partway save progress

hdr_schemata/definitions/HDRUK/DatasetType.py

@@ -1,9 +1,92 @@
 from typing import Optional
 from pydantic import RootModel,constr
+from enum import Enum
 
 #note: contructed as a string of max_length=100
 #      in the future we may want to limit this with Enums
 class DatasetType(RootModel):
     root: Optional[constr(min_length=2, max_length=100)]
 
+class DatasetTypeV2(Enum):
+    HEALTH_AND_DISEASE = 'Health and disease'
+    TREATMENTS_INTERVENTIONS = 'Treatments/Interventions'
+    MEASUREMENTS_TESTS = 'Measurements/Tests'
+    IMAGING_TYPES = 'Imaging types'
+    IMAGING_AREA_OF_THE_BODY = 'Imaging area of the body'
+    OMICS = 'Omics'
+    SOCIOECONOMIC = 'Socioeconomic'
+    LIFESTYLE = 'Lifestyle'
+    REGISTRY = 'Registry'
+    ENVIRONMENT_AND_ENERGY = 'Environment and energy'
+    INFORMATION_AND_COMMUNICATION = 'Information and communication'
+    POLITICS = 'Politics'
 
+class DatasetSubType(Enum):
+    MENTAL_HEALTH = 'Mental health'
+    CARDIOVASCULAR = 'Cardiovascular'
+    CANCER = 'Cancer'
+    RARE_DISEASES = 'Rare diseases'
+    METABOLIC_AND_ENDOCRINE = 'Metabolic and Endocrine'
+    NEUROLOGICAL = 'Neurological'
+    REPRODUCTIVE = 'Reproductive'
+    MATERNITY_AND_NEONATOLOGY = 'Maternity and neonatology'
+    RESPIRATORY = 'Respiratory'
+    IMMUNITY = 'Immunity'
+    MUSCULOSKELETAL = 'Musculoskeletal'
+    VISION = 'Vision'
+    RENAL_AND_UROGENITAL = 'Renal and urogenital'
+    ORAL_AND_GASTROINTESTINAL = 'Oral and Gastrointestinal'
+    COGNITIVE_FUNCTION = 'Cognitive Function'
+    HEARING = 'Hearing'
+    OTHERS = 'Others'
+    VACCINES = 'Vaccines'
+    PREVENTIVE = 'Preventive'
+    THERAPEUTIC = 'Therapeutic'
+    # OTHERS = 'Others'
+    LABORATORY = 'Laboratory'
+    OTHER_DIAGNOSTICS = 'Other diagnostics'
+    CT = 'CT'
+    MRI = 'MRI'
+    PET = 'PET'
+    X_RAY = 'X-ray'
+    ULTRASOUND = 'Ultrasound'
+    PATHOLOGY = 'Pathology'
+    # OTHERS = 'Others'
+    HEAD = 'Head'
+    CHEST = 'Chest'
+    ARM = 'Arm'
+    ABDOMEN = 'Abdomen'
+    LEG = 'Leg'
+    # OTHERS = 'Others'
+    PROTEOMICS = 'Proteomics'
+    TRANSCRIPTOMICS = 'Transcriptomics'
+    EPIGENOMICS = 'Epigenomics'
+    METABOLOMICS = 'Metabolomics'
+    MULTIOMICS = 'Multiomics'
+    METAGENOMICS = 'Metagenomics'
+    GENOMICS = 'Genomics'
+    # OTHERS = 'Others'
+    EDUCATION = 'Education'
+    CRIME_AND_JUSTICE = 'Crime and Justice'
+    ETHNICITY = 'Ethnicity'
+    HOUSING_ = 'Housing '
+    LABOUR = 'Labour'
+    AGEING_ = 'Ageing '
+    ECONOMICS = 'Economics'
+    MARITAL_STATUS = 'Marital status'
+    SOCIAL_SUPPORT = 'Social support'
+    DEPRIVATION = 'Deprivation'
+    RELIGION = 'Religion'
+    OCCUPATION = 'Occupation'
+    FINANCES = 'Finances'
+    FAMILY_CIRCUMSTANCE = 'Family circumstance'
+    # OTHERS = 'Others'
+    SMOKING = 'Smoking'
+    PHYSICAL_ACTIVITY = 'Physical Activity'
+    DIETARY_HABITS = 'Dietary habits'
+    ALCOHOL = 'Alcohol'
+    # OTHERS = 'Others'
+    DISEASE_REGISTRY_RESEARCH = 'Disease Registry (research)'
+    NATIONAL_DISEASE_REGISTRIES_AND_AUDITS = 'National Disease Registries and Audits'
+    BIRTHS_AND_DEATHS = 'Births and Deaths'
+    # OTHERS = 'Others'

hdr_schemata/definitions/HDRUK/Periodicity.py

@@ -20,4 +20,19 @@ class Periodicity(Enum):
     OTHER = 'OTHER'
     NoneType_None = None
 
-
+class PeriodicityV2(Enum):
+    STATIC = 'Static'
+    IRREGULAR = 'Irregular'
+    CONTINUOUS = 'Continuous'
+    BIENNIAL = 'Biennial'
+    ANNUAL = 'Annual'
+    BIANNUAL = 'Biannual'
+    QUARTERLY = 'Quarterly'
+    BIMONTHLY = 'Bimonthly'
+    MONTHLY = 'Monthly'
+    BIWEEKLY = 'Biweekly'
+    WEEKLY = 'Weekly'
+    TWICE_A_WEEK = 'Twice a week'
+    DAILY = 'Daily'
+    OTHER = 'Other'
+    NoneType_None = None

hdr_schemata/definitions/HDRUK/Purpose.py

@@ -15,4 +15,15 @@ class Purpose(Enum):
     OTHER = 'OTHER'
     NoneType_None = None
 
-
+class PurposeV2(Enum):
+    RESEARCH_COHORT = 'Research cohort'
+    STUDY = 'Study'
+    DISEASE_REGISTRY = 'Disease registry'
+    TRIAL = 'Trial'
+    CARE = 'Care'
+    AUDIT = 'Audit'
+    ADMINISTRATIVE = 'Administrative'
+    FINANCIAL = 'Financial'
+    STATUATORY = 'Statuatory'
+    OTHER = 'Other'
+    NoneType_None = None

hdr_schemata/definitions/HDRUK/Setting.py

@@ -17,3 +17,29 @@ class Setting(Enum):
     OTHER = 'OTHER'
 
 
+class SettingV2(Enum):
+    COHORT_STUDY_TRIAL = 'Cohort, study, trial'
+    CLINIC = 'Clinic'
+    PRIMARY_CARE_REFERRALS = 'Primary care - Referrals'
+    PRIMARY_CARE_CLINIC = 'Primary care - Clinic'
+    PRIMARY_CARE_OUT_OF_HOURS = 'Primary care - Out of hours'
+    SECONDARY_CARE_ACCIDENT_AND_EMERGENCY = 'Secondary care - Accident and Emergency'
+    SECONDARY_CARE_OUTPATIENTS = 'Secondary care - Outpatients'
+    SECONDARY_CARE_INPATIENTS = 'Secondary care - In-patients'
+    SECONDARY_CARE_AMBULANCE = 'Secondary care - Ambulance'
+    SECONDARY_CARE_ICU = 'Secondary care - ICU'
+    PRESCRIBING_COMMUNITY_PHARMACY = 'Prescribing - Community pharmacy'
+    PRESCRIBING_HOSPITAL = 'Prescribing - Hospital'
+    PATIENT_REPORT_OUTCOME = 'Patient report outcome'
+    WEARABLES = 'Wearables'
+    LOCAL_AUTHORITY = 'Local authority'
+    NATIONAL_GOVERNMENT = 'National government'
+    COMMUNITY = 'Community'
+    SERVICES = 'Services'
+    HOME = 'Home'
+    PRIVATE = 'Private'
+    SOCIAL_CARE_HEALTH_CARE_AT_HOME = 'Social care - Health care at home'
+    SOCIAL_CARE_OTHER_SOCIAL_DATA = 'Social care - Other social data'
+    CENSUS = 'Census'
+    OTHER = 'Other'
+    NoneType_None = None

hdr_schemata/definitions/HDRUK/Source.py

@@ -10,4 +10,11 @@ class Source(Enum):
     MACHINE_GENERATED = 'MACHINE GENERATED'
     OTHER = 'OTHER'
 
-
+class SourceV2(Enum):
+    EPR = 'EPR'
+    ELECTRONIC_SURVEY = 'Electronic survey'
+    LIMS = 'LIMS'
+    PAPER_BASED = 'Paper-based'
+    FREE_TEXT_NLP = 'Free text NLP'
+    MACHINE_GENERATED = 'Machine generated'
+    OTHER = 'Other'

hdr_schemata/definitions/HDRUK/Ternary.py

@@ -0,0 +1,6 @@
+from enum import Enum
+
+class Ternary(Enum):
+    YES = 'Yes'
+    NO = 'No'
+    NOT_STATED = 'Not stated'

hdr_schemata/definitions/HDRUK/TimeLag.py

@@ -13,4 +13,14 @@ class TimeLag(Enum):
     OTHER = 'OTHER'
     NoneType_None = None
 
+class TimeLagV2(Enum):
+    LESS_THAN_1_WEEK = 'Less than 1 week'
+    ONE_TWO_WEEKS = '1-2 weeks'
+    TWO_FOUR_WEEKS = '2-4 weeks'
+    ONE_TWO_MONTHS = '1-2 months'
+    TWO_SIX_MONTHS = '2-6 months'
+    SIX_MONTHS_PLUS = '6 months plus'
+    VARIABLE = 'Variable'
+    NOT_APPLICABLE = 'Not applicable'
+    OTHER = 'Other'
 

hdr_schemata/definitions/HDRUK/__init__.py

@@ -6,7 +6,7 @@
 from .ControlledVocabulary import ControlledVocabulary
 from .ControlledVocabularyEnum import ControlledVocabularyEnum
 from .DataUseLimitation import DataUseLimitation
-from .DatasetType import DatasetType
+from .DatasetType import DatasetType, DatasetTypeV2, DatasetSubType
 from .DataUseRequirements import DataUseRequirements
 from .DeliveryLeadTime import DeliveryLeadTime
 from .Description import Description
@@ -27,18 +27,19 @@
 from .MemberOf import MemberOf
 from .Name import Name
 from .OneHundredFiftyCharacters import OneHundredFiftyCharacters
-from .Periodicity import Periodicity
+from .Periodicity import Periodicity, PeriodicityV2
 from .PhysicalSampleAvailability import PhysicalSampleAvailability
-from .Purpose import Purpose
+from .Purpose import Purpose, PurposeV2
 from .Semver import Semver
-from .Setting import Setting
+from .Setting import Setting, SettingV2
 from .ShortDescription import ShortDescription
 from .ShortTitle import ShortTitle
-from .Source import Source
+from .Source import Source, SourceV2
 from .StandardisedDataModels import StandardisedDataModels
 from .StandardisedDataModelsEnum import StandardisedDataModelsEnum
 from .StatisticalPopulationConstrained import StatisticalPopulationConstrained
-from .TimeLag import TimeLag
+from .Ternary import Ternary
+from .TimeLag import TimeLag, TimeLagV2
 from .TissueCollectionTypeEnum import TissueCollectionTypeEnum
 from .TissueDataCategoriesEnum import TissueDataCategoriesEnum
 from .TwoHundredFiftyFiveCharacters import TwoHundredFiftyFiveCharacters

hdr_schemata/models/HDRUK/2.2.1/schema.json

@@ -1473,7 +1473,7 @@
                               ],
                               "default": null,
                               "description": "Please indicate the purpose(s) that the dataset was collected.",
-                              "title": "Purpose"
+                              "title": "Purpose of dataset collection"
                         },
                         "source": {
                               "anyOf": [
@@ -1489,7 +1489,7 @@
                               ],
                               "default": null,
                               "description": "Please indicate the source of the data extraction",
-                              "title": "Source"
+                              "title": "Source of data extraction"
                         },
                         "collectionSituation": {
                               "anyOf": [