Bugfix to nimble -v command

bbimber · bbimber · commit bf4ae47053f3 · 2024-11-11T06:49:10.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -711,10 +711,15 @@ private String getVersion(PipelineStepOutput output) throws PipelineJobException
             throw new PipelineJobException("Unable to find file: " + outFile.getPath());
         }
 
-        String ret;
-        try (BufferedReader reader = Readers.getReader(outFile))
+        String ret = null;
+        try
         {
-            ret = reader.readLine();
+            ret = StringUtils.trimToNull(Files.readString(outFile.toPath()));
+            if (ret == null)
+            {
+                throw new PipelineJobException("nimble -v did not output version");
+            }
+            ret = ret.replaceAll("nimble", "").replaceAll("[\\r\\n]+", "");
         }
         catch (IOException e)
         {

Original file line number	Diff line number	Diff line change
`@@ -711,10 +711,15 @@ private String getVersion(PipelineStepOutput output) throws PipelineJobException`
`711`	`711`	`throw new PipelineJobException("Unable to find file: " + outFile.getPath());`
`712`	`712`	`}`
`713`	`713`
`714`		`- String ret;`
`715`		`- try (BufferedReader reader = Readers.getReader(outFile))`
	`714`	`+ String ret = null;`
	`715`	`+ try`
`716`	`716`	`{`
`717`		`- ret = reader.readLine();`
	`717`	`+ ret = StringUtils.trimToNull(Files.readString(outFile.toPath()));`
	`718`	`+ if (ret == null)`
	`719`	`+ {`
	`720`	`+ throw new PipelineJobException("nimble -v did not output version");`
	`721`	`+ }`
	`722`	`+ ret = ret.replaceAll("nimble", "").replaceAll("[\\r\\n]+", "");`
`718`	`723`	`}`
`719`	`724`	`catch (IOException e)`
`720`	`725`	`{`