*/
package jalview.io;
+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.datamodel.AlignedCodonFrame;
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
{
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 all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
*
* @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<String>();
- List<String> failedXrefMenuItems = new ArrayList<String>();
- List<String> failedProjectRecoveries = new ArrayList<String>();
-
+ 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[][] { { "ENSEMBL", "ENSG00000157764" },
- { "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;
// retrieve dbref
List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
- did[0], did[1]);
+ forSource, forAccession);
+ // did[0], did[1]);
if (afs.size() == 0)
{
failedDBRetr.add("Didn't retrieve " + first);
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();
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
// 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 = CrossRefAction.getHandlerFor(seqs, dna, db, af);
cra.run();
- if (cra.getXrefViews().size() == 0)
+ cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views.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);
// 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)
{
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 + "}";
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();
- if (cra.getXrefViews().size() == 0)
+ cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
+ cra, "xrefViews");
+ if (cra_views2.size() == 0)
{
failedXrefMenuItems
.add("No crossrefs retrieved for '"
+ " via '" + nextaf.getTitle() + "'");
continue;
}
- cra_views2 = cra.getXrefViews();
assertNucleotide(cra_views2.get(0),
"Nucleotide panel included proteins for '"
+ nextxref + "' to " + xrefdb
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()
pass1++;
}
} while (pass1 < 3);
- }
+
if (failedXrefMenuItems.size() > 0)
{
for (String s : failedXrefMenuItems)
}
}
+ 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++;
+ }
+ }
+ }
+ }
+
/**
* wrapper to trap known defect for AH002001 testcase
*
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())
{
* 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)
git://source.jalview.org / jalview.git / blobdiff