lamindb_setup 0.74.2__tar.gz → 0.74.3__tar.gz

{lamindb_setup-0.74.2 → lamindb_setup-0.74.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.74.2
+Version: 0.74.3
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

{lamindb_setup-0.74.2 → lamindb_setup-0.74.3}/docs/hub-cloud/04-test-bionty.ipynb

@@ -49,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lnschema_bionty import PublicSource"
+    "from lnschema_bionty import Source"
    ]
   },
   {
@@ -58,7 +58,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sources_df = pd.DataFrame(PublicSource.objects.all().values())\n",
+    "sources_df = pd.DataFrame(Source.objects.all().values())\n",
     "sources_df.head()"
    ]
   },
@@ -124,7 +124,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sources_df = pd.DataFrame(PublicSource.objects.all().values())\n",
+    "sources_df = pd.DataFrame(Source.objects.all().values())\n",
     "sources_df.head()"
    ]
   },

{lamindb_setup-0.74.2 → lamindb_setup-0.74.3}/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.74.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.74.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb_setup-0.74.2 → lamindb_setup-0.74.3}/lamindb_setup/_exportdb.py

@@ -29,7 +29,7 @@ MODELS = {
     #     "ExperimentalFactor": False,
     #     "DevelopmentalStage": False,
     #     "Ethnicity": False,
-    #     "PublicSource": False,
+    #     "Source": False,
     # },
     # "wetlab": {
     #     "ExperimentType": False,

{lamindb_setup-0.74.2 → lamindb_setup-0.74.3}/lamindb_setup/core/_setup_bionty_sources.py

@@ -9,14 +9,14 @@ if TYPE_CHECKING:
 
 
 def write_bionty_sources(isettings: InstanceSettings) -> None:
-    """Write bionty sources to PublicSource table."""
+    """Write bionty sources to Source table."""
     if "bionty" not in isettings.schema:
         return None
     import shutil
 
     import bionty_base
     from bionty_base.dev._handle_sources import parse_sources_yaml
-    from lnschema_bionty.models import PublicSource
+    from lnschema_bionty.models import Source
 
     shutil.copy(
         bionty_base.settings.current_sources, bionty_base.settings.lamindb_sources
@@ -32,16 +32,11 @@ def write_bionty_sources(isettings: InstanceSettings) -> None:
             .set_index(["entity", key])
         )
 
-    try:
-        currently_used = _get_currently_used("organism")
-        key = "organism"
-    except KeyError:
-        currently_used = _get_currently_used("species")
-        key = "species"
+    currently_used = _get_currently_used("organism")
 
     all_records = []
     for kwargs in all_sources_dict:
-        act = currently_used.loc[(kwargs["entity"], kwargs[key])].to_dict()
+        act = currently_used.loc[(kwargs["entity"], kwargs["organism"])].to_dict()
         if (act["source"] == kwargs["source"]) and (
             act["version"] == kwargs["version"]
         ):
@@ -49,15 +44,13 @@ def write_bionty_sources(isettings: InstanceSettings) -> None:
 
         # when the database is not yet migrated but setup is updated
         # won't need this once lamindb is released with the new pin
-        if hasattr(PublicSource, "species") and "organism" in kwargs:
-            kwargs["species"] = kwargs.pop("organism")
-        elif hasattr(PublicSource, "organism") and "species" in kwargs:
-            kwargs["organism"] = kwargs.pop("species")
         kwargs["run"] = None  # can't yet access tracking information
-        record = PublicSource(**kwargs)
+        kwargs["in_db"] = False
+        # kwargs["name"] = kwargs.pop("source")
+        record = Source(**kwargs)
         all_records.append(record)
 
-    PublicSource.objects.bulk_create(all_records, ignore_conflicts=True)
+    Source.objects.bulk_create(all_records, ignore_conflicts=True)
 
 
 def load_bionty_sources(isettings: InstanceSettings):
@@ -68,11 +61,11 @@ def load_bionty_sources(isettings: InstanceSettings):
     import bionty_base
     from bionty_base.dev._handle_sources import parse_currently_used_sources
     from bionty_base.dev._io import write_yaml
-    from lnschema_bionty.models import PublicSource
+    from lnschema_bionty.models import Source
 
     try:
         # need try except because of integer primary key migration
-        active_records = PublicSource.objects.filter(currently_used=True).all().values()
+        active_records = Source.objects.filter(currently_used=True).all().values()
         write_yaml(
             parse_currently_used_sources(active_records),
             bionty_base.settings.lamindb_sources,