htsjdk.samtools.util.htsget.HtsgetResponse Maven / Gradle / Ivy
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package htsjdk.samtools.util.htsget;
import htsjdk.samtools.util.RuntimeIOException;
import org.json.JSONArray;
import org.json.JSONObject;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.SequenceInputStream;
import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
/**
* Class allowing deserialization from json htsget response, as defined in https://samtools.github.io/hts-specs/htsget.html
*
* This class currently supports version 1.2.0 of the spec
*
* An example response could be as follows
* {
* "htsget" : {
* "format" : "BAM",
* "urls" : [
* {
* "url" : "data:application/vnd.ga4gh.bam;base64,QkFNAQ==",
* "class" : "header"
* },
* {
* "url" : "https://htsget.blocksrv.example/sample1234/run1.bam",
* "headers" : {
* "Authorization" : "Bearer xxxx",
* "Range" : "bytes=65536-1003750"
* },
* "class" : "body"
* }
* ],
* "md5": "abcd"
* }
* }
*/
public class HtsgetResponse {
public static class Block {
private final URI uri;
private final Map headers;
private final HtsgetClass dataClass;
public Block(final URI uri, final Map headers, final HtsgetClass dataClass) {
this.uri = uri;
this.headers = headers;
this.dataClass = dataClass;
}
public URI getUri() {
return this.uri;
}
public Map getHeaders() {
return Collections.unmodifiableMap(this.headers);
}
public HtsgetClass getDataClass() {
return this.dataClass;
}
/**
* Gets data from this block either from its base64 encoded data url or by making an http request
*
* @return InputStream of data from this block
*/
public InputStream getData() {
switch (this.getUri().getScheme()) {
case "http":
case "https":
try {
final HttpURLConnection conn = (HttpURLConnection) this.uri.toURL().openConnection();
conn.setRequestMethod("GET");
this.headers.forEach(conn::setRequestProperty);
conn.connect();
return conn.getInputStream();
} catch (final IOException e) {
throw new RuntimeIOException("Could not retrieve data from block", e);
}
case "data":
final String dataUri = this.uri.toString();
if (!dataUri.matches("^data:.*;base64,.*")) {
throw new HtsgetMalformedResponseException("data URI must be base64 encoded: " + dataUri);
}
return new ByteArrayInputStream(
Base64.getDecoder().decode(dataUri.replaceFirst("^data:.*;base64,", "")));
default:
throw new HtsgetMalformedResponseException("Unrecognized URI scheme in data block: " + this.uri.getScheme());
}
}
/**
* Parse a single data block from a json value
*
* @param blockJson json value representing a block
* @return parsed block object
*/
public static Block parse(final JSONObject blockJson) {
final String uriJson = blockJson.optString("url", null);
if (uriJson == null) {
throw new HtsgetMalformedResponseException("No URI found in Htsget data block: " +
blockJson.toString().substring(0, Math.min(100, blockJson.toString().length())));
}
final URI uri;
try {
uri = new URI(uriJson);
} catch (final URISyntaxException e) {
throw new HtsgetMalformedResponseException("Could not parse URI in Htsget data block: " + uriJson, e);
}
final String dataClassJson = blockJson.optString("class", null);
final HtsgetClass dataClass = dataClassJson == null
? null
: HtsgetClass.valueOf(dataClassJson.toLowerCase());
final JSONObject headersJson = blockJson.optJSONObject("headers");
final Map headers = headersJson == null
? null
: headersJson.toMap().entrySet().stream()
.collect(Collectors.toMap(
Map.Entry::getKey,
e -> e.getValue().toString()
));
return new Block(uri, headers, dataClass);
}
}
public HtsgetResponse(final HtsgetFormat format, final List blocks, final String md5) {
this.format = format;
this.blocks = blocks;
this.md5 = md5;
}
private final HtsgetFormat format;
private final List blocks;
private final String md5;
public HtsgetFormat getFormat() {
return this.format;
}
public List getBlocks() {
return Collections.unmodifiableList(this.blocks);
}
public String getMd5() {
return this.md5;
}
/**
* Parses HtsgetResponse object from json string
*
* @param s json string
* @return parsed HtsgetResponse object
*/
public static HtsgetResponse parse(final String s) {
final JSONObject j = new JSONObject(s);
final JSONObject htsget = j.optJSONObject("htsget");
if (htsget == null) {
throw new HtsgetMalformedResponseException("No htsget key found in response");
}
final String md5Json = htsget.optString("md5", null);
final String formatJson = htsget.optString("format", null);
final JSONArray blocksJson = htsget.optJSONArray("urls");
if (blocksJson == null) {
throw new HtsgetMalformedResponseException("No urls field found in Htsget Response");
}
final List blocks = IntStream.range(0, blocksJson.length())
.mapToObj(blocksJson::getJSONObject)
.map(Block::parse)
.collect(Collectors.toList());
return new HtsgetResponse(
formatJson == null ? null : HtsgetFormat.valueOf(formatJson.toUpperCase()),
blocks,
md5Json
);
}
/**
* Lazily generates an InputStream over this response's data from the concatenation of the InputStreams from
* each of the response's data blocks
*
* @return InputStream over this response's data
*/
public InputStream getDataStream() {
return new SequenceInputStream(new Enumeration() {
private final Iterator iterator = HtsgetResponse.this.blocks.iterator();
@Override
public boolean hasMoreElements() {
return this.iterator.hasNext();
}
@Override
public InputStream nextElement() {
return this.iterator.next().getData();
}
});
}
}