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✨ Enable to easily join features onto artifacts via Artifact.df() #2238

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merged 10 commits into from
Nov 30, 2024
Merged

✨ Enable to easily join features onto artifacts via Artifact.df() #2238

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1ec80d0
🚧 First draft
falexwolf Nov 29, 2024
c7ace67
✨ Add a new section to the registries guide
falexwolf Nov 29, 2024
41f8f82
♻️ Prettify guide
falexwolf Nov 29, 2024
3a4ea30
💚 Improve & fix
falexwolf Nov 29, 2024
5d1fc84
📝 Polish
falexwolf Nov 29, 2024
6494cbd
💚 Fix
falexwolf Nov 29, 2024
3eda92f
💚 Fix
falexwolf Nov 29, 2024
67b28e5
💚 Fixes
falexwolf Nov 29, 2024
993fe08
♻️ Upgrade lnschema-core and polish order
falexwolf Nov 30, 2024
66045c9
💚 Fix
falexwolf Nov 30, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ lamin-tutorial/
mytest/
rds/
mydb/
docs/test-registries/
docs/test-annotate-flexible/
docs/lamindb.*
lamin_sphinx
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2 changes: 1 addition & 1 deletion docs/arrays.ipynb
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Expand Up @@ -11,7 +11,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Query arrays"
"# Slice arrays"
]
},
{
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89 changes: 35 additions & 54 deletions docs/faq/search.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -8,33 +8,19 @@
"# How does search work?"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "955b6253",
"metadata": {},
"outputs": [],
"source": [
"from laminci.db import setup_local_test_postgres"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7f312433",
"metadata": {},
"outputs": [],
"source": [
"pgurl = setup_local_test_postgres()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "286aeebc",
"metadata": {},
"metadata": {
"tags": [
"hide-cell"
]
},
"outputs": [],
"source": [
"from laminci.db import setup_local_test_postgres\n",
"pgurl = setup_local_test_postgres()\n",
"!lamin init --name benchmark_search --db {pgurl} --schema bionty --storage ./benchmark_search"
]
},
Expand All @@ -43,7 +29,7 @@
"id": "40234d47",
"metadata": {},
"source": [
"Here we show how to perform text search on `Record` and evaluate some search queries."
"Here we show how to perform text search on `Record` and evaluate some search queries for the {class}`bionty.CellType` ontology."
]
},
{
Expand All @@ -54,36 +40,32 @@
"outputs": [],
"source": [
"import lamindb as ln\n",
"import bionty as bt"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "83a46a9a",
"metadata": {},
"outputs": [],
"source": [
"import bionty as bt\n",
"\n",
"SEARCH_QUERIES_EXACT = (\"t cell\", \"stem cell\", \"b cell\", \"regulatory B cell\", \"Be2 cell\", \"adipocyte\")\n",
"SEARCH_QUERIES_CONTAINS = (\"t cel\", \"t-cel\", \"neural\", \"kidney\", \"kidne\")\n",
"TOP_N = 20\n",
"\n",
"bt.CellType.import_source()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7991a73f",
"cell_type": "markdown",
"id": "799b528e",
"metadata": {},
"outputs": [],
"source": [
"SEARCH_QUERIES_EXACT = (\"t cell\", \"stem cell\", \"b cell\", \"regulatory B cell\", \"Be2 cell\", \"adipocyte\")\n",
"SEARCH_QUERIES_CONTAINS = (\"t cel\", \"t-cel\", \"neural\", \"kidney\", \"kidne\")\n",
"TOP_N = 20"
"## Search the registry"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "682fcd2f",
"metadata": {},
"metadata": {
"tags": [
"hide-output"
]
},
"outputs": [],
"source": [
"for query in SEARCH_QUERIES_EXACT:\n",
Expand All @@ -98,7 +80,11 @@
"cell_type": "code",
"execution_count": null,
"id": "ee059b0d",
"metadata": {},
"metadata": {
"tags": [
"hide-output"
]
},
"outputs": [],
"source": [
"for query in SEARCH_QUERIES_CONTAINS:\n",
Expand All @@ -116,29 +102,24 @@
"id": "f4e41c9b",
"metadata": {},
"source": [
"Also check `bionty` public ontologies search:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eb5aa05a",
"metadata": {},
"outputs": [],
"source": [
"ct_public = bt.CellType.public()"
"## Search the public ontology"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d42c3594",
"metadata": {},
"metadata": {
"tags": [
"hide-output"
]
},
"outputs": [],
"source": [
"ct_public = bt.CellType.public()\n",
"\n",
"df = ct_public.search(\"b cell\", limit=20)\n",
"assert df.iloc[0][\"name\"] == \"B cell\"\n",
"\n",
"df"
]
},
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