refine genome "is downloadable" tests

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

@@ -20,8 +20,7 @@
 import java.lang.reflect.Field;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Class of static functions for managing genome downloads
@@ -30,20 +29,27 @@ public class GenomeDownloadUtils {
 
     private static Logger log = LogManager.getLogger(GenomeDownloadUtils.class);
 
-    public static boolean isAnnotationsDownloadable(GenomeListItem item) {
-        return item.getPath().endsWith(".json");
+    public static boolean isAnnotationsDownloadable(String path) {
+        return path.endsWith(".json");
     }
 
-    public static boolean isSequenceDownloadable(GenomeListItem item) {
-        if (item.getPath().endsWith(".json")) {
+    public static boolean isSequenceDownloadable(String path) {
+        if (path != null && path.endsWith(".json")) {
             try {
-                String jsonString = HttpUtils.getInstance().getContentsAsJSON(new URL(item.getPath()));
-                return jsonString.contains("twoBitURL");
+                String jsonString = FileUtils.getContents(path);
+                GenomeConfig genomeConfig = GenomeConfig.fromJson(jsonString);
+                String sequenceURL = genomeConfig.getTwoBitURL();
+                if (sequenceURL == null) {
+                    sequenceURL = genomeConfig.getFastaURL();
+                }
+                return isRemoteURL(sequenceURL) && !disallowedBuckets.stream().anyMatch(sequenceURL::contains);
+
             } catch (IOException e) {
-                log.error("Error fetching genome json " + item.getPath());
+                log.error("Error fetching genome json " + path);
             }
         }
         return false;
+
     }
 
     public static File downloadGenome(GenomeConfig c, boolean downloadSequence, boolean downloadAnnotations) throws IOException {
@@ -161,4 +167,13 @@ private static File download(URL url, File directory) throws MalformedURLExcepti
         return localFile;
     }
 
+    private static boolean isRemoteURL(String url) {
+        return url.startsWith("http://") || url.startsWith("https://");
+    }
+
+    static Set<String> disallowedBuckets = new HashSet<>(Arrays.asList(
+            "igv.org.genomes",
+            "igv-genepattern-org",
+            "igv.broadinstitute.org"));
+
 }

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

@@ -63,6 +63,9 @@ public class GenomeConfig implements Cloneable {
     private List<List<String>> chromAliases;
 
     public static GenomeConfig fromJson(String json) {
+        if (json.contains("chromosomeOrder")) {
+            json = fixChromosomeOrder(json);
+        }
         return (new Gson()).fromJson(json, GenomeConfig.class);
     }
 
@@ -307,4 +310,21 @@ protected GenomeConfig clone() {
         }
     }
 
+    /**
+     * Fix deprecated form of chromosome order (comma delimited list of strings)
+     *
+     * @param jsonString
+     * @return
+     */
+    private static String fixChromosomeOrder(String jsonString) {
+        Map obj = (new Gson()).fromJson(jsonString, Map.class);
+        Object chromosomeOrder = obj.get("chromosomeOrder");
+        if (chromosomeOrder != null) {
+            if (chromosomeOrder instanceof String) {
+                obj.put("chromosomeOrder", Arrays.stream(((String) chromosomeOrder).split(",")).map(c -> c.trim()).toArray());
+            }
+        }
+        return (new Gson()).toJson(obj);
+    }
+
 }

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

@@ -66,10 +66,6 @@ public GenomeConfig loadGenomeConfig() throws IOException {
 
             String jsonString = ParsingUtils.readContentsFromStream(is);
 
-            if (jsonString.contains("chromosomeOrder")) {
-                jsonString = fixChromosomeOrder(jsonString);
-            }
-
             GenomeConfig genomeConfig = GenomeConfig.fromJson(jsonString);
 
             fixPaths(genomeConfig);
@@ -79,24 +75,6 @@ public GenomeConfig loadGenomeConfig() throws IOException {
         }
     }
 
-    /**
-     * Fix deprecated form of chromosome order (comma delimited list of strings)
-     *
-     * @param jsonString
-     * @return
-     */
-    private String fixChromosomeOrder(String jsonString) {
-        Map obj = (new Gson()).fromJson(jsonString, Map.class);
-        Object chromosomeOrder = obj.get("chromosomeOrder");
-        if (chromosomeOrder != null) {
-            if (chromosomeOrder instanceof String) {
-                obj.put("chromosomeOrder", Arrays.stream(((String) chromosomeOrder).split(",")).map(c -> c.trim()).toArray());
-            }
-        }
-        return (new Gson()).toJson(obj);
-
-    }
-
     /**
      * JSON paths/urls can be relative to the path to the genome json file.  This method converts them to absolulte
      * paths/urls.

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

@@ -207,8 +207,8 @@ private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
 
     private void configureDownloadButtons(GenomeListItem item) {
         if (item != null) {
-            final boolean sequenceDownloadable = GenomeDownloadUtils.isSequenceDownloadable(item);
-            final boolean annotationsDownloadable = GenomeDownloadUtils.isAnnotationsDownloadable(item);
+            final boolean sequenceDownloadable = GenomeDownloadUtils.isSequenceDownloadable(item.getPath());
+            final boolean annotationsDownloadable = GenomeDownloadUtils.isAnnotationsDownloadable(item.getPath());
             downloadSequenceCB.setEnabled(sequenceDownloadable);
             downloadAnnotationsCB.setEnabled(annotationsDownloadable);
         }

src/test/java/org/broad/igv/feature/genome/GenomeDownloadUtilsTest.java

@@ -0,0 +1,24 @@
+package org.broad.igv.feature.genome;
+
+import org.broad.igv.util.TestUtils;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class GenomeDownloadUtilsTest {
+
+    @Test
+    public void isAnnotationsDownloadable() {
+        assertTrue(GenomeDownloadUtils.isAnnotationsDownloadable(TestUtils.DATA_DIR +  "genomes/json/hg38_twobit.json"));
+
+    }
+
+    @Test
+    public void isSequenceDownloadable() {
+
+        assertTrue(GenomeDownloadUtils.isSequenceDownloadable(TestUtils.DATA_DIR +  "genomes/json/hg38_twobit.json"));
+        assertFalse(GenomeDownloadUtils.isSequenceDownloadable(TestUtils.DATA_DIR +  "genomes/json/hg18.unittest.json"));
+        assertFalse(GenomeDownloadUtils.isSequenceDownloadable(TestUtils.DATA_DIR +  "genomes/json/sacCer3.json"));
+
+    }
+}

test/data/genomes/json/hg38_twobit.json

@@ -0,0 +1,21 @@
+{
+  "id": "hg38",
+  "name": "Human (GRCh38/hg38)",
+  "fastaURL": "https://igv.org/genomes/data/hg38/hg38.fa",
+  "indexURL": "https://igv.org/genomes/data/hg38/hg38.fa.fai",
+  "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz",
+  "aliasURL": "https://igv.org/genomes/data/hg38/hg38_alias.tab",
+  "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
+  "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes",
+  "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY",
+  "tracks": [
+    {
+      "name": "Refseq Select",
+      "format": "refgene",
+      "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqSelect.txt.gz",
+      "indexed": false,
+      "order": 1000001,
+      "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
+    }
+  ]
+}