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sierra-moxon committed Nov 18, 2024
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2 changes: 1 addition & 1 deletion .github/CODE_OF_CONDUCT.md
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We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
identity and expression, level of experience, education, socioeconomic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

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207 changes: 125 additions & 82 deletions docs/examples/MetamodelMapping.ipynb
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"cells": [
{
"cell_type": "markdown",
"id": "20a69830e031dd42",
"metadata": {
"collapsed": false,
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"source": [
"# LinkML Metamodel Mappings\n",
"\n",
"The primary use case of LinkML is to map *data* to *data*. However, because the LinkML metamodel is\n",
"expressed as a LinkML schema, it is possible to map to and from the metamodel itself.\n",
"\n",
"__NOTE__ this workflow is not yet fully matured, and is subject to change."
],
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"source": [
"## Creation of ad-hoc metamodel\n",
"\n",
"Let's assume that we have data represented using models conforming to an ad-hoc metamodel with core constructs: `Schema`, `Table`, and `Column`. We can create a LinkML schema that represents this metamodel as follows:"
],
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{
"name": "stdout",
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"\n",
"my_metamodel = sb.as_dict()\n",
"print(yaml.dump(sb.as_dict(), sort_keys=False))"
],
]
},
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"source": [
"## Example schema conforming to ad-hoc metamodel\n",
"\n",
"Now we'll make an example schema that conforms to this metamodel; this will be a fairly boring schema with a single table `Person` with three columns: `id`, `name`, and `description`:"
],
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"source": [
"my_schema = {\n",
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" },\n",
" ]\n",
"}"
],
]
},
{
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"source": [
"## Mapping to LinkML metamodel\n",
"\n",
"Now we'll create mappings from the ad-hoc metamodel to the LinkML metamodel, where **Table** maps to a LinkML **ClassDefinition**, **Column** maps to a LinkML **SlotDefinition*."
],
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"outputs": [],
"source": [
"metamap = {\n",
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" },\n",
" }\n",
"}"
],
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{
"cell_type": "code",
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"outputs": [],
"source": [
"from linkml_map.session import Session\n",
"\n",
"session = Session()"
],
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"source": [
"from linkml_map.session import Session\n",
"\n",
"session = Session()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"outputs": [],
"source": [
"session.set_source_schema(my_metamodel)\n",
"session.set_object_transformer(metamap)"
],
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"source": [
"session.set_source_schema(my_metamodel)\n",
"session.set_object_transformer(metamap)"
]
},
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"execution_count": 6,
"id": "5fcae9c463c7146b",
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{
"name": "stderr",
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},
{
"data": {
"text/plain": "{'name': 'my_schema',\n 'id': 'https://example.org/my_schema',\n 'classes': {'Person': {'attributes': {'id': {'identifier': True,\n 'range': 'integer'},\n 'name': {'identifier': None, 'range': 'string'},\n 'description': {'identifier': None, 'range': 'string'}}}}}"
"text/plain": [
"{'name': 'my_schema',\n",
" 'id': 'https://example.org/my_schema',\n",
" 'classes': {'Person': {'attributes': {'id': {'identifier': True,\n",
" 'range': 'integer'},\n",
" 'name': {'identifier': None, 'range': 'string'},\n",
" 'description': {'identifier': None, 'range': 'string'}}}}}"
]
},
"execution_count": 6,
"metadata": {},
Expand All @@ -318,18 +363,17 @@
],
"source": [
"session.transform(my_schema)"
],
]
},
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{
"cell_type": "markdown",
"source": [
"## Customizing the LinkML model\n",
"\n",
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"- every element MUST have a definition\n",
"\n",
"**TODO**"
],
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"metadata": {
"kernelspec": {
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"language": "python",
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"nbformat": 4,
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