Merge 21.11 to develop

labkey-teamcity · labkey-teamcity · commit 6ce2e3fe5797 · 2022-01-20T18:08:06.000Z
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java b/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java
@@ -16,6 +16,7 @@
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.files.FileContentService;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
@@ -358,7 +359,7 @@ public static String getAssemblyName(ReferenceGenome rg)
     public static JSONObject getIndexedFastaAdapter(ReferenceGenome rg)
     {
         ExpData d = ExperimentService.get().getExpData(rg.getFastaExpDataId());
-        String url = d.getWebDavURL(ExpData.PathType.full);
+        String url = d.getWebDavURL(FileContentService.PathType.full);
 
         JSONObject ret = new JSONObject();
         ret.put("type", "IndexedFastaAdapter");
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
@@ -499,7 +499,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
             put(JBrowseSession.getAssemblyName(rg));
         }});
 
-        String url = targetFile.getWebDavURL(ExpData.PathType.full);
+        String url = targetFile.getWebDavURL(FileContentService.PathType.full);
         if (url == null)
         {
             log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
@@ -568,7 +568,7 @@ private JSONObject getBamTrack(Logger log, ExpData targetFile, ReferenceGenome r
             put(JBrowseSession.getAssemblyName(rg));
         }});
 
-        String url = targetFile.getWebDavURL(ExpData.PathType.full);
+        String url = targetFile.getWebDavURL(FileContentService.PathType.full);
         if (url == null)
         {
             log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
@@ -661,7 +661,7 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome
         }
         else
         {
-            url = targetFile.getWebDavURL(ExpData.PathType.full);
+            url = targetFile.getWebDavURL(FileContentService.PathType.full);
         }
 
         if (url == null)

Original file line number	Diff line number	Diff line change
`@@ -499,7 +499,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r`
`499`	`499`	`put(JBrowseSession.getAssemblyName(rg));`
`500`	`500`	`}});`
`501`	`501`
`502`		`- String url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`502`	`+ String url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`503`	`503`	`if (url == null)`
`504`	`504`	`{`
`505`	`505`	`log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());`
`@@ -568,7 +568,7 @@ private JSONObject getBamTrack(Logger log, ExpData targetFile, ReferenceGenome r`
`568`	`568`	`put(JBrowseSession.getAssemblyName(rg));`
`569`	`569`	`}});`
`570`	`570`
`571`		`- String url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`571`	`+ String url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`572`	`572`	`if (url == null)`
`573`	`573`	`{`
`574`	`574`	`log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());`
`@@ -661,7 +661,7 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome`
`661`	`661`	`}`
`662`	`662`	`else`
`663`	`663`	`{`
`664`		`- url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`664`	`+ url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`665`	`665`	`}`
`666`	`666`
`667`	`667`	`if (url == null)`