/*
 * 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 jalview.gui.JvOptionPane;
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 junit.extensions.PA;

import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
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);
  }

  @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
   * failure case.
   * 
   * @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
    // 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
    //
    //
    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
      {
        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

          List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
                forSource, forAccession);
        // 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);
        filterDbRefs(ptypes, limit);
        
        // 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<>();
            CrossRefAction cra = null;

            if (pass2 == 0)
            { // retrieve and show cross-refs in this thread
              cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
              cra.run();
              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.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<>();
            // 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.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)");
    }
  }

  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
   * 
   * @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);
    }
  }
}