ignore patch files

Mark version 0.1.0
Add python_requires
add long_description

.gitignore

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

Changelog.md

@@ -0,0 +1,7 @@
+# 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

@@ -67,6 +67,8 @@ 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

@@ -6,3 +6,5 @@
 # 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

@@ -21,6 +21,7 @@ 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,
@@ -36,6 +37,7 @@ 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

@@ -1,3 +1,12 @@
+# 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
@@ -8,7 +17,7 @@ def recurse_dir(path):
             "The given path does not exist.", status.HTTP_400_BAD_REQUEST
         )
 
-    all_entries = os.listdir(path)
+    all_entries = sorted(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)]
@@ -22,7 +31,7 @@ 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 os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
+            } for x in sorted(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):
@@ -48,7 +57,7 @@ def recurse_dir(path):
                 "type": "neither",
             }
 
-    return [make_entry(x) for x in os.listdir(path)]
+    return [make_entry(x) for x in all_entries]
 
 
 def render_entries(entries):

cellxgene_gateway/flask_util.py

@@ -1,3 +1,12 @@
+# 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/gateway.py

@@ -23,7 +23,7 @@ from flask import (
     url_for,
 )
 from flask_api import status
-from werkzeug import secure_filename
+from werkzeug.utils import secure_filename
 
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache

cellxgene_gateway/process_exception.py

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

cellxgene_gateway/subprocess_backend.py

@@ -11,30 +11,32 @@ import logging
 import subprocess
 
 from flask_api import status
-from cellxgene_gateway.env import enable_annotations
+from cellxgene_gateway.env import enable_annotations, enable_backed_mode
 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 == "":
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
+                extra_args = f" --annotations-dir {make_annotations(file_path)}"
             else:
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
+                extra_args = f" --annotations-file {annotation_file_path}"
         else:
-            annotation_args = ""
+            extra_args = " --disable-annotations"
+        if enable_backed_mode:
+            extra_args += " --backed"
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
             + " --port "
             + str(port)
             + " --host 127.0.0.1"
-            + annotation_args
+            + extra_args
         )
 
         for s in scripts:

environment.yml

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

requirements.txt

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

setup.cfg

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

setup.py

@@ -1,6 +1,23 @@
 import os
-from setuptools import setup
+import codecs
+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 = []
@@ -9,6 +26,8 @@ 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()
 
@@ -16,11 +35,13 @@ setup(
     # mandatory
     name="cellxgene-gateway",
     # mandatory
-    version="0.1",
+    version=get_version("cellxgene_gateway/__init__.py"),
     # 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",
@@ -31,10 +52,11 @@ setup(
             "static/nibr.ico",
             "templates/*.html"
     ]},
-    data_files=[('', ['Readme.md', 'LICENSE.txt'])],
+    data_files=[('', ['README.md', 'LICENSE'])],
     install_requires=install_reqs,
     entry_points={
         "console_scripts": ["cellxgene-gateway=cellxgene_gateway.gateway:main"]
     },
     classifiers=["Topic :: Scientific/Engineering :: Visualization"],
+    python_requires='>=3.6',
 )