diff --git a/server/app/app.py b/server/app/app.py
index 09b8d9d5..f3eb05ea 100644
--- a/server/app/app.py
+++ b/server/app/app.py
@@ -1,7 +1,7 @@
import os
import datetime
-from flask import Flask, redirect, current_app, make_response, render_template
+from flask import Flask, redirect, current_app, make_response, render_template, abort
from flask import Blueprint, request, send_from_directory
from flask_caching import Cache
from flask_compress import Compress
@@ -14,7 +14,7 @@ import server.common.rest as common_rest
from server.common.errors import DatasetAccessError
from server.common.utils import path_join, Float32JSONEncoder
from server.common.data_locator import DataLocator
-from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
+from server.data_common.matrix_loader import MatrixDataLoader
from functools import wraps
@@ -85,12 +85,8 @@ def static_redirect(dataset, therest):
return redirect(f"/static/{therest}", code=301)
-def dataroot_index():
- # FIXME with a splash screen that includes a listing of all the datasets.
- # or perhaps a login screen if this is a hosted environment,
- # or have a configuration option to redirect to a user specified page.
-
- # the following is just for demo purposes...
+def dataroot_test_index():
+ # the following index page is meant for testing/debugging purposes
data = ''
data += 'Hosted Cellxgene'
data += 'Welcome to cellxgene
'
@@ -101,9 +97,12 @@ def dataroot_index():
datasets = []
for fname in locator.ls():
location = path_join(config.dataroot, fname)
- matrix_data_loader = MatrixDataLoader(location)
- if matrix_data_loader.etype != MatrixDataType.UNKNOWN:
+ try:
+ MatrixDataLoader(location, app_config=config)
datasets.append(fname)
+ except DatasetAccessError:
+ # skip over invalid datasets
+ pass
data += '
Select one of these datasets...
'
data += ''
@@ -118,6 +117,17 @@ def dataroot_index():
return make_response(data)
+def dataroot_index():
+ # Handle the base url for the cellxgene server when running in multi dataset mode
+ config = current_app.app_config
+ if not config.multi_dataset_index:
+ abort(404)
+ elif config.multi_dataset_index is True:
+ return dataroot_test_index()
+ else:
+ return redirect(config.dataroot_index)
+
+
class SchemaAPI(Resource):
@rest_get_data_adaptor
def get(self, data_adaptor):
diff --git a/server/common/app_config.py b/server/common/app_config.py
index f2b54811..e8798e1e 100644
--- a/server/common/app_config.py
+++ b/server/common/app_config.py
@@ -35,6 +35,15 @@ class AppConfig(object):
self.enable_reembedding = False
self.anndata_backed = False
+ # The index page when in multi-dataset mode:
+ # False or None: this returns a 404 code
+ # True: loads a test index page, which links to the datasets that are available in the dataroot
+ # string/URL: redirect to this URL: flask.redirect(config.multi_dataset_index)
+ self.multi_dataset_index = False
+
+ # A list of allowed matrix types. If an empty list, then all matrix types are allowed
+ self.multi_dataset_allowed_matrix_type = []
+
# TODO these options may not apply to all datasets in the multi dataset.
# may need to invent a way to associate these config parameters with
# specific datasets.
@@ -58,12 +67,13 @@ class AppConfig(object):
"anndata_backed",
"disable_diffexp",
"enable_reembedding",
+ "multi_dataset_index",
+ "multi_dataset_allowed_matrix_type",
]
self.update(inputs, kw)
def update(self, inputs, kw):
-
for k, v in kw.items():
if k in inputs:
setattr(self, k, v)
diff --git a/server/common/rest.py b/server/common/rest.py
index 0845b945..a446ae02 100644
--- a/server/common/rest.py
+++ b/server/common/rest.py
@@ -68,11 +68,12 @@ def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
def annotations_obs_put(request, data_adaptor, annotations):
- anno_collection = request.args.get("annotation-collection-name", default=None)
- fbs = request.get_data()
if annotations is None:
return make_response("Error, annotations are not configured", HTTPStatus.BAD_REQUEST)
+ anno_collection = request.args.get("annotation-collection-name", default=None)
+ fbs = request.get_data()
+
if anno_collection is not None:
if not annotations.is_safe_collection_name(anno_collection):
return make_response(f"Error, bad annotation collection name", HTTPStatus.BAD_REQUEST)
@@ -130,11 +131,14 @@ def data_var_put(request, data_adaptor):
def diffexp_obs_post(request, data_adaptor):
+ if data_adaptor.config.disable_diffexp:
+ return make_response(f"diffexp not supported.", HTTPStatus.BAD_REQUEST)
+
args = request.get_json()
# confirm mode is present and legal
try:
mode = DiffExpMode(args["mode"])
- except KeyError:
+ except (KeyError, TypeError):
return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
except ValueError:
return make_response(f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST)
diff --git a/server/data_common/matrix_loader.py b/server/data_common/matrix_loader.py
index 41a32f7d..e684d730 100644
--- a/server/data_common/matrix_loader.py
+++ b/server/data_common/matrix_loader.py
@@ -119,7 +119,7 @@ class MatrixDataCacheManager(object):
del self.datasets[oldest_key]
last_accessed = time.time()
- loader = MatrixDataLoader(location)
+ loader = MatrixDataLoader(location, app_config=app_config)
cache_item = MatrixDataCacheItem(loader)
self.datasets[location] = (cache_item, last_accessed)
try:
@@ -136,24 +136,31 @@ class MatrixDataType(Enum):
class MatrixDataLoader(object):
- def __init__(self, location, etype=None):
+ def __init__(self, location, matrix_data_type=None, app_config=None):
""" location can be a string or DataLocator """
self.location = DataLocator(location)
- if etype is None:
- self.etype = self.matrix_data_type()
- else:
- self.etype = etype
+ # matrix_data_type is an enum value of type MatrixDataType
+ self.matrix_data_type = matrix_data_type
+ # matrix_type is a DataAdaptor type, which corresonds to the matrix_data_type
self.matrix_type = None
- if self.etype == MatrixDataType.H5AD:
+
+ if matrix_data_type is None:
+ self.matrix_data_type = self.__matrix_data_type()
+
+ if not self.__matrix_data_type_allowed(app_config):
+ raise DatasetAccessError(
+ f"{self.location} does not have an allowed type: {str(self.matrix_data_type)}")
+
+ if self.matrix_data_type == MatrixDataType.H5AD:
from server.data_anndata.anndata_adaptor import AnndataAdaptor
self.matrix_type = AnndataAdaptor
- elif self.etype == MatrixDataType.CXG:
+ elif self.matrix_data_type == MatrixDataType.CXG:
from server.data_cxg.cxg_adaptor import CxgAdaptor
self.matrix_type = CxgAdaptor
- def matrix_data_type(self):
+ def __matrix_data_type(self):
if self.location.path.endswith(".h5ad"):
return MatrixDataType.H5AD
elif ".cxg" in self.location.path:
@@ -161,8 +168,31 @@ class MatrixDataLoader(object):
else:
return MatrixDataType.UNKNOWN
+ def __matrix_data_type_allowed(self, app_config):
+ if self.matrix_data_type == MatrixDataType.UNKNOWN:
+ return False
+
+ if not app_config:
+ return True
+ if not app_config.dataroot:
+ return True
+ if len(app_config.multi_dataset_allowed_matrix_type) == 0:
+ return True
+
+ for val in app_config.multi_dataset_allowed_matrix_type:
+ try:
+ if self.matrix_data_type == MatrixDataType(val):
+ return True
+ except ValueError:
+ # Check case where multi_dataset_allowed_matrix_type does not have a
+ # valid MatrixDataType value. TODO: Add a feature to check
+ # the AppConfig for errors on startup
+ return False
+
+ return False
+
def pre_load_validation(self):
- if self.etype == MatrixDataType.UNKNOWN:
+ if self.matrix_data_type == MatrixDataType.UNKNOWN:
raise DatasetAccessError(f"{self.location} does not have a recognized type: .h5ad or .cxg")
self.matrix_type.pre_load_validation(self.location)
diff --git a/server/eb/app.py b/server/eb/app.py
index 98cdfe90..5ff0600e 100644
--- a/server/eb/app.py
+++ b/server/eb/app.py
@@ -45,7 +45,9 @@ try:
obs_names=None,
var_names=None,
anndata_backed=False,
- disable_diffexp=False,
+ disable_diffexp=True,
+ multi_dataset_index=None,
+ multi_dataset_allowed_matrix_type=["cxg"],
)
matrix_data_cache_manager = MatrixDataCacheManager()