diff --git a/server/app/rest_api/rest.py b/server/app/rest_api/rest.py index d9b10ad9..95dc7e17 100644 --- a/server/app/rest_api/rest.py +++ b/server/app/rest_api/rest.py @@ -193,7 +193,6 @@ class CellsAPI(Resource): def get(self): from app import data payload = { - "cellids": [], "metadata": [], "cellcount": 0, "graph": [], @@ -205,8 +204,7 @@ class CellsAPI(Resource): payload["metadata"] = data.metadata(filtered_data) payload["ranges"] = data.metadata_ranges(filtered_data) payload["graph"] = data.create_graph(filtered_data) - payload["cellids"] = data.cellids(filtered_data) - payload["cellcount"] = len(payload["cellids"]) + payload["cellcount"] = data.cell_count return make_payload(payload) diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py index c5e682b9..142f87a7 100644 --- a/server/app/scanpy_engine/scanpy_engine.py +++ b/server/app/scanpy_engine/scanpy_engine.py @@ -13,12 +13,15 @@ class ScanpyEngine(CXGDriver): def __init__(self, data, schema=None, graph_method="umap", diffexp_method="ttest"): self.data = self._load_data(data) self.schema = self._load_or_infer_schema(data, schema) - self._set_cell_ids() + self._set_cell_names() self.cell_count = self.data.shape[0] self.gene_count = self.data.shape[1] self.graph_method = graph_method self.diffexp_method = diffexp_method + def _set_cell_names(self): + self.data.obs["cell_name"] = list(self.data.obs.index) + @staticmethod def _load_data(data): return sc.read(os.path.join(data, "data.h5ad")) @@ -32,20 +35,9 @@ class ScanpyEngine(CXGDriver): data_schema = parse_schema(os.path.join(data, schema)) return data_schema - def _set_cell_ids(self): - self.data.obs["cxg_cell_id"] = list(range(self.data.obs.shape[0])) - self.data.obs["cell_name"] = list(self.data.obs.index) - self.data.obs.set_index("cxg_cell_id", inplace=True) - def cells(self): return list(self.data.obs.index) - def cellids(self, df=None): - if df: - return list(df.obs.index) - else: - return list(self.data.obs.index) - def genes(self): return self.data.var.index.tolist()