ambit2.core.io.json

Class SubstanceStudyParser

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.json.SubstanceStudyParser

All Implemented Interfaces:

ICiteable, IRawReader<IStructureRecord>, Closeable, AutoCloseable, Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

public class SubstanceStudyParser
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
implements IRawReader<IStructureRecord>, ICiteable

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
protected com.fasterxml.jackson.databind.ObjectMapper	dx
protected int	index
protected static Logger	logger
protected SubstanceRecord	record
protected com.fasterxml.jackson.databind.node.ArrayNode	study
protected com.fasterxml.jackson.databind.node.ArrayNode	substance

Fields inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
SubstanceStudyParser(InputStreamReader reader)

Method Summary

Modifier and Type	Method and Description
void	close()
protected EffectRecord	createEffectRecord(Protocol protocol)
protected void	generateDocumentUUID(ProtocolApplication papp)
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
ILiteratureEntry	getReference()
protected void	handleException(Exception x)
boolean	hasNext()
Object	next()
IStructureRecord	nextRecord()
protected void	parseCompany(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
List<CompositionRelation>	parseComposition(com.fasterxml.jackson.databind.JsonNode node) TODO
static IParams	parseConditions(com.fasterxml.jackson.databind.ObjectMapper dx, Object json)
List<EffectRecord>	parseEffects(com.fasterxml.jackson.databind.node.ArrayNode node, Protocol protocol)
void	parseInterpretation(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	parseInterpretationCriteria(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	parseInterpretedResult(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	parseOwner(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
static IParams	parseParams(com.fasterxml.jackson.databind.node.ObjectNode node)
Protocol	parseProtocol(com.fasterxml.jackson.databind.node.ObjectNode node)
ProtocolApplication	parseProtocolApplication(com.fasterxml.jackson.databind.node.ObjectNode node)
List<ProtocolApplication>	parseProtocolApplication(Reader reader, SubstanceRecord record)
List<ProtocolApplication>	parseProtocolApplications(com.fasterxml.jackson.databind.JsonNode papps, SubstanceRecord record)
protected void	parseReliability(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
void	parseResult(com.fasterxml.jackson.databind.node.ObjectNode node, EffectRecord record)
protected void	parseStudyReference(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
SubstanceRecord	parseSubstance(com.fasterxml.jackson.databind.JsonNode node)
protected void	parseSubstance(com.fasterxml.jackson.databind.node.ObjectNode node, ProtocolApplication record)
SubstanceRecord	parseSubstance(Reader reader)
static IParams	parseTextValueProteomics(com.fasterxml.jackson.databind.ObjectMapper dx, String t)
void	parseValueAnnotated(com.fasterxml.jackson.databind.node.ObjectNode node, ValueAnnotated record)
List<ValueAnnotated>	parseValuesAnnotated(com.fasterxml.jackson.databind.node.ArrayNode node, Protocol protocol)
void	setReader(InputStream in)
void	setReader(Reader reader)
void	setReference(ILiteratureEntry reference)

Methods inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts, handleError, handleError, handleError, handleError, remove, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.io.IChemObjectReader

handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

accepts, addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Field Detail

logger

protected static Logger logger

dx

protected com.fasterxml.jackson.databind.ObjectMapper dx

substance

protected com.fasterxml.jackson.databind.node.ArrayNode substance

study

protected com.fasterxml.jackson.databind.node.ArrayNode study

index

protected int index

record

protected SubstanceRecord record

Constructor Detail

SubstanceStudyParser

public SubstanceStudyParser(InputStreamReader reader)
                     throws Exception

Throws:

Exception

Method Detail

setReader

public void setReader(Reader reader)
               throws org.openscience.cdk.exception.CDKException

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(InputStream in)
               throws org.openscience.cdk.exception.CDKException

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

Specified by:

getFormat in interface org.openscience.cdk.io.IChemObjectIO

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in interface org.openscience.cdk.io.IChemObjectIO

Throws:

IOException

generateDocumentUUID

protected void generateDocumentUUID(ProtocolApplication papp)
                             throws Exception

Throws:

Exception

handleException

protected void handleException(Exception x)

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

next

public Object next()

Specified by:

next in interface Iterator

setReference

public void setReference(ILiteratureEntry reference)

Specified by:

setReference in interface ICiteable

getReference

public ILiteratureEntry getReference()

Specified by:

getReference in interface ICiteable

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

parseSubstance

public SubstanceRecord parseSubstance(Reader reader)
                               throws Exception

Throws:

Exception

parseSubstance

public SubstanceRecord parseSubstance(com.fasterxml.jackson.databind.JsonNode node)

parseComposition

public List<CompositionRelation> parseComposition(com.fasterxml.jackson.databind.JsonNode node)

TODO

Parameters:

node -

Returns:

parseProtocolApplication

public List<ProtocolApplication> parseProtocolApplication(Reader reader,
                                                          SubstanceRecord record)
                                                   throws Exception

Throws:

Exception

parseProtocolApplications

public List<ProtocolApplication> parseProtocolApplications(com.fasterxml.jackson.databind.JsonNode papps,
                                                           SubstanceRecord record)
                                                    throws Exception

Throws:

Exception

parseProtocolApplication

public ProtocolApplication parseProtocolApplication(com.fasterxml.jackson.databind.node.ObjectNode node)

parseReliability

protected void parseReliability(com.fasterxml.jackson.databind.node.ObjectNode node,
                                ProtocolApplication record)

parseStudyReference

protected void parseStudyReference(com.fasterxml.jackson.databind.node.ObjectNode node,
                                   ProtocolApplication record)

parseCompany

protected void parseCompany(com.fasterxml.jackson.databind.node.ObjectNode node,
                            ProtocolApplication record)

parseOwner

public void parseOwner(com.fasterxml.jackson.databind.node.ObjectNode node,
                       ProtocolApplication record)

parseSubstance

protected void parseSubstance(com.fasterxml.jackson.databind.node.ObjectNode node,
                              ProtocolApplication record)

parseInterpretedResult

public void parseInterpretedResult(com.fasterxml.jackson.databind.node.ObjectNode node,
                                   ProtocolApplication record)

parseInterpretationCriteria

public void parseInterpretationCriteria(com.fasterxml.jackson.databind.node.ObjectNode node,
                                        ProtocolApplication record)

parseInterpretation

public void parseInterpretation(com.fasterxml.jackson.databind.node.ObjectNode node,
                                ProtocolApplication record)

parseParams

public static IParams parseParams(com.fasterxml.jackson.databind.node.ObjectNode node)

parseProtocol

public Protocol parseProtocol(com.fasterxml.jackson.databind.node.ObjectNode node)

createEffectRecord

protected EffectRecord createEffectRecord(Protocol protocol)

parseEffects

public List<EffectRecord> parseEffects(com.fasterxml.jackson.databind.node.ArrayNode node,
                                       Protocol protocol)

parseResult

public void parseResult(com.fasterxml.jackson.databind.node.ObjectNode node,
                        EffectRecord record)

parseValueAnnotated

public void parseValueAnnotated(com.fasterxml.jackson.databind.node.ObjectNode node,
                                ValueAnnotated record)

parseValuesAnnotated

public List<ValueAnnotated> parseValuesAnnotated(com.fasterxml.jackson.databind.node.ArrayNode node,
                                                 Protocol protocol)

parseConditions

public static IParams parseConditions(com.fasterxml.jackson.databind.ObjectMapper dx,
                                      Object json)

parseTextValueProteomics

public static IParams parseTextValueProteomics(com.fasterxml.jackson.databind.ObjectMapper dx,
                                               String t)