Bugfix to nimble metrics import

bbimber · bbimber · commit 89a95668298b · 2023-01-08T20:25:37.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -591,7 +591,13 @@ public static void importQualityMetrics(SequenceOutputFile so, PipelineJob job)
                             throw new PipelineJobException("Unexpected duplicate metric names: " + StringUtils.trim(line[0]));
                         }
 
-                        metricsMap.put(StringUtils.trim(line[0]), StringUtils.trim(line[1]));
+                        String value = StringUtils.trim(line[1]);
+                        if (value == null)
+                        {
+                            continue;
+                        }
+
+                        metricsMap.put(StringUtils.trim(line[0]), value.split(" ")[0]);
                     }
                 }
 

Original file line number	Diff line number	Diff line change
`@@ -591,7 +591,13 @@ public static void importQualityMetrics(SequenceOutputFile so, PipelineJob job)`
`591`	`591`	`throw new PipelineJobException("Unexpected duplicate metric names: " + StringUtils.trim(line[0]));`
`592`	`592`	`}`
`593`	`593`
`594`		`- metricsMap.put(StringUtils.trim(line[0]), StringUtils.trim(line[1]));`
	`594`	`+ String value = StringUtils.trim(line[1]);`
	`595`	`+ if (value == null)`
	`596`	`+ {`
	`597`	`+ continue;`
	`598`	`+ }`
	`599`	`+`
	`600`	`+ metricsMap.put(StringUtils.trim(line[0]), value.split(" ")[0]);`
`595`	`601`	`}`
`596`	`602`	`}`
`597`	`603`