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/data/var (#295)

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* Upgrade version of scanpy

* /data/var

This works for everything except the case where there is only one gene. Anndata flattens X when there is only one var thus causing the transpose to fail.

* Fix edge case when an axis (obs/var) only contains 1 element
This commit is contained in:
Charlotte Weaver
2018-10-03 15:09:46 -07:00
committed by GitHub
parent 467ae94faf
commit 187bbfdcf7
5 changed files with 221 additions and 69 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/rest_api/rest.py
+99 -2
View File
@@ -478,7 +478,7 @@ class DataObsAPI(Resource):
return make_response(e.message, HTTPStatus.BAD_REQUEST)
df = current_app.data.filter_dataframe(filter_, include_uns=False)
if accept_type and accept_type[0] == "application/json":
return make_response((jsonify(current_app.data.data_frame(df))))
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.OBS))))
# TODO support CSV
else:
return make_response(f"Unsupported accept-type: {accept_type}", HTTPStatus.NOT_ACCEPTABLE)
@@ -520,7 +520,103 @@ class DataObsAPI(Resource):
# TODO catch error for bad filter
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
if request.accept_mimetypes.best_match(['application/json']):
return make_response((jsonify(current_app.data.data_frame(df))))
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.OBS))))
# TODO support CSV
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
class DataVarAPI(Resource):
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
"tags": ["data"],
"parameters": [
{
"in": "query",
"name": "filter",
"type": "string",
"description": "axis:key:value"
},
{
"in": "query",
"name": "accept-type",
"type": "string",
"description": "MIME type"
},
],
"responses": {
"200": {
"description": "expression",
"examples": {
"application/json": {
"obs": [0, 20000],
"var": [
[1, 39483, 3902, 203, 0, 0, 28]
]
}
}
},
"400": {
"description": "Malformed filter"
},
"406": {
"description": "Unacceptable MIME type"
},
}
})
def get(self):
# request.args is immutable
args = dict(request.args)
accept_type = args.pop("accept-type", None)
try:
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
except QueryStringError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
df = current_app.data.filter_dataframe(filter_, include_uns=False)
if accept_type and accept_type[0] == "application/json":
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.VAR))))
# TODO support CSV
else:
return make_response(f"Unsupported accept-type: {accept_type}", HTTPStatus.NOT_ACCEPTABLE)
@swagger.doc({
"summary": "Get data (expression values) from the dataframe.",
"tags": ["data"],
"parameters": [
{
'name': 'filter',
'description': 'Complex Filter',
'in': 'body',
'schema': FilterModel
}
],
"responses": {
"200": {
"description": "expression",
"examples": {
"application/json": {
"obs": [0, 20000],
"var": [
[1, 39483, 3902, 203, 0, 0, 28]
]
}
}
},
"400": {
"description": "Malformed filter"
},
"406": {
"description": "Unacceptable MIME type"
},
}
})
def put(self):
if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
# TODO catch error for bad filter
df = current_app.data.filter_dataframe(request.get_json()["filter"], include_uns=False)
if request.accept_mimetypes.best_match(['application/json']):
return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.VAR))))
# TODO support CSV
else:
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
@@ -536,4 +632,5 @@ def get_api_resources():
api.add_resource(DiffExpObsAPI, "/diffexp/obs")
api.add_resource(AnnotationsVarAPI, "/annotations/var")
api.add_resource(DataObsAPI, "/data/obs")
api.add_resource(DataVarAPI, "/data/var")
return api
server/app/scanpy_engine/scanpy_engine.py
+22 -7
View File
@@ -280,7 +280,7 @@ class ScanpyEngine(CXGDriver):
return sorted(result, key=lambda gene: gene[0])
# @cache.memoize()
def data_frame(self, df):
def data_frame(self, df, axis):
"""
Retrieves data for each variable for observations in data frame
:param df: from filter_cells, dataframe
@@ -289,9 +289,24 @@ class ScanpyEngine(CXGDriver):
"obs": [cellid, var1 expression, var2 expression, ...],
}
"""
var_index = df.var.index.tolist()
expression = DataFrame(df.X, index=df.obs.index)
return {
"var": var_index,
"obs": expression.reset_index().values.tolist()
}
var_idx = df.var.index.tolist()
obs_idx = df.obs.index.tolist()
values = df.X
df_shape = df.shape
if df_shape[0] == 1:
values = values[None, :]
elif df_shape[1] == 1:
values = values[:, None]
if axis == Axis.OBS:
expression = DataFrame(values, index=obs_idx)
result = {
"var": var_idx,
"obs": expression.reset_index().values.tolist()
}
else:
expression = DataFrame(values.T, index=var_idx)
result = {
"obs": obs_idx,
"var": expression.reset_index().values.tolist(),
}
return result