Update to new parent class for PathType (#121)

labkey-jeckels · web-flow · commit 82f5ca0e5300 · 2022-01-15T14:16:50.000-08:00
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java b/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java
@@ -19,6 +19,7 @@
 import org.labkey.api.exp.api.DataType;
 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
@@ -488,7 +488,7 @@ 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());
@@ -536,7 +536,7 @@ 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());
@@ -629,7 +629,7 @@ 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
`@@ -488,7 +488,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r`
`488`	`488`	`put(JBrowseSession.getAssemblyName(rg));`
`489`	`489`	`}});`
`490`	`490`
`491`		`- String url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`491`	`+ String url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`492`	`492`	`if (url == null)`
`493`	`493`	`{`
`494`	`494`	`log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());`
`@@ -536,7 +536,7 @@ private JSONObject getBamTrack(Logger log, ExpData targetFile, ReferenceGenome r`
`536`	`536`	`put(JBrowseSession.getAssemblyName(rg));`
`537`	`537`	`}});`
`538`	`538`
`539`		`- String url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`539`	`+ String url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`540`	`540`	`if (url == null)`
`541`	`541`	`{`
`542`	`542`	`log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());`
`@@ -629,7 +629,7 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome`
`629`	`629`	`}`
`630`	`630`	`else`
`631`	`631`	`{`
`632`		`- url = targetFile.getWebDavURL(ExpData.PathType.full);`
	`632`	`+ url = targetFile.getWebDavURL(FileContentService.PathType.full);`
`633`	`633`	`}`
`634`	`634`
`635`	`635`	`if (url == null)`