updated import to reflect change in werkzeug api

.gitignore

@@ -136,6 +136,3 @@ dmypy.json
 .pyre/
 
 # End of https://www.gitignore.io/api/python
-
-*.patch
-.vscode

Changelog.md

@@ -1,7 +0,0 @@
-# 0.2.0
-
-Incrementing minor version since the changes for 0.15 are breaking, and we may want to release bugfixes from 0.1.0 branch.
-
-# 0.1.1
-
-Added support for cellxgene 0.15

Readme.md

@@ -67,8 +67,6 @@ Optional environment variables:
 * `GATEWAY_PORT` - local port that the gateway should bind to, defaults to 5005
 * `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
 * `GATEWAY_ENABLE_UPLOAD` - Set to `true` or `1` to enable HTTP uploads. This is not recommended for a public server.
-* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
-* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.  
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 

cellxgene_gateway/__init__.py

@@ -6,5 +6,3 @@
 # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
-
-__version__ = "0.2.0"

cellxgene_gateway/env.py

@@ -21,7 +21,6 @@ extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
 enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
 enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in ['true', '1']
-enable_backed_mode = os.environ.get("GATEWAY_ENABLE_BACKED_MODE", "").lower() in ['true', '1']
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
@@ -37,7 +36,6 @@ optional_env_vars = {
     "GATEWAY_TTL": ttl,
     "GATEWAY_ENABLE_UPLOAD": enable_upload,
     "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
-    "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
 }
 
 def validate():

cellxgene_gateway/filecrawl.py

@@ -1,12 +1,3 @@
-# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
-# under the Apache License, Version 2.0 (the "License"); you may not use
-# this file except in compliance with the License. You may obtain a copy
-# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
-# required by applicable law or agreed to in writing, software distributed
-# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
-# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
-# the specific language governing permissions and limitations under the License.
-
 import os
 from cellxgene_gateway import env
 from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
@@ -17,7 +8,7 @@ def recurse_dir(path):
             "The given path does not exist.", status.HTTP_400_BAD_REQUEST
         )
 
-    all_entries = sorted(os.listdir(path))
+    all_entries = os.listdir(path)
     def is_h5ad(el):
         return el.endswith('.h5ad') and os.path.isfile(os.path.join(path, el))
     h5ad_entries = [x for x in all_entries if is_h5ad(x)]
@@ -31,7 +22,7 @@ def recurse_dir(path):
                 "name": x[:-13] if (len(x) > 13 and x[-13] in ['-','_']) else (
                     x[:-4] if x.endswith('.csv') else x),
                 "path": os.path.join(full_path, x).replace(env.cellxgene_data, ""),
-            } for x in sorted(os.listdir(full_path)) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
+            } for x in os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
         return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
 
     def make_entry(el):
@@ -57,7 +48,7 @@ def recurse_dir(path):
                 "type": "neither",
             }
 
-    return [make_entry(x) for x in all_entries]
+    return [make_entry(x) for x in os.listdir(path)]
 
 
 def render_entries(entries):

cellxgene_gateway/flask_util.py

@@ -1,12 +1,3 @@
-# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
-# under the Apache License, Version 2.0 (the "License"); you may not use
-# this file except in compliance with the License. You may obtain a copy
-# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
-# required by applicable law or agreed to in writing, software distributed
-# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
-# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
-# the specific language governing permissions and limitations under the License.
-
 from flask import request
 
 def querystring():

cellxgene_gateway/process_exception.py

@@ -9,7 +9,7 @@
 
 
 class ProcessException(Exception):
-    def __init__(self, message, stdout, stderr, http_status, key):
+    def __init__(self, message, stdout, stderr, http_status, dataset):
         Exception.__init__(self)
         self.message = message
         self.stdout = stdout

cellxgene_gateway/subprocess_backend.py

@@ -11,32 +11,30 @@ import logging
 import subprocess
 
 from flask_api import status
-from cellxgene_gateway.env import enable_annotations, enable_backed_mode
+from cellxgene_gateway.env import enable_annotations
 from cellxgene_gateway.process_exception import ProcessException
 from cellxgene_gateway.dir_util import make_annotations
 from cellxgene_gateway.path_util import get_file_path, get_annotation_file_path
 
-
 class SubprocessBackend:
     def __init__(self):
         pass
 
     def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
         if enable_annotations and not annotation_file_path is None:
+            annotation_args_prefix = " --experimental-annotations"
             if annotation_file_path == "":
-                extra_args = f" --annotations-dir {make_annotations(file_path)}"
+                annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
             else:
-                extra_args = f" --annotations-file {annotation_file_path}"
+                annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
         else:
-            extra_args = " --disable-annotations"
+            annotation_args = ""
-        if enable_backed_mode:
-            extra_args += " --backed"
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
             + " --port "
             + str(port)
             + " --host 127.0.0.1"
-            + extra_args
+            + annotation_args
         )
 
         for s in scripts:

environment-dev.yml

@@ -8,4 +8,4 @@ dependencies:
 - psutil
 - pip:
   - flask-api
-  - cellxgene>=0.15
+  - cellxgene

requirements.txt

@@ -1,4 +1,4 @@
-cellxgene>=0.15
+cellxgene
 flask
 flask_api
 psutil

setup.cfg

@@ -1,2 +0,0 @@
-[metadata]
-description-file = README.md

setup.py

@@ -1,23 +1,6 @@
 import os
-import codecs
+from setuptools import setup
-from setuptools import find_packages, setup
-import sys
 
-if sys.version_info < (3,6):
-    sys.exit('Sorry, Python < 3.6 is not supported')
-
-def read(rel_path):
-    here = os.path.abspath(os.path.dirname(__file__))
-    with codecs.open(os.path.join(here, rel_path), 'r') as fp:
-        return fp.read()
-
-def get_version(rel_path):
-    for line in read(rel_path).splitlines():
-        if line.startswith('__version__'):
-            delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
-    else:
-        raise RuntimeError("Unable to find version string.")
 
 def parse_requirements():
     reqs = []
@@ -26,8 +9,6 @@ def parse_requirements():
             reqs.append(l.strip("\n"))
     return reqs
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
 
 install_reqs = parse_requirements()
 
@@ -35,13 +16,11 @@ setup(
     # mandatory
     name="cellxgene-gateway",
     # mandatory
-    version=get_version("cellxgene_gateway/__init__.py"),
+    version="0.1",
     # mandatory
     author="Niket Patel, Yohann Potier, Alok Saldanha",
     author_email="alok.saldanha@novartis.com",
     description=("Cellxgene Gateway"),
-    long_description=long_description,
-    long_description_content_type="text/markdown",
     license="MIT",
     keywords="visualization, genomics",
     url="http://github.com/Novartis/cellxgene-gateway",
@@ -52,11 +31,10 @@ setup(
             "static/nibr.ico",
             "templates/*.html"
     ]},
-    data_files=[('', ['README.md', 'LICENSE'])],
+    data_files=[('', ['Readme.md', 'LICENSE.txt'])],
     install_requires=install_reqs,
     entry_points={
         "console_scripts": ["cellxgene-gateway=cellxgene_gateway.gateway:main"]
     },
     classifiers=["Topic :: Scientific/Engineering :: Visualization"],
-    python_requires='>=3.6',
 )