Sample¶

Bases: NBOBaseClass

Represents the XML element Sample.

This field captures a description of the sample that was imaged in this experiment.

`fromBase(base)` `staticmethod` ¶

Cast a NBOBaseClass to a CMOS.

Parameters:

Name	Type	Description	Default
`base`	`NBOBaseClass`	The base class to cast	required

Returns:

Type	Description
`Sample`	The casted element, or nullptr if the cast fails

`getTypeName()` ¶

Returns the class type name.

Returns:

Type	Description
`string`	The class type name

`getXMLName()` ¶

Returns the XML element name corresponding to this class.

Returns:

Type	Description
`string`	The XML element name

`getNBOType()` ¶

Returns the NBO Type corresponding to this class.

Returns:

Type	Description
`int`	The NBO Type value

`getChildren()` ¶

Returns a list of all classes derived from this class.

Returns:

Type	Description
`List[NBOBaseClass]`	The list of derived classes

`getSubElements()` ¶

Returns a list of all child elements contained in this class.

Returns:

Type	Description
`List[NBOBaseClass]`	The list of child classes

`fromJsonFile(path, validate=True)` ¶

Populates this object from a JSON file.

Parameters:

Name	Type	Description	Default
`path`	`string`	The path to the JSON file	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`fromJsonString(json_string, validate=True)` ¶

Populates this object from a JSON string.

Parameters:

Name	Type	Description	Default
`json_string`	`string`	The JSON content as a string	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`fromXmlFile(path, validate=True)` ¶

Populates this object from a XML file.

Parameters:

Name	Type	Description	Default
`path`	`string`	The path to the XML file	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`fromXmlString(xml_string, validate=True)` ¶

Populates this object from a XML string.

Parameters:

Name	Type	Description	Default
`xml_string`	`string`	The XML content as a string	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`toXmlFile(filename, validate=True)` ¶

Serializes this object to an XML file.

Parameters:

Name	Type	Description	Default
`filename`	`string`	The path to the output XML file	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`toXmlString(validate=True)` ¶

Serializes this object to an XML string.

Parameters:

Name	Type	Description	Default
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

Returns:

Type	Description
`string`	A string containing the XML representation of this object

`setID(value, validate=True)` ¶

Sets the value of the ID attribute.

A unique identifier for this Sample.

Parameters:

Name	Type	Description	Default
`value`	`LSID_Type`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getID()` ¶

Returns the value of the ID attribute.

A unique identifier for this Sample.

Returns:

Type	Description
`LSID_Type`	The value of the attribute

`resetID()` ¶

Resets the ID attribute to an unset state.

A unique identifier for this Sample.

`hasID()` ¶

Checks whether the optional ID attribute is present.

A unique identifier for this Sample.

Returns:

Type	Description
`boolean`	true if the optional attribute has been set, false otherwise

`setName(value, validate=True)` ¶

Sets the value of the Name attribute.

A user assigned Name for this Sample.

Parameters:

Name	Type	Description	Default
`value`	`Denomination_Type`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getName()` ¶

Returns the value of the Name attribute.

A user assigned Name for this Sample.

Returns:

Type	Description
`Denomination_Type`	The value of the attribute

`resetName()` ¶

Resets the Name attribute to an unset state.

A user assigned Name for this Sample.

`hasName()` ¶

Checks whether the optional Name attribute is present.

A user assigned Name for this Sample.

Returns:

Type	Description
`boolean`	true if the optional attribute has been set, false otherwise

`setBiologicalOrigin(value, validate=True)` ¶

Sets the value of the BiologicalOrigin attribute.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

Parameters:

Name	Type	Description	Default
`value`	`boolean`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getBiologicalOrigin()` ¶

Returns the value of the BiologicalOrigin attribute.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

Returns:

Type	Description
`boolean`	The value of the attribute

`resetBiologicalOrigin()` ¶

Resets the BiologicalOrigin attribute to an unset state.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

`hasBiologicalOrigin()` ¶

Checks whether the BiologicalOrigin attribute is present.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`setSampleType(value, validate=True)` ¶

Sets the value of the SampleType attribute.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Parameters:

Name	Type	Description	Default
`value`	`SampleType_Type`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getSampleType()` ¶

Returns the value of the SampleType attribute.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Returns:

Type	Description
`SampleType_Type`	The value of the attribute

`resetSampleType()` ¶

Resets the SampleType attribute to an unset state.

If of Biological Origin, this field records a term that describes the general category of this Sample.

`hasSampleType()` ¶

Checks whether the optional SampleType attribute is present.

If of Biological Origin, this field records a term that describes the general category of this Sample.

Returns:

Type	Description
`boolean`	true if the optional attribute has been set, false otherwise

`setLiveSample(value, validate=True)` ¶

Sets the value of the LiveSample attribute.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

Parameters:

Name	Type	Description	Default
`value`	`boolean`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getLiveSample()` ¶

Returns the value of the LiveSample attribute.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

Returns:

Type	Description
`boolean`	The value of the attribute

`resetLiveSample()` ¶

Resets the LiveSample attribute to an unset state.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

`hasLiveSample()` ¶

Checks whether the LiveSample attribute is present.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`setOrganism(value, validate=True)` ¶

Sets the value of the Organism attribute.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getOrganism()` ¶

Returns the value of the Organism attribute.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Returns:

Type	Description
`string`	The value of the attribute

`resetOrganism()` ¶

Resets the Organism attribute to an unset state.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

`hasOrganism()` ¶

Checks whether the Organism attribute is present.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getOrganismAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setOrganismTermAccession(value, validate=True)` ¶

Sets the value of the OrganismTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getOrganismTermAccession()` ¶

Returns the value of the OrganismTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Returns:

Type	Description
`string`	The value of the attribute

`resetOrganismTermAccession()` ¶

Resets the OrganismTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

`hasOrganismTermAccession()` ¶

Checks whether the OrganismTermAccession attribute is present.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getOrganismTermAccessionAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setOrganismPart(value, validate=True)` ¶

Sets the value of the OrganismPart attribute.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getOrganismPart()` ¶

Returns the value of the OrganismPart attribute.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`string`	The value of the attribute

`resetOrganismPart()` ¶

Resets the OrganismPart attribute to an unset state.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

`hasOrganismPart()` ¶

Checks whether the OrganismPart attribute is present.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getOrganismPartAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setOrganismPartTermAccession(value, validate=True)` ¶

Sets the value of the OrganismPartTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getOrganismPartTermAccession()` ¶

Returns the value of the OrganismPartTermAccession attribute.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`string`	The value of the attribute

`resetOrganismPartTermAccession()` ¶

Resets the OrganismPartTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

`hasOrganismPartTermAccession()` ¶

Checks whether the OrganismPartTermAccession attribute is present.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getOrganismPartTermAccessionAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setSamplePreparationMethod(value, validate=True)` ¶

Sets the value of the SamplePreparationMethod attribute.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getSamplePreparationMethod()` ¶

Returns the value of the SamplePreparationMethod attribute.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`string`	The value of the attribute

`resetSamplePreparationMethod()` ¶

Resets the SamplePreparationMethod attribute to an unset state.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

`hasSamplePreparationMethod()` ¶

Checks whether the SamplePreparationMethod attribute is present.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getSamplePreparationMethodAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setSamplePreparationMethodTermAccession(value, validate=True)` ¶

Sets the value of the SamplePreparationMethodTermAccession attribute.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Parameters:

Name	Type	Description	Default
`value`	`string`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getSamplePreparationMethodTermAccession()` ¶

Returns the value of the SamplePreparationMethodTermAccession attribute.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`string`	The value of the attribute

`resetSamplePreparationMethodTermAccession()` ¶

Resets the SamplePreparationMethodTermAccession attribute to an unset state.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

`hasSamplePreparationMethodTermAccession()` ¶

Checks whether the SamplePreparationMethodTermAccession attribute is present.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`getSamplePreparationMethodTermAccessionAllowedValues()` `staticmethod` ¶

Returns the allowed values for this attribut.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

Returns:

Type	Description
`std::set< str,std::less< str >,std::allocator< str > >`	The list of allowed values

`setMetrologySample(value, validate=True)` ¶

Sets the value of the MetrologySample attribute.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

Parameters:

Name	Type	Description	Default
`value`	`boolean`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getMetrologySample()` ¶

Returns the value of the MetrologySample attribute.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

Returns:

Type	Description
`boolean`	The value of the attribute

`resetMetrologySample()` ¶

Resets the MetrologySample attribute to an unset state.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

`hasMetrologySample()` ¶

Checks whether the MetrologySample attribute is present.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

Returns:

Type	Description
`boolean`	true if the attribute has been set, false otherwise

`setFacingTheObjective(value, validate=True)` ¶

Sets the value of the FacingTheObjective attribute.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Parameters:

Name	Type	Description	Default
`value`	`FacingTheObjectiveChoice_Type`	The value to set	required
`validate`	`(boolean, optional)`	If true, validates constraints on value. Default is true.	`True`

`getFacingTheObjective()` ¶

Returns the value of the FacingTheObjective attribute.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Returns:

Type	Description
`FacingTheObjectiveChoice_Type`	The value of the attribute

`resetFacingTheObjective()` ¶

Resets the FacingTheObjective attribute to an unset state.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

`hasFacingTheObjective()` ¶

Checks whether the optional FacingTheObjective attribute is present.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

Returns:

Type	Description
`boolean`	true if the optional attribute has been set, false otherwise