mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-16 05:07:55 +08:00
91 lines
2.9 KiB
Python
91 lines
2.9 KiB
Python
from abc import ABCMeta, abstractmethod
|
|
|
|
from server.common.errors import DisabledFeatureError
|
|
from server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
|
|
from server.common.genesets import write_gene_sets_tidycsv
|
|
|
|
|
|
class Annotations(metaclass=ABCMeta):
|
|
"""baseclass for annotations and gene sets"""
|
|
|
|
def __init__(self, config={}):
|
|
self.config = config
|
|
|
|
def user_annotations_enabled(self):
|
|
return self.config.get("user-annotations", False)
|
|
|
|
def gene_sets_save_enabled(self):
|
|
return self.config.get("genesets-save", False)
|
|
|
|
def check_user_annotations_enabled(self):
|
|
if not self.user_annotations_enabled():
|
|
raise DisabledFeatureError("User annotations are disabled.")
|
|
|
|
def check_gene_sets_save_enabled(self):
|
|
if not self.gene_sets_save_enabled():
|
|
raise DisabledFeatureError("User gene sets save is disabled.")
|
|
|
|
def get_schema(self, data_adaptor):
|
|
schema = []
|
|
labels = self.read_labels(data_adaptor)
|
|
if labels is not None and not labels.empty:
|
|
for col in labels.columns:
|
|
col_schema = dict(name=col, writable=True)
|
|
col_schema.update(get_schema_type_hint_of_array(labels[col]))
|
|
schema.append(col_schema)
|
|
|
|
return schema
|
|
|
|
@abstractmethod
|
|
def set_collection(self, name):
|
|
"""set or create a new annotation collection"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def read_labels(self, data_adaptor):
|
|
"""Return the labels as a pandas.DataFrame"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def write_labels(self, df, data_adaptor):
|
|
"""Write the labels (df) to a persistent storage such that it can later be read"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def read_gene_sets(self, data_adaptor):
|
|
"""Return the gene sets from persistent storage"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def write_gene_sets(self, gs, tid, data_adaptor):
|
|
"""Write the gene sets (gs) to a persistent storage such that it can later be read"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def update_parameters(self, parameters, data_adaptor):
|
|
"""Update configuration parameters that describe information about the annotations feature"""
|
|
pass
|
|
|
|
@staticmethod
|
|
def gene_sets_to_csv(genesets):
|
|
"""
|
|
Convert the internal gene sets format (returned by read_gene_set) into
|
|
the simple Tidy CSV.
|
|
"""
|
|
from io import StringIO
|
|
|
|
if isinstance(genesets, dict):
|
|
genesets = genesets.values()
|
|
|
|
with StringIO() as sio:
|
|
write_gene_sets_tidycsv(sio, genesets)
|
|
return sio.getvalue()
|
|
|
|
@staticmethod
|
|
def gene_sets_to_response(genesets):
|
|
"""
|
|
Convert the internal gene sets format (returned by read_gene_set) into
|
|
the dict expected by the JSON REST API
|
|
"""
|
|
return list(genesets.values())
|