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* Copyright (c) 2007-2015 Broad Institute
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*
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package org.broad.igv.ga4gh;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.reader.AlignmentReader;
import org.broad.igv.util.HttpUtils;
import java.io.IOException;
import java.net.URL;
import java.util.*;
/**
* Class for testing GlobalAlliance API. Loads json from a text file, for development only
* <p/>
* Created by jrobinso on 7/18/14.
*/
public class Ga4ghAlignmentReader implements AlignmentReader<Alignment> {
private static Logger log = Logger.getLogger(Ga4ghAlignmentReader.class);
String readsetId;
List<String> sequenceNames;
Ga4ghProvider provider;
Map<String, String> chromosomeMappings;
public Ga4ghAlignmentReader(Ga4ghProvider provider, String readsetId) {
this.provider = provider == null ? Ga4ghAPIHelper.GA4GH_GOOGLE_PROVIDER : provider;
this.readsetId = readsetId;
this.chromosomeMappings = new HashMap<String, String>();
}
@Override
public void close() throws IOException {
}
@Override
public List<String> getSequenceNames() throws IOException {
if (sequenceNames == null) {
try {
loadMetadata();
} catch (IOException e) {
throw e;
} catch (Exception e) {
log.error("Error fetching metadata", e);
}
}
return sequenceNames;
}
@Override
public SAMFileHeader getFileHeader() {
return null;
}
@Override
public Set<String> getPlatforms() {
return null;
}
@Override
public CloseableIterator<Alignment> iterator() {
throw new RuntimeException("Iterating over ga4gh datasets is not supported");
}
/**
* Return an iterator over alignments overlapping the given region. We first try the sequence name as given,
* then try an alias if we have one. This is to handle the common 1 vs chr1 naming problem stemming from
* competing conventions.
*
* @param sequence
* @param start 0-based start location
* @param end 0-based, exclusive-end coordinate
* @param contained
* @return
* @throws IOException
*/
@Override
public CloseableIterator<Alignment> query(String sequence, int start, int end, boolean contained) throws IOException {
boolean sequenceNameConfirmed = false;
if (chromosomeMappings.containsKey(sequence)) {
sequence = chromosomeMappings.get(sequence);
sequenceNameConfirmed = true;
}
boolean handleError = sequenceNameConfirmed;
List<Alignment> alignmentList = Ga4ghAPIHelper.searchReads(provider, readsetId, sequence, start, end, handleError);
if (alignmentList != null) {
chromosomeMappings.put(sequence, sequence);
return new MIterator(alignmentList);
} else if (sequenceNameConfirmed == false && COMMON_ALIASES.containsKey(sequence)) {
String altSequence = COMMON_ALIASES.get(sequence);
log.info("Sequence \"" + sequence + "\" failed. Trying \"" + altSequence + "\"");
alignmentList = Ga4ghAPIHelper.searchReads(provider, readsetId, altSequence, start, end, true);
if (alignmentList != null) {
chromosomeMappings.put(sequence, altSequence);
}
return alignmentList == null ? null : new MIterator(alignmentList);
} else {
return null;
}
}
@Override
public boolean hasIndex() {
return true;
}
private void loadMetadata() throws IOException {
String authKey = provider.apiKey;
String baseURL = provider.baseURL;
URL url = new URL(baseURL + "/readgroupsets/" + readsetId + (authKey == null ? "" : "?key=" + authKey)); // TODO -- field selection?
Map<String, String> headers = new HashMap<String, String>();
String token = OAuthUtils.getInstance().getAccessToken();
if (token != null) {
headers.put("Authorization", "Bearer " + token);
}
String result = HttpUtils.getInstance().getContentsAsString(url, headers);
JsonParser parser = new JsonParser();
JsonObject root = parser.parse(result).getAsJsonObject();
if (root.has("referenceSetId")) {
String referenceSetId = root.getAsJsonPrimitive("referenceSetId").getAsString();
List<JsonObject> refererences = Ga4ghAPIHelper.searchReferences(provider, referenceSetId, 1000);
sequenceNames = new ArrayList();
for (JsonObject refObject : refererences) {
sequenceNames.add(refObject.getAsJsonPrimitive("name").getAsString());
}
}
}
public static boolean supportsFileType(String type) {
return type.equals(Ga4ghAPIHelper.RESOURCE_TYPE);
}
class MIterator implements CloseableIterator<Alignment> {
Iterator<Alignment> iter;
MIterator(List<Alignment> alignmentList) {
iter = alignmentList.iterator();
}
@Override
public void close() {
}
@Override
public boolean hasNext() {
return iter.hasNext();
}
@Override
public Alignment next() {
return iter.next();
}
@Override
public void remove() {
iter.remove();
}
}
static Map<String, String> COMMON_ALIASES = new HashMap<String, String>();
static {
for (int i = 1; i <= 23; i++) {
COMMON_ALIASES.put(("" + i), ("chr" + i));
COMMON_ALIASES.put(("chr" + i), ("" + i));
}
COMMON_ALIASES.put("chrX", "X");
COMMON_ALIASES.put("X", "chrX");
COMMON_ALIASES.put("chrY", "Y");
COMMON_ALIASES.put("Y", "chrY");
COMMON_ALIASES.put("chrM", "MT");
COMMON_ALIASES.put("MT", "chrM");
}
}