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refactor config to support different config options for datasets in different dataroots. (#1596)

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This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.
This commit is contained in:
bmccandless
2020-07-10 16:21:40 -07:00
committed by GitHub
parent 13246cb6d1
commit f69d141336
21 changed files with 1021 additions and 710 deletions
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server/common/rest.py
+21 -16
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@@ -97,12 +97,13 @@ def _query_parameter_to_filter(args):
return result
def schema_get_helper(data_adaptor, annotations):
def schema_get_helper(data_adaptor):
"""helper function to gather the schema from the data source and annotations"""
schema = data_adaptor.get_schema()
schema = copy.deepcopy(schema)
# add label obs annotations as needed
annotations = data_adaptor.dataset_config.user_annotations
if annotations is not None:
label_schema = annotations.get_schema(data_adaptor)
schema["annotations"]["obs"]["columns"].extend(label_schema)
@@ -110,20 +111,20 @@ def schema_get_helper(data_adaptor, annotations):
return schema
def schema_get(data_adaptor, annotations):
schema = schema_get_helper(data_adaptor, annotations)
def schema_get(data_adaptor):
schema = schema_get_helper(data_adaptor)
return make_response(jsonify({"schema": schema}), HTTPStatus.OK)
def config_get(app_config, data_adaptor, annotations):
config = app_config.get_client_config(data_adaptor, annotations)
def config_get(app_config, data_adaptor):
config = app_config.get_client_config(data_adaptor)
return make_response(jsonify(config), HTTPStatus.OK)
def annotations_obs_get(request, data_adaptor, annotations):
def annotations_obs_get(request, data_adaptor):
fields = request.args.getlist("annotation-name", None)
num_columns_requested = len(data_adaptor.get_obs_keys()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
if preferred_mimetype != "application/octet-stream":
@@ -131,6 +132,7 @@ def annotations_obs_get(request, data_adaptor, annotations):
try:
labels = None
annotations = data_adaptor.dataset_config.user_annotations
if annotations:
labels = annotations.read_labels(data_adaptor)
fbs = data_adaptor.annotation_to_fbs_matrix(Axis.OBS, fields, labels)
@@ -139,8 +141,9 @@ def annotations_obs_get(request, data_adaptor, annotations):
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
def annotations_put_fbs_helper(data_adaptor, fbs):
"""helper function to write annotations from fbs"""
annotations = data_adaptor.dataset_config.user_annotations
if annotations is None:
raise DisabledFeatureError("Writable annotations are not enabled")
@@ -150,7 +153,8 @@ def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
annotations.write_labels(new_label_df, data_adaptor)
def annotations_obs_put(request, data_adaptor, annotations):
def annotations_obs_put(request, data_adaptor):
annotations = data_adaptor.dataset_config.user_annotations
if annotations is None:
return abort(HTTPStatus.NOT_IMPLEMENTED)
@@ -163,17 +167,17 @@ def annotations_obs_put(request, data_adaptor, annotations):
annotations.set_collection(anno_collection)
try:
annotations_put_fbs_helper(data_adaptor, annotations, fbs)
annotations_put_fbs_helper(data_adaptor, fbs)
res = json.dumps({"status": "OK"})
return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"})
except (ValueError, DisabledFeatureError, KeyError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
def annotations_var_get(request, data_adaptor, annotations):
def annotations_var_get(request, data_adaptor):
fields = request.args.getlist("annotation-name", None)
num_columns_requested = len(data_adaptor.get_var_keys()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
if preferred_mimetype != "application/octet-stream":
@@ -181,6 +185,7 @@ def annotations_var_get(request, data_adaptor, annotations):
try:
labels = None
annotations = data_adaptor.dataset_config.user_annotations
if annotations is not None:
labels = annotations.read_labels(data_adaptor)
return make_response(
@@ -226,7 +231,7 @@ def data_var_get(request, data_adaptor):
def colors_get(data_adaptor):
if not data_adaptor.config.presentation__custom_colors:
if not data_adaptor.dataset_config.presentation__custom_colors:
return make_response(jsonify({}), HTTPStatus.OK)
try:
return make_response(jsonify(data_adaptor.get_colors()), HTTPStatus.OK)
@@ -235,7 +240,7 @@ def colors_get(data_adaptor):
def diffexp_obs_post(request, data_adaptor):
if not data_adaptor.config.diffexp__enable:
if not data_adaptor.dataset_config.diffexp__enable:
return abort(HTTPStatus.NOT_IMPLEMENTED)
args = request.get_json()
@@ -273,7 +278,7 @@ def diffexp_obs_post(request, data_adaptor):
def layout_obs_get(request, data_adaptor):
fields = request.args.getlist("layout-name", None)
num_columns_requested = len(data_adaptor.get_embedding_names()) if len(fields) == 0 else len(fields)
if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
return abort(HTTPStatus.BAD_REQUEST)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
@@ -296,7 +301,7 @@ def layout_obs_get(request, data_adaptor):
def layout_obs_put(request, data_adaptor):
if not data_adaptor.config.embedding__enable_reembedding:
if not data_adaptor.dataset_config.embedding__enable_reembedding:
return abort(HTTPStatus.NOT_IMPLEMENTED)
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])