mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-30 03:58:11 +08:00
Reorganize order of methods in engine and rest (#305)
This commit is contained in:
Charlotte Weaver
+187
-177
@@ -12,6 +12,13 @@ from server.app.util.filter import parse_filter, QueryStringError
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from server.app.util.models import FilterModel
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from server.app.util.utils import MimeTypeError, get_mime_type
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"""
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Sort order for routes
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1. Initialize
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2. Data & Metadata
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3. Computation
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"""
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class SchemaAPI(Resource):
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@swagger.doc({
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@@ -109,75 +116,6 @@ class ConfigAPI(Resource):
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return make_response(jsonify(config), HTTPStatus.OK)
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class LayoutObsAPI(Resource):
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@swagger.doc({
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"summary": "Get the default layout for all observations.",
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"tags": ["layout"],
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"parameters": [],
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"responses": {
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"200": {
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"description": "layout",
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"examples": {
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"application/json": {
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"layout": {
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"ndims": 2,
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"coordinates": [
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[0, 0.284483, 0.983744],
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[1, 0.038844, 0.739444]
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]
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}
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}
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}
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}
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}
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})
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def get(self):
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return make_response((jsonify({"layout": current_app.data.layout(current_app.data.data)})), HTTPStatus.OK)
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@swagger.doc({
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"summary": "Observation layout for filtered subset.",
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"tags": ["layout"],
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"parameters": [
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{
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"name": "filter",
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"description": "Complex Filter",
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"in": "body",
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"schema": FilterModel
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}
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],
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"responses": {
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"200": {
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"description": "layout",
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"examples": {
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"application/json": {
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"layout": {
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"ndims": 2,
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"coordinates": [
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[0, 0.284483, 0.983744],
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[1, 0.038844, 0.739444]
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]
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}
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}
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}
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},
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"400": {
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"description": "Malformed filter"
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},
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"403": {
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"description": "Non-interactive request"
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},
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}
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})
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def post(self):
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try:
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df = current_app.data.filter_dataframe(request.get_json()["filter"])
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except KeyError:
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return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
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if len(df.obs.index) > current_app.data.features["layout"]["obs"]["interactiveLimit"]:
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return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
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return make_response((jsonify({"layout": current_app.data.layout(df)})), HTTPStatus.OK)
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class AnnotationsObsAPI(Resource):
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@swagger.doc({
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"summary": "Fetch annotations (metadata) for all observations.",
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@@ -367,112 +305,6 @@ class AnnotationsVarAPI(Resource):
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return make_response(jsonify(annotation_response), HTTPStatus.OK)
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class DiffExpObsAPI(Resource):
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@swagger.doc({
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"summary": "Generate differential expression (DE) statistics for two specified subsets of data, "
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"as indicated by the two provided observation complex filters",
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"tags": ["diffexp"],
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# TODO sort out params
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# "parameters": [
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# # {
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# # "in": "body",
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# # "name": "mode",
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# # "type": "string",
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# # "required": True,
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# # "description": "topN or varFilter"
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# # },
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# {
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# "in": "query",
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# "name": "count",
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# "type": "int32",
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# "description": "TopN mode: how many vars to return"
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# },
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# {
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# "in": "body",
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# "name": "varFilter",
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# "schema": FilterModel,
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# "description": "varFilter: Complex filter, only var for which vars to return"
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# },
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# {
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# "in": "body",
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# "name": "set1",
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# "schema": FilterModel,
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# "required": True,
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# "description": "Complex filter, only obs - observations in set1"
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# },
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# {
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# "in": "body",
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# "name": "set2",
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# "schema": FilterModel,
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# "description": "Complex filter, only obs - observations in set2. If not included, inverse of set1."
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# },
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# ],
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"responses": {
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"200": {
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"description": "Statistics are encoded as an array of arrays, with fields ordered as: "
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"varIndex, avgDiff, pVal, pValAdj, set1AvgExp, set2AvgExp",
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"examples": {
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"application/json": [
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[328, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
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[1250, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
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]
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}
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},
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"400": {
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"description": "malformed filter"
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},
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"403": {
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"description": "non-interactive request"
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},
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"501": {
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"description": "diffexp is not implemented"
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}
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}
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})
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def post(self):
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args = request.get_json()
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# confirm mode is present and legal
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try:
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mode = DiffExpMode(args["mode"])
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except KeyError:
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return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
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except ValueError:
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return make_response(f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST)
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# Validate filters
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if mode == DiffExpMode.VAR_FILTER:
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if "varFilter" not in args:
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return make_response("varFilter is required when mode is set to varFilter ", HTTPStatus.BAD_REQUEST)
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if Axis.OBS in args["varFilter"]["filter"]:
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return make_response("Obs filter not allowed in varFilter", HTTPStatus.BAD_REQUEST)
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if "set1" not in args:
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return make_response("set1 is required.", HTTPStatus.BAD_REQUEST)
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if Axis.VAR in args["set1"]["filter"]:
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return make_response("Var filter not allowed for set1", HTTPStatus.BAD_REQUEST)
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# set2
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if "set2" not in args:
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return make_response("Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED)
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if Axis.VAR in args["set2"]["filter"]:
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return make_response("Var filter not allowed for set2", HTTPStatus.BAD_REQUEST)
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set1_filter = args["set1"]["filter"]
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set2_filter = args.get("set2", {"filter": {}})["filter"]
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if "varFilter" in args:
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set1_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
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set2_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
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df1 = current_app.data.filter_dataframe(set1_filter, include_uns=False)
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# TODO inverse
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df2 = current_app.data.filter_dataframe(set2_filter, include_uns=False)
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# exceeds size limit
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if df1.shape[0] + df2.shape[0] > current_app.data.features["diffexp"]["interactiveLimit"]:
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return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
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# mode
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count = args.get("count", None)
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try:
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diffexp = current_app.data.diffexp(df1, df2, count)
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except ValueError as ve:
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return make_response(ve.message, HTTPStatus.BAD_REQUEST)
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return make_response(jsonify(diffexp), HTTPStatus.OK)
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class DataObsAPI(Resource):
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@swagger.doc({
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"summary": "Get data (expression values) from the dataframe.",
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@@ -682,15 +514,193 @@ class DataVarAPI(Resource):
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return make_response((jsonify(current_app.data.data_frame(df, axis=Axis.VAR))), HTTPStatus.OK)
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class DiffExpObsAPI(Resource):
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@swagger.doc({
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"summary": "Generate differential expression (DE) statistics for two specified subsets of data, "
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"as indicated by the two provided observation complex filters",
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"tags": ["diffexp"],
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# TODO sort out params
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# "parameters": [
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# # {
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# # "in": "body",
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# # "name": "mode",
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# # "type": "string",
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# # "required": True,
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# # "description": "topN or varFilter"
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# # },
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# {
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# "in": "query",
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# "name": "count",
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# "type": "int32",
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# "description": "TopN mode: how many vars to return"
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# },
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# {
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# "in": "body",
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# "name": "varFilter",
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# "schema": FilterModel,
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# "description": "varFilter: Complex filter, only var for which vars to return"
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# },
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# {
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# "in": "body",
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# "name": "set1",
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# "schema": FilterModel,
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# "required": True,
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# "description": "Complex filter, only obs - observations in set1"
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# },
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# {
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# "in": "body",
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# "name": "set2",
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# "schema": FilterModel,
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# "description": "Complex filter, only obs - observations in set2. If not included, inverse of set1."
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# },
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# ],
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"responses": {
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"200": {
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"description": "Statistics are encoded as an array of arrays, with fields ordered as: "
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"varIndex, avgDiff, pVal, pValAdj, set1AvgExp, set2AvgExp",
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"examples": {
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"application/json": [
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[328, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
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[1250, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
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]
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}
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},
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"400": {
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"description": "malformed filter"
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},
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"403": {
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"description": "non-interactive request"
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},
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"501": {
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"description": "diffexp is not implemented"
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}
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}
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})
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def post(self):
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args = request.get_json()
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# confirm mode is present and legal
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try:
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mode = DiffExpMode(args["mode"])
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except KeyError:
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return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
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except ValueError:
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return make_response(f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST)
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# Validate filters
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if mode == DiffExpMode.VAR_FILTER:
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if "varFilter" not in args:
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return make_response("varFilter is required when mode is set to varFilter ", HTTPStatus.BAD_REQUEST)
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if Axis.OBS in args["varFilter"]["filter"]:
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return make_response("Obs filter not allowed in varFilter", HTTPStatus.BAD_REQUEST)
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if "set1" not in args:
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return make_response("set1 is required.", HTTPStatus.BAD_REQUEST)
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if Axis.VAR in args["set1"]["filter"]:
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return make_response("Var filter not allowed for set1", HTTPStatus.BAD_REQUEST)
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# set2
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if "set2" not in args:
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return make_response("Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED)
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if Axis.VAR in args["set2"]["filter"]:
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return make_response("Var filter not allowed for set2", HTTPStatus.BAD_REQUEST)
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set1_filter = args["set1"]["filter"]
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set2_filter = args.get("set2", {"filter": {}})["filter"]
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if "varFilter" in args:
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set1_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
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set2_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
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df1 = current_app.data.filter_dataframe(set1_filter, include_uns=False)
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# TODO inverse
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df2 = current_app.data.filter_dataframe(set2_filter, include_uns=False)
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# exceeds size limit
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if df1.shape[0] + df2.shape[0] > current_app.data.features["diffexp"]["interactiveLimit"]:
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return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
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# mode
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count = args.get("count", None)
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try:
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diffexp = current_app.data.diffexp(df1, df2, count)
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except ValueError as ve:
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return make_response(ve.message, HTTPStatus.BAD_REQUEST)
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return make_response(jsonify(diffexp), HTTPStatus.OK)
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class LayoutObsAPI(Resource):
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@swagger.doc({
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"summary": "Get the default layout for all observations.",
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"tags": ["layout"],
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"parameters": [],
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"responses": {
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"200": {
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"description": "layout",
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"examples": {
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"application/json": {
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"layout": {
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"ndims": 2,
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"coordinates": [
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[0, 0.284483, 0.983744],
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[1, 0.038844, 0.739444]
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]
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}
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}
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}
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}
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}
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})
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def get(self):
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return make_response((jsonify({"layout": current_app.data.layout(current_app.data.data)})), HTTPStatus.OK)
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@swagger.doc({
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"summary": "Observation layout for filtered subset.",
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"tags": ["layout"],
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"parameters": [
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{
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"name": "filter",
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"description": "Complex Filter",
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"in": "body",
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"schema": FilterModel
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}
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],
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"responses": {
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"200": {
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"description": "layout",
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"examples": {
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"application/json": {
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"layout": {
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"ndims": 2,
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"coordinates": [
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[0, 0.284483, 0.983744],
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[1, 0.038844, 0.739444]
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]
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}
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}
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}
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},
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"400": {
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"description": "Malformed filter"
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},
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"403": {
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"description": "Non-interactive request"
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},
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}
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})
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def post(self):
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try:
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df = current_app.data.filter_dataframe(request.get_json()["filter"])
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except KeyError:
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return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
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if len(df.obs.index) > current_app.data.features["layout"]["obs"]["interactiveLimit"]:
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return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
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return make_response((jsonify({"layout": current_app.data.layout(df)})), HTTPStatus.OK)
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def get_api_resources():
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bp = Blueprint("api", __name__, url_prefix="/api/v0.2")
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api = Api(bp, add_api_spec_resource=False)
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# Initialization routes
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api.add_resource(SchemaAPI, "/schema")
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api.add_resource(ConfigAPI, "/config")
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api.add_resource(LayoutObsAPI, "/layout/obs")
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# Data routes
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api.add_resource(AnnotationsObsAPI, "/annotations/obs")
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api.add_resource(DiffExpObsAPI, "/diffexp/obs")
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api.add_resource(AnnotationsVarAPI, "/annotations/var")
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api.add_resource(DataObsAPI, "/data/obs")
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api.add_resource(DataVarAPI, "/data/var")
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# Computation routes
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api.add_resource(DiffExpObsAPI, "/diffexp/obs")
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api.add_resource(LayoutObsAPI, "/layout/obs")
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return api
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