Merge pull request #5 from HDRUK/add/GWDM/1.0

Add/gwdm/1.0

.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+name: Pytest
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9  
+
+    - name: Install schema module
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools
+        python -m pip install -e .
+
+    - name: Run pytest
+      run: |
+        cd hdr_schemata/tests/
+        pytest  

hdr_schemata/definitions/HDRUK/DatasetType.py

@@ -0,0 +1,9 @@
+from typing import Optional
+from pydantic import RootModel,constr
+
+#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)]
+
+

hdr_schemata/definitions/HDRUK/LongAbstractText.py

@@ -0,0 +1,7 @@
+from typing import Optional
+from pydantic import RootModel,constr
+
+class LongAbstractText(RootModel):
+    root: Optional[constr(min_length=5, max_length=5000)]
+
+

hdr_schemata/definitions/HDRUK/ShortTitle.py

@@ -0,0 +1,7 @@
+from typing import Optional
+from pydantic import RootModel,constr
+
+class ShortTitle(RootModel):
+    root: Optional[constr(min_length=2, max_length=100)]
+
+

hdr_schemata/definitions/HDRUK/TwoHundredFiftyFiveCharacters.py

@@ -0,0 +1,6 @@
+from pydantic import RootModel, constr
+
+class TwoHundredFiftyFiveCharacters(RootModel):
+    root: constr(min_length=2, max_length=255)
+
+

hdr_schemata/definitions/HDRUK/__init__.py

@@ -4,6 +4,7 @@
 from .ControlledVocabulary import ControlledVocabulary
 from .ControlledVocabularyEnum import ControlledVocabularyEnum
 from .DataUseLimitation import DataUseLimitation
+from .DatasetType import DatasetType
 from .DataUseRequirements import DataUseRequirements
 from .DeliveryLeadTime import DeliveryLeadTime
 from .Description import Description
@@ -16,6 +17,7 @@
 from .Isocountrycode import Isocountrycode
 from .Language import Language
 from .LanguageEnum import LanguageEnum
+from .LongAbstractText import LongAbstractText
 from .LongDescription import LongDescription
 from .MeasuredProperty import MeasuredProperty
 from .MemberOf import MemberOf
@@ -27,10 +29,12 @@
 from .Semver import Semver
 from .Setting import Setting
 from .ShortDescription import ShortDescription
+from .ShortTitle import ShortTitle
 from .Source import Source
 from .StandardisedDataModels import StandardisedDataModels
 from .StandardisedDataModelsEnum import StandardisedDataModelsEnum
 from .StatisticalPopulationConstrained import StatisticalPopulationConstrained
 from .TimeLag import TimeLag
+from .TwoHundredFiftyFiveCharacters import TwoHundredFiftyFiveCharacters
 from .Url import Url
 from .Uuidv4 import Uuidv4

hdr_schemata/examples/GWDM/1.0/example.json

@@ -0,0 +1,126 @@
+{
+    "required": {
+        "gatewayId": "1234",
+        "gatewayPid": "5124f2",
+        "issued": "2020-08-05T14:35:59Z",
+        "modified": "2021-01-28T14:15:46Z",
+        "revisions": [
+            {
+                "version": "1.0.0",
+                "url": "https://d5faf9c6-6c34-46d7-93c4-7706a5436ed9"
+            },
+            {
+                "version": "2.0.0",
+                "url": "https://a7ddefbd-31d9-4703-a738-256e4689f76a"
+            },
+            {
+                "version": "0.0.1",
+                "url": "https://9e798632-442a-427b-8d0e-456f754d28dc"
+            },
+            {
+                "version": "2.1.1",
+                "url": "https://a7ddefbd-31d9-4703-a738-256e4689f76a"
+            }
+        ]
+    },
+    "summary": {
+        "abstract": "Publications that mention HDR-UK (or any variant thereof) in Acknowledgements or Author Affiliations",
+        "contactPoint": "[email protected]",
+        "keywords": "Preprints,Papers,HDR UK",
+        "controlledKeywords": "Papers",
+        "datasetType": "list of papers",
+        "description": "Publications that mention HDR-UK (or any variant thereof) in Acknowledgements or Author Affiliations\n\nThis will include:\n- Papers\n- COVID-19 Papers\n- COVID-19 Preprint",
+        "doiName": "10.1093/ije/dyx196",
+        "shortTitle": "HDR UK Papers & Preprints",
+        "title": "Publications that mention HDR-UK (or any variant thereof) in Acknowledgements or Author Affiliations",
+        "publisher": {
+            "publisherName": "HEALTH DATA RESEARCH UK"
+        }
+    },
+    "coverage": {
+        "pathway": "NOT APPLICABLE",
+        "physicalSampleAvailability": "NOT AVAILABLE",
+        "spatial": "https://www.geonames.org/countries/GB/united-kingdom.html",
+        "followup": "UNKNOWN",
+        "typicalAgeRange": "0-0"
+    },
+    "provenance": {
+        "origin": {
+            "purpose": "OTHER",
+            "source": "MACHINE GENERATED",
+            "collectionSituation": "OTHER"
+        },
+        "temporal": {
+            "endDate": "2022-04-30",
+            "startDate": "2020-03-31",
+            "timeLag": "NOT APPLICABLE",
+            "accrualPeriodicity": "DAILY",
+            "distributionReleaseDate": "2020-11-27"
+        }
+    },
+    "accessibility": {
+        "access": {
+            "deliveryLeadTime": "OTHER",
+            "jurisdiction": "GB-ENG",
+            "dataController": "HDR UK",
+            "dataProcessor": "HDR UK",
+            "accessRights": "https://raw.githubusercontent.com/HDRUK/papers/master/LICENSE",
+            "accessService": "https://github.com/HDRUK/papers",
+            "accessRequestCost": "Free"
+        },
+        "usage": {
+            "dataUseLimitation": "GENERAL RESEARCH USE",
+            "dataUseRequirement": "RETURN TO DATABASE OR RESOURCE",
+            "resourceCreator": "HDR UK Science Team"
+        },
+        "formatAndStandards": {
+            "vocabularyEncodingSchemes": "OTHER",
+            "conformsTo": "OTHER",
+            "languages": "en",
+            "formats": "CSV,JSON"
+        }
+    },
+    "linkage": {
+        "isGeneratedUsing": "something",
+        "dataUses": "dunno",
+        "isReferenceIn": "10.5281/zenodo.326615",
+        "tools": "https://github.com/HDRUK/papers",
+        "datasetLinkage": {
+            "isDerivedFrom": "https://web.www.healthdatagateway.org/dataset/fd8d0743-344a-4758-bb97-f8ad84a37357",
+            "isPartOf": "NOT APPLICABLE",
+            "isMemberOf": "blah",
+            "linkedDatasets": "https://web.www.healthdatagateway.org/dataset/fd8d0743-344a-4758-bb97-f8ad84a37357"
+        },
+        "investigations": "https://github.com/HDRUK/papers"
+    },
+    "observations": [
+        {
+            "observedNode": "FINDINGS",
+            "measuredValue": 575,
+            "observationDate": "2020-11-27",
+            "measuredProperty": "Count",
+            "disambiguatingDescription": "Number of papers with affiliation and/or acknowledgement to HDR UK"
+        }
+    ],
+    "structuralMetadata": [
+        {
+            "name": "table1",
+            "description": "this is table 1",
+            "columns": [
+                {
+                    "name": "column1",
+                    "description": "this is column1",
+                    "dataType": "String",
+                    "sensitive": false,
+		    "values": [
+			{
+			    "name": "value",
+			    "description": "this is value1",
+			    "frequency":50
+			}
+		    ]
+                }
+            ]
+        }
+    ]
+}