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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,319 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "boxed-professional", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Tutorial: Import and export" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "operational-honey", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n", | ||
| " \n", | ||
| "[](https://mybinder.org/v2/gh/simphony/docs/master?filepath=docs%2Fsource%2Fjupyter%2Fimport_export.ipynb \"Click to run the tutorial yourself!\")\n", | ||
| " \n", | ||
| "</figure>\n", | ||
| "\n", | ||
| "In this tutorial we will be covering the import and export capabilities of OSP-core. The utility functions that provide these functionalities are `import_cuds` and `export_cuds`, respectively." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "qualified-works", | ||
| "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", | ||
| "The full API specifictions of the import and export functions can be found in the\n", | ||
| "[utilities API reference page](../api_ref.html#osp.core.utils.export_cuds).\n", | ||
| " \n", | ||
| "</div>\n", | ||
| "</div>\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "driving-injury", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "For our running example, we'll be using the *city ontology* that was already introduces in the [cuds API tutorial](./cuds_api.html). First, make sure the city ontology is installed. If not, run the following command:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "dying-accreditation", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "INFO 2021-05-31 10:55:51,839 [osp.core.ontology.installation]: Will install the following namespaces: ['city']\n", | ||
| "INFO 2021-05-31 10:55:51,879 [osp.core.ontology.yml.yml_parser]: Parsing YAML ontology file c:\\users\\yoav\\anaconda3\\envs\\osp\\lib\\site-packages\\osp\\core\\ontology\\docs\\city.ontology.yml\n", | ||
| "INFO 2021-05-31 10:55:51,995 [osp.core.ontology.yml.yml_parser]: You can now use `from osp.core.namespaces import city`.\n", | ||
| "INFO 2021-05-31 10:55:51,996 [osp.core.ontology.parser]: Loaded 7396 ontology triples in total\n", | ||
| "INFO 2021-05-31 10:55:52,437 [osp.core.ontology.installation]: Installation successful\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "!pico install city" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "lonely-listening", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Next we create a few CUDS objects:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "id": "considered-leonard", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "<city.Citizen: 98f8ac8c-713d-4406-bc36-e0152f9e2ea3, CoreSession: @0x221b0a05250>" | ||
| ] | ||
| }, | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from osp.core.namespaces import city\n", | ||
| "\n", | ||
| "c = city.City(name=\"Freiburg\", coordinates=[47, 7])\n", | ||
| "p1 = city.Citizen(name=\"Peter\")\n", | ||
| "p2 = city.Citizen(name=\"Anne\")\n", | ||
| "c.add(p1, rel=city.hasInhabitant)\n", | ||
| "c.add(p2, rel=city.hasInhabitant)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "worth-province", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now we can use the `export_cuds` methods to export the data into a file:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "id": "monthly-anxiety", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from osp.core.utils import export_cuds\n", | ||
| "\n", | ||
| "export_cuds(c, file='./data.ttl', format='turtle')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "determined-nursing", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "This will create the file `data.ttl` with the following content:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "id": "outstanding-wound", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "@prefix city: <http://www.osp-core.com/city#> .\n", | ||
| "@prefix cuba: <http://www.osp-core.com/cuba#> .\n", | ||
| "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n", | ||
| "@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n", | ||
| "\n", | ||
| "cuba:_serialization rdf:first \"47398674-720b-4765-9047-b5351ed175c0\" .\n", | ||
| "\n", | ||
| "<http://www.osp-core.com/cuds#8a90e2b3-7cca-4103-9eba-aab55e5903b1> a city:Citizen ;\n", | ||
| " city:INVERSE_OF_hasInhabitant <http://www.osp-core.com/cuds#47398674-720b-4765-9047-b5351ed175c0> ;\n", | ||
| " city:age 25 ;\n", | ||
| " city:name \"Peter\" .\n", | ||
| "\n", | ||
| "<http://www.osp-core.com/cuds#98f8ac8c-713d-4406-bc36-e0152f9e2ea3> a city:Citizen ;\n", | ||
| " city:INVERSE_OF_hasInhabitant <http://www.osp-core.com/cuds#47398674-720b-4765-9047-b5351ed175c0> ;\n", | ||
| " city:age 25 ;\n", | ||
| " city:name \"Anne\" .\n", | ||
| "\n", | ||
| "<http://www.osp-core.com/cuds#47398674-720b-4765-9047-b5351ed175c0> a city:City ;\n", | ||
| " city:coordinates \"[47, 7]\"^^<http://www.osp-core.com/cuba#_datatypes/VECTOR-INT-2> ;\n", | ||
| " city:hasInhabitant <http://www.osp-core.com/cuds#8a90e2b3-7cca-4103-9eba-aab55e5903b1>,\n", | ||
| " <http://www.osp-core.com/cuds#98f8ac8c-713d-4406-bc36-e0152f9e2ea3> ;\n", | ||
| " city:name \"Freiburg\" .\n", | ||
| "\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from sys import platform\n", | ||
| "\n", | ||
| "if platform == 'win32':\n", | ||
| " !more data.ttl\n", | ||
| "else:\n", | ||
| " !cat data.ttl" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "offshore-cotton", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "You can change the format by entering a different value for the parameter `format`. The supported formats are “xml”, “n3”, “turtle”, “nt”, “pretty-xml”, “trix”, “trig” and “nquads”." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "derived-advancement", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "To import data, we can use the `import` method. Let's assume we wish to import data into an SQLite session. The following code will help us to achieve our aim:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "id": "stable-session", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from osp.wrappers.sqlite import SqliteSession\n", | ||
| "from osp.core.utils import import_cuds\n", | ||
| "\n", | ||
| "with SqliteSession(\"test.db\") as session:\n", | ||
| " wrapper = city.CityWrapper(session=session)\n", | ||
| " c = import_cuds('./data.ttl')\n", | ||
| " wrapper.add(c)\n", | ||
| " session.commit()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "higher-short", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now we can verify the data was indeed imported:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "suspended-albert", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "- Cuds object:\n", | ||
| " uid: 03015cb9-f88c-4ab1-9df9-bb52743b99de\n", | ||
| " type: city.CityWrapper\n", | ||
| " superclasses: city.CityWrapper, cuba.Entity, cuba.Wrapper\n", | ||
| " description: \n", | ||
| " To Be Determined\n", | ||
| "\n", | ||
| " |_Relationship city.hasPart:\n", | ||
| " - city.City cuds object named <Freiburg>:\n", | ||
| " . uid: 72595bc4-1b68-46a3-97e9-8f3de2650f2c\n", | ||
| " . coordinates: [47 7]\n", | ||
| " . |_Relationship city.hasInhabitant:\n", | ||
| " . - city.Citizen cuds object named <Anne>:\n", | ||
| " . . uid: 92a00459-0927-438c-a305-a26512ac7f03\n", | ||
| " . . age: 25\n", | ||
| " . - city.Citizen cuds object named <Peter>:\n", | ||
| " . uid: 27d1e83b-4ee9-4f4f-adb5-0b01a3cc2c1b\n", | ||
| " . age: 25\n", | ||
| " - city.City cuds object named <Freiburg>:\n", | ||
| " . uid: 47398674-720b-4765-9047-b5351ed175c0\n", | ||
| " . coordinates: [47 7]\n", | ||
| " . |_Relationship city.hasInhabitant:\n", | ||
| " . - city.Citizen cuds object named <Anne>:\n", | ||
| " . . uid: 98f8ac8c-713d-4406-bc36-e0152f9e2ea3\n", | ||
| " . . age: 25\n", | ||
| " . - city.Citizen cuds object named <Peter>:\n", | ||
| " . uid: 8a90e2b3-7cca-4103-9eba-aab55e5903b1\n", | ||
| " . age: 25\n", | ||
| " - city.City cuds object named <Freiburg>:\n", | ||
| " uid: d886f8ce-1326-40f5-a98b-c4c893b8c085\n", | ||
| " coordinates: [47 7]\n", | ||
| " |_Relationship city.hasInhabitant:\n", | ||
| " - city.Citizen cuds object named <Anne>:\n", | ||
| " . uid: 2b5d0a3f-81a5-4746-aab9-40adcb65e71f\n", | ||
| " . age: 25\n", | ||
| " - city.Citizen cuds object named <Peter>:\n", | ||
| " uid: 766b320a-7e9a-43ec-a696-96b4f9ee494d\n", | ||
| " age: 25\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from osp.core.utils import pretty_print\n", | ||
| "\n", | ||
| "with SqliteSession(\"test.db\") as session:\n", | ||
| " wrapper = city.CityWrapper(session=session)\n", | ||
| " pretty_print(wrapper) " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "virgin-river", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "<div class=\"admonition important\">\n", | ||
| "<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Notes</div></div>\n", | ||
| " \n", | ||
| "1. The format is automatically inferred from the file extension. To specify it explicitly, you can add the `format` parameter, like so: `import_cuds('./data.ttl', format='turtle')`.\n", | ||
| "1. The `session` parameter is optional and inferred automatically from the context that created by the `with` statement (see the [tutorial on multiple wrappers](./multiple_wrappers.html) for more information). You can specify the session explicitly like so: `import_cuds('./data.ttl', session=session)`.\n", | ||
| " \n", | ||
| "</div>" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3.7.4 64-bit", | ||
| "language": "python", | ||
| "name": "python37464bit7e5bfc198a4544d1be12f13215aed90d" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.8.5" | ||
| }, | ||
| "metadata": { | ||
| "interpreter": { | ||
| "hash": "301cd6007de04cbbf15bca26f0bc1cb48004d089278091d760363de622bdd0c8" | ||
| } | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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