Refactoring, streamline genome list

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

@@ -74,7 +74,7 @@ public class Genome {
     private static final int MAX_WHOLE_GENOME_LONG = 100;
     private static Logger log = LogManager.getLogger(Genome.class);
 
-    GenomeConfig config;
+
     private String id;
     private String displayName;
     private List<String> chromosomeNames;
@@ -98,9 +98,21 @@ public class Genome {
     private String defaultPos;
     private String nameSet;
     private List<Hub> trackHubs;
+    private GenomeConfig config;
+
+
+    private static Genome nullGenome = null;
+
+    public synchronized static Genome nullGenome() {
+        if (nullGenome == null) {
+            nullGenome = new Genome("None", Arrays.asList(new Chromosome(0, "", 0)));
+        }
+        return nullGenome;
+    }
 
-    public Genome(GenomeConfig config) throws IOException {
 
+    public Genome(GenomeConfig config) throws IOException {
+        this.config = config;
         id = config.getId();
         displayName = config.getName();
         nameSet = config.getNameSet();
@@ -180,7 +192,7 @@ public Genome(GenomeConfig config) throws IOException {
             }
         } else {
             // No chromosome list.  Try to fetch chromosome names from the sequence
-            if(this.chromosomeNames.isEmpty()) {
+            if (this.chromosomeNames.isEmpty()) {
                 this.chromosomeNames = sequence.getChromosomeNames();
             }
         }
@@ -228,8 +240,8 @@ public Genome(GenomeConfig config) throws IOException {
             // TODO -- no place to go
         }
 
-        if(config.getHubs() != null) {
-            for(String hubUrl : config.getHubs()) {
+        if (config.getHubs() != null) {
+            for (String hubUrl : config.getHubs()) {
                 try {
                     trackHubs.add(HubParser.loadHub(hubUrl, getUCSCId()));
                 } catch (Exception e) {
@@ -315,7 +327,7 @@ public String getCanonicalChrName(String str) {
             try {
                 ChromAlias aliasRecord = chromAliasSource.search(str);
 
-                if(aliasRecord == null && !str.equals(str.toLowerCase())) {
+                if (aliasRecord == null && !str.equals(str.toLowerCase())) {
                     aliasRecord = chromAliasSource.search(str.toLowerCase());
                 }
 
@@ -817,12 +829,21 @@ public List<Hub> getTrackHubs() {
         return trackHubs;
     }
 
-    public synchronized static Genome nullGenome() {
-        if(nullGenome == null) {
-            nullGenome = new Genome("None", Arrays.asList(new Chromosome(0, "", 0)));
+    public void addTrackHub(Hub hub) {
+
+        if(!trackHubs.stream().anyMatch(h -> h.getUrl().equals(hub.getUrl()))) {
+            trackHubs.add(hub);
+            if (config.isFromJson()) {
+                config.addHub(hub.getUrl());
+            }
         }
-        return  nullGenome;
     }
 
-    private static Genome nullGenome = null;
+    public boolean isFromJson() {
+        return config != null && config.isFromJson();
+    }
+
+    public GenomeConfig getConfig() {
+        return config;
+    }
 }

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

@@ -61,12 +61,15 @@ public class GenomeConfig implements Cloneable {
     private Sequence sequence;
     private LinkedHashMap<String, List<Cytoband>> cytobands;
     private List<List<String>> chromAliases;
+    private boolean fromJson = false;  // Until proven otherwise
 
     public static GenomeConfig fromJson(String json) {
         if (json.contains("chromosomeOrder")) {
             json = fixChromosomeOrder(json);
         }
-        return (new Gson()).fromJson(json, GenomeConfig.class);
+        GenomeConfig config = (new Gson()).fromJson(json, GenomeConfig.class);
+        config.fromJson = true;
+        return config;
     }
 
     public GenomeConfig() {
@@ -84,6 +87,13 @@ public void setHubs(List<String> hubs) {
         this.hubs = hubs;
     }
 
+    public void addHub(String hub) {
+        if (hubs == null) {
+            hubs = new ArrayList();
+        }
+        hubs.add(hub);
+    }
+
     public String getId() {
         return id;
     }
@@ -339,4 +349,7 @@ private static String fixChromosomeOrder(String jsonString) {
         return (new Gson()).toJson(obj);
     }
 
+    public boolean isFromJson() {
+        return fromJson;
+    }
 }

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

@@ -31,7 +31,7 @@ public class HubGenomeLoader extends GenomeLoader {
     static Logger log = LogManager.getLogger(HubGenomeLoader.class);
 
     public static boolean isHubURL(String obj) {
-        return obj.endsWith("/hub.txt");
+        return obj != null && obj.toLowerCase().endsWith("hub.txt");       // <= very crude, perhaps read the first line
     }
 
     public static String convertToHubURL(String accension) {
@@ -90,9 +90,22 @@ protected void done() {
         };
 
         worker.execute();
+    }
 
+    /**
+     * Shortcut method provided to support load-from-url.  The hub must be read and parsed to determine if it is an
+     * assembly hub.  This method avoids the need to load and parse again.
+     *
+     * @param hub
+     * @throws IOException
+     */
+    public static void loadAssemblyHub(Hub hub) throws IOException {
+        final GenomeConfig config = getGenomeConfig(hub);
+        File genomeFile = GenomeDownloadUtils.saveLocalGenome(config);
+        GenomeManager.getInstance().loadGenome(genomeFile.getAbsolutePath());
     }
 
+
     private static GenomeConfig getGenomeConfig(Hub hub) throws IOException {
 
         GenomeConfig config = hub.getGenomeConfig();

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

@@ -63,13 +63,9 @@ public Genome loadGenome() throws IOException {
     public GenomeConfig loadGenomeConfig() throws IOException {
 
         try (InputStream is = ParsingUtils.openInputStream(genomePath)) {
-
             String jsonString = ParsingUtils.readContentsFromStream(is);
-
             GenomeConfig genomeConfig = GenomeConfig.fromJson(jsonString);
-
             fixPaths(genomeConfig);
-
             return genomeConfig;
 
         }

src/main/java/org/broad/igv/ucsc/hub/Hub.java

@@ -50,6 +50,10 @@ public class Hub {
         }
     }
 
+    public boolean isAssemblyHub() {
+        return genomeStanza.hasProperty("twoBitPath");
+    }
+
 
     public String getShortLabel() {
         return hubStanza.hasProperty("shortLabel") ? hubStanza.getProperty("shortLabel") : this.url;

src/main/java/org/broad/igv/ucsc/hub/HubLoader.java

@@ -0,0 +1,12 @@
+package org.broad.igv.ucsc.hub;
+
+import org.broad.igv.ui.IGV;
+
+public class HubLoader {
+
+
+    static void loadHub(Hub hub) {
+
+
+    }
+}

src/main/java/org/broad/igv/ucsc/hub/HubParser.java

@@ -25,10 +25,6 @@ public static Hub loadAssemblyHub(String url) throws IOException {
 
     public static Hub loadHub(String url, String genomeId) throws IOException {
 
-        boolean assemblyHub = genomeId == null;
-
-        int idx = url.lastIndexOf("/");
-
         // Load stanzas from the hub.txt file, which might be all stanzas if 'useOneFile' is on
         List<Stanza> stanzas = HubParser.loadStanzas(url);
 
@@ -51,6 +47,14 @@ public static Hub loadHub(String url, String genomeId) throws IOException {
                 throw new RuntimeException("Unexpected hub file -- expected 'genome' stanza but found " + stanzas.get(1).type);
             }
             genomeStanza = stanzas.get(1);
+
+            if(!genomeStanza.hasProperty("twoBitPath")) {
+                // Not an assembly hub, validate genome
+                if(!genomeStanza.getProperty("genome").equals(genomeId)) {
+                    throw new RuntimeException("Hub file does not contain tracks for genome " + genomeId);
+                }
+            }
+
             trackStanzas = new ArrayList<>(stanzas.subList(2, stanzas.size()));
 
         } else {
@@ -63,6 +67,7 @@ public static Hub loadHub(String url, String genomeId) throws IOException {
             List<Stanza> genomeStanzaList = HubParser.loadStanzas(hubStanza.getProperty("genomesFile"));
 
             // Find stanza for requested genome, or if no requested genome the first.
+
             for (Stanza s : genomeStanzaList) {
                 if (genomeId == null || genomeId.equals(s.getProperty("genome"))) {
                     stanzas.add(s);
@@ -71,16 +76,16 @@ public static Hub loadHub(String url, String genomeId) throws IOException {
                     break;
                 }
             }
+            if(trackDbURL == null) {
+                throw new RuntimeException("Hub file does not contain tracks for genome " + genomeId);
+            }
         }
 
         // Assembly hub validation
-        if (assemblyHub) {
+        if (genomeId == null ) {
             if (!genomeStanza.hasProperty("twoBitPath")) {
                 throw new RuntimeException("Assembly hubs must specify 'twoBitPath'");
             }
-            if (!genomeStanza.hasProperty("groups")) {
-                throw new RuntimeException("Assembly hubs must specify 'groups'");
-            }
         }
 
         if (genomeStanza.hasProperty("groups")) {

src/main/java/org/broad/igv/ucsc/hub/TrackDbHub.java

@@ -12,7 +12,8 @@
 public class TrackDbHub {
 
 
-    static Set supportedTypes = new HashSet(Arrays.asList("bigBed", "bigWig", "bigGenePred", "vcfTabix", "refgene", "bam", "sampleInfo", "vcf.list"));
+    static Set supportedTypes = new HashSet(Arrays.asList("bigbed", "bigwig", "biggenepred", "vcftabix", "refgene",
+            "bam", "sampleinfo", "vcf.list", "ucscsnp", "bed", "tdf", "gff", "gff3", "gtf"));
 
     static Set filterTracks = new HashSet(Arrays.asList("cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
             "cpgIslandExtUnmasked", "windowMasker"));
@@ -99,7 +100,7 @@ public List<TrackConfigContainer> getGroupedTrackConfigurations(String hubName)
 
                 } else if (!filterTracks.contains(s.name) &&
                         s.hasProperty("bigDataUrl") &&
-                        supportedTypes.contains(s.format())) {
+                        supportedTypes.contains(s.format().toLowerCase())) {
 
                     final TrackConfig trackConfig = getTrackConfig(s);
                     if (parent != null) {