🚚 Rename DObject.run_id to DObject.source_id

docs/guide/02-select.ipynb

@@ -138,7 +138,7 @@
    "source": [
     "stmt = (\n",
     "    ln.select(ln.DObject, lns.User)\n",
-    "    .join(lns.Run, ln.DObject.run_id == lns.Run.id)\n",
+    "    .join(lns.Run, ln.DObject.source_id == lns.Run.id)\n",
     "    .join(lns.Notebook)\n",
     "    .join(lns.User)\n",
     ")"
@@ -171,7 +171,7 @@
    "source": [
     "stmt = (\n",
     "    ln.select(ln.DObject, lns.User.handle)\n",
-    "    .join(lns.Run, ln.DObject.run_id == lns.Run.id)\n",
+    "    .join(lns.Run, ln.DObject.source_id == lns.Run.id)\n",
     "    .join(lns.Notebook)\n",
     "    .join(lns.User)\n",
     ")"
@@ -204,7 +204,7 @@
    "source": [
     "stmt = (\n",
     "    ln.select(ln.DObject.name, ln.DObject.suffix, ln.DObject.size, lns.User.handle)\n",
-    "    .join(lns.Run, ln.DObject.run_id == lns.Run.id)\n",
+    "    .join(lns.Run, ln.DObject.source_id == lns.Run.id)\n",
     "    .join(lns.Notebook)\n",
     "    .join(lns.User)\n",
     ")"

docs/guide/run.md

@@ -15,5 +15,5 @@ For instance:
 
 It typically has inputs and outputs:
 
-- References to outputs are stored in the dobject table in the run_id column, which stores a foreign key into the run table. This is possible as every given dobject has a unique data source: the run that produced the dobject. Note that a given run may output several dobjects.
+- References to outputs are stored in the dobject table in the source_id column, which stores a foreign key into the run table. This is possible as every given dobject has a unique data source: the run that produced the dobject. Note that a given run may output several dobjects.
 - References to input dobjects are stored in the run_in table, a many-to-many link table between the dobject and run tables. Any dobject might serve as an input for many run. Similarly, any run might have many dobjects as inputs.

lamindb/_check_versions.py

@@ -7,8 +7,8 @@
 if version.parse(lndb_v) != version.parse("0.35.0"):
     raise RuntimeError("Upgrade lndb! pip install lndb==0.35.0")
 
-if version.parse(lnschema_core_v) != version.parse("0.27.2"):
-    raise RuntimeError("lamindb needs lnschema_core==0.27.2")
+if version.parse(lnschema_core_v) != version.parse("0.28.0"):
+    raise RuntimeError("lamindb needs lnschema_core==0.28.0")
 
 if version.parse(bionty_v) != version.parse("0.7.0"):
     raise RuntimeError("lamindb needs bionty==0.7.0")

lamindb/_record.py

@@ -272,7 +272,7 @@ def get_dobject_kwargs_from_data(
         name=name,
         suffix=suffix,
         hash=hash,
-        run_id=run.id,
+        source_id=run.id,
         size=size,
         storage_id=storage.id,
         source=run,

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     # Lamin pinned packages
     "lnhub_rest==0.5.0",  # NOT pinned in lndb, just a lower bound there
     "lndb==0.35.0",
-    "lnschema_core==0.27.2",
+    "lnschema_core==0.28.0",
     "lnschema_wetlab==0.13.4",
     "lnschema_bionty==0.7.0",
     "bionty==0.7.0",