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Update origin fields to be enum lists only #34

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merged 2 commits into from
Mar 25, 2024
Merged

Update origin fields to be enum lists only #34

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043185c
update origin fields to be enum only
BSnelling Mar 25, 2024
e8515b7
update markdown
BSnelling Mar 25, 2024
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138 changes: 69 additions & 69 deletions docs/HDRUK/2.2.1.md
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67 changes: 29 additions & 38 deletions docs/HDRUK/2.2.1.structure.json
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@
"examples": null,
"type": [
"EmailAddress[{'anyOf': [{'format': 'email', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.EmailAddress.EmailAddress]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -267,7 +267,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters]",
"List",
"null"
],
"is_list": false,
Expand All @@ -282,7 +282,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.ShortDescription.ShortDescription]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -385,7 +385,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"List",
"null"
],
"is_list": false,
Expand All @@ -402,7 +402,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Union[hdr_schemata.definitions.HDRUK.Url.Url, NoneType, hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters, hdr_schemata.definitions.HDRUK.IsPartOfEnum.IsPartOfEnum]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -434,7 +434,7 @@
],
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -601,13 +601,10 @@
"description": "Please indicate the purpose(s) that the dataset was collected.",
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Purpose.Purpose]",
"null"
"Purpose['STUDY','DISEASE REGISTRY','TRIAL','CARE','AUDIT','ADMINISTRATIVE','FINANCIAL','STATUTORY','OTHER',null]"
],
"is_list": false,
"is_optional": true,
"subItems": []
"is_list": true,
"is_optional": true
},
{
"name": "source",
Expand All @@ -616,13 +613,10 @@
"description": "Please indicate the source of the data extraction",
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Source.Source]",
"null"
"Source['EPR','ELECTRONIC SURVEY','LIMS','OTHER INFORMATION SYSTEM','PAPER BASED','FREETEXT NLP','MACHINE GENERATED','OTHER']"
],
"is_list": false,
"is_optional": true,
"subItems": []
"is_list": true,
"is_optional": true
},
{
"name": "collectionSituation",
Expand All @@ -631,13 +625,10 @@
"description": "Please indicate the setting(s) where data was collected. Multiple settings may be provided",
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Setting.Setting]",
"null"
"Setting['CLINIC','PRIMARY CARE','ACCIDENT AND EMERGENCY','OUTPATIENTS','IN-PATIENTS','SERVICES','COMMUNITY','HOME','PRIVATE','PHARMACY','SOCIAL CARE','LOCAL AUTHORITY','NATIONAL GOVERNMENT','OTHER']"
],
"is_list": false,
"is_optional": true,
"subItems": []
"is_list": true,
"is_optional": true
}
]
},
Expand Down Expand Up @@ -758,7 +749,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.DataUseLimitation.DataUseLimitation]",
"List",
"null"
],
"is_list": false,
Expand All @@ -773,7 +764,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.DataUseRequirements.DataUseRequirements]",
"List",
"null"
],
"is_list": false,
Expand All @@ -788,7 +779,7 @@
"examples": null,
"type": [
"ShortDescription[{'anyOf': [{'maxLength': 1000, 'minLength': 2, 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.ShortDescription.ShortDescription]]",
"List",
"null"
],
"is_list": false,
Expand All @@ -803,7 +794,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"List",
"null"
],
"is_list": false,
Expand All @@ -819,7 +810,7 @@
"type": [
"Doi[{'anyOf': [{'pattern': '^10.\\\\d{4,9}/[-._;()/:a-zA-Z0-9]+$', 'type': 'string'}, {'type': 'null'}]}]",
"str",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Doi.Doi]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -878,7 +869,7 @@
"examples": null,
"type": [
"LongDescription[{'anyOf': [{'maxLength': 50000, 'minLength': 2, 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -906,7 +897,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Isocountrycode.Isocountrycode]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -978,7 +969,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.ControlledVocabulary.ControlledVocabulary]",
"List",
"null"
],
"is_list": false,
Expand All @@ -993,7 +984,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.StandardisedDataModels.StandardisedDataModels]",
"List",
"null"
],
"is_list": false,
Expand All @@ -1008,7 +999,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Language.Language]",
"List",
"null"
],
"is_list": false,
Expand All @@ -1023,7 +1014,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[hdr_schemata.definitions.HDRUK.Format.Format]",
"List",
"null"
],
"is_list": false,
Expand Down Expand Up @@ -1055,7 +1046,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Union[hdr_schemata.definitions.HDRUK.Url.Url, NoneType, hdr_schemata.definitions.HDRUK.OneHundredFiftyCharacters.OneHundredFiftyCharacters]]",
"List",
"null"
],
"is_list": false,
Expand All @@ -1070,7 +1061,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.AbstractText.AbstractText]]",
"List",
"null"
],
"is_list": false,
Expand All @@ -1085,7 +1076,7 @@
"examples": null,
"type": [
"CommaSeparatedValues[{'anyOf': [{'pattern': '([^,]+)', 'type': 'string'}, {'type': 'null'}]}]",
"typing.List[typing.Optional[hdr_schemata.definitions.HDRUK.Url.Url]]",
"List",
"null"
],
"is_list": false,
Expand Down
9 changes: 0 additions & 9 deletions hdr_schemata/models/HDRUK/2.2.1/schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1455,9 +1455,6 @@
"properties": {
"purpose": {
"anyOf": [
{
"$ref": "#/$defs/CommaSeparatedValues"
},
{
"items": {
"$ref": "#/$defs/Purpose"
Expand All @@ -1474,9 +1471,6 @@
},
"source": {
"anyOf": [
{
"$ref": "#/$defs/CommaSeparatedValues"
},
{
"items": {
"$ref": "#/$defs/Source"
Expand All @@ -1493,9 +1487,6 @@
},
"collectionSituation": {
"anyOf": [
{
"$ref": "#/$defs/CommaSeparatedValues"
},
{
"items": {
"$ref": "#/$defs/Setting"
Expand Down
18 changes: 18 additions & 0 deletions hdr_schemata/models/HDRUK/v2_2_1/Origin.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
from typing import Optional, List, Union
from pydantic import BaseModel, Field
from hdr_schemata.definitions.HDRUK import *

from .annotations import annotations

an = annotations.provenance.origin


class Origin(BaseModel):
class Config:
extra = "forbid"

purpose: Optional[List[Purpose]] = Field(None, **an.purpose.__dict__)
source: Optional[List[Source]] = Field(None, **an.source.__dict__)
collectionSituation: Optional[
List[Setting]
] = Field(None, **an.collectionSituation.__dict__)
15 changes: 15 additions & 0 deletions hdr_schemata/models/HDRUK/v2_2_1/Provenance.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
from hdr_schemata.models.HDRUK.v2_2_0 import Provenance as BaseProvenance
from pydantic import Field
from typing import Optional
from .Origin import Origin

from .annotations import annotations

an = annotations.provenance


class Provenance(BaseProvenance):

origin: Optional[Origin] = Field(
None, description=an.origin.description, title=an.origin.title
)
7 changes: 7 additions & 0 deletions hdr_schemata/models/HDRUK/v2_2_1/__init__.py
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Expand Up @@ -5,6 +5,9 @@

from .EnrichmentAndLinkage import EnrichmentAndLinkage
from .Accessibility import Accessibility
from .Provenance import Provenance

from .annotations import annotations as an


class Hdruk221(Hdruk220):
Expand All @@ -21,6 +24,10 @@ class Hdruk221(Hdruk220):
title="Accessibility",
)

provenance: Optional[Provenance] = Field(
None, description=an.provenance.description, title=an.provenance.title
)

@classmethod
def save_schema(cls, location="./2.2.1/schema.json"):
with open(location, "w") as f:
Expand Down
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