ts_ids_components.xrd.sample module#
Sample component for XRD IDSs.
XrdSample extends the generic
Sample common component with a
pk (UUIDPrimaryKey) so
a consuming IDS can declare it as a top-level array (samples: List[XrdSample],
following the platform-wide samples top-level naming convention) and
datacubes (see ts_ids_components.xrd.datacube and
ts_ids_components.xrd.datacube_raw) can reference the specific
sample a scan was measured on via fk_sample.
- Model XrdSample[source]#
Bases:
SampleA sample measured by an XRD instrument.
Show JSON schema
{ "description": "A sample measured by an XRD instrument.", "type": "object", "properties": { "id": { "description": "Unique identifier assigned to a sample.", "type": [ "string", "null" ] }, "name": { "description": "Sample name.", "type": [ "string", "null" ] }, "barcode": { "description": "Barcode assigned to a sample.", "type": [ "string", "null" ] }, "batch": { "$ref": "#/definitions/Batch" }, "set": { "$ref": "#/definitions/Set", "description": "Sample set." }, "location": { "$ref": "#/definitions/Location", "description": "Sample location information." }, "compound": { "$ref": "#/definitions/Compound", "description": "Sample compound information." }, "properties": { "type": "array", "items": { "$ref": "#/definitions/Property" }, "description": "Sample properties." }, "labels": { "description": "Sample labels.", "items": { "$ref": "#/definitions/Label" }, "type": "array" }, "pk": { "@primary_key": true, "description": "Primary key for this sample, referenced by datacubes measured on it.", "type": "string" } }, "additionalProperties": false, "required": [ "pk" ], "definitions": { "Batch": { "additionalProperties": false, "description": "A Batch is the result of a single manufacturing run for a drug product that is made as specified groups or amounts, within a specific time frame from the same raw materials that is intended to have uniform character and quality, within specified limits.", "properties": { "id": { "description": "Unique identifier assigned to a batch.", "type": [ "string", "null" ] }, "name": { "description": "Batch name", "type": [ "string", "null" ] }, "barcode": { "description": "Barcode assigned to a batch", "type": [ "string", "null" ] } }, "type": "object" }, "Compound": { "additionalProperties": false, "description": "A Compound is a specific chemical or biochemical structure or substance that is being investigated. A Compound may be any drug substance, drug product intermediate, or drug product across small molecules, and cell and gene therapy (CGT).", "properties": { "id": { "description": "Unique identifier assigned to a compound.", "type": [ "string", "null" ] }, "name": { "description": "Compound name.", "type": [ "string", "null" ] } }, "type": "object" }, "Holder": { "additionalProperties": false, "description": "A sample container such as a microplate or a vial.", "properties": { "name": { "description": "Holder name.", "type": [ "string", "null" ] }, "type": { "description": "Holder type.", "type": [ "string", "null" ] }, "barcode": { "description": "Barcode assigned to a holder.", "type": [ "string", "null" ] } }, "type": "object" }, "Label": { "additionalProperties": false, "description": "A Label associated with a sample, along with metadata about the label including\nthe source of the label and times associated with the label such as when it was\ncreated or looked up.", "properties": { "source": { "$ref": "#/definitions/Source", "description": "Sample label data source information." }, "name": { "description": "Sample label name.", "type": "string" }, "value": { "description": "Sample label value.", "type": "string" }, "time": { "$ref": "#/definitions/SampleTime", "description": "Time associated with the sample label." } }, "required": [ "source", "name", "value", "time" ], "type": "object" }, "Location": { "additionalProperties": false, "description": "The Location of the sample within the holder, such as the location of a well in a microplate.", "properties": { "position": { "description": "Raw position string.", "type": [ "string", "null" ] }, "row": { "description": "Row index of sample location in a plate or holder.", "type": [ "number", "null" ] }, "column": { "description": "Column index of sample location in a plate or holder.", "type": [ "number", "null" ] }, "index": { "description": "Index of sample location flattened to a single dimension.", "type": [ "number", "null" ] }, "holder": { "$ref": "#/definitions/Holder", "description": "Sample holder information" } }, "type": "object" }, "Property": { "additionalProperties": false, "description": "A property has a name and a value of any type, with metadata about the\nproperty including the source of the property and times associated with it\nsuch as when the property was created or looked up.", "properties": { "source": { "$ref": "#/definitions/Source", "description": "Sample property data source information." }, "name": { "description": "Sample Property name.", "type": "string" }, "value": { "description": "The original string value of the property.", "type": "string" }, "value_data_type": { "$ref": "#/definitions/ValueDataType", "description": "This is the type of the original value." }, "string_value": { "description": "If string_value has a value, then numerical_value, numerical_value_unit, and boolean_value all have to be null.", "type": [ "string", "null" ] }, "numerical_value": { "description": "If numerical_value has a value, then string_value and boolean_value both have to be null.", "type": [ "number", "null" ] }, "numerical_value_unit": { "description": "Unit for the numerical value.", "type": [ "string", "null" ] }, "boolean_value": { "description": "If boolean_value has a value, then numerical_value, numerical_value_unit, and string_value all have to be null.", "type": [ "boolean", "null" ] }, "time": { "$ref": "#/definitions/SampleTime", "description": "Time associated with the sample property." } }, "required": [ "source", "name", "value", "value_data_type", "string_value", "numerical_value", "numerical_value_unit", "boolean_value", "time" ], "type": "object" }, "RawSampleTime": { "additionalProperties": false, "description": "The base model for time associated with a specific sample.", "properties": { "start": { "description": "Process/experiment/task start time.", "type": [ "string", "null" ] }, "created": { "description": "Data created time.", "type": [ "string", "null" ] }, "stop": { "description": "Process/experiment/task stop/finish time.", "type": [ "string", "null" ] }, "duration": { "description": "Process/experiment/task duration.", "type": [ "string", "null" ] }, "last_updated": { "description": "Data last updated time of a file/method.", "type": [ "string", "null" ] }, "acquired": { "description": "Data acquired/exported/captured time.", "type": [ "string", "null" ] }, "modified": { "description": "Data last modified/edited time.", "type": [ "string", "null" ] }, "lookup": { "description": "Raw sample data lookup time.", "type": [ "string", "null" ] } }, "required": [ "lookup" ], "type": "object" }, "SampleTime": { "additionalProperties": false, "description": "A model for experiment sample datetime values converted to a standard ISO format\nand their respective raw datetime values in the primary data.", "properties": { "start": { "description": "Process/experiment/task start time.", "type": [ "string", "null" ] }, "created": { "description": "Data created time.", "type": [ "string", "null" ] }, "stop": { "description": "Process/experiment/task stop/finish time.", "type": [ "string", "null" ] }, "duration": { "description": "Process/experiment/task duration.", "type": [ "string", "null" ] }, "last_updated": { "description": "Data last updated time of a file/method.", "type": [ "string", "null" ] }, "acquired": { "description": "Data acquired/exported/captured time.", "type": [ "string", "null" ] }, "modified": { "description": "Data last modified/edited time.", "type": [ "string", "null" ] }, "lookup": { "description": "Raw sample data lookup time.", "type": [ "string", "null" ] }, "raw": { "$ref": "#/definitions/RawSampleTime", "description": "Raw sample time values from primary data." } }, "required": [ "lookup" ], "type": "object" }, "Set": { "additionalProperties": false, "description": "A group of Samples.", "properties": { "id": { "description": "Unique identifier assigned to a set.", "type": [ "string", "null" ] }, "name": { "description": "Set name.", "type": [ "string", "null" ] } }, "type": "object" }, "Source": { "additionalProperties": false, "description": "The Source of information, such as a data file or a sample database.", "properties": { "name": { "description": "Source name.", "type": [ "string", "null" ] }, "type": { "description": "Source type.", "type": [ "string", "null" ] } }, "required": [ "name", "type" ], "type": "object" }, "ValueDataType": { "description": "Allowed data type values.", "enum": [ "string", "number", "boolean" ], "type": "string" } } }
- Validators:
- field batch: Batch#
- field compound: Compound#
Sample compound information.
- field labels: List[Label]#
Sample labels.
- field location: Location#
Sample location information.
- field pk: str#
Primary key for this sample, referenced by datacubes measured on it.
- Constraints:
func = <function validate_uuid at 0x7f1493ac61f0>
json_schema_input_type = PydanticUndefined
- field properties: List[Property]#
Sample properties.
- field set_: Set (alias 'set')#
Sample set.