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Add missing parameter inside _register_one. Add notebook example of s…
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…chema handling
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@crisely09
crisely09 committed Jun 28, 2024
1 parent 412af63 commit 3d275f5
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254 changes: 254 additions & 0 deletions examples/notebooks/use-cases/BBP KG Creating and Modifying Schemas.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "b14744df-3567-40f3-bb0c-06c6767ab695",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import json\n",
"import uuid\n",
"\n",
"from kgforge.core import KnowledgeGraphForge\n",
"from kgforge.specializations.resources import Dataset"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "72596414-c9ac-4312-a621-5bd4fdc3477b",
"metadata": {},
"outputs": [],
"source": [
"import getpass\n",
"TOKEN = getpass.getpass()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "c124caae-b9ae-4eb4-8d8e-bc437d28d3e6",
"metadata": {},
"outputs": [],
"source": [
"BUCKET = \"dke/kgforge\"\n",
"\n",
"forge = KnowledgeGraphForge(\"../use-cases/prod-forge-nexus.yml\",\n",
" bucket=BUCKET,\n",
" token=TOKEN\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "29bceff6-d7b4-4fda-9cc3-fe1923c0f865",
"metadata": {},
"outputs": [],
"source": [
"def make_id(i):\n",
" return f\"{forge._store.endpoint}/schemas/{forge._store.bucket}/dummy_schema_{i}\"\n",
"\n",
"def create_schema(i):\n",
" payload = {\n",
" \"context\": \"https://incf.github.io/neuroshapes/contexts/schema.json\",\n",
" \"id\": make_id(i),\n",
" \"type\": \"Schema\",\n",
" \"imports\": [\n",
" \"https://neuroshapes.org/commons/entity\"\n",
" ],\n",
" \"shapes\": [\n",
" {\n",
" \"@id\": f\"{make_id(i)}/shapes/DummyShape\",\n",
" \"@type\": \"NodeShape\",\n",
" \"node\": \"https://neuroshapes.org/commons/entity/shapes/EntityShape\",\n",
" }\n",
" ]\n",
" }\n",
" resource = forge.from_json(payload)\n",
" forge.register(resource, schema_id=forge._store.service.SHACL_SCHEMA)\n",
" return resource"
]
},
{
"cell_type": "markdown",
"id": "e79f1807-dbfa-4cca-ab08-4809c9962517",
"metadata": {},
"source": [
"## 1. Create dummy schemas"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "9a022c3d",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<action> _register_one\n",
"<succeeded> True\n",
"<action> _register_one\n",
"<succeeded> True\n",
"<action> _register_one\n",
"<succeeded> True\n"
]
}
],
"source": [
"dummies = [create_schema(uuid.uuid4()) for j in range(3)]"
]
},
{
"cell_type": "markdown",
"id": "d10b21d5-212b-48cc-b4a2-7ef2f739b2ed",
"metadata": {},
"source": [
"## 2. Retrieve the reciently created schemas using the ids and tag them"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "515b3e19",
"metadata": {},
"outputs": [],
"source": [
"retrieved = [forge.retrieve(dummy.id) for dummy in dummies]"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "2c5594ee",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" context: https://incf.github.io/neuroshapes/contexts/schema.json\n",
" id: https://bbp.epfl.ch/nexus/v1/schemas/dke/kgforge/dummy_schema_7fab9433-af89-43eb-878a-607389240256\n",
" type: Schema\n",
" imports:\n",
" [\n",
" https://neuroshapes.org/commons/entity\n",
" ]\n",
" shapes:\n",
" [\n",
" {\n",
" id: https://bbp.epfl.ch/nexus/v1/schemas/dke/kgforge/dummy_schema_7fab9433-af89-43eb-878a-607389240256/shapes/DummyShape\n",
" type: NodeShape\n",
" node: https://neuroshapes.org/commons/entity/shapes/EntityShape\n",
" }\n",
" ]\n",
"}\n"
]
}
],
"source": [
"print(retrieved[0])"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "efb9cb41",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"https://bluebrain.github.io/nexus/schemas/shacl-20170720.ttl\n"
]
}
],
"source": [
"print(retrieved[0]._store_metadata['_constrainedBy'])"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "a4f95633",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<action> _tag_one\n",
"<succeeded> True\n",
"<action> _tag_one\n",
"<succeeded> True\n",
"<action> _tag_one\n",
"<succeeded> True\n"
]
}
],
"source": [
"for r in retrieved:\n",
" forge.tag(r, 't01')"
]
},
{
"cell_type": "markdown",
"id": "551f3fdc-4760-4c6b-861b-6ac085f27e00",
"metadata": {},
"source": [
"## 3. Deprecate the schemas"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "e6859730",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<action> _deprecate_one\n",
"<succeeded> True\n",
"<action> _deprecate_one\n",
"<succeeded> True\n",
"<action> _deprecate_one\n",
"<succeeded> True\n"
]
}
],
"source": [
"for r in retrieved:\n",
" forge.deprecate(r)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "dev-forge",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.18"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
3 changes: 1 addition & 2 deletions kgforge/specializations/stores/bluebrain_nexus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,9 +164,8 @@ def register_callback(task: Task):

def _register_one(self, resource: Resource, schema_id: str) -> None:
method, url, resource, exception_, headers, params, payload = (
prepare_methods.prepare_create(service=self.service, resource=resource)
prepare_methods.prepare_create(service=self.service, resource=resource, schema_id=schema_id)
)

response = requests.request(
method=method,
url=url,
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