org.brapi.v2.model.geno

Class BrAPISample

java.lang.Object

org.brapi.v2.model.geno.BrAPISample

public class BrAPISample
extends Object

Sample

Constructor Summary

Constructors

Constructor and Description
BrAPISample()

Method Summary

Modifier and Type	Method and Description
BrAPISample	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPISample	column(Integer column)
boolean	equals(Object o)
BrAPISample	externalReferences(List<BrAPIExternalReference> externalReferences)
BrAPISample	germplasmDbId(String germplasmDbId)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
Integer	getColumn() The Column identifier for this samples location in the plate minimum: 1 maximum: 12
@Valid List<BrAPIExternalReference>	getExternalReferences() Get externalReferences
String	getGermplasmDbId() The ID which uniquely identifies a germplasm
String	getObservationUnitDbId() The ID which uniquely identifies an observation unit
String	getPlateDbId() The ID which uniquely identifies a plate of samples
String	getPlateName() The human readable name of a plate
String	getProgramDbId() The ID which uniquely identifies a program within the given database server
String	getRow() The Row identifier for this samples location in the plate
String	getSampleBarcode() A unique identifier physically attached to the sample
String	getSampleDbId() The ID which uniquely identifies a sample MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.
String	getSampleDescription() Description of a sample MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.
String	getSampleGroupDbId() The ID which uniquely identifies a group of samples
String	getSampleName() The name of the sample
String	getSamplePUI() A permanent unique identifier for the sample (DOI, URL, UUID, etc) MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein.
@Valid OffsetDateTime	getSampleTimestamp() The date and time a sample was collected from the field MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested
String	getSampleType() The type of sample taken.
String	getStudyDbId() The ID which uniquely identifies a study within the given database server
String	getTakenBy() The name or identifier of the entity which took the sample from the field
String	getTissueType() The type of tissue sampled.
String	getTrialDbId() The ID which uniquely identifies a trial within the given database server
String	getWell() The Well identifier for this samples location in the plate.
int	hashCode()
BrAPISample	observationUnitDbId(String observationUnitDbId)
BrAPISample	plateDbId(String plateDbId)
BrAPISample	plateName(String plateName)
BrAPISample	programDbId(String programDbId)
BrAPISample	putAdditionalInfoItem(String key, Object additionalInfoItem)
BrAPISample	row(String row)
BrAPISample	sampleBarcode(String sampleBarcode)
BrAPISample	sampleDbId(String sampleDbId)
BrAPISample	sampleDescription(String sampleDescription)
BrAPISample	sampleGroupDbId(String sampleGroupDbId)
BrAPISample	sampleName(String sampleName)
BrAPISample	samplePUI(String samplePUI)
BrAPISample	sampleTimestamp(OffsetDateTime sampleTimestamp)
BrAPISample	sampleType(String sampleType)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setColumn(Integer column)
void	setExternalReferences(List<BrAPIExternalReference> externalReferences)
void	setGermplasmDbId(String germplasmDbId)
void	setObservationUnitDbId(String observationUnitDbId)
void	setPlateDbId(String plateDbId)
void	setPlateName(String plateName)
void	setProgramDbId(String programDbId)
void	setRow(String row)
void	setSampleBarcode(String sampleBarcode)
void	setSampleDbId(String sampleDbId)
void	setSampleDescription(String sampleDescription)
void	setSampleGroupDbId(String sampleGroupDbId)
void	setSampleName(String sampleName)
void	setSamplePUI(String samplePUI)
void	setSampleTimestamp(OffsetDateTime sampleTimestamp)
void	setSampleType(String sampleType)
void	setStudyDbId(String studyDbId)
void	setTakenBy(String takenBy)
void	setTissueType(String tissueType)
void	setTrialDbId(String trialDbId)
void	setWell(String well)
BrAPISample	studyDbId(String studyDbId)
BrAPISample	takenBy(String takenBy)
BrAPISample	tissueType(String tissueType)
String	toString()
BrAPISample	trialDbId(String trialDbId)
BrAPISample	well(String well)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BrAPISample

public BrAPISample()

Method Detail

sampleDbId

public BrAPISample sampleDbId(String sampleDbId)

getSampleDbId

public String getSampleDbId()

The ID which uniquely identifies a sample MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.

Returns:

sampleDbId

setSampleDbId

public void setSampleDbId(String sampleDbId)

additionalInfo

public BrAPISample additionalInfo(com.google.gson.JsonObject additionalInfo)

putAdditionalInfoItem

public BrAPISample putAdditionalInfoItem(String key,
                                         Object additionalInfoItem)

getAdditionalInfo

public com.google.gson.JsonObject getAdditionalInfo()

Additional arbitrary info

Returns:

additionalInfo

setAdditionalInfo

public void setAdditionalInfo(com.google.gson.JsonObject additionalInfo)

column

public BrAPISample column(Integer column)

getColumn

public Integer getColumn()

The Column identifier for this samples location in the plate minimum: 1 maximum: 12

Returns:

column

setColumn

public void setColumn(Integer column)

externalReferences

public BrAPISample externalReferences(List<BrAPIExternalReference> externalReferences)

getExternalReferences

@Valid
public @Valid List<BrAPIExternalReference> getExternalReferences()

Get externalReferences

Returns:

externalReferences

setExternalReferences

public void setExternalReferences(List<BrAPIExternalReference> externalReferences)

germplasmDbId

public BrAPISample germplasmDbId(String germplasmDbId)

getGermplasmDbId

public String getGermplasmDbId()

The ID which uniquely identifies a germplasm

Returns:

germplasmDbId

setGermplasmDbId

public void setGermplasmDbId(String germplasmDbId)

observationUnitDbId

public BrAPISample observationUnitDbId(String observationUnitDbId)

getObservationUnitDbId

public String getObservationUnitDbId()

The ID which uniquely identifies an observation unit

Returns:

observationUnitDbId

setObservationUnitDbId

public void setObservationUnitDbId(String observationUnitDbId)

plateDbId

public BrAPISample plateDbId(String plateDbId)

getPlateDbId

public String getPlateDbId()

The ID which uniquely identifies a plate of samples

Returns:

plateDbId

setPlateDbId

public void setPlateDbId(String plateDbId)

plateName

public BrAPISample plateName(String plateName)

getPlateName

public String getPlateName()

The human readable name of a plate

Returns:

plateName

setPlateName

public void setPlateName(String plateName)

programDbId

public BrAPISample programDbId(String programDbId)

getProgramDbId

public String getProgramDbId()

The ID which uniquely identifies a program within the given database server

Returns:

programDbId

setProgramDbId

public void setProgramDbId(String programDbId)

row

public BrAPISample row(String row)

getRow

public String getRow()

The Row identifier for this samples location in the plate

Returns:

row

setRow

public void setRow(String row)

sampleBarcode

public BrAPISample sampleBarcode(String sampleBarcode)

getSampleBarcode

public String getSampleBarcode()

A unique identifier physically attached to the sample

Returns:

sampleBarcode

setSampleBarcode

public void setSampleBarcode(String sampleBarcode)

sampleDescription

public BrAPISample sampleDescription(String sampleDescription)

getSampleDescription

public String getSampleDescription()

Description of a sample MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.

Returns:

sampleDescription

setSampleDescription

public void setSampleDescription(String sampleDescription)

sampleGroupDbId

public BrAPISample sampleGroupDbId(String sampleGroupDbId)

getSampleGroupDbId

public String getSampleGroupDbId()

The ID which uniquely identifies a group of samples

Returns:

sampleGroupDbId

setSampleGroupDbId

public void setSampleGroupDbId(String sampleGroupDbId)

sampleName

public BrAPISample sampleName(String sampleName)

getSampleName

public String getSampleName()

The name of the sample

Returns:

sampleName

setSampleName

public void setSampleName(String sampleName)

samplePUI

public BrAPISample samplePUI(String samplePUI)

getSamplePUI

public String getSamplePUI()

A permanent unique identifier for the sample (DOI, URL, UUID, etc) MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible.

Returns:

samplePUI

setSamplePUI

public void setSamplePUI(String samplePUI)

sampleTimestamp

public BrAPISample sampleTimestamp(OffsetDateTime sampleTimestamp)

getSampleTimestamp

@Valid
public @Valid OffsetDateTime getSampleTimestamp()

The date and time a sample was collected from the field MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested

Returns:

sampleTimestamp

setSampleTimestamp

public void setSampleTimestamp(OffsetDateTime sampleTimestamp)

sampleType

public BrAPISample sampleType(String sampleType)

getSampleType

public String getSampleType()

The type of sample taken. ex. 'DNA', 'RNA', 'Tissue', etc

Returns:

sampleType

setSampleType

public void setSampleType(String sampleType)

studyDbId

public BrAPISample studyDbId(String studyDbId)

getStudyDbId

public String getStudyDbId()

The ID which uniquely identifies a study within the given database server

Returns:

studyDbId

setStudyDbId

public void setStudyDbId(String studyDbId)

takenBy

public BrAPISample takenBy(String takenBy)

getTakenBy

public String getTakenBy()

The name or identifier of the entity which took the sample from the field

Returns:

takenBy

setTakenBy

public void setTakenBy(String takenBy)

tissueType

public BrAPISample tissueType(String tissueType)

getTissueType

public String getTissueType()

The type of tissue sampled. ex. 'Leaf', 'Root', etc. MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology).

Returns:

tissueType

setTissueType

public void setTissueType(String tissueType)

trialDbId

public BrAPISample trialDbId(String trialDbId)

getTrialDbId

public String getTrialDbId()

The ID which uniquely identifies a trial within the given database server

Returns:

trialDbId

setTrialDbId

public void setTrialDbId(String trialDbId)

well

public BrAPISample well(String well)

getWell

public String getWell()

The Well identifier for this samples location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate.

Returns:

well

setWell

public void setWell(String well)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object