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Merge pull request #38 from HDRUK/GAT-3848
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Gat 3848
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@spco
spco authored Apr 23, 2024
2 parents 866da1c + 33cfa69 commit 3e128b1
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Showing 7 changed files with 128 additions and 106 deletions.
120 changes: 60 additions & 60 deletions docs/HDRUK/2.2.1.md
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44 changes: 21 additions & 23 deletions docs/HDRUK/2.2.1.structure.json
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Expand Up @@ -219,7 +219,7 @@
"examples": null,
"type": [
"EmailAddress[{'anyOf': [{'format': 'email', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.EmailAddress.EmailAddress]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -267,7 +267,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters]",
"null"
],
"is_list": false,
Expand All @@ -282,7 +282,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.ShortDescription.ShortDescription]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -385,7 +385,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"null"
],
"is_list": false,
Expand All @@ -402,7 +402,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Union[hdr_schemata.definitions.HDRUK.Url.Url, NoneType, hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters, hdr_schemata.definitions.HDRUK.IsPartOfEnum.IsPartOfEnum]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -434,7 +434,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -749,7 +749,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.DataUseLimitation.DataUseLimitation]",
"null"
],
"is_list": false,
Expand All @@ -764,7 +764,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.DataUseRequirements.DataUseRequirements]",
"null"
],
"is_list": false,
Expand All @@ -779,7 +779,7 @@
"examples": null,
"type": [
"ShortDescription[{'anyOf': [{'maxLength': 1000, 'minLength': 2, 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.ShortDescription.ShortDescription]]",
"null"
],
"is_list": false,
Expand All @@ -794,7 +794,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"null"
],
"is_list": false,
Expand All @@ -810,7 +810,7 @@
"type": [
"Doi[{'anyOf': [{'pattern': '^10.\\\\d{4,9}/[-._;()/:a-zA-Z0-9]+$', 'type': 'string'}, {'type': 'null'}]}]",
"str",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Doi.Doi]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -869,7 +869,7 @@
"examples": null,
"type": [
"LongDescription[{'anyOf': [{'maxLength': 50000, 'minLength': 2, 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -897,7 +897,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.Isocountrycode.Isocountrycode]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -969,7 +969,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.ControlledVocabulary.ControlledVocabulary]",
"null"
],
"is_list": false,
Expand All @@ -983,11 +983,9 @@
"description": "List any relevant terminologies / ontologies / controlled vocabularies, such as ICD 10 Codes, NHS Data Dictionary National Codes or SNOMED CT International, that are being used by the dataset. If the controlled vocabularies are local standards, please make that explicit. If you are using a standard that has not been included in the list, please use \u201cother\u201d and contact support desk to ask for an addition. Notes: More than one vocabulary may be provided.",
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"null"
"StandardisedDataModels[{'$defs': {'StandardisedDataModelsEnum': {'enum': ['HL7 FHIR', 'HL7 V2', 'HL7 CDA', 'HL7 CCOW', 'LOINC', 'DICOM', 'I2B2', 'IHE', 'OMOP', 'OPENEHR', 'SENTINEL', 'PCORNET', 'CDISC', 'NHS DATA DICTIONARY', 'NHS SCOTLAND DATA DICTIONARY', 'NHS WALES DATA DICTIONARY', 'LOCAL', 'OTHER'], 'title': 'StandardisedDataModelsEnum', 'type': 'string'}}, 'anyOf': [{'$ref': '#/$defs/StandardisedDataModelsEnum'}, {'type': 'null'}], 'default': null}]"
],
"is_list": false,
"is_list": true,
"is_optional": true,
"subItems": []
},
Expand All @@ -999,7 +997,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.Language.Language]",
"null"
],
"is_list": false,
Expand All @@ -1014,7 +1012,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[hdr_schemata.definitions.HDRUK.Format.Format]",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -1046,7 +1044,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Union[hdr_schemata.definitions.HDRUK.Url.Url, NoneType, hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters]]",
"null"
],
"is_list": false,
Expand All @@ -1061,7 +1059,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.AbstractText.AbstractText]]",
"null"
],
"is_list": false,
Expand All @@ -1076,7 +1074,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"List",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"null"
],
"is_list": false,
Expand Down
39 changes: 19 additions & 20 deletions hdr_schemata/definitions/HDRUK/StandardisedDataModelsEnum.py
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Expand Up @@ -3,24 +3,23 @@
from typing import List, Optional, Union
from pydantic import AnyUrl, BaseModel, EmailStr, Field, constr

class StandardisedDataModelsEnum(Enum):
HL7_FHIR = 'HL7 FHIR'
HL7_V2 = 'HL7 V2'
HL7_CDA = 'HL7 CDA'
HL7_CCOW = 'HL7 CCOW'
LOINC = 'LOINC'
DICOM = 'DICOM'
I2B2 = 'I2B2'
IHE = 'IHE'
OMOP = 'OMOP'
OPENEHR = 'OPENEHR'
SENTINEL = 'SENTINEL'
PCORNET = 'PCORNET'
CDISC = 'CDISC'
NHS_DATA_DICTIONARY = 'NHS DATA DICTIONARY'
NHS_SCOTLAND_DATA_DICTIONARY = 'NHS SCOTLAND DATA DICTIONARY'
NHS_WALES_DATA_DICTIONARY = 'NHS WALES DATA DICTIONARY'
LOCAL = 'LOCAL'
OTHER = 'OTHER'


class StandardisedDataModelsEnum(Enum):
HL7_FHIR = "HL7 FHIR"
HL7_V2 = "HL7 V2"
HL7_CDA = "HL7 CDA"
HL7_CCOW = "HL7 CCOW"
LOINC = "LOINC"
DICOM = "DICOM"
I2B2 = "I2B2"
IHE = "IHE"
OMOP = "OMOP"
OPENEHR = "OPENEHR"
SENTINEL = "SENTINEL"
PCORNET = "PCORNET"
CDISC = "CDISC"
NHS_DATA_DICTIONARY = "NHS DATA DICTIONARY"
NHS_SCOTLAND_DATA_DICTIONARY = "NHS SCOTLAND DATA DICTIONARY"
NHS_WALES_DATA_DICTIONARY = "NHS WALES DATA DICTIONARY"
LOCAL = "LOCAL"
OTHER = "OTHER"
3 changes: 0 additions & 3 deletions hdr_schemata/models/HDRUK/2.2.1/schema.json
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Expand Up @@ -929,9 +929,6 @@
},
"conformsTo": {
"anyOf": [
{
"$ref": "#/$defs/CommaSeparatedValues"
},
{
"items": {
"$ref": "#/$defs/StandardisedDataModels"
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1 change: 1 addition & 0 deletions hdr_schemata/models/HDRUK/v2_1_2/__init__.py
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Expand Up @@ -17,6 +17,7 @@
from .Observations import Observation
from .DataClass import DataClass
from .DataElement import DataElement
from .FormatAndStandards import FormatAndStandards

from .annotations import annotations as an

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10 changes: 10 additions & 0 deletions hdr_schemata/models/HDRUK/v2_2_1/Accessibility.py
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Expand Up @@ -2,7 +2,11 @@
from hdr_schemata.definitions.HDRUK import *

from hdr_schemata.models.HDRUK.v2_2_0 import Accessibility as BaseAccessibility

from typing import Optional

from .Access import Access
from .FormatAndStandards import FormatAndStandards

from .annotations import annotations

Expand All @@ -11,3 +15,9 @@

class Accessibility(BaseAccessibility):
access: Access = Field(..., description=an.description, title=an.title)

formatAndStandards: Optional[FormatAndStandards] = Field(
None,
title=an.formatAndStandards.title,
description=an.formatAndStandards.description,
)
17 changes: 17 additions & 0 deletions hdr_schemata/models/HDRUK/v2_2_1/FormatAndStandards.py
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@@ -0,0 +1,17 @@
from typing import Optional, List
from pydantic import Field
from hdr_schemata.definitions.HDRUK import *

from .annotations import annotations

an = annotations.accessibility.formatAndStandards

from hdr_schemata.models.HDRUK.v2_2_0 import (
FormatAndStandards as BaseFormatAndStandards,
)


class FormatAndStandards(BaseFormatAndStandards):
conformsTo: Optional[List[StandardisedDataModels]] = Field(
..., **an.vocabularyEncodingScheme.__dict__
)

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