Genome improvements (#1589)

Refactoring genome load management to simplify code.

src/main/java/org/broad/igv/feature/genome/Genome.java

@@ -125,7 +125,7 @@ public Genome(GenomeConfig config) throws IOException {
         } else if (config.fastaURL != null) {
             String fastaPath = config.fastaURL;
             String indexPath = config.indexURL;
-            String gziIndexPath = config.gziIndexURL;
+            String gziIndexPath = config.gziIndexURL != null ? config.gziIndexURL : config.compressedIndexURL;   // Synonyms
             uncachedSequence = fastaPath.endsWith(".gz") ?
                     new FastaBlockCompressedSequence(fastaPath, gziIndexPath, indexPath) :
                     new FastaIndexedSequence(fastaPath, indexPath);

src/main/java/org/broad/igv/feature/genome/GenomeManager.java

@@ -116,7 +116,9 @@ private GenomeManager() {
      * @throws UnsupportedEncodingException
      */
     public static File getGenomeFile(String genomePath) throws MalformedURLException, UnsupportedEncodingException {
+
         File archiveFile;
+
         if (HttpUtils.isRemoteURL(genomePath.toLowerCase())) {
             // We need a local copy, as there is no http zip file reader
             URL genomeArchiveURL = HttpUtils.createURL(genomePath);
@@ -195,10 +197,11 @@ public Genome loadGenome(String genomePath) throws IOException {
             Genome newGenome = GenomeLoader.getLoader(genomePath).loadGenome();
 
             // Load user-defined chr aliases, if any.  This is done last so they have priority
+            final File genomeCacheDirectory = DirectoryManager.getGenomeCacheDirectory();
             try {
-                String aliasPath = (new File(DirectoryManager.getGenomeCacheDirectory(), newGenome.getId() + "_alias.tab")).getAbsolutePath();
+                String aliasPath = (new File(genomeCacheDirectory, newGenome.getId() + "_alias.tab")).getAbsolutePath();
                 if (!(new File(aliasPath)).exists()) {
-                    aliasPath = (new File(DirectoryManager.getGenomeCacheDirectory(), newGenome.getId() + "_alias.tab.txt")).getAbsolutePath();
+                    aliasPath = (new File(genomeCacheDirectory, newGenome.getId() + "_alias.tab.txt")).getAbsolutePath();
                 }
                 if ((new File(aliasPath)).exists()) {
                     newGenome.addChrAliases(ChromAliasParser.loadChrAliases(aliasPath));
@@ -212,7 +215,13 @@ public Genome loadGenome(String genomePath) throws IOException {
                 IGV.getInstance().resetSession(null);
             }
 
-            setCurrentGenome(genomePath, newGenome);
+            // If the genome is loaded from anywhere other than the cache directory add an entry to the pulldown
+            if(newGenome != null && !(new File(genomePath).getParentFile().equals(genomeCacheDirectory))) {
+                GenomeListItem genomeListItem = new GenomeListItem(newGenome.getDisplayName(), genomePath, newGenome.getId());
+                GenomeListManager.getInstance().addGenomeItem(genomeListItem, true);
+            }
+
+            setCurrentGenome(newGenome);
 
             return currentGenome;
 
@@ -226,13 +235,7 @@ public Genome loadGenome(String genomePath) throws IOException {
         }
     }
 
-    public void setCurrentGenome(String genomePath, Genome newGenome) {
-
-        GenomeListItem genomeListItem = new GenomeListItem(newGenome.getDisplayName(), genomePath, newGenome.getId());
-        final Set<String> serverGenomeIDs = genomeListManager.getServerGenomeIDs();
-
-        boolean userDefined = !serverGenomeIDs.contains(newGenome.getId());
-        genomeListManager.addGenomeItem(genomeListItem, userDefined);
+    public void setCurrentGenome(Genome newGenome) {
 
         this.currentGenome = newGenome;
 
@@ -354,26 +357,32 @@ public Genome getCurrentGenome() {
     }
 
 
-    public boolean downloadGenome(GenomeListItem item, boolean downloadSequence) {
+    public boolean downloadGenome(GenomeListItem item, boolean downloadDataFiles) {
 
         boolean success;
         try {
-            File genomeFile = getGenomeFile(item.getPath());                  // Has side affect of downloading .genome file
-            if (downloadSequence) {
-                String fastaPath = null;
+            File genomeFile = getGenomeFile(item.getPath()); // Has side affect of downloading .genome file
+
+            if (downloadDataFiles) {
+
+
                 if (item.getPath().endsWith(".genome")) {
                     GenomeDescriptor genomeDescriptor = GenomeDescriptor.parseGenomeArchiveFile(genomeFile);
-                    fastaPath = genomeDescriptor.getSequencePath();
+                    String fastaPath = genomeDescriptor.getSequencePath();
+                    if (fastaPath != null && FileUtils.isRemote(fastaPath)) {
+                        File localFile = downloadFasta(fastaPath);
+                        if (localFile != null) {
+                            addLocalFasta(item.getId(), localFile);
+                        }
+                    }
+
                 } else if (item.getPath().endsWith(".json")) {
+
                     JsonGenomeLoader.GenomeDescriptor desc = (new JsonGenomeLoader(item.getPath())).loadDescriptor();
-                    fastaPath = desc.getFastaURL();
-                }
-                if (fastaPath != null && FileUtils.isRemote(fastaPath)) {
-                    File localFile = downloadFasta(fastaPath);
-                    if (localFile != null) {
-                        addLocalFasta(item.getId(), localFile);
-                    }
+
+
                 }
+
             }
 
             success = true;
@@ -391,7 +400,6 @@ public boolean downloadGenome(GenomeListItem item, boolean downloadSequence) {
         }
 
         return success;
-
     }
 
 
@@ -466,11 +474,4 @@ private static void updateSequenceMapFile() {
         }
     }
 
-    public void refreshHostedGenome(String genomeId) {
-
-        Map<String, GenomeListItem> itemMap = GenomeListManager.getInstance().getServerGenomeMap();
-        if (itemMap.containsKey(genomeId)) {
-            downloadGenome(itemMap.get(genomeId), false);
-        }
-    }
 }

src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java

@@ -98,6 +98,19 @@ private String fixChromosomeOrder(String jsonString) {
      * @return
      */
     private GenomeConfig fixPaths(GenomeConfig config) {
+
+        if (config.chromAliasBbURL != null) {
+            config.chromAliasBbURL = FileUtils.getAbsolutePath(config.chromAliasBbURL, genomePath);
+        }
+        if (config.twoBitURL != null) {
+            config.twoBitURL = FileUtils.getAbsolutePath(config.twoBitURL, genomePath);
+        }
+        if (config.cytobandBbURL != null) {
+            config.cytobandBbURL = FileUtils.getAbsolutePath(config.cytobandBbURL, genomePath);
+        }
+        if (config.chromSizesURL != null) {
+            config.chromSizesURL = FileUtils.getAbsolutePath(config.chromSizesURL, genomePath);
+        }
         if (config.fastaURL != null) {
             config.fastaURL = FileUtils.getAbsolutePath(config.fastaURL, genomePath);
         }
@@ -107,6 +120,9 @@ private GenomeConfig fixPaths(GenomeConfig config) {
         if (config.gziIndexURL != null) {
             config.gziIndexURL = FileUtils.getAbsolutePath(config.gziIndexURL, genomePath);
         }
+        if (config.compressedIndexURL != null) {
+            config.compressedIndexURL = FileUtils.getAbsolutePath(config.compressedIndexURL, genomePath);
+        }
         if (config.cytobandURL != null) {
             config.cytobandURL = FileUtils.getAbsolutePath(config.cytobandURL, genomePath);
         }

src/main/java/org/broad/igv/ui/IGV.java

@@ -1943,7 +1943,7 @@ public void run() {
 
                     if (!genomeLoaded) {
                         Genome genome = Genome.nullGenome();
-                        GenomeManager.getInstance().setCurrentGenome("", genome);
+                        GenomeManager.getInstance().setCurrentGenome(genome);
 
 
                         //GenomeManager.getInstance().setCurrentGenome(Genome.NoneGenome());

src/main/java/org/broad/igv/ui/IGVMenuBar.java

@@ -41,7 +41,6 @@
 import org.broad.igv.feature.genome.GenomeUtils;
 import org.broad.igv.track.AttributeManager;
 import org.broad.igv.track.Track;
-import org.broad.igv.ui.commandbar.GenomeComboBox;
 import org.broad.igv.ui.commandbar.GenomeListManager;
 import org.broad.igv.ui.commandbar.GenomeSelectionDialog;
 import org.broad.igv.util.GoogleUtils;
@@ -435,7 +434,7 @@ private JMenu createGenomesMenu() {
         JMenu menu = new JMenu("Genomes");
 
         loadGenomeFromServerMenuItem = new JMenuItem("Download Hosted Genome...");
-        loadGenomeFromServerMenuItem.addActionListener(e -> GenomeComboBox.loadGenomeFromServer());
+        loadGenomeFromServerMenuItem.addActionListener(e -> GenomeSelectionDialog.selectGenomesFromServer());
         loadGenomeFromServerMenuItem.setToolTipText(LOAD_GENOME_SERVER_TOOLTIP);
         menu.add(loadGenomeFromServerMenuItem);
 

src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java

@@ -30,6 +30,7 @@
 package org.broad.igv.ui.action;
 
 import org.broad.igv.Globals;
+import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.load.HubGenomeLoader;
 import org.broad.igv.logging.*;
 import org.broad.igv.feature.genome.GenomeManager;
@@ -81,6 +82,7 @@ public void actionPerformed(ActionEvent e) {
 
             if (!dlg.isCanceled()) {
 
+
                 String inputURLs = dlg.getFileURL();
                 if (inputURLs != null && inputURLs.trim().length() > 0) {
 
@@ -89,7 +91,7 @@ public void actionPerformed(ActionEvent e) {
                     if (inputs.length == 1 && HubGenomeLoader.isHubURL(inputs[0])) {
                         LongRunningTask.submit(() -> {
                             try {
-                               GenomeManager.getInstance().loadGenome(inputs[0]);
+                               Genome newGenome = GenomeManager.getInstance().loadGenome(inputs[0]);
                             } catch (IOException ex) {
                                 log.error("Error loading tack hub", ex);
                                 MessageUtils.showMessage("Error loading track hub: " + ex.getMessage());

src/main/java/org/broad/igv/ui/action/UCSCGenArkAction.java

@@ -27,12 +27,14 @@
 
 import org.broad.igv.Globals;
 import org.broad.igv.feature.genome.Genome;
+import org.broad.igv.feature.genome.GenomeListItem;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.feature.genome.load.HubGenomeLoader;
 import org.broad.igv.logging.LogManager;
 import org.broad.igv.logging.Logger;
 import org.broad.igv.track.AttributeManager;
 import org.broad.igv.ui.IGV;
+import org.broad.igv.ui.commandbar.GenomeListManager;
 import org.broad.igv.ui.table.SearchableTableDialog;
 import org.broad.igv.ui.table.SearchableTableModel;
 import org.broad.igv.ui.table.SearchableTableRecord;

src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java

@@ -1,26 +1,20 @@
 package org.broad.igv.ui.commandbar;
 
 import org.broad.igv.logging.*;
-import org.broad.igv.DirectoryManager;
-import org.broad.igv.event.GenomeResetEvent;
-import org.broad.igv.event.IGVEventBus;
 import org.broad.igv.feature.genome.GenomeListItem;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.UIConstants;
 import org.broad.igv.ui.util.MessageUtils;
-import org.broad.igv.ui.util.UIUtilities;
 import org.broad.igv.util.LongRunningTask;
 
 import javax.swing.*;
 import javax.swing.border.EmptyBorder;
 import java.awt.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
-import java.util.List;
 
 /**
  * Created by jrobinso on 7/6/17.
@@ -100,7 +94,7 @@ private void loadGenomeListItem(final GenomeListItem genomeListItem) {
                 if (genomeListItem != null && genomeListItem.getPath() != null) {
 
                     if (genomeListItem == GenomeListItem.DOWNLOAD_ITEM) {
-                        loadGenomeFromServer();
+                        GenomeSelectionDialog.selectGenomesFromServer();
                     } else {
 
                         try {
@@ -197,76 +191,4 @@ public Component getListCellRendererComponent(JList list, Object value, int inde
     }
 
 
-    /**
-     * Open a selection list to load a genome from the server.   This method is static because its used by multiple
-     * UI elements  (menu bar and genome selection pulldown).
-     */
-    public static void loadGenomeFromServer() {
-
-        Runnable showDialog = () -> {
-
-            Collection<GenomeListItem> inputListItems = GenomeListManager.getInstance().getServerGenomeList();
-            if (inputListItems == null) {
-                return;
-            }
-            GenomeSelectionDialog dialog = new GenomeSelectionDialog(IGV.getInstance().getMainFrame(), inputListItems);
-            UIUtilities.invokeAndWaitOnEventThread(() -> dialog.setVisible(true));
-
-            if (dialog.isCanceled()) {
-                IGVEventBus.getInstance().post(new GenomeResetEvent());
-            } else {
-                List<GenomeListItem> selectedValueList = dialog.getSelectedValues();
-                GenomeListItem firstItem = null;
-                for (GenomeListItem selectedValue : selectedValueList) {
-                    if (selectedValue != null) {
-                        boolean downloadSequence = false;
-                        boolean success = GenomeManager.getInstance().downloadGenome(selectedValue, downloadSequence);
-                        if (success) {
-                            GenomeListManager.getInstance().addServerGenomeItem(selectedValue);
-                            firstItem = selectedValue;
-                        }
-                    }
-                }
-                if (firstItem != null && selectedValueList.size() == 1) {
-                    try {
-
-                        GenomeManager.getInstance().loadGenome(firstItem.getPath());
-                        // If the user has previously defined this genome, remove it.
-                        GenomeListManager.getInstance().removeUserDefinedGenome(firstItem.getId());
-
-                        // If this is a .json genome, attempt to remove existing .genome files
-                        if (firstItem.getPath().endsWith(".json")) {
-                            removeDotGenomeFile(firstItem.getId());
-                        }
-
-
-                    } catch (IOException e) {
-                        GenomeListManager.getInstance().removeGenomeListItem(firstItem);
-                        MessageUtils.showErrorMessage("Error loading genome " + firstItem.getDisplayableName(), e);
-                        log.error("Error loading genome " + firstItem.getDisplayableName(), e);
-                    }
-                }
-            }
-        };
-
-        if (SwingUtilities.isEventDispatchThread()) {
-            LongRunningTask.submit(showDialog);
-        } else {
-            showDialog.run();
-        }
-    }
-
-    public static void removeDotGenomeFile(String id) {
-        try {
-            File dotGenomeFile = new File(DirectoryManager.getGenomeCacheDirectory(), id + ".genome");
-            if (dotGenomeFile.exists()) {
-                dotGenomeFile.delete();
-            }
-        } catch (Exception e) {
-            // If anything goes wrong, just log it, this cleanup is not essential
-            log.error("Error deleting .genome file", e);
-        }
-    }
-
-
 }