Simplify 10ktp

Signed-off-by: zethson <lukas.heumos@posteo.net>

.gitignore

@@ -28,3 +28,4 @@ __pycache__/
 *.pye
 
 Sandbox.ipynb
+test.ipynb

data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_make_vitessce.py

@@ -1,18 +1,8 @@
-# ADJUST
-uid = "10ktp"
-
-# Setup before running this script for the first time
-#   1) Ensure you have a lamin.ai account
-#   2) Run `lamin login` to authenticate
-#   3) Activate lamin db connection with `lamin load scverse/spatialdata-db`
-#   4) Execute script once and replace the stem_uid for this file
+theislab_uid = "10ktp"
 
 import lamindb as ln
 
-ln.settings.transform.stem_uid = "5PYtTxDE7LvE"
-ln.settings.transform.version = "1"
-
-ln.track()
+ln.context.track("5PYtTxDE7LvE")
 
 from vitessce import (
     VitessceConfig,
@@ -31,7 +21,7 @@
 from lamindb.integrations import save_vitessce_config
 
 
-artifact = ln.Artifact.filter(ulabels__name=uid).one()
+artifact = ln.Artifact.filter(ulabels__name=theislab_uid).one()
 
 vc = VitessceConfig(
     schema_version="1.0.16",
@@ -49,4 +39,4 @@
 dataset = vc.add_dataset(name='Visium demo').add_object(wrapper)
 spatial = vc.add_view("spatialBeta", dataset=dataset)
 vc.layout(spatial)
-view = save_vitessce_config(vc, description="Visium HD demo vitessce config")
+view = save_vitessce_config(vc, description="Visium HD demo vitessce config")

data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp_to_lamin.py

@@ -1,42 +1,31 @@
-# ADJUST
-uid = "10ktp"
-
-# Setup before running this script for the first time
-#   1) Ensure you have a lamin.ai account
-#   2) Run `lamin login` to authenticate
-#   3) Activate lamin db connection with `lamin load scverse/spatialdata-db`
-#   4) Execute script once and replace the stem_uid for this file
+theislab_uid = "10ktp"
 
 import lamindb as ln
+from spatialdata_db import load_10x_metadata
 
-ln.settings.transform.stem_uid = "KgGzOw8PUYKO"
-ln.settings.transform.version = "3"
 ln.track("KgGzOw8PUYKO7CpM")
+
 try:
-    artifact = ln.Artifact.filter(ulabels__name=uid).one()
+    artifact = ln.Artifact.filter(ulabels__name=theislab_uid).one()
     artifact.delete(permanent=True)
 except:
     pass
 
-### From here on we assume Lamin is set up correctly
 DATASET_PATH = "/lustre/groups/ml01/projects/2024_spatialdata_db/data/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0/10ktp__10X__Visium__Mouse__brain__20200623__v1.1.0.zarr"
 
 artifact = ln.Artifact(DATASET_PATH, description="10X, Visium, Mouse, Brain")
-artifact.save() # transfers to Lamin
+artifact.save()
 
 # Associate ID with the artifact so we can retrieve afterwards
 tuid_parent = ln.ULabel.filter(name="theislab unique ID").one()
-tuid = ln.ULabel(name=uid).save()
+tuid = ln.ULabel(name=theislab_uid).save()
 tuid.parents.add(tuid_parent)
 artifact.labels.add(tuid)
 
 # load 10X metadata we have on disk
-import pandas as pd
-from spatialdata_db import load_10x_metadata
-
 all_metadata_10x = load_10x_metadata()
-assert len(all_metadata_10x.query(f"uid == '{uid}'")) == 1
-metadata = all_metadata_10x.query(f"uid == '{uid}'").iloc[0]
+assert len(all_metadata_10x.query(f"uid == '{theislab_uid}'")) == 1
+metadata = all_metadata_10x.query(f"uid == '{theislab_uid}'").iloc[0]
 
 # Associate metadata as features
 import bionty as bt
@@ -45,39 +34,18 @@
 organism_lo = bt.Organism.public().lookup()
 tissue_lo = bt.Tissue.public().lookup()
 
-# Species --
-
-if metadata["Species"].lower() == "mouse":
-    feature_organism = bt.Organism.from_public(name=organism_lo.mouse.name)
-elif metadata["Species"].lower() == "human":
-    feature_organism = bt.Organism.from_public(name=organism_lo.human.name)
-else:
-    raise NotImplementedError("Unknown species!")
-
-feature_organism.save()
-
-# Tissue
+# Species (Organism)
+organisms = bt.Organism.from_values(metadata["Species"].lower(), field="name")
+ln.save(organisms)
 
+# Orgna (Tissue)
 if metadata["organ"].lower() == "olfactory_bulb":
     metadata["organ"] = "olfactorybulb"
-
-if metadata["organ"].lower() == "brain":
-    feature_tissue = bt.Tissue.from_public(name=tissue_lo.brain.name)
-elif metadata["organ"].lower() == "kidney":
-    feature_tissue = bt.Tissue.from_public(name=tissue_lo.kidney.name)
-elif metadata["organ"].lower() == "colon":
-    feature_tissue = bt.Tissue.from_public(name=tissue_lo.colon.name)
-else:
-    raise NotImplementedError("Unknown tissue!")
-
-feature_tissue.save()
+tissues = bt.Tissue.from_values(metadata["organ"].lower(), field="name")
+ln.save(tissues)
 
 # Associate bionty terms to artifact
+artifact.organism.set(organisms)
+artifact.tissue.set(tissues)
 
-artifact.labels.add(feature_organism, feature=feature_lo.organism)
-artifact.labels.add(feature_tissue, feature=feature_lo.tissue)
-
-
-# finish for tracing in Lamin
-
-ln.finish()
+ln.context.finish()

pyproject.toml

@@ -25,7 +25,11 @@ dependencies = [
   "anndata",
   # for debug logging (referenced from the issue template)
   "session-info",
-  "lamindb[aws,bionty,jupyter]"
+  "lamindb[aws,bionty,jupyter]",
+  "vitessce",
+  "spatialdata",
+  "spatialdata-io",
+  "spatialdata-plot"
 ]
 optional-dependencies.dev = [
   "pre-commit",