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fix: Handle non-categorical columns with colors + update deprecated AnnData API (#2758)

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Yeah that makes sense! Mergingg
This commit is contained in:
rwbaber
2026-02-24 21:37:57 +00:00
committed by GitHub
parent 7c7203bdfe
commit 5eb3021752
4 changed files with 11 additions and 10 deletions
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8
server/cli/prepare.py
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@@ -128,12 +128,12 @@ def prepare(
raise click.FileError(data, hint="not a valid file or path")
if not set_obs_names == "":
if set_obs_names not in adata.obs_keys():
raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
if set_obs_names not in list(adata.obs.keys()):
raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
adata.obs_names = adata.obs[set_obs_names]
if not set_var_names == "":
if set_var_names not in adata.var_keys():
raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
if set_var_names not in list(adata.var.keys()):
raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
adata.var_names = adata.var[set_var_names]
if make_obs_names_unique:
adata.obs.index = make_index_unique(adata.obs.index)

2
server/common/colors.py
View File

@@ -228,6 +228,6 @@ def convert_anndata_category_colors_to_cxg_category_colors(data):
# create the cellxgene color entry for this category
cxg_colors[category_name] = dict(
zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
zip(data.obs[category_name].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
)
return cxg_colors

2
server/common/corpora.py
View File

@@ -22,7 +22,7 @@ def corpora_get_versions_from_anndata(adata):
"""
# per Corpora AnnData spec, this is a corpora file if the following is true
if "version" not in adata.uns_keys():
if "version" not in list(adata.uns.keys()):
return None
version = adata.uns["version"]
if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:

9
server/data_anndata/anndata_adaptor.py
View File

@@ -1,4 +1,5 @@
import warnings
import importlib.metadata
import anndata
import numpy as np
@@ -16,7 +17,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
from server.data_common.data_adaptor import DataAdaptor
from server.common.fbs.matrix import encode_matrix_fbs
anndata_version = version.parse(str(anndata.__version__)).release
anndata_version = version.parse(str(importlib.metadata.version('anndata'))).release
def anndata_version_is_pre_070():
@@ -63,7 +64,7 @@ class AnndataAdaptor(DataAdaptor):
return "cellxgene anndata adaptor version"
def get_library_versions(self):
return dict(anndata=str(anndata.__version__))
return dict(anndata=str(importlib.metadata.version('anndata')))
@staticmethod
def _create_unique_column_name(df, col_name_prefix):
@@ -313,11 +314,11 @@ class AnndataAdaptor(DataAdaptor):
layouts = self.dataset_config.embeddings__names
if layouts is None or len(layouts) == 0:
layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
layouts = [key[2:] for key in list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
# remove invalid layouts
valid_layouts = []
obsm_keys = self.data.obsm_keys()
obsm_keys = list(self.data.obsm.keys())
for layout in layouts:
layout_name = f"X_{layout}"
if layout_name not in obsm_keys: