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some cleanup for the output system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-03-18 12:54:39 +00:00
parent c78fc23ec5
commit 8a5f0b746e
16 changed files with 806 additions and 409 deletions
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49
java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
View File

@ -1,7 +1,30 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.Datum;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.playground.utils.report.tags.Table;
import org.broadinstitute.sting.utils.StingException;
@ -23,9 +46,9 @@ import java.util.Map;
public class AnalysisModuleScanner {
// what we extracted from the class
private Map<Param, Field> parameters = new HashMap<Param, Field>(); // the parameter annotations
private Map<Table, Field> tables = new HashMap<Table, Field>(); // the table annotations
private Map<Datum, Field> datums = new HashMap<Datum, Field>(); // the data we've discovered
private Map<Field, Param> parameters = new HashMap<Field, Param>(); // the parameter annotations
private Map<Field, Table> tables = new HashMap<Field, Table>(); // the table annotations
private Map<Field, DataPoint> datums = new HashMap<Field, DataPoint>(); // the data we've discovered
private Analysis analysis; // the analysis annotation
// private storage of the class type
@ -68,11 +91,11 @@ public class AnalysisModuleScanner {
for (Field f : cls.getDeclaredFields())
for (Annotation annotation : f.getAnnotations()) {
if (annotation.annotationType().equals(Param.class))
parameters.put((Param) annotation, f);
parameters.put(f, (Param) annotation);
if (annotation.annotationType().equals(Table.class))
tables.put((Table) annotation, f);
if (annotation.annotationType().equals(Datum.class))
datums.put((Datum) annotation, f);
tables.put(f,(Table) annotation);
if (annotation.annotationType().equals(DataPoint.class))
datums.put(f,(DataPoint) annotation);
}
}
@ -80,7 +103,7 @@ public class AnalysisModuleScanner {
*
* @return get the list of parameters we found
*/
public Map<Param, Field> getParameters() {
public Map<Field, Param> getParameters() {
return parameters;
}
@ -88,7 +111,7 @@ public class AnalysisModuleScanner {
*
* @return a list of table annotations found
*/
public Map<Table, Field> getTables() {
public Map<Field,Table> getTables() {
return tables;
}
@ -96,7 +119,7 @@ public class AnalysisModuleScanner {
*
* @return a map of the datum annotations found
*/
public Map<Datum, Field> getData() {
public Map<Field, DataPoint> getData() {
return datums;
}
@ -107,4 +130,8 @@ public class AnalysisModuleScanner {
public Analysis getAnalysis() {
return analysis;
}
public Class getModuleClass() {
return cls;
}
}

88
java/src/org/broadinstitute/sting/playground/utils/report/Marshaller.java
View File

@ -1,88 +0,0 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.playground.utils.report.formats.OutputFormater;
import org.broadinstitute.sting.playground.utils.report.tags.*;
import org.broadinstitute.sting.utils.StingException;
import java.util.Collection;
/**
* @author aaron
* <p/>
* Class Marshaller
* <p/>
* Given an analysis scan, an object, and a formatter, this class emits
* a report to disk (or other source).
*/
public class Marshaller {
private String report;
private OutputFormater formatter;
/**
* create a report
* @param reportName the report name
* @param formater the formater to use
*/
public void createReport(String reportName, OutputFormater formater) {
this.formatter = formater;
report = reportName;
formatter.startReport(report);
}
/**
* add an analysis module to the output source
* @param toMarshall the object to marshall
*/
public void write(Object toMarshall) {
AnalysisModuleScanner moduleScanner = new AnalysisModuleScanner(toMarshall);
formatter.addAnalysis(moduleScanner.getAnalysis());
for (Param p : moduleScanner.getParameters().keySet())
try {
formatter.addParam(p, moduleScanner.getParameters().get(p).get(toMarshall).toString());
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + moduleScanner.getParameters().get(p), e);
}
for (Datum d : moduleScanner.getData().keySet())
try {
formatter.addDatum(d, moduleScanner.getData().get(d).get(toMarshall).toString());
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + moduleScanner.getParameters().get(d), e);
}
for (Table t : moduleScanner.getTables().keySet())
try {
formatter.addTable(t, new TableContainer((Collection<Object>) moduleScanner.getTables().get(t).get(toMarshall),t.columns()));
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + moduleScanner.getParameters().get(t), e);
}
}
public void endReport() {
formatter.endReport();
}
}

205
java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java 100644
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@ -0,0 +1,205 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
import freemarker.template.Configuration;
import freemarker.template.DefaultObjectWrapper;
import freemarker.template.Template;
import freemarker.template.TemplateException;
import org.broadinstitute.sting.playground.utils.report.chunks.AnalysisChunk;
import org.broadinstitute.sting.playground.utils.report.chunks.DataPointChunk;
import org.broadinstitute.sting.playground.utils.report.chunks.ParameterChunk;
import org.broadinstitute.sting.playground.utils.report.chunks.TableChunk;
import org.broadinstitute.sting.utils.Pair;
import java.io.*;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author aaron
* <p/>
* Class ReportMarshaller
* <p/>
* marshall report data out of the GATK.
*/
public class ReportMarshaller {
private Template temp;
// the aggregation of all our analyses
private HashMap map;
private List<Map> analysisObjects;
private final File writeLocation;
/**
* create a marshaled object
*
* @param reportName the report name
* @param template the template to use
*/
public ReportMarshaller(String reportName, File filename, Template template) {
map = new HashMap();
analysisObjects = new ArrayList<Map>();
map.put("title",reportName);
temp = template;
this.writeLocation = filename;
}
/**
* create a marshaled object
*
* @param reportName the report name
*/
public ReportMarshaller(String reportName, File filename) {
map = new HashMap();
analysisObjects = new ArrayList<Map>();
map.put("title",reportName);
temp = createTemplate();
this.writeLocation = filename;
}
/**
* add an analysis module to the output source
*
* @param toMarshall the object to marshall
*/
public void write(Object toMarshall) {
// Create a context to add data to
HashMap analysisMap = new HashMap();
AnalysisModuleScanner moduleScanner = new AnalysisModuleScanner(toMarshall);
Pair<String,Object> pair;
pair = addAnalysis(moduleScanner);
analysisMap.put(pair.first,pair.second);
pair = addParameters(toMarshall, moduleScanner);
analysisMap.put(pair.first,pair.second);
pair = addDataPoints(toMarshall, moduleScanner);
analysisMap.put(pair.first,pair.second);
pair = addTables(toMarshall, moduleScanner);
analysisMap.put(pair.first,pair.second);
// add it to the list of analysis maps we have
analysisObjects.add(analysisMap);
}
private Pair<String, Object> addAnalysis(AnalysisModuleScanner moduleScanner) {
AnalysisChunk chunk = new AnalysisChunk(moduleScanner);
return new Pair<String, Object>("analysis",chunk);
}
/**
* output the Params objects we find
*
* @param toMarshall the object to output
* @param moduleScanner our scanner, which stores the annotated field information
* @return a pair of a string and the list of Chunk objects
*/
private Pair<String, Object> addParameters(Object toMarshall, AnalysisModuleScanner moduleScanner) {
List<ParameterChunk> chunks = new ArrayList<ParameterChunk>();
for (Field f : moduleScanner.getParameters().keySet()) {
ParameterChunk chunk = new ParameterChunk(f, moduleScanner.getParameters(), toMarshall);
if (chunk.isValid()) chunks.add(chunk);
}
return new Pair<String, Object>("parameters",chunks);
}
/**
* output the Table objects we find
*
* @param toMarshall the object to output
* @param moduleScanner our scanner, which stores the annotated field information
* @return a pair of a string and the list of Chunk objects
*/
private Pair<String, Object> addTables(Object toMarshall, AnalysisModuleScanner moduleScanner) {
List<TableChunk> chunks = new ArrayList<TableChunk>();
for (Field f : moduleScanner.getTables().keySet()) {
TableChunk chunk = new TableChunk(f, moduleScanner.getTables(), toMarshall);
if (chunk.isValid()) chunks.add(chunk);
}
return new Pair<String, Object>("tables",chunks);
}
/**
* output the DataPoint objects we find
*
* @param toMarshall the object to output
* @param moduleScanner our scanner, which stores the annotated field information
* @return a pair of a string and the list of Chunk objects
*/
private Pair<String, Object> addDataPoints(Object toMarshall, AnalysisModuleScanner moduleScanner) {
List<DataPointChunk> chunks = new ArrayList<DataPointChunk>();
for (Field f : moduleScanner.getData().keySet()) {
DataPointChunk chunk = new DataPointChunk(f, moduleScanner.getData(), toMarshall);
if (chunk.isValid()) chunks.add(chunk);
}
return new Pair<String, Object>("datapoints",chunks);
}
/** call the method to finalize the report */
public void close() {
map.put("analyses",this.analysisObjects);
Writer out = null;
try {
out = new OutputStreamWriter(new FileOutputStream(this.writeLocation));
} catch (FileNotFoundException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
try {
temp.process(map, out);
out.flush();
} catch (TemplateException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
}
private Template createTemplate() {
Configuration cfg = new Configuration();
try {
cfg.setDirectoryForTemplateLoading(new File("templates"));
} catch (IOException e) {
e.printStackTrace();
}
cfg.setObjectWrapper(new DefaultObjectWrapper());
Template temp = null;
try {
temp = cfg.getTemplate("myTestTemp.ftl");
} catch (IOException e) {
e.printStackTrace();
}
return temp;
}
}

68
java/src/org/broadinstitute/sting/playground/utils/report/TableContainer.java
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@ -1,68 +0,0 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
import java.util.*;
/**
*
* @author aaron
*
* Class TableContainer
*
* represents a table of data, and formats according to column count. Do not use,
* needs improvement. This is a stand-in for something better.
*/
public class TableContainer {
private List<Object> tableEntries;
private int columns = 2; // default to two
public TableContainer(Collection<Object> tbl, int columns) {
tableEntries = new ArrayList<Object>();
if (tbl instanceof List || tbl instanceof Vector || tbl instanceof Set)
tableEntries.addAll(tbl);
if (tbl instanceof Map)
for (Object key : ((Map)tbl).keySet()) {
tableEntries.add(key);
tableEntries.add(((Map) tbl).get(key));
}
this.columns = columns;
}
public List<List<Object>> toRows() {
ArrayList<List<Object>> list = new ArrayList<List<Object>>();
List<Object> currentRow = new ArrayList<Object>();
for (Object obj : tableEntries) {
if (currentRow.size() >= columns) {
list.add(currentRow);
currentRow = new ArrayList<Object>();
}
currentRow.add(obj);
}
list.add(currentRow);
return list;
}
}

99
java/src/org/broadinstitute/sting/playground/utils/report/TableFormatter.java 100644
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@ -0,0 +1,99 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
/**
*
* @author aaron
*
* Class TableFormatter
*
* a helper class for formatting a table of data. Given a collection, it formats it into rows and columns.
* If it's a Map, values are emited as key, value, key, value, so it may make sense to have colums set to 2.
*
* TODO: Needs some cleanup
*
*/
public class TableFormatter {
public Object tableEntries; // data storage
private int columns = 2; // default to two columns of data, overridden in the constructor
public TableFormatter(Collection<Object> tbl, int columns) {
tableEntries = tbl;
this.columns = columns;
}
public TableFormatter(Object tbl) {
tableEntries = tbl;
}
/**
* convert the underlying object to a list of lists, for convenient output
* @return a list of list of objects (a list for each row, then a list of row members)
*/
public List<List<Object>> toRows() {
if (tableEntries instanceof Collection)
return collectionToTable(((Collection)tableEntries));
else if (tableEntries instanceof Map)
return mapToTable(((Map)tableEntries));
else
throw new UnsupportedOperationException("underlying collection must be an instance of type Collection or of type Map");
}
private List<List<Object>> mapToTable(Map collection) {
ArrayList<List<Object>> list = new ArrayList<List<Object>>();
for (Object obj : collection.keySet()) {
List<Object> currentRow = new ArrayList<Object>();
currentRow.add(obj);
Object data = collection.get(obj);
currentRow.add(data.toString());
list.add(currentRow);
}
return list;
}
private List<List<Object>> collectionToTable(Collection collection) {
ArrayList<List<Object>> list = new ArrayList<List<Object>>();
List<Object> currentRow = new ArrayList<Object>();
for (Object obj : collection) {
if (currentRow.size() >= columns) {
list.add(currentRow);
currentRow = new ArrayList<Object>();
}
currentRow.add(obj);
}
list.add(currentRow);
return list;
}
}

85
java/src/org/broadinstitute/sting/playground/utils/report/chunks/AnalysisChunk.java 100644
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@ -0,0 +1,85 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.chunks;
import org.broadinstitute.sting.playground.utils.report.AnalysisModuleScanner;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
/**
* @author aaron
* <p/>
* Class AnalysisChunk
* <p/>
* The basic data we've decorated an analysis with
*/
public class AnalysisChunk implements Chunk {
public String name;
public String description;
public String version;
public String className;
/**
* extract the analysis data from an analysis annotation using the module scanner.
* @param moduleScanner the module scanner
*/
public AnalysisChunk(AnalysisModuleScanner moduleScanner) {
Analysis a = moduleScanner.getAnalysis();
name = (a.name().equals("") ? moduleScanner.getModuleClass().getSimpleName() : a.name());
description = a.description();
version = a.version().equals("") ? "unknown" : a.version();
className = moduleScanner.getModuleClass().getName();
}
public String getName() {
return name;
}
public String getDescription() {
return description;
}
public String getVersion() {
return version;
}
public String getClassName() {
return className;
}
/**
* is the chunk we've created valid? Invalid chunk would contain null data, or various other
* factors that eliminate a chunk from being outputted.
*
* @return true if it's valid, false if not.
*/
@Override
public boolean isValid() {
if (name == null || name.equals("")) return false;
if (description == null || description.equals("")) return false;
if (version == null) return false;
if (className == null || className.equals("")) return false;
return true;
}
}

41
java/src/org/broadinstitute/sting/playground/utils/report/chunks/Chunk.java 100644
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@ -0,0 +1,41 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.chunks;
/**
* @author aaron
* <p/>
* Interface Chunk
* <p/>
* the basics of what a report data chunk needs to have
*/
public interface Chunk {
/**
* is the chunk we've created valid? Invalid chunk would contain null data, or various other
* factors that eliminate a chunk from being outputted.
*
* @return true if it's valid, false if not.
*/
public boolean isValid();
}

88
java/src/org/broadinstitute/sting/playground/utils/report/chunks/DataPointChunk.java 100644
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@ -0,0 +1,88 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.chunks;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.util.Map;
/**
* @author aaron
* <p/>
* Class DataPointChunk
* <p/>
* a data point chunk
*/
public class DataPointChunk implements Chunk {
public String name;
public String description;
public String value;
/**
* create a DataPointChunk from extracted information
*
* @param dpf the datapoint field
* @param mappings the mapping of datapoints to fields in the analysis object
* @param toMarshall the object we're marshaling from
*/
public DataPointChunk(Field dpf, Map<Field, DataPoint> mappings, Object toMarshall) {
try {
// make sure we can access the field
dpf.setAccessible(true);
name = mappings.get(dpf).name().equals("") ? dpf.getName() : mappings.get(dpf).name();
description = mappings.get(dpf).description();
value = dpf.get(toMarshall).toString();
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + mappings.get(mappings.get(dpf)), e);
}
}
public String getName() {
return name;
}
public String getDescription() {
return description;
}
public String getValue() {
return value;
}
/**
* is the chunk we've created valid? Invalid chunk would contain null data, or various other
* factors that eliminate a chunk from being outputted.
*
* @return true if it's valid, false if not.
*/
@Override
public boolean isValid() {
if (name == null || name.equals("")) return false;
if (description == null || description.equals("")) return false;
return value != null;
}
}

89
java/src/org/broadinstitute/sting/playground/utils/report/chunks/ParameterChunk.java 100644
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@ -0,0 +1,89 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.chunks;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.util.Map;
/**
* @author aaron
* <p/>
* Class ParameterChunk
* <p/>
* The basics of a parameter
*/
public class ParameterChunk implements Chunk {
public String name;
public String description;
public String value;
/**
* create a ParameterChunk from extracted information
*
* @param pf the parameter annotated field
* @param mappings the mapping of params to fields in the analysis object
* @param toMarshall the object we're marshaling from
*/
public ParameterChunk(Field pf, Map<Field, Param> mappings, Object toMarshall) {
try {
// make sure we can access the field
pf.setAccessible(true);
name = mappings.get(pf).name().equals("") ? pf.getName() : mappings.get(pf).name();
description = mappings.get(pf).description();
value = pf.get(toMarshall).toString();
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + pf, e);
}
}
public String getName() {
return name;
}
public String getDescription() {
return description;
}
public String getValue() {
return value;
}
/**
* is the chunk we've created valid? Invalid chunk would contain null data, or various other
* factors that eliminate a chunk from being outputted.
*
* @return true if it's valid, false if not.
*/
@Override
public boolean isValid() {
if (name == null || name.equals("")) return false;
if (description == null || description.equals("")) return false;
if (value == null) return false;
return true;
}
}

109
java/src/org/broadinstitute/sting/playground/utils/report/chunks/TableChunk.java 100644
View File

@ -0,0 +1,109 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.chunks;
import org.broadinstitute.sting.playground.utils.report.TableFormatter;
import org.broadinstitute.sting.playground.utils.report.tags.Table;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.util.List;
import java.util.Map;
/**
* @author aaron
* <p/>
* Class TableChunk
* <p/>
* all the information we gleam from a Table annotation, including the table entries
*/
public class TableChunk implements Chunk {
public final String name;
public final String header;
public final String description;
public final int columns;
public final TableFormatter table;
/**
* create a TableChunk from extracted information
*
* @param tbf the Table annotated field
* @param mappings the mapping of datapoints to fields in the analysis object
* @param toMarshall the object we're marshaling from
*/
public TableChunk(Field tbf, Map<Field, Table> mappings, Object toMarshall) {
try {
// make sure we can access the field
tbf.setAccessible(true);
name = mappings.get(tbf).name().equals("") ? tbf.getName() : mappings.get(tbf).name();
description = mappings.get(tbf).description();
header = mappings.get(tbf).header();
columns = mappings.get(tbf).columns();
table = new TableFormatter(tbf.get(toMarshall));
} catch (IllegalAccessException e) {
throw new StingException("Unable to access variable " + tbf, e);
}
}
public String getName() {
return name;
}
public String getHeader() {
return header;
}
public String getDescription() {
return description;
}
public int getColumns() {
return columns;
}
public TableFormatter getTable() {
return table;
}
public List<List<Object>> getRows() {
return table.toRows();
}
/**
* is the chunk we've created valid? Invalid chunk would contain null data, or various other
* factors that eliminate a chunk from being outputted.
*
* @return true if it's valid, false if not.
*/
@Override
public boolean isValid() {
if (this.name == null || this.name.equals("")) return false;
if (this.header == null || this.header.equals("")) return false;
if (this.description == null) return false;
if (columns < 1) return false;
if (table == null || table.tableEntries == null) return false;
return true;
}
}

80
java/src/org/broadinstitute/sting/playground/utils/report/formats/OutputFormater.java
View File

@ -1,80 +0,0 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.formats;
import org.broadinstitute.sting.playground.utils.report.TableContainer;
import org.broadinstitute.sting.playground.utils.report.tags.*;
/**
*
* @author aaron
*
* Class OutputFormater
*
* The formatter defines a perticular output format style. The formatter methods
* are required to be called in the following order:
*
* 1. startReport()
* 2. for each analysis module:
* addAnalysis()
* with many addParam(), addTable(), and addDatum() in no particular order promised
* 3. endReport()
*/
public interface OutputFormater {
/**
* start the report, given the report tag
* @param reportName the report name.
*/
public void startReport(String reportName);
/**
* add an analysis to the report
* @param analysisTag the analysis tag
*/
public void addAnalysis(Analysis analysisTag);
/**
* add a parameter value to the output location
* @param value
*/
public void addParam(Param paramTag, String value);
/**
* add a parameter value to the output location
* @param value
*/
public void addTable(Table tableTag, TableContainer value);
/**
* add a datum object to the output location
* @param value
*/
public void addDatum(Datum datumTag, String value);
/**
* end the report
*/
public void endReport();
}

130
java/src/org/broadinstitute/sting/playground/utils/report/formats/SimpleTextOutputer.java
View File

@ -1,130 +0,0 @@
/*
* Copyright (c) 2010. The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.utils.report.formats;
import org.broadinstitute.sting.playground.utils.report.TableContainer;
import org.broadinstitute.sting.playground.utils.report.tags.*;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.util.List;
/**
*
* @author aaron
*
* Class SimpleTextOutputer
*
* a very small demo of text output, just to use for testing and development
*/
public class SimpleTextOutputer implements OutputFormater {
protected PrintWriter out;
protected String terminator = "\n";
protected String spacer = "\t\t\t";
/**
* create a simple text output format given the output file
* @param outputFile
*/
public SimpleTextOutputer(File outputFile) {
try {
FileOutputStream stream = new FileOutputStream(outputFile);
out = new PrintWriter(stream);
} catch (FileNotFoundException e) {
throw new StingException("Unable to find file ",e);
}
}
/**
* start the report, given the report tag
*
* @param reportTag the report tag, which describes the basics of the report
*/
@Override
public void startReport(String reportTag) {
out.write("----------------" + reportTag + "----------------" + terminator);
}
/**
* add an analysis to the report
*
* @param analysisTag the analysis tag
*/
@Override
public void addAnalysis(Analysis analysisTag) {
out.write("----------------" + analysisTag.name() + "----------------" + terminator);
out.write(String.format("Name%s%s%s",spacer,analysisTag.name(),terminator));
out.write(String.format("Description\t\t%s%s",analysisTag.description(),terminator));
out.write(String.format("Version%s%s%s",spacer,analysisTag.version(),terminator));
}
/**
* add a parameter value to the output location
*
* @param value
*/
@Override
public void addParam(Param paramTag, String value) {
out.write(String.format("Param %s%s%s%s",paramTag.name(),spacer,value,terminator));
}
/**
* add a parameter value to the output location
*
* @param value
*/
@Override
public void addTable(Table tableTag, TableContainer value) {
out.write(tableTag.name());
boolean first = false;
for (List<Object> row : value.toRows()) {
if (!first) first = true;
else out.write("\t");
out.write("\t\t");
for (Object obj: row) out.write(obj+",");
out.write(terminator);
}
}
/**
* add a datum object to the output location
*
* @param value
*/
@Override
public void addDatum(Datum datumTag, String value) {
out.write("Datum "+datumTag.name()+spacer+value+terminator);
}
/**
* end the report
*
*/
@Override
public void endReport() {
out.write("----------------" + "----------------" + terminator);
out.close();
}
}

4
java/src/org/broadinstitute/sting/playground/utils/report/tags/Analysis.java
View File

@ -12,7 +12,7 @@ import java.lang.annotation.RetentionPolicy;
*/
@Retention(RetentionPolicy.RUNTIME)
public @interface Analysis {
String name(); // the name of the analysis
String name() default ""; // the name of the analysis
String description(); // its description, required
String version() default "unversioned"; // the version, not always used
String version() default ""; // the version, not always used
}

10
java/src/org/broadinstitute/sting/playground/utils/report/tags/Datum.java → java/src/org/broadinstitute/sting/playground/utils/report/tags/DataPoint.java
View File

@ -29,13 +29,13 @@ import java.lang.annotation.RetentionPolicy;
/**
* @author aaron
* <p/>
* Annotation Datum
* Annotation DataPoint
* <p/>
* The basic Datum annotation, for fields in an analysis that
* The basic DataPoint annotation, for fields in an analysis that
* are to be output as data.
*/
@Retention(RetentionPolicy.RUNTIME)
public @interface Datum {
String name(); // the name, required
String description(); // a description
public @interface DataPoint {
String name() default ""; // the name, required
String description(); // a description
}

22
java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerTest.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.playground.utils.report.tags.Table;
import org.junit.Assert;
@ -25,12 +26,12 @@ public class AnalysisModuleScannerTest extends BaseTest {
AnalysisModuleScanner scanner = new AnalysisModuleScanner(FakeAnalysis.class);
// check we found one param, and check its description
Assert.assertEquals(1, scanner.getParameters().size());
Assert.assertTrue("basic description".equals(scanner.getParameters().keySet().iterator().next().description()));
Assert.assertEquals(3, scanner.getParameters().size());
Assert.assertTrue("basic description".equals(scanner.getParameters().values().iterator().next().description()));
// check that we've found a table, and check its description
Assert.assertEquals(1, scanner.getTables().size());
Assert.assertTrue("Generate a table from this data".equals(scanner.getTables().keySet().iterator().next().description()));
Assert.assertTrue("Generate a table from this data".equals(scanner.getTables().values().iterator().next().description()));
// check that the analysis name and description were set
Assert.assertTrue("testAnalysis".equals(scanner.getAnalysis().name()));
@ -48,6 +49,21 @@ class FakeAnalysis {
@Param(description = "basic description")
public String text = "GRRR";
@Param(description = "basic description")
public String text2superlonganme = "GRRR";
@Param(description = "basic description")
public String text3 = "GRRR";
@DataPoint(description = "basic description")
public String text4 = "GRRR";
@DataPoint(description = "basic description")
public String text5 = "GRRR";
@DataPoint(description = "basic description")
public String text6 = "GRRR";
@Table(name="FakeTable", description = "Generate a table from this data",columns=3)
public List<Integer> values = new ArrayList<Integer>();

48
java/test/org/broadinstitute/sting/playground/utils/report/MarshallerTest.java → java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerTest.java
View File

@ -24,35 +24,39 @@
package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.playground.utils.report.formats.SimpleTextOutputer;
import org.junit.Test;
import java.io.File;
/**
*
* @author aaron
*
* Class MarshallerTest
*
* test out the marshaller
* @author aaron
* <p/>
* Class ReportMarshallerTest
* <p/>
* test out the marshaller
*/
public class MarshallerTest extends BaseTest {
public class ReportMarshallerTest extends BaseTest {
@Test
public void testMarshalling() {
// output file
/*File fl = new File("testfile.txt");
fl.deleteOnExit();
Marshaller m = new Marshaller();
SimpleTextOutputer format = new SimpleTextOutputer(fl);
/*Configuration cfg = new Configuration();
try {
cfg.setDirectoryForTemplateLoading(new File("templates"));
} catch (IOException e) {
e.printStackTrace();
}
cfg.setObjectWrapper(new DefaultObjectWrapper());
Template temp = null;
try {
temp = cfg.getTemplate("myTestTemp.ftl");
} catch (IOException e) {
e.printStackTrace();
}
FakeAnalysis fa = new FakeAnalysis();
// start the marshall
m.createReport("Fake Report",format);
m.write(fa);
m.write(fa);
m.write(fa);
m.endReport();*/
File fl = new File("testFile.out");
fl.deleteOnExit();
ReportMarshaller marsh = new ReportMarshaller("report",fl,temp);
marsh.write(fa);
marsh.write(fa);
marsh.write(fa);
marsh.close();*/
}
}