Yanked

This release has been yanked by its maintainers, and will be ignored by installers, except when explicitly specified.
Consider using release 2.2.0 instead.
Reason given by maintainers: customers are encouraged to contact TetraScience to install the latest version from TS JFrog

Welcome to ts-ids-core's documentation!

ts-ids-core provides a programmatic way of defining TetraScience Intermediate Data Schema (IDS). An IDS defined using the ts-ids-core framework can be exported to IDS JSON (jsonschema v7) and is thus compatible with the Tetra Data Platform (TDP).

Install

pip install ts-ids-core

Quickstart

To define your own Programmatic IDS (PIDS), inherit from classes in ts_ids_core.schema; ts_ids_core.schema.IdsSchema contains the IDS metadata fields, e.g. IDS version, and should be the parent class to your top-level IDS class.

In addition to defining IDS metadata fields, in the example below we add a field named "samples" that conforms to the predefined component, Schema.

from typing import List

from ts_ids_core.schema import IdsSchema, Sample
from ts_ids_core.base.ids_field import IdsField
from ts_ids_core.base.ids_element import SchemaExtraMetadataType


class DemoIdsSchema(IdsSchema):
    #: The type hint `SchemaExtraMetadataType` is required.
    schema_extra_metadata: SchemaExtraMetadataType = {
        "$id": "https://ids.tetrascience.com/my_namespace/demo_ids/v1.0.0/schema.json",
        "$schema": "http://json-schema.org/draft-07/schema#",
    }

    ids_namespace: str = IdsField('my_namespace', const=True)
    ids_type: str = IdsField('my_unique_ids_name', const=True)
    ids_version: str = IdsField('v1.0.0', const=True)

    samples: List[Sample] = IdsField()

That's it! You just defined an IDS class. To export the IDS to JSON Schema used by the TDP, run the following code:

ids_json_schema = DemoIdsSchema.schema_json(indent=2)

When printed, output will look like this:

Expand to show output

{
  "$id": "https://ids.tetrascience.com/my_namespace/my_unique_ids_name/v1.0.0/schema.json",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "description": "Top-level schema.",
  "type": "object",
  "properties": {
    "ids_type": {
      "const": "my_unique_ids_name",
      "type": "string"
    },
    "ids_version": {
      "const": "v1.0.0",
      "type": "string"
    },
    "@idsConventionVersion": {
      "const": "v1.0.0",
      "type": "string"
    },
    "ids_namespace": {
      "const": "my_namespace",
      "type": "string"
    },
    "samples": {
      "type": "array",
      "items": {
        "$ref": "#/definitions/Sample"
      }
    }
  },
  "additionalProperties": false,
  "definitions": {
    "Batch": {
      "type": "object",
      "properties": {
        "id": {
          "type": [
            "string",
            "null"
          ]
        },
        "name": {
          "type": [
            "string",
            "null"
          ]
        },
        "barcode": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "additionalProperties": false
    },
    "Set": {
      "type": "object",
      "properties": {
        "id": {
          "type": [
            "string",
            "null"
          ]
        },
        "name": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "additionalProperties": false
    },
    "Lot": {
      "type": "object",
      "properties": {
        "id": {
          "type": [
            "string",
            "null"
          ]
        },
        "name": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "additionalProperties": false
    },
    "Holder": {
      "type": "object",
      "properties": {
        "name": {
          "type": [
            "string",
            "null"
          ]
        },
        "type": {
          "type": [
            "string",
            "null"
          ]
        },
        "barcode": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "additionalProperties": false
    },
    "Location": {
      "type": "object",
      "properties": {
        "position": {
          "type": [
            "string",
            "null"
          ]
        },
        "row": {
          "type": [
            "number",
            "null"
          ]
        },
        "column": {
          "type": [
            "number",
            "null"
          ]
        },
        "index": {
          "type": [
            "number",
            "null"
          ]
        },
        "holder": {
          "$ref": "#/definitions/Holder"
        }
      },
      "additionalProperties": false
    },
    "Source": {
      "type": "object",
      "properties": {
        "name": {
          "type": [
            "string",
            "null"
          ]
        },
        "type": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "required": [
        "name",
        "type"
      ],
      "additionalProperties": false
    },
    "ValueDataType": {
      "title": "ValueDataType",
      "description": "An enumeration.",
      "enum": [
        "string",
        "number",
        "boolean"
      ],
      "type": "string"
    },
    "RawSampleTime": {
      "type": "object",
      "properties": {
        "start": {
          "type": [
            "string",
            "null"
          ]
        },
        "created": {
          "type": [
            "string",
            "null"
          ]
        },
        "stop": {
          "type": [
            "string",
            "null"
          ]
        },
        "duration": {
          "type": [
            "string",
            "null"
          ]
        },
        "last_updated": {
          "type": [
            "string",
            "null"
          ]
        },
        "acquired": {
          "type": [
            "string",
            "null"
          ]
        },
        "modified": {
          "type": [
            "string",
            "null"
          ]
        },
        "lookup": {
          "type": [
            "string",
            "null"
          ]
        }
      },
      "required": [
        "lookup"
      ],
      "additionalProperties": false
    },
    "SampleTime": {
      "type": "object",
      "properties": {
        "start": {
          "type": [
            "string",
            "null"
          ]
        },
        "created": {
          "type": [
            "string",
            "null"
          ]
        },
        "stop": {
          "type": [
            "string",
            "null"
          ]
        },
        "duration": {
          "type": [
            "string",
            "null"
          ]
        },
        "last_updated": {
          "type": [
            "string",
            "null"
          ]
        },
        "acquired": {
          "type": [
            "string",
            "null"
          ]
        },
        "modified": {
          "type": [
            "string",
            "null"
          ]
        },
        "lookup": {
          "type": [
            "string",
            "null"
          ]
        },
        "raw": {
          "$ref": "#/definitions/RawSampleTime"
        }
      },
      "required": [
        "lookup"
      ],
      "additionalProperties": false
    },
    "Property": {
      "type": "object",
      "properties": {
        "source": {
          "$ref": "#/definitions/Source"
        },
        "name": {
          "description": "This is the property name",
          "type": "string"
        },
        "value": {
          "description": "The original string value of the parameter",
          "type": "string"
        },
        "value_data_type": {
          "description": "This is the type of the original value",
          "$ref": "#/definitions/ValueDataType"
        },
        "string_value": {
          "description": "If string_value has a value, then numerical_value,\nnumerical_value_unit, and boolean_value all have to be null",
          "type": [
            "string",
            "null"
          ]
        },
        "numerical_value": {
          "description": "If numerical_value has a value, then string_value and\nboolean_value both have to be null",
          "type": [
            "number",
            "null"
          ]
        },
        "numerical_value_unit": {
          "type": [
            "string",
            "null"
          ]
        },
        "boolean_value": {
          "description": "If boolean_value has a value, then numerical_value, numerical_value_unit,\nand string_value all have to be null",
          "type": [
            "boolean",
            "null"
          ]
        },
        "time": {
          "$ref": "#/definitions/SampleTime"
        }
      },
      "required": [
        "source",
        "name",
        "value",
        "value_data_type",
        "string_value",
        "numerical_value",
        "numerical_value_unit",
        "boolean_value",
        "time"
      ],
      "additionalProperties": false
    },
    "Label": {
      "type": "object",
      "properties": {
        "source": {
          "$ref": "#/definitions/Source"
        },
        "name": {
          "type": "string"
        },
        "value": {
          "type": "string"
        },
        "time": {
          "$ref": "#/definitions/SampleTime"
        }
      },
      "required": [
        "source",
        "name",
        "value",
        "time"
      ],
      "additionalProperties": false
    },
    "Sample": {
      "description": "See [here](https://developers.tetrascience.com/docs/ids-design-conventions-schema-templates#samples)\nfor specification of \"samples\". An instance of this class is one item in the\n`samples` array.",
      "type": "object",
      "properties": {
        "id": {
          "type": [
            "string",
            "null"
          ]
        },
        "name": {
          "type": [
            "string",
            "null"
          ]
        },
        "barcode": {
          "type": [
            "string",
            "null"
          ]
        },
        "batch": {
          "$ref": "#/definitions/Batch"
        },
        "set": {
          "$ref": "#/definitions/Set"
        },
        "lot": {
          "$ref": "#/definitions/Lot"
        },
        "location": {
          "$ref": "#/definitions/Location"
        },
        "properties": {
          "type": "array",
          "items": {
            "$ref": "#/definitions/Property"
          }
        },
        "labels": {
          "type": "array",
          "items": {
            "$ref": "#/definitions/Label"
          }
        }
      },
      "additionalProperties": false
    }
  }
}

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

ts-ids-core-0.1.0a4.tar.gz (23.8 kB view details)

Uploaded Jul 8, 2022 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

ts_ids_core-0.1.0a4-py3-none-any.whl (25.3 kB view details)

Uploaded Jul 8, 2022 Python 3

File details

Details for the file ts-ids-core-0.1.0a4.tar.gz.

File metadata

Download URL: ts-ids-core-0.1.0a4.tar.gz
Upload date: Jul 8, 2022
Size: 23.8 kB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: poetry/1.1.13 CPython/3.9.11 Darwin/20.6.0

File hashes

Hashes for ts-ids-core-0.1.0a4.tar.gz
Algorithm	Hash digest
SHA256	`c15e92e7c6963d71ddfdc37781e2765d9eddc6b986cabf7c6e8b36ffe2b93a62`
MD5	`c122f6bd2e465ebe0a3966fcd69f1e79`
BLAKE2b-256	`037bd10c308ee3a4c4494800791b0216bc44785f2c7959e34bac65de0459629b`

See more details on using hashes here.

File details

Details for the file ts_ids_core-0.1.0a4-py3-none-any.whl.

File metadata

Download URL: ts_ids_core-0.1.0a4-py3-none-any.whl
Upload date: Jul 8, 2022
Size: 25.3 kB
Tags: Python 3
Uploaded using Trusted Publishing? No
Uploaded via: poetry/1.1.13 CPython/3.9.11 Darwin/20.6.0

File hashes

Hashes for ts_ids_core-0.1.0a4-py3-none-any.whl
Algorithm	Hash digest
SHA256	`64ae5c06701bef4baa20dcfc179e1d5c490740a7a19b180004b2977b12f6706f`
MD5	`50351b664f6d21add52394393aa7ee89`
BLAKE2b-256	`d58425fdb20640a7aa2ad4fa47e848d1e4f44c1ab8632ab03cb759525e2445cc`