avp
- .getAlignViewport());
- cra = new CrossRefAction(nextaf, xrseqs, avp.getAlignViewport()
- .isNucleotide(), xrefdb);
+ if (pass2 == 0)
+ { // retrieve and show cross-refs in this thread
+ cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs found for '" + nextxref + "' to "
- + xrefdb + " via '" + nextaf.getTitle() + "'");
- // save views for analysis
- viewxrefview.put(avp, cra.getXrefViews());
- for (AlignmentViewPanel nextavp : 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.getInstance().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(),
+ 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())
+ {
+ // top view, then bottom
+ cra_views.add(af2.getViewport().getAlignPanel());
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+
+ }
+ else
{
+ // bottom view, then top
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+ cra_views.add(af2.getViewport().getAlignPanel());
- viewsourcedb.put(nextavp, nextxref + " -> " + xrefdb);
}
}
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
+ // first save/verify views.
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+ "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();
+
+ List<String> _xrptypes = (seqs == null || seqs.length == 0)
+ ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(
+ avp.getAlignViewport().isNucleotide());
+
+ 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)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
+ {
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
+ int q = 0;
+ String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
+ + "}";
+
+ if (pass3 == 0)
+ {
+ SequenceI[] xrseqs = avp.getAlignment()
+ .getSequencesArray();
+ AlignFrame nextaf = Desktop
+ .getAlignFrameFor(avp.getAlignViewport());
+
+ cra = CrossRefAction.getHandlerFor(xrseqs,
+ avp.getAlignViewport().isNucleotide(), xrefdb,
+ nextaf);
+ cra.run();
+ 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.getInstance().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(),
+ 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())
+ {
+ // top view, then bottom
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+
+ }
+ else
+ {
+ // bottom view, then top
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ }
+ Assert.assertEquals(cra_views2.size(), 2);
+ Assert.assertNotNull(cra_views2.get(0));
+ Assert.assertNotNull(cra_views2.get(1));
+ }
+
+ for (AlignmentViewPanel nextavp : cra_views2)
+ {
+ 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);
+ }
+ } // 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++;
}
}
}
- Thread.sleep(50000);
}
+ /**
+ * 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() + " ]");
+ }
+ }
+
+ /**
+ * first time called, record strings derived from alignment and
+ * alignedcodonframes, and save view to a project file. Second time called,
+ * compare strings to existing ones. org.testng.Assert.assertTrue on
+ * stringmatch
+ *
+ * @param dbtoviewBit
+ * map between xrefpath and view string
+ * @param savedProjects
+ * - map from xrefpath to saved project filename (createTempFile)
+ * @param xrefpath
+ * - xrefpath - unique ID for this context (composed of sequence of
+ * db-fetch/cross-ref actions preceeding state)
+ * @param avp
+ * - viewpanel to store (for viewpanels in splitframe, the same
+ * project should be written for both panels, only one needs
+ * recovering for comparison on the next stringify call, but each
+ * viewpanel needs to be called with a distinct xrefpath to ensure
+ * each one's strings are compared)
+ */
+ 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);
+ }
+ }
+ else
+ {
+ System.out.println("Stringify check on view from '" + xrefpath
+ + "' [ possibly retrieved from '"
+ + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
+
+ }
+ }
+
+ StringBuilder sbr = new StringBuilder();
+ sbr.append(avp.getAlignment().toString());
+ sbr.append("\n");
+ sbr.append("<End of alignment>");
+ sbr.append("\n");
+ sbr.append(avp.getAlignment().getDataset());
+ sbr.append("\n");
+ sbr.append("<End of dataset>");
+ sbr.append("\n");
+ int p = 0;
+ if (avp.getAlignment().getCodonFrames() != null)
+ {
+ for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
+ {
+ sbr.append("<AlignedCodonFrame " + p++ + ">");
+ sbr.append("\n");
+ sbr.append(ac.toString());
+ sbr.append("\n");
+ }
+ }
+ String dbt = dbtoviewBit.get(xrefpath);
+ if (dbt == null)
+ {
+ dbtoviewBit.put(xrefpath, sbr.toString());
+ }
+ else
+ {
+ Assert.assertEquals(sbr.toString(), dbt,
+ "stringify mismatch for " + xrefpath);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff