From 1e44bb7f1e09dceb7e124502a709a8afdd834963 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 29 Jul 2010 18:17:34 +0000
Subject: [PATCH] - no complaints about more than one Summary file, the values
of the first file found are taken - added some more properties - started with
lane summary, not yet used
SVN: 17296
---
.../cisd/dsu/dss/plugins/IlluminaSummary.java | 13 ++
.../IlluminaSummaryReportingPlugin.java | 159 ++++++++++++++----
.../dsu/dss/plugins/LaneResultsSummary.java | 109 ++++++++++++
3 files changed, 249 insertions(+), 32 deletions(-)
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
index e413f57456d..b75d90f40e1 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
@@ -40,6 +40,8 @@ class IlluminaSummary
{
private ChipResultsSummary chipResultsSummary;
+ private LaneResultsSummary LaneResultsSummary;
+
private String Software;
@XmlElement(name = "ChipResultsSummary")
@@ -53,6 +55,17 @@ class IlluminaSummary
this.chipResultsSummary = chipResultsSummary;
}
+ @XmlElement(name = "LaneResultsSummary")
+ public LaneResultsSummary getLaneResultsSummary()
+ {
+ return LaneResultsSummary;
+ }
+
+ public void setLaneResultsSummary(LaneResultsSummary laneResultsSummary)
+ {
+ LaneResultsSummary = laneResultsSummary;
+ }
+
@XmlElement(name = "Software")
public String getSoftware()
{
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 cb311ebd484..cd65b689f79 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
@@ -19,21 +19,25 @@ package ch.ethz.bsse.cisd.dsu.dss.plugins;
import java.io.File;
import java.io.FileFilter;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.xml.JaxbXmlParser;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
* Reporting plugin which shows numbers of the Summary file generated from the Illumina Sequencer.
@@ -47,6 +51,14 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
private static final String SUMMARY_FILE_NAME = "Summary.xml";
+ private static final String DATA_INTENSITIES_BASE_CALLS_PATH = "/Data/Intensities/BaseCalls";
+
+ private static final String GERALD_DIR = "GERALD";
+
+ private static final String[] PROPERTIES =
+ { "GENOME_ANALYZER", "END_TYPE", "ILLUMINA_PIPELINE_VERSION",
+ "CYCLES_REQUESTED_BY_CUSTOMER" };
+
public IlluminaSummaryReportingPlugin(Properties properties, File storeRoot)
{
super(properties, storeRoot);
@@ -60,30 +72,67 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
builder.addHeader("Clusters (PF)");
builder.addHeader("Yield (kbases)");
builder.addHeader("Software");
+ for (String property : PROPERTIES)
+ {
+ builder.addHeader(property);
+ }
+ builder.addHeader("PhiX: Clusters");
+ builder.addHeader("PhiX: ClustersPF");
+ builder.addHeader("PhiX: Yield (kbases)");
+ builder.addHeader("PhiX: % Align (PF)");
for (DatasetDescription dataset : datasets)
{
File originalData = getDataSubDir(dataset);
- File summaryFile = extractSummaryFile(dataset, originalData);
- describe(builder, dataset, summaryFile);
+
+ // set the directory containing the Summary.xml
+ File childDirectory =
+ new File(originalData, dataset.getSampleCode()
+ + DATA_INTENSITIES_BASE_CALLS_PATH);
+ File[] files = childDirectory.listFiles(new FileFilter()
+ {
+ public boolean accept(File file)
+ {
+ return file.isDirectory() && file.getName().startsWith(GERALD_DIR);
+ }
+ });
+
+ System.out.println(files[0]);
+ if (files.length == 1)
+ {
+ File geraldDir = files[0];
+ File summaryFile = new File(geraldDir, SUMMARY_FILE_NAME);
+ describe(builder, dataset, summaryFile);
+ } else
+ {
+ // throw new EnvironmentFailureException(String.format("More than one ..."));
+ }
+ // if (childDirectory.exists())
+ // {
+ // File summaryFile = extractSummaryFile(dataset, childDirectory);
+ // describe(builder, dataset, summaryFile);
+ // } else
+ // {
+ // File summaryFile = extractSummaryFile(dataset, originalData);
+ // }
}
return builder.getTableModel();
}
- 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)
- {
- return files.get(0);
- } else
- {
- throw new EnvironmentFailureException(String.format(
- "%s file was found for the dataset %s (%s).", (size == 0) ? "No summary"
- : " More than one", dataset.getDatasetCode(), dataset.getSampleCode()));
- }
- }
+ // 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)
+ // {
+ // return files.get(0);
+ // } else
+ // {
+ // throw new EnvironmentFailureException(String.format(
+ // "%s file was found for the dataset %s (%s).", (size == 0) ? "No summary"
+ // : " More than one", dataset.getDatasetCode(), dataset.getSampleCode()));
+ // }
+ // }
private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset,
File summaryFile)
@@ -103,27 +152,74 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
software_version = "Not available";
}
- List<ISerializableComparable> row =
- Arrays.<ISerializableComparable> asList(
- new StringTableCell(dataset.getSampleCode()), new IntegerTableCell(
- chipResultSummary.getClusterCountRaw()), new IntegerTableCell(
- chipResultSummary.getClusterCountPF()), new IntegerTableCell(
- chipResultSummary.getYield() / 1000), new StringTableCell(
- software_version));
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+ row.add(new StringTableCell(dataset.getSampleCode()));
+ row.add(new IntegerTableCell(chipResultSummary.getClusterCountRaw()));
+ row.add(new IntegerTableCell(chipResultSummary.getClusterCountPF()));
+ row.add(new IntegerTableCell(chipResultSummary.getYield() / 1000));
+ row.add(new StringTableCell(software_version));
+ addPropertyColumnValues(dataset, row);
+ // just dummies
+ row.add(new IntegerTableCell(1));
+ row.add(new IntegerTableCell(1));
+ row.add(new IntegerTableCell(1));
+ row.add(new DoubleTableCell(1.0));
builder.addRow(row);
}
- private static FileFilter createIlluminaSummaryFileFilter()
+ private static void addPropertyColumnValues(DatasetDescription dataset,
+ List<ISerializableComparable> row)
{
- return new FileFilter()
+ Sample sample = getSample(dataset);
+ for (String propertyCode : PROPERTIES)
+ {
+ boolean found = false;
+ for (IEntityProperty property : sample.getProperties())
{
- public boolean accept(File file)
+ if (property.getPropertyType().getCode().equals(propertyCode))
{
- return file.isFile() && file.getName().equals(SUMMARY_FILE_NAME);
+ row.add(new StringTableCell(property.tryGetAsString()));
+ found = true;
+ break;
}
- };
+ }
+ if (found == false)
+ {
+ row.add(new StringTableCell(""));
+ }
+ }
}
+ private static Sample getSample(DatasetDescription dataset)
+ {
+ String spaceCode = dataset.getGroupCode();
+ String sampleCode = dataset.getSampleCode();
+ String databaseInstanceCode = dataset.getDatabaseInstanceCode();
+ SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new SpaceIdentifier(databaseInstanceCode, spaceCode),
+ sampleCode);
+ Sample sampleOrNull =
+ ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
+ if (sampleOrNull == null)
+ {
+ throw new EnvironmentFailureException(String.format(
+ "Couldn't get sample %s for dataset %s.", dataset.getSampleCode(),
+ dataset.getDatasetCode()));
+ }
+ return sampleOrNull;
+ }
+
+ // private static FileFilter createIlluminaSummaryFileFilter()
+ // {
+ // return new FileFilter()
+ // {
+ // public boolean accept(File file)
+ // {
+ // return file.isFile() && file.getName().equals(SUMMARY_FILE_NAME);
+ // }
+ // };
+ // }
+
/**
* Loader of Illumina summary XML file.
* <p>
@@ -145,5 +241,4 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
}
}
-
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
new file mode 100644
index 00000000000..7f6865e89ec
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.ethz.bsse.cisd.dsu.dss.plugins;
+
+/**
+ * <pre>
+ * <LaneResultsSummary>
+ * <Read>
+ * <readNumber>1</readNumber>
+ * <Lane>
+ * <laneNumber>1</laneNumber>
+ * <clusterCountPF>
+ * <mean>251107</mean>
+ * <stdev>9934</stdev>
+ * <sumsq>11841370000</sumsq>
+ * </clusterCountPF>
+ * <clusterCountRaw>
+ * <mean>290967</mean>
+ * <stdev>12357</stdev>
+ * <sumsq>18322720000</sumsq>
+ * </clusterCountRaw>
+ * <laneYield>2290093</laneYield>
+ * <oneSig>
+ * <mean>497</mean>
+ * <stdev>61</stdev>
+ * <sumsq>447654</sumsq>
+ * </oneSig>
+ * <percentClustersPF>
+ * <mean>86.32</mean>
+ * <stdev>1.66</stdev>
+ * <sumsq>331.22</sumsq>
+ * </percentClustersPF>
+ * <signal20AsPctOf1>
+ * <mean>81.60</mean>
+ * <stdev>6.26</stdev>
+ * <sumsq>4700.89</sumsq>
+ * </signal20AsPctOf1>
+ * </Lane>
+ * ...
+ * </Read>
+ * </LaneResultsSummary>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+
+public class LaneResultsSummary
+{
+ private String Read;
+
+ private Long clusterCountPF;
+
+ private Long clusterCountRaw;
+
+ private Long laneyield;
+
+ public String getRead()
+ {
+ return Read;
+ }
+
+ public void setRead(String read)
+ {
+ Read = read;
+ }
+ public Long getClusterCountPF()
+ {
+ return clusterCountPF;
+ }
+
+ public void setClusterCountPF(Long clusterCountPF)
+ {
+ this.clusterCountPF = clusterCountPF;
+ }
+
+ public Long getClusterCountRaw()
+ {
+ return clusterCountRaw;
+ }
+
+ public void setClusterCountRaw(Long clusterCountRaw)
+ {
+ this.clusterCountRaw = clusterCountRaw;
+ }
+
+ public Long getLaneyield()
+ {
+ return laneyield;
+ }
+
+ public void setLaneyield(Long laneyield)
+ {
+ this.laneyield = laneyield;
+ }
+}
\ No newline at end of file
--
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