diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java index 7c5514a8e6faa552fdf5719e76636a17562511bb..3f8ec99b3bcf79047e62c9f91741ec10ee2b2eb3 100644 --- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java +++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java @@ -61,22 +61,20 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl for (DatasetDescription dataset : datasets) { File originalData = getDataSubDir(dataset); - describe(builder, dataset, originalData); + File summaryFile = extractSummaryFile(dataset, originalData); + describe(builder, dataset, summaryFile); } return builder.getTableModel(); } - private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset, - File originalData) + private static File extractSummaryFile(DatasetDescription dataset, File originalData) { List<File> files = new ArrayList<File>(); FileUtilities.findFiles(originalData, files, createIlluminaSummaryFileFilter()); int size = files.size(); if (size == 1) { - File file = files.get(0); - IlluminaSummary summary = new IlluminaSummaryXMLLoader(false).readSummaryXML(file); - describeSummary(builder, summary, dataset); + return files.get(0); } else { throw new EnvironmentFailureException(String.format( @@ -85,8 +83,15 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl } } - private static void describeSummary(SimpleTableModelBuilder builder, IlluminaSummary summary, - DatasetDescription dataset) + private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset, + File summaryFile) + { + IlluminaSummary summary = new IlluminaSummaryXMLLoader(false).readSummaryXML(summaryFile); + describeSummary(builder, dataset, summary); + } + + private static void describeSummary(SimpleTableModelBuilder builder, + DatasetDescription dataset, IlluminaSummary summary) { ChipResultsSummary chipResultSummary = summary.getChipResultsSummary(); List<ISerializableComparable> row =