add a script to create an example and add enums for collection type

hdr_schemata/definitions/HDRUK/TissueCollectionTypeEnum.py

@@ -0,0 +1,14 @@
+from enum import Enum
+
+
+class TissueCollectionTypeEnum(Enum):
+    CASE_CONTROL = "Case-control"
+    COHORT = "Cohort"
+    CROSS_SECTIONAL = "Cross-sectional"
+    LONGITUDINAL = "Longitudinal"
+    TWIN_STUDY = "Twin-study"
+    QUALITY_CONTROL = "Quality control"
+    POPULATION_BASED = "Population-based"
+    DISEASE_SPECIFIC = "Disease specific"
+    BIRTH_COHORT = "Birth cohort"
+    OTHER = "Other"

hdr_schemata/models/HDRUK/v2_2_0/TissuesSampleCollection.py

@@ -3,6 +3,7 @@
 from .TissueSampleMetadata import TissueSampleMetadata
 from hdr_schemata.definitions.HDRUK import (
     TissueDataCategoriesEnum,
+    TissueCollectionTypeEnum,
     MaterialTypeCategories,
 )
 
@@ -11,17 +12,23 @@ class TissuesSampleCollection(BaseModel):
     dataCategories: Optional[List[TissueDataCategoriesEnum]] = Field(
         None,
         title="Data Categories",
-        description="Data categories related to the tissue sample collection",
+        description="The type of data that is associated with the samples in the study. Can be several values MIABIS-2.0-13",
     )
 
     materialType: Optional[List[MaterialTypeCategories]] = Field(
         None,
         title="Material Type",
-        description="Material type of the tissue sample collection",
+        description="The biospecimen saved from a biological entity for propagation e.g. testing, diagnostics, treatment or research purposes. Can be several values MIABIS-2.0-14",
     )
 
     tissueSampleMetadata: Optional[TissueSampleMetadata] = Field(
         None,
         title="Tissue Sample Metadata",
         description="Metadata related to the tissue sample",
     )
+
+    collectionType: Optional[TissueCollectionTypeEnum] = Field(
+        None,
+        title="Collection Type",
+        description="The type of the sample collection. Can be several values [MIABIS-2.0-16](https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#collection-type)",
+    )

hdr_schemata/utils/create_example.py

@@ -0,0 +1,19 @@
+import json
+
+data = json.load(open("temp.json"))
+
+
+def get_subItems(item):
+    return (
+        {subItem["name"]: get_subItems(subItem) for subItem in item["subItems"]}
+        if item.get("subItems")
+        else " | ".join(item["type"])
+    )
+
+
+example = {item["name"]: get_subItems(item) for item in data}
+print(json.dumps(example, indent=6))
+with open("temp2.json", "w") as f:
+    json.dump(example, f, indent=6)
+
+# print(json.dumps(data, indent=6))