bug fix -- not all fields in genome.json were handled for local genom…

…es with relative paths.
igvteam · Sep 27, 2024 · f3233fc · f3233fc
1 parent 51e5288
commit f3233fc
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Showing 4 changed files with 41 additions and 10 deletions.
diff --git a/src/main/java/org/broad/igv/feature/genome/Genome.java b/src/main/java/org/broad/igv/feature/genome/Genome.java
@@ -124,7 +124,7 @@ 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);

diff --git a/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java b/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
@@ -99,6 +99,19 @@ 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);
         }
@@ -108,6 +121,9 @@ 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);
         }

diff --git a/src/main/java/org/broad/igv/ui/commandbar/GenomeListManager.java b/src/main/java/org/broad/igv/ui/commandbar/GenomeListManager.java
@@ -258,15 +258,28 @@ private static Map<String, GenomeListItem> getCachedGenomeList() {
                         JsonObject json = rootElement.getAsJsonObject();
                         JsonElement id = json.get("id");
                         JsonElement name = json.get("name");
-                        JsonElement fastaURL = json.get("fastaURL");
-                        if (id != null && name != null && fastaURL != null) {
-                            if (cachedGenomes.containsKey(id.getAsString())) {
-                                File prevFile = new File(cachedGenomes.get(id.getAsString()).getPath());
-                                prevFile.delete();
-                            }
-                            GenomeListItem item = new GenomeListItem(name.getAsString(), file.getAbsolutePath(), id.getAsString());
-                            cachedGenomes.put(item.getId(), item);
+                        JsonElement fasta = json.get("fastaURL");
+                        JsonElement twobit = json.get("twoBitURL");
+                        if (id == null) {
+                            log.error("Error parsing " + file.getName() + ". \"id\" is required");
+                            continue;
+                        }
+                        if (name == null) {
+                            log.error("Error parsing " + file.getName() + ". \"name\" is required");
+                            continue;
+                        }
+                        if (id == null) {
+                            log.error("Error parsing " + file.getName() + ". \"id\" is required");
+                            continue;
+                        }
+                        if (fasta == null && twobit == null) {
+                            log.error("Error parsing " + file.getName() + ". One of either \"fastaURL\" or \"twoBitURL\" is required");
+                            continue;
                         }
+
+                        GenomeListItem item = new GenomeListItem(name.getAsString(), file.getAbsolutePath(), id.getAsString());
+                        cachedGenomes.put(item.getId(), item);
+
                     }
                 } catch (Exception e) {
                     log.error("Error parsing genome json: " + file.getAbsolutePath(), e);
@@ -316,7 +329,7 @@ public void removeGenomeListItem(GenomeListItem genomeListItem) {
 
         // If this is a cached genome remove it from cache
         Map<String, GenomeListItem> cachedItems = getCachedGenomeList();
-        if(cachedItems.containsKey(id)){
+        if (cachedItems.containsKey(id)) {
             try {
                 (new File(genomeListItem.getPath())).delete();
             } catch (Exception e) {

diff --git a/src/main/java/org/broad/igv/util/FileUtils.java b/src/main/java/org/broad/igv/util/FileUtils.java
@@ -364,9 +364,11 @@ public static String getFileExtension(String filePath) {
      * @return
      */
     public static String getAbsolutePath(String inputPath, String referencePath) {
+
         if (isRemote(inputPath) || referencePath == null) {
             return inputPath;
         }
+
         File inFile = new File(inputPath);
         if (inFile.isAbsolute()) {
             return inFile.getAbsolutePath();