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362 changes: 181 additions & 181 deletions docs/developers/operations.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "edcc1fd6-2474-4d15-8355-084ef85bc748",
"metadata": {},
"source": [
"# Operations development"
]
},
{
"cell_type": "markdown",
"id": "e191786a-786a-418e-886a-a4da0c2d741e",
"metadata": {},
"source": [
"SimPhoNy operations are actions (written in Python) that can be executed on\n",
"demand on any ontology individual belonging to the ontology class they\n",
"are defined for."
]
},
{
"cell_type": "markdown",
"id": "7ea449f9-bc08-4ddc-a8a8-13c6d3ade2ef",
"metadata": {},
"source": [
"<div class=\"admonition important\">\n",
"<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Tip</div></div>\n",
" \n",
"File uploads and downloads in SimPhoNy are an example of SimPhoNy operations.\n",
"Head to the [assertional knowledge](../usage/assertional_knowledge.html#Operations) section to see them in action.\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "ee275d73-f2ef-4418-bc94-cec8458c803c",
"metadata": {},
"source": [
"\n",
"SimPhoNy operations are distributed as (or as part of) Python packages. \n",
"Developing operations for an ontology class is fairly simple. To do so, import the [Operations abstract class](../api_reference.md#simphony_osp.development.Operations) from the `simphony_osp.development` module, and create an implementation by subclassing it.\n",
"\n",
"Then, define an `iri` attribute having as value the IRI of the ontology class that the\n",
"operation should be associated to. Every public method ([not starting with\n",
"an underscore](https://peps.python.org/pep-0008/#method-names-and-instance-variables)) defined on the implementation is automatically detected and\n",
"assigned as an operation to said ontology class. The\n",
"[ontology individual object](../usage/assertional_knowledge.ipynb#Ontology-individual-objects)\n",
"on which the operation is called is available as the private attribute\n",
"`_individual` on every instance of the implementation. For a specific \n",
"ontology individual, the implementation gets instantiated the first time that \n",
"any operation defined on it is called by the user.\n",
"\n",
"Finally, define an\n",
"[entry point](https://packaging.python.org/en/latest/specifications/entry-points/#entry-points-specification)\n",
"(or many if implementing operations for several ontology classes) under the\n",
"`simphony_osp.ontology.operations`\n",
"[group](https://packaging.python.org/en/latest/specifications/entry-points/#data-model)\n",
"that points to your\n",
"implementation of the `Operations` abstract class.\n",
"\n",
"An example implementation of an operation that takes advantage of\n",
"[geopy](https://pypi.org/project/geopy/) to compute the distance between \n",
"two points on Earth defined using the \n",
"[WGS84 Geo Positioning vocabulary](https://www.w3.org/2003/01/geo/wgs84_pos)\n",
"is shown below."
]
},
{
"cell_type": "markdown",
"id": "0fffa052-186a-46b7-9076-8acfed6b1ee0",
"metadata": {},
"source": [
"```python\n",
"\"\"\"Operations for classes from the WGS84 Geo Positioning vocabulary.\"\"\"\n",
"\n",
"from geopy import distance\n",
"from simphony_osp.namespaces import wgs84_pos\n",
"from simphony_osp.ontology import OntologyIndividual\n",
"from simphony_osp.ontology.operations import Operations\n",
"\n",
"\n",
"class Wgs84Pos(Operations):\n",
" \"\"\"Operations for the Point ontology class.\"\"\"\n",
"\n",
" iri = wgs84_pos.Point.iri\n",
"\n",
" def distance(self, other: OntologyIndividual) -> float:\n",
" \"\"\"Compute the distance between two points on Earth.\n",
" \n",
" Args:\n",
" other: Another point with respect to which the distance will be computed. \n",
" \n",
" Returns:\n",
" The distance between this point and the given one in km.\n",
" \"\"\"\n",
" lat_self = float(self._individual[wgs84_pos.latitude].one())\n",
" long_self = float(self._individual[wgs84_pos.longitude].one())\n",
" lat_other = float(other[wgs84_pos.latitude].one())\n",
" long_other = float(other[wgs84_pos.longitude].one())\n",
" return distance.geodesic(\n",
" (lat_self, long_self),\n",
" (lat_other, long_other),\n",
" ellipsoid=\"WGS-84\"\n",
" ).km\n",
"\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "744e037f-aabe-4bdf-a994-8787f3f039b1",
"metadata": {},
"source": [
"<div class=\"admonition note\">\n",
"<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Note</div></div>\n",
" \n",
"Remember that the implementation above is still not enough for the operation to\n",
"work: the corresponding \n",
"[entry point](https://packaging.python.org/en/latest/specifications/entry-points/#entry-points-specification)\n",
"for `Wgs84Pos` must have been defined and the `wgs84_pos` vocabulary needs to be installed using [pico](../usage/ontologies/pico.html).\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "d3db93d6-e26f-4831-b9a2-d9223cc4a51f",
"metadata": {},
"source": [
"The operation can be used as follows."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "40a97048-80ea-4d99-8711-3ecd6ab5598b",
"metadata": {},
"outputs": [
"cells": [
{
"cell_type": "markdown",
"id": "edcc1fd6-2474-4d15-8355-084ef85bc748",
"metadata": {},
"source": [
"# Operations development"
]
},
{
"cell_type": "markdown",
"id": "e191786a-786a-418e-886a-a4da0c2d741e",
"metadata": {},
"source": [
"SimPhoNy operations are actions (written in Python) that can be executed on\n",
"demand on any ontology individual belonging to the ontology class they\n",
"are defined for."
]
},
{
"data": {
"text/plain": [
"417.4695920611045"
"cell_type": "markdown",
"id": "7ea449f9-bc08-4ddc-a8a8-13c6d3ade2ef",
"metadata": {},
"source": [
"<div class=\"admonition important\">\n",
"<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Tip</div></div>\n",
" \n",
"File uploads and downloads in SimPhoNy are an example of SimPhoNy operations.\n",
"Head to the [assertional knowledge](../usage/assertional_knowledge.html#Operations) section to see them in action.\n",
" \n",
"</div>"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
},
{
"cell_type": "markdown",
"id": "ee275d73-f2ef-4418-bc94-cec8458c803c",
"metadata": {},
"source": [
"\n",
"SimPhoNy operations are distributed as (or as part of) Python packages. \n",
"Developing operations for an ontology class is fairly simple. To do so, import the [Operations abstract class](../api_reference.md#simphony_osp.development.Operations) from the `simphony_osp.development` module, and create an implementation by subclassing it.\n",
"\n",
"Then, define an `iri` attribute having as value the IRI of the ontology class that the\n",
"operation should be associated to. Every public method ([not starting with\n",
"an underscore](https://peps.python.org/pep-0008/#method-names-and-instance-variables)) defined on the implementation is automatically detected and\n",
"assigned as an operation to said ontology class. The\n",
"[ontology individual object](../usage/assertional_knowledge.ipynb#Ontology-individual-objects)\n",
"on which the operation is called is available as the private attribute\n",
"`_individual` on every instance of the implementation. For a specific \n",
"ontology individual, the implementation gets instantiated the first time that \n",
"any operation defined on it is called by the user.\n",
"\n",
"Finally, define an\n",
"[entry point](https://packaging.python.org/en/latest/specifications/entry-points/#entry-points-specification)\n",
"(or many if implementing operations for several ontology classes) under the\n",
"`simphony_osp.ontology.operations`\n",
"[group](https://packaging.python.org/en/latest/specifications/entry-points/#data-model)\n",
"that points to your\n",
"implementation of the `Operations` abstract class.\n",
"\n",
"An example implementation of an operation that takes advantage of\n",
"[geopy](https://pypi.org/project/geopy/) to compute the distance between \n",
"two points on Earth defined using the \n",
"[WGS84 Geo Positioning vocabulary](https://www.w3.org/2003/01/geo/wgs84_pos)\n",
"is shown below."
]
},
{
"cell_type": "markdown",
"id": "0fffa052-186a-46b7-9076-8acfed6b1ee0",
"metadata": {},
"source": [
"```python\n",
"\"\"\"Operations for classes from the WGS84 Geo Positioning vocabulary.\"\"\"\n",
"\n",
"from geopy import distance\n",
"from simphony_osp.namespaces import wgs84_pos\n",
"from simphony_osp.ontology import OntologyIndividual\n",
"from simphony_osp.ontology.operations import Operations\n",
"\n",
"\n",
"class Wgs84Pos(Operations):\n",
" \"\"\"Operations for the Point ontology class.\"\"\"\n",
"\n",
" iri = wgs84_pos.Point.iri\n",
"\n",
" def distance(self, other: OntologyIndividual) -> float:\n",
" \"\"\"Compute the distance between two points on Earth.\n",
" \n",
" Args:\n",
" other: Another point with respect to which the distance will be computed. \n",
" \n",
" Returns:\n",
" The distance between this point and the given one in km.\n",
" \"\"\"\n",
" lat_self = float(self._individual[wgs84_pos.latitude].one())\n",
" long_self = float(self._individual[wgs84_pos.longitude].one())\n",
" lat_other = float(other[wgs84_pos.latitude].one())\n",
" long_other = float(other[wgs84_pos.longitude].one())\n",
" return distance.geodesic(\n",
" (lat_self, long_self),\n",
" (lat_other, long_other),\n",
" ellipsoid=\"WGS-84\"\n",
" ).km\n",
"\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "744e037f-aabe-4bdf-a994-8787f3f039b1",
"metadata": {},
"source": [
"<div class=\"admonition note\">\n",
"<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Note</div></div>\n",
" \n",
"Remember that the implementation above is still not enough for the operation to\n",
"work: the corresponding \n",
"[entry point](https://packaging.python.org/en/latest/specifications/entry-points/#entry-points-specification)\n",
"for `Wgs84Pos` must have been defined and the `wgs84_pos` vocabulary needs to be installed using [pico](../usage/ontologies/pico.html).\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "d3db93d6-e26f-4831-b9a2-d9223cc4a51f",
"metadata": {},
"source": [
"The operation can be used as follows."
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "40a97048-80ea-4d99-8711-3ecd6ab5598b",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"417.4695920611045"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from simphony_osp.namespaces import wgs84_pos\n",
"\n",
"location_freiburg = wgs84_pos.Point()\n",
"location_freiburg[wgs84_pos.latitude] = 47.997791\n",
"location_freiburg[wgs84_pos.longitude] = 7.842609\n",
"\n",
"location_paris = wgs84_pos.Point()\n",
"location_paris[wgs84_pos.latitude] = 48.85333\n",
"location_paris[wgs84_pos.longitude] = 2.34885\n",
"\n",
"location_freiburg.operations.distance(location_paris)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.8.12"
}
],
"source": [
"from simphony_osp.namespaces import wgs84_pos\n",
"\n",
"location_freiburg = wgs84_pos.Point()\n",
"location_freiburg[wgs84_pos.latitude] = 47.997791\n",
"location_freiburg[wgs84_pos.longitude] = 7.842609\n",
"\n",
"location_paris = wgs84_pos.Point()\n",
"location_paris[wgs84_pos.latitude] = 48.85333\n",
"location_paris[wgs84_pos.longitude] = 2.34885\n",
"\n",
"location_freiburg.operations.distance(location_paris)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.8.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
"nbformat": 4,
"nbformat_minor": 5
}
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