Prepare for 0.3.12 release

Bump flask from 2.2.2 to 2.2.5

.github/workflows/pr-checks.yaml

@@ -6,7 +6,7 @@ on: [push, pull_request]
 
 jobs:
   black:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         name: Checkout repository
@@ -25,7 +25,7 @@ jobs:
           black . --check
   # This job is copied over from `deploy.yaml`
   run-tests:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
 

Changelog.md

@@ -1,3 +1,17 @@
+# 0.3.12
+
+* #81 List gene set annotations when cell annotations not present
+* #86 Upgrade pip within docker image
+* #73 Moved new link to front
+* #87 Temporarily pin versions of werkzeug and flask
+
+
+# 0.3.11
+
+* #81 added support for gene sets
+* #79 added example for cellxgene-gateway customized docker image
+* #78 prune directories that do not contain h5ad files
+
 # 0.3.10
 
 * #65 Added GATEWAY_EXPIRE_SECONDS to set how long cellxgene servers can remain idle before being terminated.

Dockerfile

@@ -1,6 +1,7 @@
 FROM python:3.9
 
-RUN pip install cellxgene-gateway 'MarkupSafe<2.1'
+RUN pip install --upgrade pip \
+    && pip install cellxgene-gateway 'MarkupSafe<2.1'
 
 ENV CELLXGENE_DATA=/cellxgene-data
 ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene

README.md

@@ -75,7 +75,7 @@ Optional environment variables:
 * `GATEWAY_PORT` - local port that the gateway should bind to, defaults to 5005
 * `GATEWAY_EXPIRE_SECONDS` - time in seconds that a cellxgene process will remain idle before being terminated. Defaults to 3600 (one hour)
 * `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
-* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
+* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations and gene sets.
 * `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.
 * `GATEWAY_LOG_LEVEL` - default is `INFO`. set to `DEBUG` to increase logging and to `WARNING` to decrease logging.
 * `S3_ENABLE_LISTINGS_CACHE` - Set to `true` or to `1` to cache listings of S3 folders for performance. If the cache becomes stale, set `filecrawl.html?refresh=true` query parameter to refresh the cache.
@@ -186,21 +186,6 @@ pip install isort flake8 black
 isort -rc . # rc means recursive, and was deprecated in dev version of isort
 black .
 ```
-## Dependency management
-
-We use the following files for dependency management:
-
-* environment.yml - specifies a conda environment sufficient to run the packages
-* setup.cfg - lists static dependency information, both minimal and extra dependencies
-* setup.py - dynamically generated package information
-* requirements.txt - simple wrapper invoking setup.py
-
-For more details, see the folloiwng links:
-
-* https://towardsdatascience.com/setuptools-python-571e7d5500f2
-* https://towardsdatascience.com/requirements-vs-setuptools-python-ae3ee66e28af
-
-
 
 # Getting Help
 

cellxgene_gateway/__init__.py

@@ -7,4 +7,4 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-__version__ = "0.3.10"
+__version__ = "0.3.12"

cellxgene_gateway/cache_entry.py

@@ -58,7 +58,6 @@ class CacheEntry:
 
     @classmethod
     def for_key(cls, key, port):
-
         return cls(
             None,
             key,

cellxgene_gateway/filecrawl.py

@@ -7,31 +7,32 @@
 # 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
+import html
 import urllib.parse
 
-from cellxgene_gateway import env, flask_util
+from cellxgene_gateway import flask_util
 from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.dir_util import annotations_suffix, make_annotations, make_h5ad
+from cellxgene_gateway.env import enable_annotations
 
 
 def render_annotations(item, item_source):
+    if not enable_annotations:
+        return ""
     url = flask_util.view_url(
         item_source.get_annotations_subpath(item), item_source.name
     )
-    new_annotation = f"<a class='new' href='{url}'>new</a>"
+    new_annotation = [f"<a class='new' href='{url}'>new</a>"]
+
     annotations = (
-        ", ".join(
-            [
-                f"<a href='{CacheKey(item, item_source, a).view_url}/'>{a.name}</a>"
-                for a in item.annotations
-            ]
-        )
-        + ", "
+        [
+            f"<a href='{CacheKey(item, item_source, a).view_url}/'>{html.escape(a.name)}</a>"
+            for a in item.annotations
+        ]
         if item.annotations
-        else ""
+        else []
     )
-    return " | annotations: " + annotations + new_annotation
+    return "| annotations: " + ", ".join(new_annotation + annotations)
 
 
 def render_item(item, item_source):

cellxgene_gateway/flask_util.py

@@ -26,8 +26,8 @@ def url(endpoint, descriptor, source_name):
 
 
 def view_url(descriptor, source_name):
-    return url("gateway_blueprint.do_view", descriptor, source_name)
+    return url("do_view", descriptor, source_name)
 
 
 def relaunch_url(descriptor, source_name):
-    return url("gateway_blueprint.do_relaunch", descriptor, source_name)
+    return url("do_relaunch", descriptor, source_name)

cellxgene_gateway/gateway.py

@@ -1,15 +1,45 @@
+# 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 BaseHTTPServer
+import json
 import logging
 import os
+import urllib.parse
+from threading import Lock, Thread
 
-import typer
-from flask import Flask
+from flask import (
+    Flask,
+    make_response,
+    redirect,
+    render_template,
+    request,
+    send_from_directory,
+    url_for,
+)
 from werkzeug.middleware.proxy_fix import ProxyFix
 
-from cellxgene_gateway import env, flask_util, gateway_blueprint
+from cellxgene_gateway import env, flask_util
+from cellxgene_gateway.backend_cache import BackendCache
+from cellxgene_gateway.cache_entry import CacheEntryStatus
+from cellxgene_gateway.cache_key import CacheKey
+from cellxgene_gateway.cellxgene_exception import CellxgeneException
+from cellxgene_gateway.extra_scripts import get_extra_scripts
+from cellxgene_gateway.filecrawl import render_item_source
+from cellxgene_gateway.process_exception import ProcessException
+from cellxgene_gateway.prune_process_cache import PruneProcessCache
 from cellxgene_gateway.util import current_time_stamp
 
 app = Flask(__name__)
 
+item_sources = []
+default_item_source = None
+
 
 def _force_https(app):
     def wrapper(environ, start_response):
@@ -20,6 +50,14 @@ def _force_https(app):
     return wrapper
 
 
+def set_no_cache(resp):
+    resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
+    resp.headers["Pragma"] = "no-cache"
+    resp.headers["Expires"] = "0"
+    resp.headers["Cache-Control"] = "public, max-age=0"
+    return resp
+
+
 app.wsgi_app = _force_https(app.wsgi_app)
 if (
     env.proxy_fix_for > 0
@@ -37,8 +75,227 @@ if (
         x_prefix=env.proxy_fix_prefix,
     )
 
+cache = BackendCache()
 
-def main(prometheus: bool = False):
+
+@app.errorhandler(CellxgeneException)
+def handle_invalid_usage(error):
+    message = f"{error.http_status} Error : {error.message}"
+
+    return (
+        render_template(
+            "cellxgene_error.html",
+            extra_scripts=get_extra_scripts(),
+            message=message,
+        ),
+        error.http_status,
+    )
+
+
+@app.errorhandler(ProcessException)
+def handle_invalid_process(error):
+    message = []
+
+    message.append(error.message)
+    message.append(f"{error.http_status} Error.")
+    message.append(f"Stdout: {error.stdout}")
+    message.append(f"Stderr: {error.stderr}")
+
+    return (
+        render_template(
+            "process_error.html",
+            extra_scripts=get_extra_scripts(),
+            message=error.message,
+            http_status=error.http_status,
+            stdout=error.stdout,
+            stderr=error.stderr,
+            relaunch_url=error.key.relaunch_url(),
+            annotation_file=error.key.annotation_descriptor,
+        ),
+        error.http_status,
+    )
+
+
+@app.route("/favicon.ico")
+def favicon():
+    return send_from_directory(
+        os.path.join(app.root_path, "static"),
+        "nibr.ico",
+        mimetype="image/vnd.microsof.icon",
+    )
+
+
+@app.route("/")
+def index():
+    return render_template(
+        "index.html",
+        ip=env.ip,
+        cellxgene_data=env.cellxgene_data,
+        extra_scripts=get_extra_scripts(),
+    )
+
+
+@app.route("/filecrawl.html")
+@app.route("/filecrawl/<path:path>")
+def filecrawl(path=None):
+    source_name = request.args.get("source")
+    sources = (
+        filter(
+            lambda x: x.name == urllib.parse.unquote_plus(source_name),
+            item_sources,
+        )
+        if source_name
+        else item_sources
+    )
+    # loop all data sources --
+    rendered_sources = [
+        render_item_source(item_source, path) for item_source in sources
+    ]  # will we need to make this async in the page???
+    rendered_html = "\n".join(rendered_sources)
+
+    resp = make_response(
+        render_template(
+            "filecrawl.html",
+            extra_scripts=get_extra_scripts(),
+            rendered_html=rendered_html,
+            path=path,
+        )
+    )
+    set_no_cache(resp)
+    return resp
+
+
+entry_lock = Lock()
+
+
+def matching_source(source_name):
+    if source_name is None:
+        source_name = default_item_source.name
+    matching = [i for i in item_sources if i.name == source_name]
+    if len(matching) != 1:
+        raise Exception(f"Could not find matching item source {source_name}")
+    source = matching[0]
+    return source
+
+
+@app.route(
+    "/source/<path:source_name>/view/<path:path>",
+    methods=["GET", "PUT", "POST"],
+)
+@app.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
+def do_view(path, source_name=None):
+    source = matching_source(source_name)
+    match = cache.check_path(source, path)
+
+    if match is None:
+        lookup = source.lookup(path)
+        if lookup is None:
+            raise CellxgeneException(
+                f"Could not find item for path {path} in source {source.name}",
+                404,
+            )
+        key = CacheKey.for_lookup(source, lookup)
+        print(
+            f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
+        )
+        with entry_lock:
+            match = cache.check_entry(key)
+            if match is None:
+                uascripts = get_extra_scripts()
+                match = cache.create_entry(key, uascripts)
+
+    match.timestamp = current_time_stamp()
+
+    if (
+        match.status == CacheEntryStatus.loaded
+        or match.status == CacheEntryStatus.loading
+    ):
+        if source.is_authorized(match.key.descriptor):
+            return match.serve_content(path)
+        else:
+            raise CellxgeneException("User not authorized to access this data", 403)
+    elif match.status == CacheEntryStatus.error:
+        raise ProcessException.from_cache_entry(match)
+
+
+@app.route("/cache_status", methods=["GET"])
+def do_GET_status():
+    return render_template(
+        "cache_status.html",
+        entry_list=cache.entry_list,
+        extra_scripts=get_extra_scripts(),
+    )
+
+
+@app.route("/cache_status.json", methods=["GET"])
+def do_GET_status_json():
+    return json.dumps(
+        {
+            "launchtime": app.launchtime,
+            "entry_list": [
+                {
+                    "dataset": entry.key.dataset,
+                    "annotation_file": entry.key.annotation_file,
+                    "launchtime": entry.launchtime,
+                    "last_access": entry.timestamp,
+                    "status": entry.status,
+                }
+                for entry in cache.entry_list
+            ],
+        }
+    )
+
+
+@app.route("/relaunch/<path:path>", methods=["GET"])
+def do_relaunch(path):
+    source_name = request.args.get("source_name") or default_item_source.name
+    source = matching_source(source_name)
+    key = CacheKey.for_lookup(source, source.lookup(path))
+    match = cache.check_entry(key)
+    if not match is None:
+        match.terminate()
+    return redirect(
+        key.view_url,
+        code=302,
+    )
+
+
+@app.route("/terminate/<path:path>", methods=["GET"])
+def do_terminate(path):
+    source_name = request.args.get("source_name") or default_item_source.name
+    source = matching_source(source_name)
+    key = CacheKey.for_lookup(source, source.lookup(path))
+    match = cache.check_entry(key)
+    if not match is None:
+        match.terminate()
+    return redirect(url_for("do_GET_status"), code=302)
+
+
+@app.route("/metadata/ip_address", methods=["GET"])
+def ip_address():
+    resp = make_response(env.ip)
+    return set_no_cache(resp)
+
+
+def launch():
+    env.validate()
+    if not item_sources or not len(item_sources):
+        raise Exception("No data sources specified for Cellxgene Gateway")
+
+    global default_item_source
+    if default_item_source is None:
+        default_item_source = item_sources[0]
+
+    pruner = PruneProcessCache(cache)
+
+    background_thread = Thread(target=pruner)
+    background_thread.start()
+
+    app.launchtime = current_time_stamp()
+    app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
+
+
+def main():
     logging.basicConfig(
         level=env.log_level,
         format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
@@ -49,33 +306,19 @@ def main(prometheus: bool = False):
     if cellxgene_bucket is not None:
         from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
 
-        gateway_blueprint.item_sources.append(S3ItemSource(cellxgene_bucket, name="s3"))
+        item_sources.append(S3ItemSource(cellxgene_bucket, name="s3"))
         default_item_source = "s3"
     if cellxgene_data is not None:
         from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 
-        gateway_blueprint.item_sources.append(
-            FileItemSource(cellxgene_data, name="local")
-        )
+        item_sources.append(FileItemSource(cellxgene_data, name="local"))
         default_item_source = "local"
-    if len(gateway_blueprint.item_sources) == 0:
+    if len(item_sources) == 0:
         raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
-    flask_util.include_source_in_url = len(gateway_blueprint.item_sources) > 1
+    flask_util.include_source_in_url = len(item_sources) > 1
 
-    if prometheus:
-        from cellxgene_gateway.prometheus import add_metrics
-
-        add_metrics(app)
-    app.register_blueprint(gateway_blueprint.gateway_blueprint)
-    gateway_blueprint.launch()
-
-    app.launchtime = current_time_stamp()
-    app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
-
-
-def run():
-    typer.run(main)
+    launch()
 
 
 if __name__ == "__main__":
-    run()
+    main()

cellxgene_gateway/gateway_blueprint.py

@@ -1,266 +0,0 @@
-# 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 BaseHTTPServer
-import json
-import os
-import urllib.parse
-from threading import Lock, Thread
-
-from flask import (
-    Blueprint,
-    current_app,
-    make_response,
-    redirect,
-    render_template,
-    request,
-    send_from_directory,
-    url_for,
-)
-
-from cellxgene_gateway import env
-from cellxgene_gateway.backend_cache import BackendCache
-from cellxgene_gateway.cache_entry import CacheEntryStatus
-from cellxgene_gateway.cache_key import CacheKey
-from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.extra_scripts import get_extra_scripts
-from cellxgene_gateway.filecrawl import render_item_source
-from cellxgene_gateway.process_exception import ProcessException
-from cellxgene_gateway.prune_process_cache import PruneProcessCache
-from cellxgene_gateway.util import current_time_stamp
-
-gateway_blueprint = Blueprint("gateway_blueprint", __name__)
-item_sources = []
-default_item_source = None
-
-
-def set_no_cache(resp):
-    resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
-    resp.headers["Pragma"] = "no-cache"
-    resp.headers["Expires"] = "0"
-    resp.headers["Cache-Control"] = "public, max-age=0"
-    return resp
-
-
-cache = BackendCache()
-
-
-@gateway_blueprint.errorhandler(CellxgeneException)
-def handle_invalid_usage(error):
-
-    message = f"{error.http_status} Error : {error.message}"
-
-    return (
-        render_template(
-            "cellxgene_error.html",
-            extra_scripts=get_extra_scripts(),
-            message=message,
-        ),
-        error.http_status,
-    )
-
-
-@gateway_blueprint.errorhandler(ProcessException)
-def handle_invalid_process(error):
-
-    message = []
-
-    message.append(error.message)
-    message.append(f"{error.http_status} Error.")
-    message.append(f"Stdout: {error.stdout}")
-    message.append(f"Stderr: {error.stderr}")
-
-    return (
-        render_template(
-            "process_error.html",
-            extra_scripts=get_extra_scripts(),
-            message=error.message,
-            http_status=error.http_status,
-            stdout=error.stdout,
-            stderr=error.stderr,
-            relaunch_url=error.key.relaunch_url(),
-            annotation_file=error.key.annotation_descriptor,
-        ),
-        error.http_status,
-    )
-
-
-@gateway_blueprint.route("/favicon.ico")
-def favicon():
-    return send_from_directory(
-        os.path.join(current_app.root_path, "static"),
-        "nibr.ico",
-        mimetype="image/vnd.microsof.icon",
-    )
-
-
-@gateway_blueprint.route("/")
-def index():
-    return render_template(
-        "index.html",
-        ip=env.ip,
-        cellxgene_data=env.cellxgene_data,
-        extra_scripts=get_extra_scripts(),
-    )
-
-
-@gateway_blueprint.route("/filecrawl.html")
-@gateway_blueprint.route("/filecrawl/<path:path>")
-def filecrawl(path=None):
-    source_name = request.args.get("source")
-    sources = (
-        filter(
-            lambda x: x.name == urllib.parse.unquote_plus(source_name),
-            item_sources,
-        )
-        if source_name
-        else item_sources
-    )
-    # loop all data sources --
-    rendered_sources = [
-        render_item_source(item_source, path) for item_source in sources
-    ]  # will we need to make this async in the page???
-    rendered_html = "\n".join(rendered_sources)
-
-    resp = make_response(
-        render_template(
-            "filecrawl.html",
-            extra_scripts=get_extra_scripts(),
-            rendered_html=rendered_html,
-            path=path,
-        )
-    )
-    set_no_cache(resp)
-    return resp
-
-
-entry_lock = Lock()
-
-
-def matching_source(source_name):
-    if source_name is None:
-        source_name = default_item_source.name
-    matching = [i for i in item_sources if i.name == source_name]
-    if len(matching) != 1:
-        raise Exception(f"Could not find matching item source {source_name}")
-    source = matching[0]
-    return source
-
-
-@gateway_blueprint.route(
-    "/source/<path:source_name>/view/<path:path>",
-    methods=["GET", "PUT", "POST"],
-)
-@gateway_blueprint.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
-def do_view(path, source_name=None):
-    source = matching_source(source_name)
-    match = cache.check_path(source, path)
-
-    if match is None:
-        lookup = source.lookup(path)
-        if lookup is None:
-            raise CellxgeneException(
-                f"Could not find item for path {path} in source {source.name}",
-                404,
-            )
-        key = CacheKey.for_lookup(source, lookup)
-        print(
-            f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
-        )
-        with entry_lock:
-            match = cache.check_entry(key)
-            if match is None:
-                uascripts = get_extra_scripts()
-                match = cache.create_entry(key, uascripts)
-
-    match.timestamp = current_time_stamp()
-
-    if (
-        match.status == CacheEntryStatus.loaded
-        or match.status == CacheEntryStatus.loading
-    ):
-        if source.is_authorized(match.key.descriptor):
-            return match.serve_content(path)
-        else:
-            raise CellxgeneException("User not authorized to access this data", 403)
-    elif match.status == CacheEntryStatus.error:
-        raise ProcessException.from_cache_entry(match)
-
-
-@gateway_blueprint.route("/cache_status", methods=["GET"])
-def do_GET_status():
-    return render_template(
-        "cache_status.html",
-        entry_list=cache.entry_list,
-        extra_scripts=get_extra_scripts(),
-    )
-
-
-@gateway_blueprint.route("/cache_status.json", methods=["GET"])
-def do_GET_status_json():
-    return json.dumps(
-        {
-            "launchtime": current_app.launchtime,
-            "entry_list": [
-                {
-                    "dataset": entry.key.dataset,
-                    "annotation_file": entry.key.annotation_file,
-                    "launchtime": entry.launchtime,
-                    "last_access": entry.timestamp,
-                    "status": entry.status,
-                }
-                for entry in cache.entry_list
-            ],
-        }
-    )
-
-
-@gateway_blueprint.route("/relaunch/<path:path>", methods=["GET"])
-def do_relaunch(path):
-    source_name = request.args.get("source_name") or default_item_source.name
-    source = matching_source(source_name)
-    key = CacheKey.for_lookup(source, source.lookup(path))
-    match = cache.check_entry(key)
-    if not match is None:
-        match.terminate()
-    return redirect(
-        key.view_url,
-        code=302,
-    )
-
-
-@gateway_blueprint.route("/terminate/<path:path>", methods=["GET"])
-def do_terminate(path):
-    source_name = request.args.get("source_name") or default_item_source.name
-    source = matching_source(source_name)
-    key = CacheKey.for_lookup(source, source.lookup(path))
-    match = cache.check_entry(key)
-    if not match is None:
-        match.terminate()
-    return redirect(url_for("gateway_blueprint.do_GET_status"), code=302)
-
-
-@gateway_blueprint.route("/metadata/ip_address", methods=["GET"])
-def ip_address():
-    resp = make_response(env.ip)
-    return set_no_cache(resp)
-
-
-def launch():
-    env.validate()
-    if not item_sources or not len(item_sources):
-        raise Exception("No data sources specified for Cellxgene Gateway")
-
-    global default_item_source
-    if default_item_source is None:
-        default_item_source = item_sources[0]
-
-    pruner = PruneProcessCache(cache)
-
-    background_thread = Thread(target=pruner)
-    background_thread.start()

cellxgene_gateway/items/file/fileitem_source.py

@@ -24,17 +24,22 @@ class FileItemSource(ItemSource):
         h5ad_suffix=dir_util.h5ad_suffix,
         annotation_dir_suffix=dir_util.annotations_suffix,
         annotation_file_suffix=".csv",
+        gene_set_file_suffix="_gene_sets.csv",
     ):
         self._name = name
         self.base_path = base_path
         self.h5ad_suffix = h5ad_suffix
         self.annotation_dir_suffix = annotation_dir_suffix
         self.annotation_file_suffix = annotation_file_suffix
+        self.gene_set_file_suffix = gene_set_file_suffix
 
     @property
     def name(self):
         return self._name or f"Files:{self.base_path}"
 
+    def is_gene_set(self, path: str) -> bool:
+        return path.endswith(self.gene_set_file_suffix)
+
     def is_h5ad_file(self, path: str) -> bool:
         return path.endswith(self.h5ad_suffix) and os.path.isfile(path)
 
@@ -63,7 +68,7 @@ class FileItemSource(ItemSource):
 
         return item_tree
 
-    def scan_directory(self, subpath="") -> dict:
+    def scan_directory(self, subpath: str = "") -> ItemTree:
         base_path = os.path.join(self.base_path, subpath)
 
         if not os.path.exists(base_path):
@@ -100,6 +105,11 @@ class FileItemSource(ItemSource):
             branches = [
                 self.scan_directory(os.path.join(subpath, subdir)) for subdir in subdirs
             ]
+            # Exclude branches without files as leaves. Since traversal is applied pre-order,
+            # branch.branches has already been processed and we don't need to check deeper nesting.
+            branches = [
+                branch for branch in branches if branch.items or branch.branches
+            ]
 
         return ItemTree(subpath, items, branches)
 
@@ -176,11 +186,29 @@ class FileItemSource(ItemSource):
         annotations_subpath = self.get_annotations_subpath(item)
         annotations_fullpath = self.full_path(annotations_subpath)
         if os.path.isdir(annotations_fullpath):
-            return [
+            sorted_files = sorted(os.listdir(annotations_fullpath))
+            annotation_files = [
                 self.make_fileitem_from_path(annotation, annotations_subpath, True)
-                for annotation in sorted(os.listdir(annotations_fullpath))
+                for annotation in sorted_files
                 if annotation.endswith(self.annotation_file_suffix)
+                and not self.is_gene_set(annotation)
                 and os.path.isfile(os.path.join(annotations_fullpath, annotation))
             ]
+
+            # Catch gene sets without accompanying [annotations].csv
+            gene_sets_files = [
+                self.make_fileitem_from_path(
+                    annotation[: -len(self.gene_set_file_suffix)] + ".csv",
+                    annotations_subpath,
+                    True,
+                )
+                for annotation in sorted_files
+                if self.is_gene_set(annotation)
+                and annotation[: -len(self.gene_set_file_suffix)]
+                not in [a.name for a in annotation_files]
+                and os.path.isfile(os.path.join(annotations_fullpath, annotation))
+            ]
+
+            return sorted(annotation_files + gene_sets_files, key=lambda x: x.name)
         else:
             return None

cellxgene_gateway/items/s3/s3item_source.py

@@ -116,6 +116,9 @@ class S3ItemSource(ItemSource):
         branches = None
         if len(subdir_keys) > 0:
             branches = [self.scan_directory(key) for key in subdir_keys]
+            branches = [
+                branch for branch in branches if branch.items or branch.branches
+            ]
 
         return ItemTree(directory_key, items, branches)
 

cellxgene_gateway/prometheus.py

@@ -1,9 +0,0 @@
-from prometheus_flask_exporter import PrometheusMetrics
-
-from cellxgene_gateway import __version__
-
-
-def add_metrics(app):
-    metrics = PrometheusMetrics(app)
-    metrics.info("app_info", "Application info", version=__version__)
-    return metrics

cellxgene_gateway/subprocess_backend.py

@@ -30,8 +30,11 @@ class SubprocessBackend:
                 extra_args = f" --annotations-dir {make_annotations(file_path)}"
             else:
                 extra_args = f" --annotations-file {annotation_file_path}"
+                gene_sets_file_path = annotation_file_path[:-4] + "_gene_sets.csv"
+                extra_args += f" --gene-sets-file {gene_sets_file_path}"
         else:
             extra_args = " --disable-annotations"
+            extra_args += " --disable-gene-sets-save"
         if enable_backed_mode:
             extra_args += " --backed"
         if not cellxgene_args is None:

cellxgene_gateway/templates/cache_status.html

@@ -61,7 +61,7 @@
                     <td>
                          {% if entry.status.name == 'loaded' %}
                          <a
-                              href="{{ url_for('gateway_blueprint.do_terminate', path=entry.key.descriptor, source_name=entry.key.source_name) }}">
+                              href="{{ url_for('do_terminate', path=entry.key.descriptor, source_name=entry.key.source_name) }}">
                               terminate </a>
                          {% endif %}
                     </td>

cellxgene_gateway/templates/cellxgene_error.html

@@ -28,11 +28,11 @@
           
      <h4>{{ message }}</h4>
 
-     <a href="{{ url_for('gateway_blueprint.filecrawl') }}">
+     <a href="{{ url_for('filecrawl') }}">
           Please click here to be redirected to the file directory.
      </a>
      <br>
-     <a href="{{ url_for('gateway_blueprint.index') }}">
+     <a href="{{ url_for('index') }}">
           Please click here to return to the homepage.
      </a>
      </div>

cellxgene_gateway/templates/filecrawl.html

@@ -36,10 +36,10 @@
           Navigation:
      <ul>
      {% if path %}
-     <li><a href="{{ url_for('gateway_blueprint.filecrawl') }}">top level</a></li>
+     <li><a href="{{ url_for('filecrawl') }}">top level</a></li>
      {% else %}
      {% endif %}
-     <li><a href="{{ url_for('gateway_blueprint.index') }}">homepage</a></li>
+     <li><a href="{{ url_for('index') }}">homepage</a></li>
      </ul>
      </p>
      <script>

cellxgene_gateway/templates/index.html

@@ -35,12 +35,12 @@
 		Links:	
 	</h1>
 	<div class="list-group" style="width:50%;padding-left:65px">
-	  <a href="{{ url_for('gateway_blueprint.filecrawl') }}" class="list-group-item list-group-item-action">
+	  <a href="{{ url_for('filecrawl') }}" class="list-group-item list-group-item-action">
 		  <u>File Crawler: Allows you to view all uploaded data.</u></a>
 		  
 	</div>
 	<div class="list-group" style="width:50%;padding-left:65px">
-		<a href="{{ url_for('gateway_blueprint.do_GET_status') }}" class="list-group-item list-group-item-action">
+		<a href="{{ url_for('do_GET_status') }}" class="list-group-item list-group-item-action">
 			<u>Cache Status: view status of launched cellxgene servers.</u></a>
 	</div>
 	

cellxgene_gateway/templates/loading.html

@@ -35,11 +35,11 @@
           The page will refresh shortly.
      </p>
 
-     <a href="{{ url_for('gateway_blueprint.filecrawl') }}">
+     <a href="{{ url_for('filecrawl') }}">
           Please click here to be redirected to the file directory.
      </a>
      <br>
-     <a href="{{ url_for('gateway_blueprint.index') }}">
+     <a href="{{ url_for('index') }}">
           Please click here to return to the homepage.
      </a>
      </div>

cellxgene_gateway/templates/process_error.html

@@ -39,10 +39,10 @@
           <li><a href="{{ relaunch_url }}">
                     Attempt to relaunch the cellxgene server.
                </a></li>
-          <li><a href="{{ url_for('gateway_blueprint.filecrawl') }}">
+          <li><a href="{{ url_for('filecrawl') }}">
                Return to the file directory.
           </a></li>
-          <li><a href="{{ url_for('gateway_blueprint.index') }}">
+          <li><a href="{{ url_for('index') }}">
                Return to the homepage.
           </a></li>
      </ul>

environment.yml

@@ -4,10 +4,9 @@ channels:
 dependencies:
 - python=3.9
 - requests
-- flask
+- flask==2.2.5
 - psutil
 - black
-- typer
 - twine
 - isort
 - coverage
@@ -15,6 +14,5 @@ dependencies:
 - pip:
   - pre_commit
   - flask-api
-  - werkzeug
+  - werkzeug==2.3.8
   - cellxgene
-  - prometheus-flask-exporter

examples/customized_docker_image/Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.9
+
+RUN pip install cellxgene-gateway 'MarkupSafe<2.1'
+
+COPY customize_ui.sh customize_ui.sh
+RUN CELLXGENE_GATEWAY_DIR=/usr/local/lib/python3.9/site-packages/cellxgene_gateway . ./customize_ui.sh
+
+ENV CELLXGENE_DATA=/cellxgene-data
+ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene
+EXPOSE 5005
+
+RUN mkdir /cellxgene-data
+
+CMD ["cellxgene-gateway"]

examples/customized_docker_image/README.md

@@ -0,0 +1,14 @@
+# Purpose
+
+This is a simple example of how to make a small script to customize the UI of cellxgene-gateway. The script that does the customization is `customize_ui.sh`, it simply makes the main header green using CSS but you could do anything you want there (including adding more script tags, etc).
+
+# Usage
+
+```
+docker build -t cellxgene_custom .
+CELLXGENE_DATA=`pwd`/../../../cellxgene_data
+docker run -p 5005:5005 --mount src=$CELLXGENE_DATA,target=/cellxgene-data,type=bind cellxgene_custom
+```
+
+If you now open http://localhost:5005 you should see a green cellxgene gateway header.
+

examples/customized_docker_image/customize_ui.sh

@@ -0,0 +1,3 @@
+# make the header bright green
+find "${CELLXGENE_GATEWAY_DIR}/templates" -name index.html -exec sed -i -e 's/<head>/<head>\
+> <style> header h3 {color: #0F0;} <\/style>/g' {} \;

requirements.txt

@@ -1,9 +1,6 @@
- # requirements.txt
- #
- # installs dependencies from ./setup.py, and the package itself,
- # in editable mode
- -e .[prometheus]
-
- # (the -e above is optional). you could also just install the package
- # normally with just the line below (after uncommenting)
- # .
+cellxgene
+flask==2.2.5
+flask-api
+werkzeug==2.3.8
+psutil
+requests

setup.cfg

@@ -1,30 +1,2 @@
 [metadata]
-description_file = README.md
-description = "Cellxgene Gateway"
-author = "Niket Patel, Yohann Potier, Alok Saldanha"
-author_email = "alok.saldanha@novartis.com"
-long_description_content_type="text/markdown"
-license = "MIT"
-keywords ="visualization, genomics"
-url = "http://github.com/Novartis/cellxgene-gateway"
-python_requires = ">=3.6"
-classifier =
-    "Topic :: Scientific/Engineering :: Visualization"
-
-[options]
-install_requires =
-    cellxgene
-    flask
-    flask-api
-    werkzeug
-    psutil
-    requests
-    typer
-
-[options.extras_require]
-prometheus =
-    prometheus-flask-exporter
-
-[entry_points]
-console_scripts =
-    cellxgene-gateway = cellxgene_gateway.cli:run
+description-file = README.md

setup.py

@@ -4,6 +4,9 @@ import sys
 
 from setuptools import find_packages, setup
 
+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__))
@@ -20,15 +23,33 @@ def get_version(rel_path):
         raise RuntimeError("Unable to find version string.")
 
 
+def parse_requirements():
+    reqs = []
+    with open("requirements.txt", "r") as f:
+        for line in f.readlines():
+            reqs.append(line.strip("\n"))
+    return reqs
+
+
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
+install_reqs = parse_requirements()
+
 setup(
+    # mandatory
+    name="cellxgene-gateway",
     # mandatory
     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,
-    name="cellxgene-gateway",
+    long_description_content_type="text/markdown",
+    license="MIT",
+    keywords="visualization, genomics",
+    url="http://github.com/Novartis/cellxgene-gateway",
     packages=find_packages(),
     package_data={
         "cellxgene_gateway": [
@@ -39,4 +60,10 @@ setup(
         ]
     },
     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",
 )

tests/items/s3/test_s3item_source.py

@@ -1,9 +1,7 @@
 import unittest
 from unittest.mock import MagicMock, Mock, patch
 
-from flask import Flask
-
-from cellxgene_gateway.gateway_blueprint import gateway_blueprint
+from cellxgene_gateway.gateway import app
 from cellxgene_gateway.items.item import ItemType
 from cellxgene_gateway.items.s3.s3item import S3Item
 from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
@@ -84,8 +82,6 @@ class TestScanDirectory(unittest.TestCase):
 
         s3func.return_value = S3Mock
         source = S3ItemSource("my-bucket")
-        app = Flask(__name__)
-        app.register_blueprint(gateway_blueprint)
         with app.test_request_context(query_string="refresh=true") as test_context:
             tree = source.scan_directory()
 

tests/test_cache_entry.py

@@ -5,7 +5,7 @@ from flask import Flask
 from cellxgene_gateway import flask_util
 from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
 from cellxgene_gateway.cache_key import CacheKey
-from cellxgene_gateway.gateway_blueprint import gateway_blueprint
+from cellxgene_gateway.gateway import app
 from cellxgene_gateway.items.file.fileitem import FileItem
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 from cellxgene_gateway.items.item import ItemType
@@ -18,8 +18,7 @@ key = CacheKey(
 
 class TestRenderEntry(unittest.TestCase):
     def setUp(self):
-        self.app = Flask(__name__)
-        self.app.register_blueprint(gateway_blueprint)
+        self.app = app
         self.app_context = self.app.test_request_context()
         self.app_context.push()
         self.client = self.app.test_client()

tests/test_filecrawl.py

@@ -1,5 +1,6 @@
 import unittest
-from unittest.mock import MagicMock, patch
+from collections import defaultdict
+from unittest.mock import patch
 
 from cellxgene_gateway.filecrawl import (
     render_item,
@@ -13,26 +14,79 @@ from cellxgene_gateway.items.item import ItemTree, ItemType
 source = FileItemSource("/tmp")
 
 
+def make_entry(subpath="somepath", annotations=None):
+    return FileItem(
+        subpath=subpath,
+        name="entry",
+        ext=".h5ad",
+        type=ItemType.h5ad,
+        annotations=annotations,
+    )
+
+
 class TestRenderEntry(unittest.TestCase):
     def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="/somepath/", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="/somepath/")
         rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
 
     def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="/somepath", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="/somepath")
         rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
 
     def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath/", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="somepath/")
         rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
 
     def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath", name="entry", type=ItemType.h5ad)
+        entry = make_entry(subpath="somepath")
         rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
+
+
+class TestRenderAnnotation(unittest.TestCase):
+    @patch("cellxgene_gateway.filecrawl.enable_annotations", new=True)
+    def test_GIVEN_no_annotation_THEN_new_alone(self):
+        entry = make_entry(annotations=None)
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a></li>",
+            rendered,
+        )
+
+    @patch("cellxgene_gateway.filecrawl.enable_annotations", new=True)
+    def test_GIVEN_annotation_THEN_new_before(self):
+        annotation = FileItem(
+            subpath="somepath/entry_annotations",
+            name="annot",
+            ext=".csv",
+            type=ItemType.annotation,
+        )
+        entry = make_entry(annotations=[annotation])
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a>,"
+            " <a href='/source/Files:/tmp/view/somepath/entry_annotations/annot.csv/'>annot</a></li>",
+            rendered,
+        )
+
+    @patch("cellxgene_gateway.filecrawl.enable_annotations", new=True)
+    def test_GIVEN_annotation_THEN_escaped(self):
+        annotation = FileItem(
+            subpath="somepath/entry_annotations",
+            name="hot&cold",
+            ext=".csv",
+            type=ItemType.annotation,
+        )
+        entry = make_entry(annotations=[annotation])
+        rendered = render_item(entry, source)
+        self.assertIn(
+            "> | annotations: <a class='new' href='/source/Files:/tmp/view/somepath/entry_annotations'>new</a>,"
+            " <a href='/source/Files:/tmp/view/somepath/entry_annotations/hot&cold.csv/'>hot&amp;cold</a></li>",
+            rendered,
+        )
 
 
 class TestRenderItemSource(unittest.TestCase):
@@ -48,12 +102,47 @@ class TestRenderItemSource(unittest.TestCase):
 
 
 class TestRenderItemTree(unittest.TestCase):
+    def setUp(self):
+        from cellxgene_gateway.gateway import app
+
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
     @patch("cellxgene_gateway.items.file.fileitem_source.FileItemSource")
     def test_GIVEN_deep_nested_dirs_THEN_includes_dirs_in_output(self, item_source):
         item_source.name = "FakeSource"
-        item_tree = ItemTree("foo/bar/baz", [], [])
+        item_source.get_annotations_subpath = lambda _: "FakeAnnotations"
+        file_item = FileItem(
+            subpath="foo/bar/baz", name="file.h5ad", type=ItemType.h5ad
+        )
+        item_tree = ItemTree("foo/bar/baz", [file_item], [])
         rendered = render_item_tree(item_tree, item_source)
         self.assertEqual(
             rendered,
-            "<li><a href='/filecrawl/foo/bar/baz?source=FakeSource'>baz</a><ul></ul></li>",
+            "<li><a href='/filecrawl/foo/bar/baz?source=FakeSource'>baz</a><ul>"
+            "<li> <a href='/source/FakeSource/view/foo/bar/baz/file.h5ad/'>file.h5ad</a>"
+            " </li></ul></li>",
+        )
+
+    @patch(
+        "os.listdir",
+        side_effect=lambda parent: defaultdict(
+            list, {"tmp": ["foo"], "tmp/foo": ["bar"]}
+        )[parent],
+    )
+    @patch("os.path.exists", return_value=True)
+    def test_GIVEN_dirs_without_h5ad_THEN_excludes_dirs_in_output(
+        self, listdir, exists
+    ):
+        # Directories:
+        # - tmp
+        #   - foo
+        #     - bar (no h5ad files)
+        item_source = FileItemSource("tmp", name="local")
+        item_tree = item_source.list_items("foo")
+        rendered = render_item_tree(item_tree, item_source)
+        self.assertEqual(
+            rendered,
+            "<li><a href='/filecrawl/foo?source=local'>foo</a><ul></ul></li>",
         )

tests/test_subprocess_backend.py

@@ -1,7 +1,6 @@
 import unittest
 from unittest.mock import MagicMock, patch
 
-from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cache_entry import CacheEntry
 from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.items.file.fileitem import FileItem
@@ -33,10 +32,46 @@ class TestSubprocessBackend(unittest.TestCase):
             backend.launch(cellxgene_loc, scripts, entry)
         popen.assert_called_once_with(
             [
-                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --scripts http://example.com/script.js --scripts http://example.com/script2.js"
+                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --disable-annotations --disable-gene-sets-save --scripts http://example.com/script.js --scripts http://example.com/script2.js"
             ],
             shell=True,
             stderr=-1,
             stdout=-1,
         )
         self.assertEqual("An unexpected error", context.exception.stderr)
+
+    @patch("subprocess.Popen")
+    def test_launch_GIVEN_annotations_enabled_THEN_set_flags(self, popen):
+        subprocess = MagicMock()
+        subprocess.stdout.readline().decode.return_value = (
+            "[cellxgene] Type CTRL-C at any time to exit.\n"
+        )
+        subprocess.stderr.read().decode.return_value = ""
+        popen.return_value = subprocess
+
+        key = CacheKey(
+            FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+            FileItemSource("/tmp", "local"),
+            FileItem(
+                "/czi/pbmc3k_annotations/", name="foo.csv", type=ItemType.annotation
+            ),
+        )
+        entry = CacheEntry.for_key(key, 8000)
+        import cellxgene_gateway.subprocess_backend
+
+        cellxgene_gateway.subprocess_backend.enable_annotations = True
+        try:
+            backend = cellxgene_gateway.subprocess_backend.SubprocessBackend()
+            cellxgene_loc = "/some/cellxgene"
+
+            backend.launch(cellxgene_loc, [], entry)
+        finally:
+            cellxgene_gateway.subprocess_backend.enable_annotations = False
+        popen.assert_called_once_with(
+            [
+                "yes | /some/cellxgene launch /tmp/czi/pbmc3k.h5ad --port 8000 --host 127.0.0.1 --annotations-file /tmp/czi/pbmc3k_annotations/foo.csv --gene-sets-file /tmp/czi/pbmc3k_annotations/foo_gene_sets.csv"
+            ],
+            shell=True,
+            stderr=-1,
+            stdout=-1,
+        )