mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-26 00:18:12 +08:00
Makefile modularity, test targets, and auto-formatting (#1070)
* Fix Makefile whitespace and .PHONY use
* Fix Makefile filename
* Modularize Makefile into client and server Makefiles
Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.
This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.
* Add auto-formatting to client and server modules
One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.
* Add yapf for automatic code formatting
* Add a root test target that calls sub-tests
* Apply yapf to python files
* Do not duplicate npm commands, simply pass through
* Update documentation
* Do not shadow reserved word len
* Add general test target
* Fix make call in dev-env
* Use black instead of yapf
* Run flake8 from the root directory
* Revert "Apply yapf to python files"
This reverts commit cdca128a01.
* Apply black to python code
* Resolve lint errors resulting from black format
* Add explanation of server unit tests in dev guidelines
This commit is contained in:
Matt Weiden
+34
-91
@@ -8,13 +8,7 @@ from flask_restful import Api, Resource
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from server import __version__ as cellxgene_version
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from anndata import __version__ as anndata_version
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from server.app.util.constants import (
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Axis,
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DiffExpMode,
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JSON_NaN_to_num_warning_msg,
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CXGUID,
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CXG_ANNO_COLLECTION
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)
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from server.app.util.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg, CXGUID, CXG_ANNO_COLLECTION
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from server.app.util.errors import (
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FilterError,
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InteractiveError,
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@@ -40,41 +34,18 @@ class ConfigAPI(Resource):
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config = {
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"config": {
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"features": [
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{
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"method": "POST",
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"path": "/cluster/",
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**current_app.data.features["cluster"],
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},
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{
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"method": "POST",
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"path": "/layout/obs",
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**current_app.data.features["layout"]["obs"],
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},
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{
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"method": "POST",
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"path": "/layout/var",
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**current_app.data.features["layout"]["var"],
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},
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{
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"method": "POST",
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"path": "/diffexp/",
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**current_app.data.features["diffexp"],
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},
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{"method": "POST", "path": "/cluster/", **current_app.data.features["cluster"]},
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{"method": "POST", "path": "/layout/obs", **current_app.data.features["layout"]["obs"]},
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{"method": "POST", "path": "/layout/var", **current_app.data.features["layout"]["var"]},
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{"method": "POST", "path": "/diffexp/", **current_app.data.features["diffexp"]},
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],
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"displayNames": {
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"engine": f"cellxgene Scanpy engine version ",
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"dataset": current_app.config["DATASET_TITLE"],
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},
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"links": {
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"about-dataset": current_app.config["ABOUT_DATASET"]
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},
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"parameters": {
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**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)
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},
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"library_versions": {
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"cellxgene": cellxgene_version,
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"anndata": anndata_version
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}
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"links": {"about-dataset": current_app.config["ABOUT_DATASET"]},
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"parameters": {**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)},
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"library_versions": {"cellxgene": cellxgene_version, "anndata": anndata_version},
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}
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}
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@@ -84,17 +55,13 @@ class ConfigAPI(Resource):
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class AnnotationsObsAPI(Resource):
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def get(self):
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fields = request.args.getlist("annotation-name", None)
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/octet-stream"]
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)
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preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
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cxguid = get_userid(session)
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anno_collection = get_anno_collection(session)
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try:
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if preferred_mimetype == "application/octet-stream":
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fbs = current_app.data.annotation_to_fbs_matrix("obs", fields, uid=cxguid, collection=anno_collection)
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return make_response(fbs,
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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return make_response(fbs, HTTPStatus.OK, {"Content-Type": "application/octet-stream"})
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except KeyError:
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@@ -115,9 +82,7 @@ class AnnotationsObsAPI(Resource):
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try:
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fbs = request.get_data()
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res = current_app.data.annotation_put_fbs("obs", fbs, uid=cxguid, collection=anno_collection)
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return make_response(
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res, HTTPStatus.OK, {"Content-Type": "application/json"}
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)
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return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"})
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except (ValueError, DisabledFeatureError, KeyError) as e:
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return make_response(str(e), HTTPStatus.BAD_REQUEST)
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except Exception as e:
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@@ -127,14 +92,14 @@ class AnnotationsObsAPI(Resource):
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class AnnotationsVarAPI(Resource):
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def get(self):
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fields = request.args.getlist("annotation-name", None)
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/octet-stream"]
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)
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preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
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try:
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if preferred_mimetype == "application/octet-stream":
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return make_response(current_app.data.annotation_to_fbs_matrix("var", fields),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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return make_response(
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current_app.data.annotation_to_fbs_matrix("var", fields),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"},
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)
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except KeyError:
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@@ -145,19 +110,16 @@ class AnnotationsVarAPI(Resource):
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class DataVarAPI(Resource):
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def put(self):
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/octet-stream"]
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)
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preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
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try:
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if preferred_mimetype == "application/octet-stream":
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filter_json = request.get_json()
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filter = filter_json["filter"] if filter_json else None
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return make_response(
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current_app.data.data_frame_to_fbs_matrix(
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filter, axis=Axis.VAR
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),
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current_app.data.data_frame_to_fbs_matrix(filter, axis=Axis.VAR),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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{"Content-Type": "application/octet-stream"},
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)
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except FilterError as e:
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@@ -175,35 +137,23 @@ class DiffExpObsAPI(Resource):
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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(
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f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST
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)
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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 or "varFilter" in args:
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# not NOT_IMPLEMENTED
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return make_response(
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"mode=varfilter not implemented", HTTPStatus.NOT_IMPLEMENTED
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)
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return make_response("mode=varfilter not implemented", HTTPStatus.NOT_IMPLEMENTED)
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if mode == DiffExpMode.TOP_N and "count" not in args:
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return make_response(
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"mode=topN requires a count parameter", HTTPStatus.BAD_REQUEST
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)
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return make_response("mode=topN requires a count parameter", 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(
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"Var filter not allowed for set1", HTTPStatus.BAD_REQUEST
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)
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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(
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"Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED
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)
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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(
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"Var filter not allowed for set2", HTTPStatus.BAD_REQUEST
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)
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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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@@ -214,14 +164,9 @@ class DiffExpObsAPI(Resource):
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count = args.get("count", None)
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try:
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diffexp = current_app.data.diffexp_topN(
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set1_filter,
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set2_filter,
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count,
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current_app.data.features["diffexp"]["interactiveLimit"],
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)
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return make_response(
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diffexp, HTTPStatus.OK, {"Content-Type": "application/json"}
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set1_filter, set2_filter, count, current_app.data.features["diffexp"]["interactiveLimit"],
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)
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return make_response(diffexp, HTTPStatus.OK, {"Content-Type": "application/json"})
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except (ValueError, FilterError) as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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except InteractiveError:
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@@ -236,14 +181,12 @@ class DiffExpObsAPI(Resource):
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class LayoutObsAPI(Resource):
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def get(self):
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/octet-stream"]
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)
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preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
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try:
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if preferred_mimetype == "application/octet-stream":
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return make_response(current_app.data.layout_to_fbs_matrix(),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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return make_response(
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current_app.data.layout_to_fbs_matrix(), HTTPStatus.OK, {"Content-Type": "application/octet-stream"}
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)
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except PrepareError as e:
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@@ -278,7 +221,7 @@ def is_safe_collection_name(name):
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"""
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if name is None:
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return False
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return re.match(r'^\w+$', name) is not None
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return re.match(r"^\w+$", name) is not None
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def get_api_resources():
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