Add user-generated annotations tests to the server (#1164)

* Add user-generated annotations tests to the server

Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969

* Auto-format python code

* @skip_if: passing lambdas > than property strings

* Respond to feedback from @bkmartinjr
This commit is contained in:
Matt Weiden
2020-02-23 15:32:13 -08:00
committed by GitHub
parent fb1f0c6469
commit c7f2032dd7
65 changed files with 377 additions and 223 deletions
+4 -4
View File
@@ -23,7 +23,6 @@ def anndata_version_is_pre_070():
class AnndataAdaptor(DataAdaptor):
def __init__(self, data_locator, config=None):
super().__init__(config)
self.data = None
@@ -127,7 +126,6 @@ class AnndataAdaptor(DataAdaptor):
"dataframe": {"nObs": self.cell_count, "nVar": self.gene_count, "type": str(self.data.X.dtype)},
"annotations": {
"obs": {"index": self.parameters.get("obs_names"), "columns": []},
"var": {"index": self.parameters.get("var_names"), "columns": []},
},
"layout": {"obs": []},
@@ -177,8 +175,10 @@ class AnndataAdaptor(DataAdaptor):
def _validate_and_initialize(self):
if anndata_version_is_pre_070() and self.config.anndata_backed:
warnings.warn(f"Use of --backed mode with anndata versions older than 0.7 will have serious "
"performance issues. Please update to at least anndata 0.7 or later.")
warnings.warn(
f"Use of --backed mode with anndata versions older than 0.7 will have serious "
"performance issues. Please update to at least anndata 0.7 or later."
)
# var and obs column names must be unique
if not self.data.obs.columns.is_unique or not self.data.var.columns.is_unique: