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Commit 09314e01 authored by kohleman's avatar kohleman
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adopted test to cover new XML elements 

SVN: 18418
parent b337f25d
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deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
+ 134
− 6
View file @ 09314e01
......@@ -37,18 +37,34 @@ public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
IlluminaSummaryReportingPlugin.IlluminaSummaryXMLLoader.readSummaryXML(file);
ChipResultsSummary chipResultsSummary = summary.getChipResultsSummary();
LaneResultsSummary laneResultsSummary = summary.getLaneResultsSummary();
assertEquals(new Long(98792458L), chipResultsSummary.getClusterCountPF());
assertEquals(new Long(158466917L), chipResultsSummary.getClusterCountRaw());
assertEquals(new Long(3556528488L), chipResultsSummary.getYield());
if (summary.getSoftware() == null)
// if not there yhen take the init value
assertEquals(new Double(0.0), chipResultsSummary.getDensityRatio());
assertEquals(new Long(381287L), laneResultsSummary.getRead().getLanes().get(0)
.getClusterCountRaw().getMean());
assertEquals(new Long(277736L), laneResultsSummary.getRead().getLanes().get(0)
.getClusterCountPF().getMean());
assertEquals(new Integer(1199819), laneResultsSummary.getRead().getLanes().get(0)
.getLaneYield());
assertEquals(new Double(79.37), laneResultsSummary.getRead().getLanes().get(0)
.getPercentUniquelyAlignedPF().getMean());
if (summary.getSoftware() == "")
{
assertEquals(null, summary.getSoftware());
assertEquals("", summary.getSoftware());
} else
{
assertEquals("CASAVA-1.6.0", summary.getSoftware());
}
}
/**
*
*/
protected static final String EXAMPLE = "<?xml version='1.0' ?>\n "
+ "<?xml-stylesheet type='text/xsl' href='Summary.xsl' ?>\n "
+ "<Summary> "
......@@ -63,10 +79,122 @@ public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
+ " <RunFolder>090916_42R0CAAXX</RunFolder> "
+ " </ChipSummary> "
+ " <Date>Tue Oct 20 18:15:43 2009</Date> "
+ " <ExpandedLaneSummary/> "
+ " <LaneParameterSummary/> "
+ " <LaneResultsSummary/> "
+ " <ExpandedLaneSummary> "
+ " <Read> "
+ " <readNumber>1</readNumber> "
+ " <Lane> "
+ " <laneNumber>1</laneNumber> "
+ " <clusterCountRaw> "
+ " <mean>381286.80</mean> "
+ " <stdev>28613.35</stdev> "
+ " <sumsq>98246880000.00</sumsq> "
+ " </clusterCountRaw> "
+ " <errorPF> "
+ " <mean>0.72</mean> "
+ " <stdev>0.49</stdev> "
+ " <sumsq>90.37</sumsq> "
+ " </errorPF> "
+ " <errorRaw> "
+ " <mean>0.83</mean> "
+ " <stdev>0.48</stdev> "
+ " <sumsq>110.63</sumsq> "
+ " </errorRaw> "
+ " <infoContentPF> "
+ " <mean>213494</mean> "
+ " <stdev>9929</stdev> "
+ " <sumsq>5481321756576</sumsq> "
+ " </infoContentPF> "
+ " <infoContentRaw> "
+ " <mean>229532</mean> "
+ " <stdev>11786</stdev> "
+ " <sumsq>6338734406410</sumsq> "
+ " </infoContentRaw> "
+ " <percentClustersPF> "
+ " <mean>73.03</mean> "
+ " <stdev>2.72</stdev> "
+ " <sumsq>890.49</sumsq> "
+ " </percentClustersPF> "
+ " <percentUniquelyAlignedPF> "
+ " <mean>79.37</mean> "
+ " <stdev>0.86</stdev> "
+ " <sumsq>755955.73</sumsq> "
+ " </percentUniquelyAlignedPF> "
+ " <phasingApplied>0.8203</phasingApplied> "
+ " <prephasingApplied>0.3881</prephasingApplied> "
+ " <signalAverage1to3> "
+ " <mean>526.07</mean> "
+ " <stdev>43.17</stdev> "
+ " <sumsq>223675.10</sumsq> "
+ " </signalAverage1to3> "
+ " <signalAverage2to4> "
+ " <mean>519.91</mean> "
+ " <stdev>41.72</stdev> "
+ " <sumsq>208871.60</sumsq> "
+ " </signalAverage2to4> "
+ " <signalLoss10to20> "
+ " <mean>1.01</mean> "
+ " <stdev>0.40</stdev> "
+ " <sumsq>19.25</sumsq> "
+ " </signalLoss10to20> "
+ " <signalLoss2to10> "
+ " <mean>0.45</mean> "
+ " <stdev>0.53</stdev> "
+ " <sumsq>33.94</sumsq> "
+ " </signalLoss2to10> "
+ " </Lane> "
+ " </Read> "
+ " </ExpandedLaneSummary> "
+ " <LaneParameterSummary/> "
+ " <LaneResultsSummary> "
+ " <Read> "
+ " <readNumber>1</readNumber> "
+ " <Lane> "
+ " <laneNumber>1</laneNumber> "
+ " <averageAlignScorePF> "
+ " <mean>94.25</mean> "
+ " <stdev>3.64</stdev> "
+ " <sumsq>1067460.47</sumsq> "
+ " </averageAlignScorePF> "
+ " <clusterCountPF> "
+ " <mean>277736</mean> "
+ " <stdev>11981</stdev> "
+ " <sumsq>17224950000</sumsq> "
+ " </clusterCountPF> "
+ " <clusterCountRaw> "
+ " <mean>381287</mean> "
+ " <stdev>28613</stdev> "
+ " <sumsq>98246880000</sumsq> "
+ " </clusterCountRaw> "
+ "<errorPF> "
+ "<mean>0.72</mean> "
+ "<stdev>0.49</stdev> "
+ "<sumsq>90.37</sumsq> "
+ "</errorPF> "
+ "<laneYield>1199819</laneYield> "
+ "<oneSig> "
+ "<mean>536</mean> "
+ "<stdev>46</stdev> "
+ "<sumsq>256164</sumsq> "
+ "</oneSig> "
+ "<percentClustersPF> "
+ "<mean>73.03</mean> "
+ "<stdev>2.72</stdev> "
+ "<sumsq>890.49</sumsq> "
+ "</percentClustersPF> "
+ "<percentUniquelyAlignedPF> "
+ "<mean>79.37</mean> "
+ "<stdev>0.86</stdev> "
+ "<sumsq>755955.73</sumsq> "
+ "</percentUniquelyAlignedPF> "
+ "<signal20AsPctOf1> "
+ "<mean>82.19</mean> "
+ "<stdev>5.09</stdev> "
+ "<sumsq>3103.16</sumsq> "
+ "</signal20AsPctOf1> "
+ " </Lane> "
+ " </Read> "
+ " </LaneResultsSummary> "
+ " <TileErrorsByLane/> "
// + " <Software>CASAVA-1.6.0</Software> "
+ " <Software>CASAVA-1.6.0</Software> "
+ "</Summary>";
}
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