🏗️ Persist the session

docs/guide/07-link-samples.ipynb

@@ -117,11 +117,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5e532d56",
+   "id": "7117701d-eda9-4a1a-a011-f2fb1b9c49ff",
    "metadata": {},
    "outputs": [],
    "source": [
-    "readout.dobjects.append(dobject)"
+    "dobject.readouts.append(readout)"
    ]
   },
   {
@@ -177,9 +177,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "biosample.species_id = (\n",
-    "    species.id\n",
-    ")  # need to have a better UX around this that clarifies why we have to do this"
+    "# the species record already exists, hence we only link the id instead of adding the full record\n",
+    "# need to have a more intuitive UX around this that clarifies why we have to do this\n",
+    "biosample.species_id = species.id"
    ]
   },
   {
@@ -259,11 +259,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f4c14773-eeac-4db8-95e5-364b5e7cd532",
+   "id": "d0a3783a-370d-4648-8bd1-6776f014b0f5",
    "metadata": {},
    "outputs": [],
    "source": [
-    "biosample.dobjects.append(dobject)"
+    "dobject.biosamples.append(biosample)"
    ]
   },
   {

lamindb/_check_versions.py

@@ -5,8 +5,8 @@
 from nbproject import __version__ as nbproject_v
 from packaging import version
 
-if version.parse(lndb_setup_v) != version.parse("0.17.0"):
-    raise RuntimeError("lamindb needs lndb_setup==0.17.0")
+if version.parse(lndb_setup_v) != version.parse("0.18.0"):
+    raise RuntimeError("lamindb needs lndb_setup==0.18.0")
 
 if version.parse(lnschema_core_v) != version.parse("0.20.0"):
     raise RuntimeError("lamindb needs lnschema_core==0.20.0")

lamindb/_delete.py

@@ -24,29 +24,27 @@ def delete(record: sqm.SQLModel):
     Args:
         record: One or multiple records as instances of `SQLModel`.
     """
-    with sqm.Session(settings.instance.db_engine()) as session:
-        if isinstance(record, DObject):
-            # delete usage events related to the dobject that's to be deleted
-            events = session.exec(
-                sqm.select(Usage).where(Usage.dobject_id == record.id)
-            )
-            for event in events:
-                session.delete(event)
-            session.commit()
-            # delete run_ins related to the dobject that's to be deleted
-            run_ins = session.exec(
-                sqm.select(RunIn).where(RunIn.dobject_id == record.id)
-            )
-            for run_in in run_ins:
-                session.delete(run_in)
-            session.commit()
-        session.delete(record)
+    session = settings.instance.session()
+    if isinstance(record, DObject):
+        # delete usage events related to the dobject that's to be deleted
+        events = session.exec(sqm.select(Usage).where(Usage.dobject_id == record.id))
+        for event in events:
+            session.delete(event)
         session.commit()
-        settings.instance._update_cloud_sqlite_file()
-        logger.success(
-            f"Deleted {colors.yellow(f'row {record}')} in"
-            f" {colors.blue(f'table {type(record).__name__}')}."
-        )
+        # delete run_ins related to the dobject that's to be deleted
+        run_ins = session.exec(sqm.select(RunIn).where(RunIn.dobject_id == record.id))
+        for run_in in run_ins:
+            session.delete(run_in)
+        session.commit()
+    session.delete(record)
+    session.commit()
+    settings.instance._update_cloud_sqlite_file()
+    logger.success(
+        f"Deleted {colors.yellow(f'row {record}')} in"
+        f" {colors.blue(f'table {type(record).__name__}')}."
+    )
+    if settings.instance._session is None:
+        session.close()
     if isinstance(record, DObject):
         # TODO: do not track deletes until we come up
         # with a good design that respects integrity

lamindb/_load.py

@@ -1,5 +1,4 @@
 import lnschema_core as core
-import sqlmodel as sqm
 from lamin_logger import logger
 from lndb_setup import settings
 
@@ -9,18 +8,20 @@
 
 
 def populate_runin(dobject: core.DObject, run: core.Run):
-    with sqm.Session(settings.instance.db_engine()) as session:
-        result = session.get(core.RunIn, (run.id, dobject.id))
-        if result is None:
-            session.add(
-                core.RunIn(
-                    run_id=run.id,
-                    dobject_id=dobject.id,
-                )
+    session = settings.instance.session()
+    result = session.get(core.RunIn, (run.id, dobject.id))
+    if result is None:
+        session.add(
+            core.RunIn(
+                run_id=run.id,
+                dobject_id=dobject.id,
             )
-            session.commit()
-            logger.info(f"Added dobject ({dobject.id}) as input for run ({run.id}).")
-            settings.instance._update_cloud_sqlite_file()
+        )
+        session.commit()
+        logger.info(f"Added dobject ({dobject.id}) as input for run ({run.id}).")
+        settings.instance._update_cloud_sqlite_file()
+    if settings.instance._session is None:
+        session.close()
 
 
 def load(dobject: core.DObject, stream: bool = False):

lamindb/dev/db/_add.py

@@ -54,12 +54,14 @@ def add(  # type: ignore  # no support of different naming of args across overlo
     for record in records:
         if isinstance(record, DObject) and hasattr(record, "_local_filepath"):
             upload_data_object(record, **kwargs)
-    with sqm.Session(settings.instance.db_engine(), expire_on_commit=False) as session:
-        for record in records:
-            session.add(record)
-        session.commit()
-        for record in records:
-            session.refresh(record)
+    session = settings.instance.session()
+    for record in records:
+        session.add(record)
+    session.commit()
+    for record in records:
+        session.refresh(record)
+    if settings.instance._session is None:
+        session.close()
     settings.instance._update_cloud_sqlite_file()
     if len(records) > 1:
         return records

lamindb/dev/db/_core.py

@@ -7,4 +7,4 @@ def session() -> sqm.Session:
 
     Returns a `sqlmodel.Session` object.
     """
-    return sqm.Session(settings.instance.db_engine())
+    return settings.instance.session()

lamindb/dev/db/_select.py

@@ -106,11 +106,16 @@ def __init__(self, *, tables, stmt, _settings_store: InstanceSettingsStore = Non
     def _execute(self):
         # cache the query result for the lifetime of the object
         if self._result is None:
-            with sqm.Session(
-                settings._instance(self._settings_store).db_engine(),
-                expire_on_commit=False,
-            ) as session:
-                self._result = session.exec(self._stmt).all()
+            if self._settings_store is not None:
+                session = sqm.Session(
+                    settings._instance(self._settings_store).db_engine(),
+                    expire_on_commit=False,
+                )
+            else:
+                session = settings.instance.session()
+            self._result = session.exec(self._stmt).all()
+            if settings.instance._session is None:
+                session.close()
 
     def all(self):
         """Return all result as a list."""

pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
     # Lamin pinned packages
-    "lndb_setup==0.17.0",
+    "lndb_setup==0.18.0",
     "lnschema_core==0.20.0",
     "lnschema_wetlab==0.10.0",
     "lnschema_bionty==0.6.0",