Issue 50861: Pass around properly encoded WebDav URLs (#320)

Author: labkey-jeckels

jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java

@@ -29,6 +29,7 @@
 import org.labkey.jbrowse.JBrowseSchema;
 
 import java.io.File;
+import java.net.URI;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -361,12 +362,12 @@ public static String getAssemblyName(ReferenceGenome rg)
     public static JSONObject getIndexedFastaAdapter(ReferenceGenome rg)
     {
         ExpData d = ExperimentService.get().getExpData(rg.getFastaExpDataId());
-        String url = d.getWebDavURL(FileContentService.PathType.full);
+        URI url = d.getWebDavURL(FileContentService.PathType.full);
 
         JSONObject ret = new JSONObject();
         ret.put("type", "IndexedFastaAdapter");
         ret.put("fastaLocation", new JSONObject(){{
-            put("uri", url);
+            put("uri", url.toString());
         }});
         ret.put("faiLocation", new JSONObject(){{
             put("uri", url + ".fai");
@@ -378,7 +379,7 @@ public static JSONObject getIndexedFastaAdapter(ReferenceGenome rg)
     public static JSONObject getBgZippedIndexedFastaAdapter(ReferenceGenome rg)
     {
         ExpData d = ExperimentService.get().getExpData(rg.getFastaExpDataId());
-        String url = d.getWebDavURL(FileContentService.PathType.full);
+        URI url = d.getWebDavURL(FileContentService.PathType.full);
 
         JSONObject ret = new JSONObject();
         ret.put("type", "BgzipFastaAdapter");

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -50,6 +50,7 @@
 import org.labkey.api.util.JobRunner;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
+import org.labkey.api.util.UnexpectedException;
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.jbrowse.JBrowseLuceneSearch;
 import org.labkey.jbrowse.JBrowseManager;
@@ -59,6 +60,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.nio.file.Files;
 import java.sql.SQLException;
 import java.util.Arrays;
@@ -512,7 +515,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
             put(JBrowseSession.getAssemblyName(rg));
         }});
 
-        String url = targetFile.getWebDavURL(FileContentService.PathType.full);
+        URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
         if (url == null)
         {
             log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
@@ -522,7 +525,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
         ret.put("adapter", new JSONObject(){{
             put("type", "ExtendedVariantAdapter");
             put("vcfGzLocation", new JSONObject(){{
-                put("uri", url);
+                put("uri", url.toString());
             }});
 
             put("index", new JSONObject(){{
@@ -596,7 +599,7 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
             put(JBrowseSession.getAssemblyName(rg));
         }});
 
-        String url = targetFile.getWebDavURL(FileContentService.PathType.full);
+        URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
         if (url == null)
         {
             log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
@@ -612,7 +615,7 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
                 put("type", type);
                 put("bamLocation", new JSONObject()
                 {{
-                    put("uri", url);
+                    put("uri", url.toString());
                 }});
 
                 put("index", new JSONObject()
@@ -667,7 +670,7 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom
             put(getCategory());
         }});
 
-        String url = targetFile.getWebDavURL(FileContentService.PathType.full);
+        URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
         if (url == null)
         {
             log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
@@ -677,7 +680,7 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom
         ret.put("adapter", new JSONObject(){{
             put("type", "BigWigAdapter");
             put("bigWigLocation", new JSONObject(){{
-                put("uri", url);
+                put("uri", url.toString());
                 put("locationType", "UriLocation");
             }});
         }});
@@ -747,7 +750,7 @@ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, Referen
 
         // if not gzipped, we need to process it:
         File gzipped = prepareResource(u, log, true, false);
-        final String url;
+        final URI url;
         if (!getExpData().getFile().equals(gzipped))
         {
             url = getWebDavURL(gzipped);
@@ -1192,7 +1195,7 @@ public File getExpectedLocationOfIndexFile(String extension, boolean throwIfNotF
         return ret;
     }
 
-    private String getWebDavURL(File input)
+    private URI getWebDavURL(File input)
     {
         java.nio.file.Path path = input.toPath();
         if (getContainerObj() == null)
@@ -1221,7 +1224,14 @@ private String getWebDavURL(File input)
                 relPath = Path.parse(FilenameUtils.separatorsToUnix(relPath)).toString();
             }
 
-            return AppProps.getInstance().getBaseServerUrl() + root.getWebdavURL() + relPath;
+            try
+            {
+                return new URI(AppProps.getInstance().getBaseServerUrl() + root.getWebdavURL() + relPath);
+            }
+            catch (URISyntaxException e)
+            {
+                throw UnexpectedException.wrap(e);
+            }
         }
 
         return null;