--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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.Jalview2XML;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class CrossRef2xmlTests extends Jalview2xmlBase
+{
+
+ /**
+ * 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<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
+ // show xrefs - verify expected type of frame is shown for each xref
+ // show xrefs again
+ // - verify original -> xref -> xref(original) recovers frame containing at
+ // least the first retrieved sequence
+ // store
+ // 1. whole project
+ // 2. individual frames
+ // 3. load each one back and verify
+ // . aligned sequences (.toString() )
+ // . xrefs (.toString() )
+ // . codonframes
+ //
+ //
+ HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
+ List<String> keyseq = new ArrayList<String>();
+ HashMap<String, File> savedProjects = new HashMap<String, File>();
+
+ for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+ { "UNIPROT", "P01731" } })
+ {
+ // 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
+ {
+ String first = 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(
+ did[0], did[1]);
+ if (afs.size() == 0)
+ {
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
+ }
+ keyseq.add(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();
+ seqs = retral.getSequencesArray();
+
+ }
+ else
+ {
+ Desktop.instance.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);
+
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
+ {
+
+ 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<AlignmentViewPanel>();
+ CrossRefAction cra = null;
+
+ if (pass2 == 0)
+ { // retrieve and show cross-refs in this thread
+ cra = new CrossRefAction(af, seqs, dna, db);
+ cra.run();
+ 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)
+ .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());
+
+ }
+ }
+ HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+ // 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<AlignmentViewPanel>();
+ 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.run();
+ 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)
+ .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)");
+ }
+ }
+
+ /**
+ * 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<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() + " ]");
+ }
+ }
+
+ /**
+ * 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(HashMap<String, String> dbtoviewBit,
+ HashMap<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