Tetra Data Domain-Specific Components Documentation

ts-ids-components is home to domain-specific common components for use in programmatic IDSs. For getting started with programmatic IDS or documentation about creating and using Tetra Data models, see ids.tetrascience.com.

These components can be used in any IDS as a way to build upon existing data models. When multiple IDSs use the same common components, accessing data becomes more consistent by enabling reuse of search queries and application code.

Version

v0.15.0

Install

pip install ts-ids-components

Quickstart

After installing this package, components can be imported and used in any programmatic IDS definition.

Here is an example of a complete IDS definition which uses the {py:class}Filter <ts_ids_components.plate_reader.Filter> component:

from typing import List

from ts_ids_core.schema import (
    IdsElement,
    IdsField,
    Required,
    SchemaExtraMetadataType,
    TetraDataSchema,
)

from ts_ids_components.plate_reader import Filter


class InstrumentMethod(IdsElement):
    """Methods defined for the instrument run"""

    protocol_id: str = IdsField(description="Identifier for the protocol used")
    filter: Filter


class MyPlateReaderModel(TetraDataSchema):
    """IDS demonstrating plate reader components"""

    schema_extra_metadata: SchemaExtraMetadataType = {
        "$id": "https://ids.tetrascience.com/common/plate-reader-component-demo/v1.0.0/schema.json",
        "$schema": "http://json-schema.org/draft-07/schema",
    }

    ids_type: Required[str] = IdsField(
        default="plate-reader-component-demo", alias="@idsType", const=True
    )
    ids_version: Required[str] = IdsField(
        default="v1.0.0", alias="@idsVersion", const=True
    )
    ids_namespace: Required[str] = IdsField(
        default="common", alias="@idsNamespace", const=True
    )

    methods: List[InstrumentMethod]

See {external+ts-ids-core:doc}ts-ids-core export-schema <cli/export_schema> documentation for an explanation of generating JSON Schema from a programmatic IDS.

Expand to show JSON schema for `MyPlateReaderModel`

{
  "description": "IDS demonstrating plate reader components",
  "type": "object",
  "properties": {
    "@idsType": {
      "const": "plate-reader-component-demo",
      "type": "string"
    },
    "@idsVersion": {
      "const": "v1.0.0",
      "type": "string"
    },
    "@idsNamespace": {
      "const": "common",
      "type": "string"
    },
    "@idsConventionVersion": {
      "description": "IDS convention version. Defined by TetraScience.",
      "const": "v1.0.0",
      "type": "string"
    },
    "methods": {
      "type": "array",
      "items": {
        "$ref": "#/definitions/InstrumentMethod"
      }
    }
  },
  "required": [
    "@idsType",
    "@idsVersion",
    "@idsNamespace",
    "@idsConventionVersion"
  ],
  "additionalProperties": false,
  "$id": "https://ids.tetrascience.com/common/plate-reader-component-demo/v1.0.0/schema.json",
  "$schema": "http://json-schema.org/draft-07/schema",
  "definitions": {
    "ValueUnit": {
      "type": "object",
      "properties": {
        "value": {
          "type": [
            "number",
            "null"
          ]
        },
        "unit": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "required": [
        "value",
        "unit"
      ],
      "additionalProperties": false
    },
    "Filter": {
      "description": "Optical filter properties",
      "type": "object",
      "properties": {
        "position": {
          "description": "Position of this filter in a container like a filter wheel",
          "type": [
            "string",
            "null"
          ]
        },
        "bandwidth": {
          "description": "The range of frequencies associated with this filter",
          "$ref": "#/definitions/ValueUnit"
        },
        "wavelength": {
          "description": "Characteristic wavelength of this filter",
          "$ref": "#/definitions/ValueUnit"
        }
      },
      "additionalProperties": false
    },
    "InstrumentMethod": {
      "description": "Methods defined for the instrument run",
      "type": "object",
      "properties": {
        "protocol_id": {
          "description": "Identifier for the protocol used",
          "type": "string"
        },
        "filter": {
          "$ref": "#/definitions/Filter"
        }
      },
      "additionalProperties": false
    }
  }
}

License

License information can be found here: LICENSE.

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