lamindb_setup 0.74.2__py2.py3-none-any.whl → 0.74.3__py2.py3-none-any.whl

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/_exportdb.py

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

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,

{lamindb_setup-0.74.2.dist-info → lamindb_setup-0.74.3.dist-info}/METADATA

@@ -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.dist-info → lamindb_setup-0.74.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=uZ5-AbjJbOWBYvG9QbuADUZdJM1pp0IM2p7E75AoVnU,1542
+lamindb_setup/__init__.py,sha256=FLoipEAQXtUmcK_Dwo1brKCnl2kfCxuCwN6GTe1FgxU,1542
 lamindb_setup/_cache.py,sha256=wA7mbysANwe8hPNbjDo9bOmXJ0xIyaS5iyxIpxSWji4,846
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=cNEL9Q4yPpmEkGKHH8JgullWl1VUZwALJ4RHn9wZypY,2613
@@ -6,7 +6,7 @@ lamindb_setup/_close.py,sha256=1QS9p2SCacgovYn6xqWU4zFvwHN1RgIccvzwJgFvKgU,1186
 lamindb_setup/_connect_instance.py,sha256=dWqvNBBxqCG6xOiY_fI-P5ccyzno_ePGP3Rp1rgNq3g,12512
 lamindb_setup/_delete.py,sha256=Y8KSFYgY0UHAvjd7cCL6hZ_XiLeJwx50BguVATcj_Xo,5524
 lamindb_setup/_django.py,sha256=EoyWvFzH0i9wxjy4JZhcoXCTckztP_Mrl6FbYQnMmLE,1534
-lamindb_setup/_exportdb.py,sha256=uTIZjKKTB7arzEr1j0O6lONiT2pRBKeOFdLvOV8ZwzE,2120
+lamindb_setup/_exportdb.py,sha256=43g77-tH-vAlTn8ig1mMD9-KXLKvxUeDLaq0gVu3l-c,2114
 lamindb_setup/_importdb.py,sha256=yYYShzUajTsR-cTW4CZ-UNDWZY2uE5PAgNbp-wn8Ogc,1874
 lamindb_setup/_init_instance.py,sha256=jcKtXLOwkoq7bC-0j0xnNU4_up9nPl0iKQPNoJbBts8,12078
 lamindb_setup/_migrate.py,sha256=P4n3x0SYzO9szjF2-JMa7z4mQadtWjHv5ow4HbCDZLI,8864
@@ -33,14 +33,14 @@ lamindb_setup/core/_settings_save.py,sha256=n_tYfb9EBSxwm4LHyPRHJptE5uB8lmHhcRkz
 lamindb_setup/core/_settings_storage.py,sha256=65aobewYX6VfOeYZjZQOOI7ZD_3b4QA9TDmrduU0m4c,13262
 lamindb_setup/core/_settings_store.py,sha256=VEE8Ff2A7y4j8ksOaa7g48jNaOqe1PBnBjb1PKKGUKU,2115
 lamindb_setup/core/_settings_user.py,sha256=P2lC4WDRAFfT-Xq3MlXJ-wMKIHCoGNhMTQfRGIAyUNQ,1344
-lamindb_setup/core/_setup_bionty_sources.py,sha256=h_pBANsSGK6ujAFsG21mtADHVJoMLKDR4eGgRP4Fgls,3072
+lamindb_setup/core/_setup_bionty_sources.py,sha256=i_fVCnoh38ouTKKeM-MUXQbkkxMcrSz5dTM_mOCHUcU,2732
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=reu02M4aE2BT_A5AFqwhv48l91mOMyQ4zTd-hh-wtuU,6922
 lamindb_setup/core/django.py,sha256=QUQm3zt5QIiD8uv6o9vbSm_bshqiSWzKSkgD3z2eJCg,3542
 lamindb_setup/core/exceptions.py,sha256=eoI7AXgATgDVzgArtN7CUvpaMUC067vsBg5LHCsWzDM,305
 lamindb_setup/core/hashing.py,sha256=_JliYeCcjT_foOUJ5ck1rvcCo9q7r4b4SaSclQ_w4Qo,3071
 lamindb_setup/core/types.py,sha256=bcYnZ0uM_2NXKJCl94Mmc-uYrQlRUUVKG3sK2N-F-N4,532
 lamindb_setup/core/upath.py,sha256=dwudkTVsXuyjS-2xR16WomcWtXJAEfRZ0ZzFq8_EDhE,27157
-lamindb_setup-0.74.2.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-0.74.2.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
-lamindb_setup-0.74.2.dist-info/METADATA,sha256=_3FEUyj8OTeA3negmlHl0mXYPprbhDrgq8jU-1DKtUk,1638
-lamindb_setup-0.74.2.dist-info/RECORD,,
+lamindb_setup-0.74.3.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-0.74.3.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
+lamindb_setup-0.74.3.dist-info/METADATA,sha256=dqS1Dfpqk1G-BoZzexMF8b1wv_MxWPuqKwKMM1rvWx8,1638
+lamindb_setup-0.74.3.dist-info/RECORD,,