✨ Adopt QueryDB for rxrx (#44)

Signed-off-by: Lukas Heumos <[email protected]>

Author: Zethson

.github/workflows/build.yml

@@ -20,11 +20,11 @@ jobs:
     timeout-minutes: 30
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           repository: laminlabs/lndocs
           ssh-key: ${{ secrets.READ_LNDOCS }}

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/rbubley/mirrors-prettier

docs/rxrx.ipynb

@@ -22,8 +22,8 @@
     "\n",
     "High numbers of fluorescent microscopy images characterize cellular phenotypes in vitro based on morphology and protein expression (5-10 stains) across a range of conditions.\n",
     "\n",
-    "- In this guide, you'll see how to query some of these data using LaminDB.\n",
-    "- If you'd like to transfer data into your own LaminDB instance, see the [transfer guide](inv:docs#transfer)."
+    "In this guide, you'll see how to query some of these data using LaminDB.\n",
+    "If you'd like to transfer data into your own LaminDB instance, see the [transfer guide](inv:docs#transfer)."
    ]
   },
   {
@@ -32,21 +32,45 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install 'lamindb[bionty,jupyter,gcp,wetlab]' duckdb\n",
-    "!lamin connect laminlabs/lamindata"
+    "# !pip install 'lamindb[gcp]' duckdb\n",
+    "!lamin init --modules bionty,wetlab --storage ./test-rxrx"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "import lamindb as ln\n",
     "import bionty as bt\n",
     "import wetlab as wl"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create the central query object for this instance:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "lamindata_db = ln.QueryDB(\"laminlabs/lamindata\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -64,10 +88,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "df = wl.GeneticPerturbation.df()\n",
+    "df = lamindata_db.genetic_perturbations.to_dataframe()\n",
     "df.shape"
    ]
   },
@@ -81,10 +109,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "sirnas = wl.GeneticPerturbation.filter(system=\"siRNA\").lookup(return_field=\"name\")"
+    "sirnas = lamindata_db.genetic_perturbations.filter(system=\"siRNA\").lookup(\n",
+    "    return_field=\"name\"\n",
+    ")"
    ]
   },
   {
@@ -97,11 +131,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "cell_lines = bt.CellLine.lookup(return_field=\"abbr\")\n",
-    "wells = wl.Well.lookup(return_field=\"name\")"
+    "cell_lines = lamindata_db.cell_lines.lookup(return_field=\"abbr\")\n",
+    "wells = lamindata_db.wells.lookup(return_field=\"name\")"
    ]
   },
   {
@@ -135,7 +173,7 @@
    },
    "outputs": [],
    "source": [
-    "collection = ln.Collection.get(\"Br2Z1lVSQBAkkbbt7ILu\")\n",
+    "collection = lamindata_db.collections.get(\"Br2Z1lVSQBAkkbbt7ILu\")\n",
     "collection.view_lineage()\n",
     "collection.describe()"
    ]
@@ -150,7 +188,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "collection.meta_artifact.load().head()"
@@ -189,7 +231,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "query = df[\n",
@@ -212,7 +258,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "collection.data_artifact.storage.root"
@@ -221,7 +271,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "images = [f\"{collection.data_artifact.storage.root}/{key}\" for key in query.path]\n",
@@ -238,7 +292,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "path = ln.UPath(images[1])\n",
@@ -248,7 +306,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "from IPython.display import Image\n",
@@ -273,22 +335,25 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "import duckdb\n",
     "\n",
-    "features = ln.Feature.lookup(return_field=\"name\")\n",
+    "features = lamindata_db.features.lookup(return_field=\"name\")\n",
     "\n",
     "filter = (\n",
     "    f\"{features.cell_line} == '{cell_lines.hep_g2_cell}' and {features.sirna} ==\"\n",
     "    f\" '{sirnas.s15652}' and {features.well} == '{wells.m15}' and \"\n",
     "    f\"{features.plate} == '1' and {features.site} == '2'\"\n",
     ")\n",
     "\n",
-    "region = ln.setup.settings.storage.region\n",
     "parquet_data = duckdb.from_parquet(\n",
-    "    collection.meta_artifact.path.as_posix() + f\"?s3_region={region}\"\n",
+    "    collection.meta_artifact.path.as_posix() + \"?s3_region=us-east-1\"\n",
     ")\n",
     "\n",
     "parquet_data.filter(filter)"

docs/vitessce.ipynb

@@ -41,7 +41,7 @@
    "source": [
     "# pip install \"vitessce[all]>=3.5.0\"\n",
     "# pip install \"generate-tiff-offsets>=0.1.9\"\n",
-    "# pip install \"lamindb[jupyter,bionty]\"\n",
+    "# pip install lamindb\n",
     "!lamin connect laminlabs/lamin-dev  # <-- replace with your instance"
    ]
   },