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clean-up before annotating VariantEval2 for output. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3055 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-03-22 07:39:20 +00:00
parent 076d21d394
commit 439c34ed38
12 changed files with 208 additions and 528 deletions
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12
java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
View File

@ -26,7 +26,6 @@ package org.broadinstitute.sting.playground.utils.report;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param; import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.playground.utils.report.tags.Table;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.lang.annotation.Annotation; import java.lang.annotation.Annotation;
@ -47,7 +46,6 @@ public class AnalysisModuleScanner {
// what we extracted from the class // what we extracted from the class
private Map<Field, Param> parameters = new HashMap<Field, Param>(); // the parameter annotations 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 Map<Field, DataPoint> datums = new HashMap<Field, DataPoint>(); // the data we've discovered
private Analysis analysis; // the analysis annotation private Analysis analysis; // the analysis annotation
@ -92,8 +90,6 @@ public class AnalysisModuleScanner {
for (Annotation annotation : f.getAnnotations()) { for (Annotation annotation : f.getAnnotations()) {
if (annotation.annotationType().equals(Param.class)) if (annotation.annotationType().equals(Param.class))
parameters.put(f, (Param) annotation); parameters.put(f, (Param) annotation);
if (annotation.annotationType().equals(Table.class))
tables.put(f,(Table) annotation);
if (annotation.annotationType().equals(DataPoint.class)) if (annotation.annotationType().equals(DataPoint.class))
datums.put(f,(DataPoint) annotation); datums.put(f,(DataPoint) annotation);
} }
@ -107,14 +103,6 @@ public class AnalysisModuleScanner {
return parameters; return parameters;
} }
/**
*
* @return a list of table annotations found
*/
public Map<Field,Table> getTables() {
return tables;
}
/** /**
* *
* @return a map of the datum annotations found * @return a map of the datum annotations found

119
java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
View File

@ -27,17 +27,15 @@ import freemarker.template.Configuration;
import freemarker.template.DefaultObjectWrapper; import freemarker.template.DefaultObjectWrapper;
import freemarker.template.Template; import freemarker.template.Template;
import freemarker.template.TemplateException; import freemarker.template.TemplateException;
import org.broadinstitute.sting.playground.utils.report.chunks.AnalysisChunk; import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
import org.broadinstitute.sting.playground.utils.report.chunks.DataPointChunk; import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.playground.utils.report.chunks.ParameterChunk; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.playground.utils.report.chunks.TableChunk;
import org.broadinstitute.sting.utils.Pair;
import java.io.*; import java.io.*;
import java.lang.reflect.Field; import java.lang.reflect.Field;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap; import java.util.HashMap;
import java.util.List;
import java.util.Map; import java.util.Map;
@ -52,9 +50,8 @@ public class ReportMarshaller {
private Template temp; private Template temp;
// the aggregation of all our analyses // the aggregation of all our analyses
private HashMap map; private Node root;
private List<Map> analysisObjects; private File writeLocation;
private final File writeLocation;
/** /**
* create a marshaled object * create a marshaled object
* *
@ -62,10 +59,15 @@ public class ReportMarshaller {
* @param template the template to use * @param template the template to use
*/ */
public ReportMarshaller(String reportName, File filename, Template template) { public ReportMarshaller(String reportName, File filename, Template template) {
map = new HashMap(); init(reportName, filename);
analysisObjects = new ArrayList<Map>();
map.put("title",reportName);
temp = template; temp = template;
}
private void init(String reportName, File filename) {
root = new Node(reportName);
Node title= new Node("title");
title.addChild(new Node(reportName));
root.addChild(title);
this.writeLocation = filename; this.writeLocation = filename;
} }
@ -75,11 +77,8 @@ public class ReportMarshaller {
* @param reportName the report name * @param reportName the report name
*/ */
public ReportMarshaller(String reportName, File filename) { public ReportMarshaller(String reportName, File filename) {
map = new HashMap(); init(reportName,filename);
analysisObjects = new ArrayList<Map>();
map.put("title",reportName);
temp = createTemplate(); temp = createTemplate();
this.writeLocation = filename;
} }
@ -93,28 +92,21 @@ public class ReportMarshaller {
HashMap analysisMap = new HashMap(); HashMap analysisMap = new HashMap();
AnalysisModuleScanner moduleScanner = new AnalysisModuleScanner(toMarshall); AnalysisModuleScanner moduleScanner = new AnalysisModuleScanner(toMarshall);
Pair<String,Object> pair; Node analysis = addAnalysis(moduleScanner);
pair = addAnalysis(moduleScanner); analysis.addAllChildren(getParameterNodes(toMarshall, moduleScanner));
analysisMap.put(pair.first,pair.second); analysis.addAllChildren(getDataPointNodes(toMarshall, moduleScanner));
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);
// add this analysis to the root node
root.addChild(analysis);
} }
private Pair<String, Object> addAnalysis(AnalysisModuleScanner moduleScanner) { private Node addAnalysis(AnalysisModuleScanner moduleScanner) {
AnalysisChunk chunk = new AnalysisChunk(moduleScanner); Node analysis = new Node(moduleScanner.getAnalysis().name());
return new Pair<String, Object>("analysis",chunk); Node description = new Node("description");
description.createSubNode(moduleScanner.getAnalysis().description());
analysis.addChild(description);
return analysis;
} }
/** /**
@ -124,29 +116,14 @@ public class ReportMarshaller {
* @param moduleScanner our scanner, which stores the annotated field information * @param moduleScanner our scanner, which stores the annotated field information
* @return a pair of a string and the list of Chunk objects * @return a pair of a string and the list of Chunk objects
*/ */
private Pair<String, Object> addParameters(Object toMarshall, AnalysisModuleScanner moduleScanner) { private Collection<Node> getParameterNodes(Object toMarshall, AnalysisModuleScanner moduleScanner) {
List<ParameterChunk> chunks = new ArrayList<ParameterChunk>(); Collection<Node> nodes = new ArrayList<Node>();
for (Field f : moduleScanner.getParameters().keySet()) { for (Field f : moduleScanner.getParameters().keySet()) {
ParameterChunk chunk = new ParameterChunk(f, moduleScanner.getParameters(), toMarshall); Node node = new Node(moduleScanner.getParameters().get(f).name().equals("") ? f.getName() : moduleScanner.getParameters().get(f).name());
if (chunk.isValid()) chunks.add(chunk); addChildNodeFromField(toMarshall, f, node);
nodes.add(node);
} }
return new Pair<String, Object>("parameters",chunks); return nodes;
}
/**
* 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);
} }
/** /**
@ -156,18 +133,18 @@ public class ReportMarshaller {
* @param moduleScanner our scanner, which stores the annotated field information * @param moduleScanner our scanner, which stores the annotated field information
* @return a pair of a string and the list of Chunk objects * @return a pair of a string and the list of Chunk objects
*/ */
private Pair<String, Object> addDataPoints(Object toMarshall, AnalysisModuleScanner moduleScanner) { private Collection<Node> getDataPointNodes(Object toMarshall, AnalysisModuleScanner moduleScanner) {
List<DataPointChunk> chunks = new ArrayList<DataPointChunk>(); Collection<Node> nodes = new ArrayList<Node>();
for (Field f : moduleScanner.getData().keySet()) { for (Field f : moduleScanner.getData().keySet()) {
DataPointChunk chunk = new DataPointChunk(f, moduleScanner.getData(), toMarshall); Node node = new Node(moduleScanner.getData().get(f).name().equals("") ? f.getName() : moduleScanner.getData().get(f).name());
if (chunk.isValid()) chunks.add(chunk); addChildNodeFromField(toMarshall, f, node);
nodes.add(node);
} }
return new Pair<String, Object>("datapoints",chunks); return nodes;
} }
/** call the method to finalize the report */ /** call the method to finalize the report */
public void close() { public void close() {
map.put("analyses",this.analysisObjects);
Writer out = null; Writer out = null;
try { try {
out = new OutputStreamWriter(new FileOutputStream(this.writeLocation)); out = new OutputStreamWriter(new FileOutputStream(this.writeLocation));
@ -175,6 +152,9 @@ public class ReportMarshaller {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
} }
try { try {
// add the data to a map
Map map = new HashMap();
map.put("root",root);
temp.process(map, out); temp.process(map, out);
out.flush(); out.flush();
} catch (TemplateException e) { } catch (TemplateException e) {
@ -194,12 +174,27 @@ public class ReportMarshaller {
cfg.setObjectWrapper(new DefaultObjectWrapper()); cfg.setObjectWrapper(new DefaultObjectWrapper());
Template temp = null; Template temp = null;
try { try {
temp = cfg.getTemplate("myTestTemp.ftl"); temp = cfg.getTemplate("machineReadable.ftl");
} catch (IOException e) { } catch (IOException e) {
e.printStackTrace(); e.printStackTrace();
} }
return temp; return temp;
} }
/**
* helper method for adding a Node to the specified node, given the field
* @param toMarshall the object which contains the specified field
* @param f the field
* @param node the node to add a child node to
*/
private static void addChildNodeFromField(Object toMarshall, Field f, Node node) {
f.setAccessible(true);
try {
node.addAllChildren(ComplexDataUtils.resolveObjects(f.get(toMarshall)));
} catch (IllegalAccessException e) {
throw new StingException("Unable to access field " + f);
}
}
} }

85
java/src/org/broadinstitute/sting/playground/utils/report/chunks/AnalysisChunk.java
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@ -1,85 +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.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
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@ -1,41 +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.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
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@ -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.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
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@ -1,89 +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.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
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@ -1,109 +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.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;
}
}

20
java/src/org/broadinstitute/sting/playground/utils/report/tags/Table.java
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@ -1,20 +0,0 @@
package org.broadinstitute.sting.playground.utils.report.tags;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
/**
* @author aaron
* <p/>
* Annotation Table
* <p/>
* tells the report system to make a table out of the annotated field. The field
* can be of type List<>, Map<>, Vector<>, Collection<> or primative array.
*/
@Retention(RetentionPolicy.RUNTIME)
public @interface Table {
String name(); // the name
String header() default ""; // any text representing the table header
String description(); // a description of the table
int columns() default -1; // the number of columns to divide the data into
}

81
java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java 100644
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@ -0,0 +1,81 @@
package org.broadinstitute.sting.playground.utils.report.utils;
import java.util.*;
/**
*
* @author aaron
*
* Class ComplexDataUtils
*
* This class contains methods and techniques for breaking down complex data in the output system
*/
public class ComplexDataUtils {
/**
* convert any string -> object pairing into a string keyed tree
* @param obj the object
* @return a mapping of the name to the associated value tree. All non-leaf nodes will be Strings
*/
public static Collection<Node> resolveObjects(Object obj) { // TODO: fix this, we need a way to get the name of the list from the data point
Collection<Node> nodes = new ArrayList<Node>();
// the simplest case
if (obj == null) nodes.add(new Node("<null>")); // throw new IllegalStateException("object is null");
else if (obj instanceof TableType)
nodes.add(tableToNode((TableType)obj, ((TableType)obj).getName()));
else if (obj instanceof Map) {
for (Object key : ((Map)obj).keySet()) {
Node keyNode = new Node(key.toString());
nodes.add(keyNode);
keyNode.addAllChildren(resolveObjects(((Map)obj).get(key)));
}
} else if (obj instanceof Collection)
nodes.addAll(listToNode((Collection)obj, "collection"));
else if (obj.getClass().isArray())
nodes.addAll(listToNode(Arrays.asList(obj),"array"));
else
nodes.add(new Node(obj.toString()));
return nodes;
}
/**
* given a TableType object, make it into a tree using maps.
* @param table the table type to convert into a map
* @return
*/
private static Node tableToNode(TableType table, String name) {
Node root = new Node(name);
Object[] rows = table.getRowKeys();
Object[] cols = table.getColumnKeys();
for (int x = 0; x < table.getRowKeys().length; x++) {
Node row = new Node(rows[x].toString());
root.addChild(row);
for (int y = 0; y < table.getRowKeys().length; y++) {
Node col = new Node(cols[y].toString());
row.addChild(col);
col.addChild(new Node(table.getCell(x,y)));
}
}
return root;
}
/**
* given a Collection object, make it into a tree using maps.
* @param coll the collection to iterate, and turn into a list
* @return a mapping of String to Object
*/
private static Collection<Node> listToNode(Collection coll, String name) {
Collection<Node> nodes = new ArrayList<Node>();
Iterator<Object> iter = coll.iterator();
for (int x = 0; x < coll.size(); x++) {
Node value = new Node(String.valueOf(x));
value.addChild(new Node(iter.next().toString()));
nodes.add(value);
}
return nodes;
}
}

49
java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java 100644
View File

@ -0,0 +1,49 @@
package org.broadinstitute.sting.playground.utils.report.utils;
import java.util.Collection;
import java.util.LinkedHashSet;
/**
* a node, extracted using the new report output system.
*/
public class Node {
public String value;
public String description; // if one is available
public Collection<Node> children;
public Node(String value) {
this.value = value;
}
public void addChild(Node child) {
if (children == null) children = new LinkedHashSet<Node>();
children.add(child);
}
public void addAllChildren(Collection<Node> children) {
if (this.children == null) this.children = new LinkedHashSet<Node>();
this.children.addAll(children);
}
public Boolean getComplex() { return (children != null && children.size() > 0); }
/**
* a convenience method for adding a new sub-node with the specified value
* @param value the value of the sub-node
*/
public void createSubNode(String value) {
addChild(new Node(value));
}
public String getValue() {
return value;
}
public String getDescription() {
return description;
}
public Collection<Node> getChildren() {
return children;
}
}

17
java/src/org/broadinstitute/sting/playground/utils/report/utils/TableType.java 100644
View File

@ -0,0 +1,17 @@
package org.broadinstitute.sting.playground.utils.report.utils;
/**
*
* @author aaron
*
* Class TableType
*
* an interface for turning arbritary objects into tables
*/
public interface TableType {
public Object[] getRowKeys();
public Object[] getColumnKeys();
public String getCell(int x, int y);
public String getName();
}

18
java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerTest.java
View File

@ -4,13 +4,9 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis; 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.DataPoint;
import org.broadinstitute.sting.playground.utils.report.tags.Param; import org.broadinstitute.sting.playground.utils.report.tags.Param;
import org.broadinstitute.sting.playground.utils.report.tags.Table;
import org.junit.Assert; import org.junit.Assert;
import org.junit.Test; import org.junit.Test;
import java.util.ArrayList;
import java.util.List;
/** /**
* @author aaron * @author aaron
@ -29,10 +25,6 @@ public class AnalysisModuleScannerTest extends BaseTest {
Assert.assertEquals(3, scanner.getParameters().size()); Assert.assertEquals(3, scanner.getParameters().size());
Assert.assertTrue("basic description".equals(scanner.getParameters().values().iterator().next().description())); 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().values().iterator().next().description()));
// check that the analysis name and description were set // check that the analysis name and description were set
Assert.assertTrue("testAnalysis".equals(scanner.getAnalysis().name())); Assert.assertTrue("testAnalysis".equals(scanner.getAnalysis().name()));
Assert.assertTrue("The is just a simple description".equals(scanner.getAnalysis().description())); Assert.assertTrue("The is just a simple description".equals(scanner.getAnalysis().description()));
@ -64,17 +56,7 @@ class FakeAnalysis {
@DataPoint(description = "basic description") @DataPoint(description = "basic description")
public String text6 = "GRRR"; public String text6 = "GRRR";
@Table(name="FakeTable", description = "Generate a table from this data",columns=3)
public List<Integer> values = new ArrayList<Integer>();
public FakeAnalysis() { public FakeAnalysis() {
values.add(1);
values.add(2);
values.add(3);
values.add(4);
values.add(5);
values.add(6);
} }
} }