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Merge pull request #10 from linkml/refactored-docs
Reorganized docs
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| copyright = f"{date.today().year}, Author 1 <[email protected]>" | ||
| author = "Author 1 <[email protected]>" | ||
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| # -- General configuration --------------------------------------------------- | ||
| # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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| # from https://github.com/cthoyt/ontoportal-client/blob/9862e26f8e374c3aef8707e3d5d69526c4d0fcd5/docs/source/conf.py | ||
| # If true, the current module name will be prepended to all description | ||
| # unit titles (such as .. function::). | ||
| add_module_names = False | ||
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| # A list of prefixes that are ignored when creating the module index. (new in Sphinx 0.6) | ||
| modindex_common_prefix = ["linkml_store."] | ||
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| extensions = [ | ||
| "sphinx.ext.autosummary", | ||
| "sphinx.ext.autodoc", | ||
| "sphinx.ext.githubpages", | ||
| "sphinx_rtd_theme", | ||
| "sphinx_click", | ||
| "sphinx.ext.viewcode", | ||
| "sphinx_autodoc_typehints", | ||
| "sphinx_automodapi.automodapi", | ||
| "sphinx_automodapi.smart_resolver", | ||
| "myst_parser", | ||
| "nbsphinx", | ||
| ] | ||
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| # generate autosummary pages | ||
| autosummary_generate = True | ||
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@@ -54,6 +69,15 @@ | |
| html_favicon = 'https://linkml.io/uploads/linkml-logo_color-no-words.png' | ||
| html_static_path = ["_static"] | ||
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| # https://stackoverflow.com/questions/5599254/how-to-use-sphinxs-autodoc-to-document-a-classs-init-self-method | ||
| autodoc_default_options = { | ||
| 'members': True, | ||
| 'member-order': 'bysource', | ||
| 'special-members': '__init__', | ||
| 'undoc-members': True, | ||
| 'exclude-members': '__weakref__' | ||
| } | ||
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| # The name of an image file (relative to this directory) to place at the top | ||
| # of the sidebar. | ||
| # | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,261 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "# How to Check Referential Integrity\n", | ||
| "\n", | ||
| "This example uses MongoDB" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "fc4794dd116ed21" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from linkml_store import Client\n", | ||
| "\n", | ||
| "client = Client()" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.760981Z", | ||
| "start_time": "2024-05-04T19:51:08.378243Z" | ||
| } | ||
| }, | ||
| "id": "initial_id" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "outputs": [], | ||
| "source": [ | ||
| "db = client.attach_database(\"mongodb://localhost:27017\", \"test\")\n", | ||
| "db.metadata.ensure_referential_integrity = True\n", | ||
| "db.set_schema_view(\"../../tests/input/countries/countries.linkml.yaml\")\n", | ||
| "countries_coll = db.create_collection(\"Country\", alias=\"countries\", recreate_if_exists=True)\n", | ||
| "routes_coll = db.create_collection(\"Route\", alias=\"routes\", recreate_if_exists=True)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.788932Z", | ||
| "start_time": "2024-05-04T19:51:09.771112Z" | ||
| } | ||
| }, | ||
| "id": "cc164c0acbe4c39d" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "outputs": [], | ||
| "source": [ | ||
| "COUNTRIES = \"../../tests/input/countries/countries.jsonl\"\n", | ||
| "ROUTES = \"../../tests/input/countries/routes.csv\"" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.789681Z", | ||
| "start_time": "2024-05-04T19:51:09.786454Z" | ||
| } | ||
| }, | ||
| "id": "5286ef4e9dd0f316" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": "[{'origin': 'DE', 'destination': 'FR', 'method': 'rail'}]" | ||
| }, | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from linkml_store.utils.format_utils import load_objects\n", | ||
| "\n", | ||
| "countries = load_objects(COUNTRIES)\n", | ||
| "routes = load_objects(ROUTES)\n", | ||
| "routes" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.795894Z", | ||
| "start_time": "2024-05-04T19:51:09.790413Z" | ||
| } | ||
| }, | ||
| "id": "2e21988e4fc13f58" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "outputs": [], | ||
| "source": [ | ||
| "countries_coll.insert(countries)\n", | ||
| "routes_coll.insert(routes)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.803272Z", | ||
| "start_time": "2024-05-04T19:51:09.798758Z" | ||
| } | ||
| }, | ||
| "id": "668e59a8f28e7bfe" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": "[{'origin': 'DE', 'destination': 'FR', 'method': 'rail'}]" | ||
| }, | ||
| "execution_count": 6, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "routes_coll.find().rows" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.810617Z", | ||
| "start_time": "2024-05-04T19:51:09.804004Z" | ||
| } | ||
| }, | ||
| "id": "995e63f873ea9353" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "outputs": [], | ||
| "source": [ | ||
| "for result in db.iter_validate_database():\n", | ||
| " print(result)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.956191Z", | ||
| "start_time": "2024-05-04T19:51:09.809082Z" | ||
| } | ||
| }, | ||
| "id": "a8ef16a3fbc6bfe6" | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "## Inserting invalid data\n", | ||
| "\n", | ||
| "We will intentionally insert an invalid row" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "24fb15bce092c2d1" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "outputs": [], | ||
| "source": [ | ||
| "routes_coll.insert({\"origin\": \"ZZZ\", \"destination\": \"YYY\", \"method\": \"rail\"})" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.961815Z", | ||
| "start_time": "2024-05-04T19:51:09.956721Z" | ||
| } | ||
| }, | ||
| "id": "f712a82be775f413" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 9, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": " origin destination method\n0 DE FR rail\n1 ZZZ YYY rail", | ||
| "text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>origin</th>\n <th>destination</th>\n <th>method</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>DE</td>\n <td>FR</td>\n <td>rail</td>\n </tr>\n <tr>\n <th>1</th>\n <td>ZZZ</td>\n <td>YYY</td>\n <td>rail</td>\n </tr>\n </tbody>\n</table>\n</div>" | ||
| }, | ||
| "execution_count": 9, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "routes_coll.find().rows_dataframe" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:51:09.974226Z", | ||
| "start_time": "2024-05-04T19:51:09.961675Z" | ||
| } | ||
| }, | ||
| "id": "18ffa996e3893b96" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "type='ReferentialIntegrity' severity=<Severity.ERROR: 'ERROR'> message='Referential integrity error: Country not found' instance='ZZZ' instance_index=None instantiates='Country'\n", | ||
| "type='ReferentialIntegrity' severity=<Severity.ERROR: 'ERROR'> message='Referential integrity error: Country not found' instance='YYY' instance_index=None instantiates='Country'\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "results = list(db.iter_validate_database())\n", | ||
| "for result in results:\n", | ||
| " print(result)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-04T19:52:20.044928Z", | ||
| "start_time": "2024-05-04T19:52:19.996008Z" | ||
| } | ||
| }, | ||
| "id": "c67517aece5d47c5" | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 2 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython2", | ||
| "version": "2.7.6" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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