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Do not calculate layout, used saved layout instead (#343)

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* Do not calculate layout, used saved layout instead

See for rationale: https://docs.google.com/document/d/1HJFvbdDHxxgkCW0DZzdTZ9CUMgc2ef2rQFukATBQWvE/edit

* Error handling for when layout has not been precomputed

* Server error (500) not client error (400) for unprepared data
This commit is contained in:
Charlotte Weaver
2018-10-18 11:51:38 -07:00
committed by GitHub
parent 2616b5c185
commit 06f402ab0a
5 changed files with 92 additions and 70 deletions
Download Patch File Download Diff File Expand all files Collapse all files
docs/REST_API.md
+5 -1
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@@ -460,8 +460,12 @@ Get the _default_ layout for all observations or (_future_) all variables. Retur
}
}
```
**Response code:**
### PUT /layout/obs, (_future_) PUT /layout/var
- 200 - success
- 500 Internal Server Error - unprepared data, layout has not been stored in the input data
### (_future_) PUT /layout/obs, (_future_) PUT /layout/var
Generate layout for the caller-specified subset of data, as indicated by the filter. This operation implicitly requests a re-layout operation to be performed on the specified data. This operation will _commonly_ return the same results for any given caller-specified filter, but this behavior is not guaranteed.
server/app/rest_api/rest.py
+53 -46
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@@ -10,7 +10,7 @@ from werkzeug.datastructures import ImmutableMultiDict
from server.app.util.constants import Axis, DiffExpMode
from server.app.util.filter import parse_filter, QueryStringError
from server.app.util.models import FilterModel
from server.app.util.utils import FilterError, InteractiveError, MimeTypeError, get_mime_type
from server.app.util.utils import FilterError, InteractiveError, MimeTypeError, PrepareError, get_mime_type
"""
Sort order for routes
@@ -630,56 +630,63 @@ class LayoutObsAPI(Resource):
}
}
}
},
"400": {
"description": "Data preparation error"
}
}
})
def get(self):
return make_response((jsonify({"layout": current_app.data.layout({})})), HTTPStatus.OK)
@swagger.doc({
"summary": "Observation layout for filtered subset.",
"tags": ["layout"],
"parameters": [
{
"name": "filter",
"description": "Complex Filter",
"in": "body",
"schema": FilterModel
}
],
"responses": {
"200": {
"description": "layout",
"examples": {
"application/json": {
"layout": {
"ndims": 2,
"coordinates": [
[0, 0.284483, 0.983744],
[1, 0.038844, 0.739444]
]
}
}
}
},
"400": {
"description": "Malformed filter"
},
"403": {
"description": "Non-interactive request"
},
}
})
def put(self):
try:
filter = request.get_json()["filter"]
interactive_limit = current_app.data.features["layout"]["obs"]["interactiveLimit"]
layout = current_app.data.layout(filter, interactive_limit=interactive_limit)
return make_response(jsonify({"layout": layout}), HTTPStatus.OK)
except FilterError as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except InteractiveError:
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
layout = current_app.data.layout({})
except PrepareError as e:
return make_response(e.message, HTTPStatus.INTERNAL_SERVER_ERROR)
return make_response((jsonify({"layout": layout})), HTTPStatus.OK)
# @swagger.doc({
# "summary": "Observation layout for filtered subset.",
# "tags": ["layout"],
# "parameters": [
# {
# "name": "filter",
# "description": "Complex Filter",
# "in": "body",
# "schema": FilterModel
# }
# ],
# "responses": {
# "200": {
# "description": "layout",
# "examples": {
# "application/json": {
# "layout": {
# "ndims": 2,
# "coordinates": [
# [0, 0.284483, 0.983744],
# [1, 0.038844, 0.739444]
# ]
# }
# }
# }
# },
# "400": {
# "description": "Malformed filter"
# },
# "403": {
# "description": "Non-interactive request"
# },
# }
# })
# def put(self):
# try:
# filter = request.get_json()["filter"]
# interactive_limit = current_app.data.features["layout"]["obs"]["interactiveLimit"]
# layout = current_app.data.layout(filter, interactive_limit=interactive_limit)
# return make_response(jsonify({"layout": layout}), HTTPStatus.OK)
# except FilterError as e:
# return make_response(e.message, HTTPStatus.BAD_REQUEST)
# except InteractiveError:
# return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
def get_api_resources():
server/app/scanpy_engine/scanpy_engine.py
+9 -4
View File
@@ -9,7 +9,7 @@ from scipy import stats
from server.app.app import cache
from server.app.driver.driver import CXGDriver
from server.app.util.constants import Axis, DEFAULT_TOP_N, DiffExpMode
from server.app.util.utils import FilterError, InteractiveError
from server.app.util.utils import FilterError, InteractiveError, PrepareError
"""
Sort order for methods
@@ -30,7 +30,6 @@ class ScanpyEngine(CXGDriver):
self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1]
self._create_schema()
self.layout({})
def _create_schema(self):
self.schema = {
@@ -340,8 +339,14 @@ class ScanpyEngine(CXGDriver):
# TODO Filtering cells is fine, but filtering genes does nothing because the neighbors are
# calculated using the original vars (geneset) and this doesn’t get updated when you use less.
# Need to recalculate neighbors (long) if user requests new layout filtered by var
getattr(sc.tl, self.layout_method)(df, random_state=123)
df_layout = df.obsm[f"X_{self.layout_method}"]
# TODO for MVP we are pushing computation of layout to preprocessing and not allowing re-layout
# this will probably change after user feedback
# getattr(sc.tl, self.layout_method)(df, random_state=123)
try:
df_layout = df.obsm[f"X_{self.layout_method}"]
except ValueError as e:
raise PrepareError(f"Layout has not been calculated using {self.layout_method}, "
f"please prepare your datafile and relaunch cellxgene") from e
normalized_layout = DataFrame((df_layout - df_layout.min()) / (df_layout.max() - df_layout.min()),
index=df.obs.index)
return {
server/app/util/utils.py
+6
View File
@@ -30,6 +30,12 @@ class InteractiveError(Exception):
self.message = message
class PrepareError(Exception):
def __init__(self, message):
self.message = message
def get_mime_type(default="application/json", acceptable_types=["application/json", "text/csv"], query_param=None,
header=None):
mime_type = default
server/test/test_api.py
+19 -19
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@@ -70,27 +70,27 @@ class EndPoints(unittest.TestCase):
self.assertEqual(result_data["layout"]["ndims"], 2)
self.assertEqual(len(result_data["layout"]["coordinates"]), 2638)
def test_put_layout(self):
endpoint = "layout/obs"
url = f"{URL_BASE}{endpoint}"
obs_filter = {
"filter": {
"obs": {
"annotation_value": [
{"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
{"name": "n_counts", "min": 3000},
],
"index": [1, 99, [1000, 2000]]
}
}
}
result = self.session.put(url, json=obs_filter)
self.assertEqual(result.status_code, HTTPStatus.OK)
result_data = result.json()
self.assertEqual(len(result_data["layout"]["coordinates"]), 15)
# def test_put_layout(self):
# endpoint = "layout/obs"
# url = f"{URL_BASE}{endpoint}"
# obs_filter = {
# "filter": {
# "obs": {
# "annotation_value": [
# {"name": "louvain", "values": ["NK cells", "CD8 T cells"]},
# {"name": "n_counts", "min": 3000},
# ],
# "index": [1, 99, [1000, 2000]]
# }
# }
# }
# result = self.session.put(url, json=obs_filter)
# self.assertEqual(result.status_code, HTTPStatus.OK)
# result_data = result.json()
# self.assertEqual(len(result_data["layout"]["coordinates"]), 15)
def test_bad_filter(self):
endpoints = ["layout/obs", "annotations/obs", "annotations/var", "data/obs", "data/var"]
endpoints = ["annotations/obs", "annotations/var", "data/obs", "data/var"]
for endpoint in endpoints:
url = f"{URL_BASE}{endpoint}"
result = self.session.put(url, json=BAD_FILTER)