Package htsjdk.samtools.util.htsget

Class HtsgetPOSTRequest

java.lang.Object

htsjdk.samtools.util.htsget.HtsgetRequest

htsjdk.samtools.util.htsget.HtsgetPOSTRequest

public class HtsgetPOSTRequest
extends HtsgetRequest

Builder for an htsget POST request that allows opening a connection using the request after validating that it is properly formed.

This class is experimental and subject to change as the POST api evolves.

See https://github.com/samtools/hts-specs/pull/285 for the API specification.

Field Summary

Fields inherited from class htsjdk.samtools.util.htsget.HtsgetRequest

ACCEPT_TYPE, dataClass, fields, format, interval, notags, PROTOCOL_VERSION, tags, UNMAPPED_UNPLACED_INTERVAL

Constructor Summary

Constructors

Constructor	Description
HtsgetPOSTRequest(HtsgetRequest req)
HtsgetPOSTRequest(URI endpoint)	Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server

Method Summary

Modifier and Type	Method	Description
void	addInterval(Locatable interval)
void	addIntervals(Collection<Locatable> intervals)
protected HttpURLConnection	getConnection()
org.json.JSONObject	queryBody()
void	setInterval(Locatable interval)
URI	toURI()	Convert request to a URI which can be used to make http request for data blocks
void	validateRequest()	Validates that the user query obeys htsget spec
HtsgetPOSTRequest	withDataClass(HtsgetClass dataClass)
HtsgetPOSTRequest	withField(HtsgetRequestField field)
HtsgetPOSTRequest	withFields(Collection<HtsgetRequestField> fields)
HtsgetPOSTRequest	withFormat(HtsgetFormat format)
HtsgetPOSTRequest	withInterval(Locatable interval)
HtsgetPOSTRequest	withIntervals(Collection<Locatable> intervals)
HtsgetPOSTRequest	withNotag(String notag)
HtsgetPOSTRequest	withNotags(Collection<String> notags)
HtsgetPOSTRequest	withTag(String tag)
HtsgetPOSTRequest	withTags(Collection<String> tags)

Methods inherited from class htsjdk.samtools.util.htsget.HtsgetRequest

addField, addFields, addNotag, addNotags, addTag, addTags, getDataClass, getEndpoint, getFields, getFormat, getInterval, getNoTags, getResponse, getTags, setDataClass, setFormat

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

HtsgetPOSTRequest

public HtsgetPOSTRequest(URI endpoint)

Construct an HtsgetRequest from a URI identifying a valid resource on a htsget server

Parameters:

endpoint - the full URI including both server path and the ID of the htsget resource, without the filtering parameters defined in the htsget spec such as start or referenceName

HtsgetPOSTRequest

public HtsgetPOSTRequest(HtsgetRequest req)

Method Details

setInterval

public void setInterval(Locatable interval)

Overrides:

setInterval in class HtsgetRequest

addInterval

public void addInterval(Locatable interval)

addIntervals

public void addIntervals(Collection<Locatable> intervals)

withFormat

public HtsgetPOSTRequest withFormat(HtsgetFormat format)

Overrides:

withFormat in class HtsgetRequest

withDataClass

public HtsgetPOSTRequest withDataClass(HtsgetClass dataClass)

Overrides:

withDataClass in class HtsgetRequest

withInterval

public HtsgetPOSTRequest withInterval(Locatable interval)

Overrides:

withInterval in class HtsgetRequest

withIntervals

public HtsgetPOSTRequest withIntervals(Collection<Locatable> intervals)

withField

public HtsgetPOSTRequest withField(HtsgetRequestField field)

Overrides:

withField in class HtsgetRequest

withFields

public HtsgetPOSTRequest withFields(Collection<HtsgetRequestField> fields)

Overrides:

withFields in class HtsgetRequest

withTag

public HtsgetPOSTRequest withTag(String tag)

Overrides:

withTag in class HtsgetRequest

withTags

public HtsgetPOSTRequest withTags(Collection<String> tags)

Overrides:

withTags in class HtsgetRequest

withNotag

public HtsgetPOSTRequest withNotag(String notag)

Overrides:

withNotag in class HtsgetRequest

withNotags

public HtsgetPOSTRequest withNotags(Collection<String> notags)

Overrides:

withNotags in class HtsgetRequest

validateRequest

public void validateRequest()

Description copied from class: HtsgetRequest

Validates that the user query obeys htsget spec

Overrides:

validateRequest in class HtsgetRequest

toURI

public URI toURI()

Description copied from class: HtsgetRequest

Convert request to a URI which can be used to make http request for data blocks

Overrides:

toURI in class HtsgetRequest

queryBody

public org.json.JSONObject queryBody()

getConnection

protected HttpURLConnection getConnection()

Overrides:

getConnection in class HtsgetRequest