Feature/cruk schemata v2

available.json

@@ -13,7 +13,11 @@
             "1.0",
             "1.1",
             "1.2",
-            "2.0"
+            "2.0",
+            "2.1"
+      ],
+      "CRUK": [
+            "1.0.0"
       ],
       "SchemaOrg": [
             "BioSchema",

examples

@@ -0,0 +1 @@
+hdr_schemata/examples

hdr_schemata/examples/CRUK/1.0.0/example.json

@@ -0,0 +1,109 @@
+{
+    "identifier": "a7ddefbd-31d9-4703-a738-256e4689f76a",
+    "version": "1.0.0",
+    "revisions": [
+        {
+            "version": "1.0.0",
+            "url": "https://example.org/datasets/a7ddefbd-31d9-4703-a738-256e4689f76a"
+        }
+    ],
+    "issued": "2020-08-05T14:35:59Z",
+    "modified": "2021-01-28T14:15:46Z",
+    "summary": {
+        "title": "CRUK DataHub Example Dataset",
+        "abstract": "Example CRUK dataset record extending HDRUK 4.0.0 with CRUK-specific fields.",
+        "dataCustodian": {
+            "identifier": "hdr-uk",
+            "name": "HEALTH DATA RESEARCH UK",
+            "contactPoint": "susheel.varma@hdruk.ac.uk"
+        },
+        "populationSize": 575,
+        "keywords": [
+            "Cancer",
+            "CRUK",
+            "Example"
+        ],
+        "doiName": "10.1093/ije/dyx196",
+        "contactPoint": "susheel.varma@hdruk.ac.uk"
+    },
+    "accessibility": {
+        "formatAndStandards": {
+            "language": [
+                "en"
+            ],
+            "vocabularyEncodingScheme": [
+                "OTHER"
+            ],
+            "format": [
+                "CSV",
+                "JSON"
+            ],
+            "conformsTo": [
+                "OTHER"
+            ]
+        },
+        "usage": {
+            "dataUseLimitation": [
+                "General research use"
+            ],
+            "resourceCreator": "HDR UK Science Team",
+            "dataUseRequirements": [
+                "Return to database or resource"
+            ]
+        },
+        "access": {
+            "dataController": "HDR UK",
+            "jurisdiction": [
+                "GB-ENG"
+            ],
+            "dataProcessor": "HDR UK",
+            "accessService": "https://github.com/HDRUK/papers",
+            "accessRights": "https://raw.githubusercontent.com/HDRUK/papers/master/LICENSE",
+            "accessRequestCost": "Free",
+            "deliveryLeadTime": "Other"
+        }
+    },
+    "observations": [
+        {
+            "observedNode": "Findings",
+            "measuredValue": 575,
+            "disambiguatingDescription": "Example observation count",
+            "observationDate": "2020-11-27",
+            "measuredProperty": "Count"
+        }
+    ],
+    "datasetFilters": [
+        {
+            "id": "1",
+            "label": "Breast",
+            "category": "Cancer",
+            "primaryGroup": "cancer-type",
+            "description": "Breast cancer"
+        }
+    ],
+    "icons": [
+        "icon-a",
+        "icon-b"
+    ],
+    "erd": null,
+    "projectGrants": [
+        {
+            "pid": "CRUK-PROJ-001",
+            "projectGrantName": "CRUK Example Grant Title",
+            "leadResearcher": "Dr Smith",
+            "leadResearchInstitute": "Sussex University",
+            "grantNumber": "ABC123",
+            "projectGrantStartDate": "2020-01-01",
+            "projectGrantEndDate": "2024-12-31",
+            "projectGrantScope": "Longitudinal genomic data including somatic mutations"
+        }
+    ],
+    "otherDataTypes": [
+        {
+            "title": "Mammograms",
+            "description": "2D images of both normal and malignant breasts",
+            "format": "image/jpeg"
+        }
+    ]
+}
+

hdr_schemata/models/CRUK/__init__.py

@@ -0,0 +1,2 @@
+from .v1_0_0 import Cruk100
+

hdr_schemata/models/CRUK/create_json_schema.py

@@ -0,0 +1,4 @@
+import v1_0_0
+
+v1_0_0.Cruk100.save_schema()
+

hdr_schemata/models/CRUK/v1_0_0/__init__.py

@@ -0,0 +1,180 @@
+import json
+from typing import List, Literal, Optional
+
+from pydantic import BaseModel, Field, constr
+
+from hdr_schemata.definitions.HDRUK import (
+    Format,
+    OneHundredFiftyCharacters,
+    ShortDescription,
+    Url,
+)
+from hdr_schemata.models.HDRUK.v4_0_0 import Hdruk400
+
+
+class DatasetFilter(BaseModel):
+    class Config:
+        extra = "forbid"
+
+    id: constr(pattern=r"(\d+_){0,5}\d+") = Field(..., title="Id")
+    label: constr(min_length=0, max_length=150) = Field(..., title="Label")
+    category: constr(min_length=0, max_length=150) = Field(..., title="Category")
+    primaryGroup: Literal["cancer-type", "data-type", "access-type"] = Field(
+        ..., title="Primary group"
+    )
+    description: constr(min_length=0, max_length=150) = Field(..., title="Description")
+
+
+class DataTable(BaseModel):
+    class Config:
+        extra = "forbid"
+
+    size: Optional[int] = Field(
+        None,
+        title="Table size",
+        description="Number of Complete Entries.",
+        json_schema_extra={
+            "guidance": (
+                "Provides a measure of the completeness of the data set. A row which includes n/a against "
+                "columns that are not relevant or not applicable should still be counted as complete."
+            )
+        },
+    )
+
+
+class OtherDataType(BaseModel):
+    class Config:
+        extra = "forbid"
+
+    title: OneHundredFiftyCharacters = Field(
+        ...,
+        title="Title",
+        json_schema_extra={"guidance": "Short descriptive titles"},
+        examples=["Mammograms", "Patient recordings"],
+    )
+    description: ShortDescription = Field(
+        ...,
+        title="Data description",
+        json_schema_extra={"guidance": "A description of the data type."},
+        examples=[
+            "2D images of both normal and malignant breasts",
+            "audio-tapes of oncology consultations",
+        ],
+    )
+    format: Format = Field(
+        ...,
+        title="Format",
+        description="Format drawn from https://www.iana.org/assignments/media-types/media-types.xhtml.",
+        json_schema_extra={
+            "guidance": (
+                "https://www.iana.org/assignments/media-types/media-types.xhtml lists the commonly used "
+                "formats for different media (such as video/image/audio) etc. If your format is not "
+                "included in the list set out there, please indicate other and specify in the description."
+            )
+        },
+    )
+
+
+class ProjectGrant(BaseModel):
+    pid: Optional[OneHundredFiftyCharacters] = Field(
+        None,
+        title="Persistent identifier of the study",
+    )
+    projectGrantName: OneHundredFiftyCharacters = Field(
+        ...,
+        title="Project Grant Title",
+        description=(
+            "The Project Grant Title should be unique to the CRUK datahub. "
+            "(Add your institute or name if necessary to disambiguate."
+        ),
+    )
+    leadResearcher: OneHundredFiftyCharacters = Field(
+        ...,
+        title="Lead Researcher",
+        examples=["Dr Smith"],
+    )
+    leadResearchInstitute: OneHundredFiftyCharacters = Field(
+        ...,
+        title="Lead Research Institute",
+        examples=["Sussex University"],
+    )
+    grantNumber: str = Field(
+        ...,
+        title="Grant number(s)",
+        description="List of CRUK and any other grant numbers.",
+        examples=["ABC123"],
+        json_schema_extra={"guidance": "Normally specified on the grant acceptance letter"},
+    )
+    projectGrantStartDate: str = Field(
+        ...,
+        title="Project Start Date",
+        description="Starting date of projectGrant grant.",
+        json_schema_extra={
+            "guidance": (
+                "Date on which the dataset projectGrant starts. This is normally set out in the grant "
+                "contract and will be different from the start of any data collection"
+            )
+        },
+    )
+    projectGrantEndDate: Optional[str] = Field(
+        ...,
+        title="Project End Date",
+        description="Current end date of project grant.",
+        json_schema_extra={
+            "guidance": (
+                "Date on which the dataset project is currently projected to finish. This is normally set "
+                "out in the grant contract and will be different from the end of any data collection"
+            )
+        },
+    )
+    projectGrantScope: Optional[constr(min_length=5, max_length=500)] = Field(
+        None,
+        title="Project Scope",
+        description="data and biospecimens expected to result from the grant.",
+        examples=["Longitudinal genomic data including somatic mutations"],
+        json_schema_extra={
+            "guidance": (
+                "Short paragraph setting out the types of data / biospecimens likely to result from the "
+                "grant and the cancers covered"
+            )
+        },
+    )
+
+
+class Cruk100(Hdruk400):
+    class Config:
+        extra = "forbid"
+
+    datasetFilters: Optional[List[DatasetFilter]] = Field(
+        None,
+        title="Dataset Filters",
+    )
+    icons: Optional[List[str]] = Field(
+        None,
+        title="Icons",
+        description="Calculated categorization icons added during export.",
+    )
+    erd: Optional[Url] = Field(
+        None,
+        title="Entity Relationship Diagram",
+        description="Visual representation of data table relationships.",
+        json_schema_extra={
+            "guidance": (
+                "Please upload an image file (max 5MB) showing the relationship between the different tables"
+            )
+        },
+    )
+    projectGrants: Optional[List[ProjectGrant]] = Field(
+        None,
+        title="Associated Project Grants",
+    )
+    otherDataTypes: Optional[List[OtherDataType]] = Field(
+        None,
+        title="Other data types",
+    )
+
+    @classmethod
+    def save_schema(cls, location: str = "./1.0.0/schema.json") -> None:
+        with open(location, "w") as f:
+            json.dump(cls.model_json_schema(), f, indent=6)
+