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org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource Maven / Gradle / Ivy
package org.molgenis.omx.das.impl;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.ServletContext;
import com.google.common.collect.Iterables;
import org.apache.commons.lang3.StringUtils;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.Query;
import org.molgenis.data.support.GenomeConfig;
import org.molgenis.data.support.QueryImpl;
import org.molgenis.omx.das.RangeHandlingDataSource;
import uk.ac.ebi.mydas.configuration.DataSourceConfiguration;
import uk.ac.ebi.mydas.configuration.PropertyType;
import uk.ac.ebi.mydas.datasource.RangeHandlingAnnotationDataSource;
import uk.ac.ebi.mydas.exceptions.BadReferenceObjectException;
import uk.ac.ebi.mydas.exceptions.DataSourceException;
import uk.ac.ebi.mydas.model.DasAnnotatedSegment;
import uk.ac.ebi.mydas.model.DasFeature;
import uk.ac.ebi.mydas.model.DasMethod;
import uk.ac.ebi.mydas.model.DasType;
import static org.molgenis.util.ApplicationContextProvider.*;
public class RepositoryRangeHandlingDataSource extends RangeHandlingDataSource implements
RangeHandlingAnnotationDataSource
{
private final DataService dataService;
private final GenomeConfig config;
private DasType mutationType;
private DasMethod method;
private String type;
@Override
public void init(ServletContext servletContext, Map globalParameters,
DataSourceConfiguration dataSourceConfig) throws DataSourceException
{
this.type = dataSourceConfig.getDataSourceProperties().get("type").getValue();
this.mutationType = new DasType(type, null, "?", type);
this.method = new DasMethod("not_recorded", "not_recorded", "ECO:0000037");
}
public RepositoryRangeHandlingDataSource() throws DataSourceException
{
dataService = getApplicationContext().getBean(DataService.class);
config = getApplicationContext().getBean(GenomeConfig.class);
}
@Override
public DasAnnotatedSegment getFeatures(String segmentParamString, int start, int stop, Integer maxbins)
throws BadReferenceObjectException, DataSourceException
{
String[] segmentParts = segmentParamString.split(",");
String dataSet = null;
String customParam;
String segmentId = null;
String posAttribute = null;
String chromosomeAttribute = null;
String idAttribute = null;
String stopAttribute = null;
String refAttribute = null;
String altAttribute = null;
String descriptionAttribute = null;
String nameAttribute = null;
String linkAttribute = null;
String patientAttribute = null;
if (segmentParts.length > 1)
{
segmentId = segmentParts[0];
customParam = segmentParts[1];
if (customParam.indexOf(DasURLFilter.DATASET_PREFIX) != -1)
{
dataSet = customParam.substring(11);
}
}
if (maxbins == null || maxbins < 0)
{
maxbins = 1000;
}
Iterable entityIterable = queryDataSet(segmentId, dataSet, maxbins);
List features = new ArrayList();
Integer score = 0;
Map patients = new HashMap();
for (Entity entity : entityIterable)
{
DasFeature feature;
Integer valueStart = null;
Integer valueStop = null;
String valueDescription = null;
String valueIdentifier = null;
String valueName = null;
String valueLink = null;
String valuePatient = null;
String valueRef = null;
String valueAlt = null;
posAttribute = getAttributeName(posAttribute, config.GENOMEBROWSER_POS, entity);
chromosomeAttribute = getAttributeName(chromosomeAttribute, config.GENOMEBROWSER_CHROM, entity);
idAttribute = getAttributeName(idAttribute, config.GENOMEBROWSER_ID, entity);
stopAttribute = getAttributeName(stopAttribute, config.GENOMEBROWSER_STOP, entity);
descriptionAttribute = getAttributeName(descriptionAttribute, config.GENOMEBROWSER_DESCRIPTION, entity);
refAttribute = getAttributeName(refAttribute, config.GENOMEBROWSER_REF, entity);
altAttribute = getAttributeName(altAttribute, config.GENOMEBROWSER_ALT, entity);
nameAttribute = getAttributeName(nameAttribute, config.GENOMEBROWSER_NAME, entity);
linkAttribute = getAttributeName(linkAttribute, config.GENOMEBROWSER_LINK, entity);
patientAttribute = getAttributeName(patientAttribute, config.GENOMEBROWSER_PATIENT_ID , entity);
try
{
valueStart = entity.getInt(posAttribute);
valueIdentifier = StringUtils.isNotEmpty(idAttribute)&&StringUtils.isNotEmpty(entity.getString(idAttribute))?entity.getString(idAttribute):"-";
}
catch (ClassCastException e)
{
// start of identifier not correctly specified? exclude this mutation fore it can not be plotted
break;
}
// no end position? assume mutation of 1 position, so stop == start
Iterable attributes = entity.getAttributeNames();
valueStop = Iterables.contains(attributes, stopAttribute) ? entity.getInt(stopAttribute) : valueStart;
valueDescription = Iterables.contains(attributes, descriptionAttribute) ? entity
.getString(descriptionAttribute) : "";
valueName = Iterables.contains(attributes, nameAttribute) ? entity.getString(nameAttribute) : "";
valueLink = Iterables.contains(attributes, linkAttribute) ? entity.getString(linkAttribute) : "";
valuePatient = Iterables.contains(attributes, patientAttribute) ? entity.getString(patientAttribute) : "";
valueRef = StringUtils.isNotEmpty(refAttribute)&&StringUtils.isNotEmpty(entity.getString(refAttribute))?entity.getString(refAttribute):"";
valueAlt = StringUtils.isNotEmpty(altAttribute)&&StringUtils.isNotEmpty(entity.getString(altAttribute))?entity.getString(altAttribute):"";
List notes = new ArrayList();
if(StringUtils.isNotEmpty(valueRef)) notes.add(refAttribute+"~"+valueRef);
if(StringUtils.isNotEmpty(valueAlt)) notes.add(altAttribute+"~"+valueAlt);
if (valueStart != null
&& ((valueStart >= start && valueStart <= stop) || (valueStop >= start && valueStop <= stop)))
{
DasType type;// used for label colours in Dalliance
if (!StringUtils.isEmpty(valueRef)&&!StringUtils.isEmpty(valueAlt))
{
if(valueRef.length()==1&&valueAlt.length()==1)
type = new DasType(valueAlt, "", "", "");
else if(valueRef.length()==1&&valueAlt.length()>1){
type = new DasType("insert", "", "", "");
}
else if(valueRef.length()>1&&valueAlt.length()==1){
type = new DasType("delete", "", "", "");
}
else{
type = new DasType("delete", "", "", "");;
}
}
else if (patients.containsKey(valuePatient))
{
type = patients.get(valuePatient);
}
else
{
type = new DasType(score.toString(), "", "", "");
patients.put(valuePatient, type);
++score;
}
feature = createDasFeature(valueStart, valueStop, valueIdentifier, valueName, valueDescription,
valueLink, type, method, dataSet, valuePatient, notes);
features.add(feature);
}
}
DasAnnotatedSegment segment = new DasAnnotatedSegment(segmentId, start, stop, "1.00", segmentId, features);
return segment;
}
public String getAttributeName(String attribute, String fieldName, Entity entity) {
if (attribute == null)
{
attribute = config.getAttributeNameForAttributeNameArray(fieldName,
entity.getEntityMetaData());
}
return attribute;
}
protected Iterable queryDataSet(String segmentId, String dataSet, int maxbins)
{
String chromosomeAttribute = config.getAttributeNameForAttributeNameArray(config.GENOMEBROWSER_CHROM,
dataService.getEntityMetaData(dataSet));
Query q = new QueryImpl().eq(chromosomeAttribute, segmentId);
q.pageSize(maxbins);
return dataService.findAll(dataSet, q);
}
@Override
public Integer getTotalCountForType(DasType type) throws DataSourceException
{
return 1000;
}
@Override
public Collection getTypes() throws DataSourceException
{
return Collections.singleton(mutationType);
}
}
