made pruner a daemon thread

Gunicorn support for now. Will revisit populating item sources on module load to improve reusability of module (specifically in tests for now).

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,67 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '18 6 * * 6'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'javascript', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.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
 
@@ -52,9 +52,39 @@ jobs:
           eval "$(conda shell.bash hook)"
           conda activate cellxgene-gateway
           coverage report --fail-under 41
+          coverage report > coverage.txt
+          coverage html -i
           coverage xml -i
 
-      - name: "Upload coverage to Codecov"
+      - name: Upload coverage HTML report
-        uses: codecov/codecov-action@v1
+        uses: actions/upload-artifact@v4
         with:
-          fail_ci_if_error: true
+          name: coverage-html
+          path: htmlcov/
+          retention-days: 30
+
+      - name: Upload coverage xml
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+          retention-days: 30
+
+      - name: Upload coverage summary
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-summary
+          path: coverage.txt
+          retention-days: 30
+      # - name: "Upload coverage to Codecov"
+      #   if: ${{ github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository) }}
+      #   uses: codecov/codecov-action@v1
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}
+      #     files: ./coverage.xml
+      #     flags: unittests
+      #     env_vars: OS,PYTHON
+      #     name: codecov-umbrella
+      #     fail_ci_if_error: true
+      #     path_to_write_report: ./codecov_report.txt
+      #     verbose: true

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
       types: [python]
       stages: [commit]
     - id: black
-      language_version: python3.6+
       name: black
       language: system
       entry: black

Changelog.md

@@ -1,6 +1,77 @@
+# 0.4.0
+
+* Removed dependency on flask-api
+* Updated dependencies (python 3.11, numpy, unpinned flask, werkzeug)
+
+# 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.
+* Added GATEWAY_LOG_LEVEL to set the log level
+* #68 Close connections after reading response
+* #68 Background thread reads from output of cellxgene process until it exits
+
+# 0.3.9
+
+* Added S3_ENABLE_LISTINGS_CACHE variable (See README.md)
+
+# 0.3.8
+
+* Fixed bug #57 affecting deeply nested subdirectory listing
+
+# 0.3.7
+
+* added back /metadata/ip_address endpoint
+
+# 0.3.6
+
+* pinned version of werkzeug
+
+# 0.3.5
+
+* Pinned flask version to match cellxgene 0.17.0
+
+# 0.3.4
+
+* Fixed bug #50 affecting subdirectory listing
+
+# 0.3.3
+
+* Fixed bug #48 affecting cache pruning
+
+# 0.3.2
+
+ * Fixed bug #45 affecting multi-level S3 folders
+ * Added extra_scripts to cache_status page
+
+# 0.3.1
+
+ * Added missing __init__.py
+
+# 0.3.0
+
+ * Added support for itemsource interface, allowing s3 hosting
+ * Removed support for http file uploads
+ * Only set wsgi.url_scheme when EXTERNAL_PROTOCOL is set (see issue #43) 
+ * Dropped flake8 due to conflicts with black
+ * Added code coverage metrics
+
 # 0.2.3
 
-* Added support for ProxyFix
+ * Added support for ProxyFix
 
 # 0.2.2
 

Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.11
+
+RUN pip install --upgrade pip
+RUN pip install "cellxgene-gateway>=0.4"
+
+ENV CELLXGENE_DATA=/cellxgene-data
+ENV CELLXGENE_LOCATION=/usr/local/bin/cellxgene
+
+CMD ["cellxgene-gateway"]

README.md

@@ -2,6 +2,8 @@
 
 Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available  proxies requests to that server.
 
+[![codecov](https://codecov.io/gh/Novartis/cellxgene-gateway/branch/master/graph/badge.svg?token=ndEFSzRKJn)](https://codecov.io/gh/Novartis/cellxgene-gateway) [![PyPI](https://img.shields.io/pypi/v/cellxgene-gateway)](https://pypi.org/project/cellxgene-gateway/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/cellxgene-gateway)](https://pypistats.org/packages/cellxgene-gateway)
+
 # Running locally
 
 ## Prequisites
@@ -71,9 +73,12 @@ Optional environment variables:
 * `EXTERNAL_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy that performs https termination. Default value "http"
 * `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions. Defaults to `socket.gethostbyname(socket.gethostname())`
 * `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.
 
 If any of the following optional variables are set, [ProxyFix](https://werkzeug.palletsprojects.com/en/1.0.x/middleware/proxy_fix/) will be used.
 * `PROXY_FIX_FOR` - Number of upstream proxies setting X-Forwarded-For
@@ -84,6 +89,48 @@ If any of the following optional variables are set, [ProxyFix](https://werkzeug.
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 
+## Running cellxgene-gateway with Docker
+
+First, build Docker image:
+
+```bash
+docker build -t cellxgene-gateway .
+```
+
+Then, cellxgene-gateway can be launched as such:
+
+```bash
+docker run -it --rm \
+-v <local_data_dir>:/cellxgene-data \
+-p 5005:5005 \
+cellxgene-gateway
+```
+
+Additional environment variables can be provided with the `-e` parameter:
+
+```bash
+docker run -it --rm \
+-v ../cellxgene_data:/cellxgene-data \
+-e GATEWAY_PORT=8080 \
+-p 8080:8080 \
+cellxgene-gateway
+```
+## Running cellxgene gateway with start scripts
+
+For your convenience, we provide start scripts for flask, gunicorn and uwsgi.
+
+First, set up a .env
+```bash
+cp env_example .env
+# edit .env
+open .env
+```
+
+Then run the scripts in a subshell
+```bash
+( ./start_flask.sh )
+```
+
 # Customization
 
 The current paradigm for customization is to modify files during a build or deployment phase:
@@ -159,6 +206,35 @@ black .
 
 If you need help for any reason, please make a github ticket. One of the contributors should help you out.
 
+# Releasing New Versions
+
+## How to prepare for release
+
+- Update Changelog.md and version number in __init__.py
+- Cut a release on github
+	- Go to your project homepage on GitHub
+	- On right side, you will see [Releases](https://github.com/Novartis/cellxgene-gateway/releases) link. Click on it.
+	- Click on Draft a new release
+	- Fill in all the details
+		- Tag version should be the version number of your package release
+		- Release Title can be anything you want, but we use v0.3.11 (the same as the tag to be created on publish)
+		- Description should be changelog
+	- Click Publish release at the bottom of the page
+	- Now under Releases you can view all of your releases.
+	- Copy the download link (tar.gz) and save it somewhere
+
+## How to publish to PyPI
+
+Make sure your `.pypirc` is set up for testpypi and pypi index servers.
+ 
+
+```bash
+rm -rf dist
+python setup.py sdist bdist_wheel
+python -m twine upload --repository testpypi dist/*
+python -m twine upload dist/*
+```
+
 # Contributors
 
 * Niket Patel - https://github.com/NiketPatel9

SECURITY.md

@@ -0,0 +1,15 @@
+# Security Policy
+
+## Supported Versions
+
+Use this section to tell people about which versions of your project are
+currently being supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 0.3.2   | :white_check_mark: |
+| <= 0.3.1   | :x:                |
+
+## Reporting a Vulnerability
+
+Please file a bug report issue.

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__ = "0.2.3"
+__version__ = "0.4.0"

cellxgene_gateway/backend_cache.py

@@ -8,11 +8,10 @@
 # the specific language governing permissions and limitations under the License.
 
 import time
+from http import HTTPStatus
 from threading import Thread
 from typing import List
 
-from flask_api import status
-
 from cellxgene_gateway import env
 from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
 from cellxgene_gateway.cache_key import CacheKey
@@ -53,7 +52,7 @@ class BackendCache:
             return matches[0]
         else:
             raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
+                HTTPStatus.INTERNAL_SERVER_ERROR,
                 "Found " + str(len(matches)) + " for " + path,
             )
 
@@ -71,7 +70,7 @@ class BackendCache:
             return matches[0]
         else:
             raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
+                HTTPStatus.INTERNAL_SERVER_ERROR,
                 "Found " + str(len(matches)) + " for " + key.dataset,
             )
 

cellxgene_gateway/cache_entry.py

@@ -9,7 +9,6 @@
 import datetime
 import logging
 import re
-import urllib.parse
 from enum import Enum
 
 import psutil
@@ -22,6 +21,8 @@ from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.flask_util import querystring
 from cellxgene_gateway.util import current_time_stamp
 
+logger = logging.getLogger(__name__)
+
 
 class CacheEntryStatus(Enum):
     loaded = "loaded"
@@ -57,7 +58,6 @@ class CacheEntry:
 
     @classmethod
     def for_key(cls, key, port):
-
         return cls(
             None,
             key,
@@ -111,7 +111,7 @@ class CacheEntry:
             except psutil.NoSuchProcess:
                 pass
 
-            logging.getLogger("cellxgene_gateway").info(f"terminated {terminated}")
+            logger.info(f"terminated {terminated}")
         self.status = CacheEntryStatus.terminated
 
     def rewrite_text_content(self, cellxgene_content):
@@ -148,7 +148,7 @@ class CacheEntry:
         headers = {}
         copy_headers = [
             "accept",
-            "accept-encoding",
+            # "accept-encoding" - removed: let requests library handle compression/decompression
             "accept-language",
             "cache-control",
             "connection",
@@ -168,39 +168,43 @@ class CacheEntry:
                 headers[h] = request.headers[h]
 
         full_path = self.cellxgene_basepath() + subpath + querystring()
+        cellxgene_response = None
+        try:
+            if request.method in ["GET", "HEAD", "OPTIONS"]:
+                cellxgene_response = get(full_path, headers=headers)
+            elif request.method == "PUT":
+                cellxgene_response = put(
+                    full_path,
+                    headers=headers,
+                    data=request.data,
+                )
+            elif request.method == "POST":
+                cellxgene_response = post(
+                    full_path,
+                    headers=headers,
+                    data=request.data,
+                )
+            else:
+                raise CellxgeneException(f"Unexpected method {request.method}", 400)
+            content_type = cellxgene_response.headers["content-type"]
+            if "text" in content_type:
+                gateway_content = self.rewrite_text_content(
+                    cellxgene_response.content.decode()
+                )
+            else:
+                gateway_content = cellxgene_response.content
 
-        if request.method in ["GET", "HEAD", "OPTIONS"]:
+            resp_headers = {}
-            cellxgene_response = get(full_path, headers=headers)
+            for h in copy_headers:
-        elif request.method == "PUT":
+                if h in cellxgene_response.headers:
-            cellxgene_response = put(
+                    resp_headers[h] = cellxgene_response.headers[h]
-                full_path,
-                headers=headers,
-                data=request.data,
-            )
-        elif request.method == "POST":
-            cellxgene_response = post(
-                full_path,
-                headers=headers,
-                data=request.data,
-            )
-        else:
-            raise CellxgeneException(f"Unexpected method {request.method}", 400)
-        content_type = cellxgene_response.headers["content-type"]
-        if "text" in content_type:
-            gateway_content = self.rewrite_text_content(
-                cellxgene_response.content.decode()
-            )
-        else:
-            gateway_content = cellxgene_response.content
 
-        resp_headers = {}
+            gateway_response = make_response(
-        for h in copy_headers:
+                gateway_content,
-            if h in cellxgene_response.headers:
+                cellxgene_response.status_code,
-                resp_headers[h] = cellxgene_response.headers[h]
+                resp_headers,
-
+            )
-        gateway_response = make_response(
+        finally:
-            gateway_content,
+            if cellxgene_response is not None:
-            cellxgene_response.status_code,
+                cellxgene_response.close()
-            resp_headers,
-        )
         return gateway_response

cellxgene_gateway/dir_util.py

@@ -9,49 +9,9 @@
 
 import os
 
-from flask_api import status
-
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 
-
-def is_subdir(full_path, parent_path):
-    subdir = os.path.realpath(full_path)
-    parent = os.path.realpath(parent_path)
-    return subdir.startswith(parent)
-
-
-def create_dir(parent_path, dir_name):
-    full_path = os.path.join(parent_path, dir_name)
-
-    if "/" in dir_name:
-        raise CellxgeneException(
-            "Please have no slashes in the intended directory.",
-            status.HTTP_400_BAD_REQUEST,
-        )
-    elif not os.path.exists(parent_path):
-        raise CellxgeneException(
-            "The selected User directory does not exist.",
-            status.HTTP_400_BAD_REQUEST,
-        )
-    elif os.path.exists(full_path):
-        raise CellxgeneException(
-            "The provided subdirectory already exists within Directory.",
-            status.HTTP_400_BAD_REQUEST,
-        )
-    elif not is_subdir(full_path, parent_path):
-        raise CellxgeneException(
-            "The directory must be a subdirectory of the parent path.",
-            status.HTTP_400_BAD_REQUEST,
-        )
-    elif not os.path.isdir(parent_path):
-        raise CellxgeneException(
-            "The parent is not a directory.", status.HTTP_400_BAD_REQUEST
-        )
-    else:
-        os.mkdir(full_path)
-
-
 annotations_suffix = "_annotations"
 h5ad_suffix = ".h5ad"
 

cellxgene_gateway/env.py

@@ -9,7 +9,6 @@
 
 import logging
 import os
-import socket
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
@@ -20,11 +19,13 @@ external_host = os.environ.get(
     os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"),
 )
 external_protocol = os.environ.get(
-    "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http")
+    "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", None)
 )
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
-ttl = os.environ.get("GATEWAY_TTL")
+expire_seconds = int(
+    os.environ.get("GATEWAY_EXPIRE_SECONDS", os.environ.get("GATEWAY_TTL", "3600"))
+)
 enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in [
     "true",
     "1",
@@ -33,6 +34,7 @@ enable_backed_mode = os.environ.get("GATEWAY_ENABLE_BACKED_MODE", "").lower() in
     "true",
     "1",
 ]
+log_level = logging.getLevelName(os.environ.get("GATEWAY_LOG_LEVEL", "INFO"))
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
@@ -50,9 +52,10 @@ optional_env_vars = {
     "GATEWAY_IP": ip,
     "GATEWAY_PORT": gateway_port,
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
-    "GATEWAY_TTL": ttl,
+    "GATEWAY_EXPIRE_SECONDS": expire_seconds,
     "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
     "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
+    "GATEWAY_LOG_LEVEL": log_level,
     "CELLXGENE_ARGS": cellxgene_args,
     "CELLXGENE_DATA": cellxgene_data,
     "PROXY_FIX_FOR": proxy_fix_for,

cellxgene_gateway/extra_scripts.py

@@ -8,6 +8,7 @@
 # the specific language governing permissions and limitations under the License.
 
 from json import loads
+from json.decoder import JSONDecodeError
 
 from cellxgene_gateway import env
 
@@ -17,4 +18,9 @@ def get_extra_scripts():
     # ['https://www.googletagmanager.com/gtag/js?id=UA-123456-2',
     #  f"{env.external_protocol}://{env.external_host}/static/js/google_ua.js"]
     # where google_ua.js is a script you add to the static/js folder prior to deployment.
-    return [] if env.extra_scripts is None else loads(env.extra_scripts)
+    try:
+        return [] if env.extra_scripts is None else loads(env.extra_scripts)
+    except JSONDecodeError as exc:
+        raise Exception(
+            f'Error parsing GATEWAY_EXTRA_SCRIPTS, expected JSON array e.g. ["https://example.com/path/to/script.js"]'
+        ) from exc

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}/'>{html.escape(a.name)}</a>"
-                f"<a href='{CacheKey(item, item_source, a).view_url}/'>{a.name}</a>"
+            for a in item.annotations
-                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):
@@ -54,7 +55,7 @@ def render_item_tree(item_tree, item_source):
     if item_tree.descriptor:
         descriptor = item_tree.descriptor.lstrip("/")
         url = f"/filecrawl/{descriptor}?source={item_source.name}"
-        name = descriptor.rsplit("/")[1] if descriptor.find("/") >= 0 else descriptor
+        name = descriptor.rsplit("/", 1)[-1]
         return f"<li><a href='{url}'>{name}</a>{html}</li>"
     else:
         return html
@@ -62,5 +63,6 @@ def render_item_tree(item_tree, item_source):
 
 def render_item_source(item_source, filter=None):
     item_tree = item_source.list_items(filter)
-    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a></h6>"
+    filterpart = "" if filter is None else ":" + filter
+    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a>{filterpart}</h6>"
     return heading + render_item_tree(item_tree, item_source)

cellxgene_gateway/gateway.py

@@ -22,16 +22,13 @@ from flask import (
     send_from_directory,
     url_for,
 )
-from flask_api import status
 from werkzeug.middleware.proxy_fix import ProxyFix
-from werkzeug.utils import secure_filename
 
 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.dir_util import create_dir, is_subdir
 from cellxgene_gateway.extra_scripts import get_extra_scripts
 from cellxgene_gateway.filecrawl import render_item_source
 from cellxgene_gateway.process_exception import ProcessException
@@ -43,15 +40,30 @@ app = Flask(__name__)
 item_sources = []
 default_item_source = None
 
+# Guard for lazy initialization so tests can import this module without
+# triggering environment-dependent side effects. initialize_data_sources()
+# will set this to True when it has run.
+data_sources_initialized = False
+data_sources_init_lock = Lock()
+
 
 def _force_https(app):
     def wrapper(environ, start_response):
-        environ["wsgi.url_scheme"] = env.external_protocol
+        if env.external_protocol is not None:
+            environ["wsgi.url_scheme"] = env.external_protocol
         return app(environ, start_response)
 
     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
@@ -69,12 +81,89 @@ if (
         x_prefix=env.proxy_fix_prefix,
     )
 
+
+# WSGI middleware to ensure data sources are initialized before the first
+# WSGI request is handled. This guarantees initialization works under
+# Gunicorn/uWSGI (which import the module but don't call main()). The
+# initialize_data_sources() function is idempotent-protected by
+# data_sources_initialized and data_sources_init_lock.
+def _init_on_first_wsgi_request(wsgi_app):
+    def middleware(environ, start_response):
+        global data_sources_initialized
+        if not data_sources_initialized:
+            with data_sources_init_lock:
+                if not app.extensions.get("cellxgene_gateway", {}).get("launchtime"):
+                    app.extensions.setdefault("cellxgene_gateway", {})[
+                        "launchtime"
+                    ] = current_time_stamp()
+
+                if not data_sources_initialized:
+                    initialize_data_sources()
+
+                    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]
+
+                    data_sources_initialized = True
+        return wsgi_app(environ, start_response)
+
+    return middleware
+
+
+# Wrap the WSGI app so Gunicorn/uWSGI will trigger initialization when the
+# first request comes in. Tests that need initialization can call
+# initialize_data_sources() directly.
+app.wsgi_app = _init_on_first_wsgi_request(app.wsgi_app)
+
 cache = BackendCache()
 
 
+# Initialize data sources - this is defined later in the file but called here
+# to ensure initialization happens when WSGI servers (Gunicorn) import the module
+def initialize_data_sources():
+    """Initialize data sources from environment variables.
+    Called at module import time for WSGI server compatibility (Gunicorn).
+    Uses a guard flag to prevent double initialization within a process."""
+    global default_item_source
+
+    logging.basicConfig(
+        level=env.log_level,
+        format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
+    )
+    logger = logging.getLogger(__name__)
+
+    cellxgene_data = os.environ.get("CELLXGENE_DATA", None)
+    cellxgene_bucket = os.environ.get("CELLXGENE_BUCKET", None)
+
+    if cellxgene_bucket is not None:
+        from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
+
+        s3_source = S3ItemSource(cellxgene_bucket, name="s3")
+        item_sources.append(s3_source)
+        default_item_source = s3_source
+        logger.info("Initialized S3 data source")
+        logger.debug(f"S3 bucket: {cellxgene_bucket}")
+    if cellxgene_data is not None:
+        from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+
+        file_source = FileItemSource(cellxgene_data, name="local")
+        item_sources.append(file_source)
+        default_item_source = file_source
+        logger.info("Initialized local file data source")
+        logger.debug(f"Data directory: {cellxgene_data}")
+    if len(item_sources) == 0:
+        raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
+    flask_util.include_source_in_url = len(item_sources) > 1
+
+
 @app.errorhandler(CellxgeneException)
 def handle_invalid_usage(error):
-
     message = f"{error.http_status} Error : {error.message}"
 
     return (
@@ -89,7 +178,6 @@ def handle_invalid_usage(error):
 
 @app.errorhandler(ProcessException)
 def handle_invalid_process(error):
-
     message = []
 
     message.append(error.message)
@@ -157,10 +245,7 @@ def filecrawl(path=None):
             path=path,
         )
     )
-    resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
+    set_no_cache(resp)
-    resp.headers["Pragma"] = "no-cache"
-    resp.headers["Expires"] = "0"
-    resp.headers["Cache-Control"] = "public, max-age=0"
     return resp
 
 
@@ -168,7 +253,7 @@ entry_lock = Lock()
 
 
 def matching_source(source_name):
-    if source_name is None:
+    if source_name is None and default_item_source is not None:
         source_name = default_item_source.name
     matching = [i for i in item_sources if i.name == source_name]
     if len(matching) != 1:
@@ -209,40 +294,64 @@ def do_view(path, source_name=None):
         match.status == CacheEntryStatus.loaded
         or match.status == CacheEntryStatus.loading
     ):
-        return match.serve_content(path)
+        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)
+    else:
+        raise CellxgeneException(
+            f"Unexpected cache entry status {match.status} for key {match.key.descriptor}",
+            500,
+        )
 
 
 @app.route("/cache_status", methods=["GET"])
 def do_GET_status():
-    return render_template("cache_status.html", entry_list=cache.entry_list)
+    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():
+    def map_entry(entry):
+        dataset = entry.key.h5ad_item.descriptor
+        annotation_file = entry.key.annotation_descriptor
+        return {
+            "dataset": dataset,
+            "annotation_file": annotation_file,
+            "launchtime": entry.launchtime,
+            "last_access": entry.timestamp,
+            "status": entry.status.name,
+        }
+
     return json.dumps(
         {
-            "launchtime": app.launchtime,
+            "launchtime": app.extensions.get("cellxgene_gateway", {}).get("launchtime"),
-            "entry_list": [
+            "entry_list": [map_entry(entry) for entry in cache.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 get_cache_key(path):
-def do_relaunch(path):
+    if request.args.get("source_name"):
-    source_name = request.args.get("source_name") or default_item_source.name
+        source_name = request.args.get("source_name")
+    elif default_item_source:
+        source_name = default_item_source.name
+    else:
+        source_name = None
     source = matching_source(source_name)
     key = CacheKey.for_lookup(source, source.lookup(path))
+    return key
+
+
+@app.route("/relaunch/<path:path>", methods=["GET"])
+def do_relaunch(path):
+    key = get_cache_key(path)
     match = cache.check_entry(key)
     if not match is None:
         match.terminate()
@@ -254,55 +363,42 @@ def do_relaunch(path):
 
 @app.route("/terminate/<path:path>", methods=["GET"])
 def do_terminate(path):
-    source_name = request.args.get("source_name") or default_item_source.name
+    key = get_cache_key(path)
-    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)
 
 
-def launch():
+@app.route("/metadata/ip_address", methods=["GET"])
-    env.validate()
+def ip_address():
-    if not item_sources or not len(item_sources):
+    resp = make_response(env.ip)
-        raise Exception("No data sources specified for Cellxgene Gateway")
+    return set_no_cache(resp)
 
-    global default_item_source
-    if default_item_source is None:
-        default_item_source = item_sources[0]
 
+def start_pruner_thread():
     pruner = PruneProcessCache(cache)
-
+    # Run the pruner as a daemon thread so it won't block interpreter
-    background_thread = Thread(target=pruner)
+    # shutdown (for example when Ctrl-C is used in the main thread).
+    # This avoids "Exception ignored in: <module 'threading'...>" at exit.
+    background_thread = Thread(target=pruner, daemon=True)
     background_thread.start()
 
-    app.launchtime = current_time_stamp()
+
+def launch():
+    start_pruner_thread()
+
+    app.extensions.setdefault("cellxgene_gateway", {})[
+        "launchtime"
+    ] = current_time_stamp()
     app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
 
 
+app.extensions.setdefault("cellxgene_gateway", {})["launchtime"] = None
+
+
 def main():
-    logging.basicConfig(
+    """CLI entry point for Flask development server."""
-        level=logging.INFO,
-        format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
-    )
-    cellxgene_data = os.environ.get("CELLXGENE_DATA", None)
-    cellxgene_bucket = os.environ.get("CELLXGENE_BUCKET", None)
-
-    if cellxgene_bucket is not None:
-        from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
-
-        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
-
-        item_sources.append(FileItemSource(cellxgene_data, name="local"))
-        default_item_source = "local"
-    if len(item_sources) == 0:
-        raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
-    flask_util.include_source_in_url = len(item_sources) > 1
-
     launch()
 
 

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)
 
@@ -51,7 +56,7 @@ class FileItemSource(ItemSource):
         return self.convert_h5ad_path_to_annotation(item.descriptor)
 
     def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory()
+        item_tree = self.scan_directory("" if filter is None else filter)
 
         """def get_items(dir):
             if dir.branches:
@@ -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)
 
@@ -121,6 +131,9 @@ class FileItemSource(ItemSource):
         if self.is_h5ad_file(full_path):
             return self.shallowitem_from_descriptor(descriptor)
 
+    def is_authorized(self, descriptor):
+        return True
+
     def lookup(self, indescriptor: str) -> LookupResult:
         descriptor = indescriptor.strip("/")
         if descriptor.endswith(self.annotation_file_suffix):
@@ -173,11 +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/item_source.py

@@ -40,6 +40,10 @@ class ItemSource(ABC):
     def update(self, item: Item) -> None:
         raise Exception('"update" unimplemented')
 
+    @abstractmethod
+    def is_authorized(self, descriptor: str) -> bool:
+        raise Exception('"is_authorized" unimplemented')
+
     @abstractmethod
     def lookup(self, descriptor: str) -> LookupResult:
         raise Exception('"lookup" unimplemented')

cellxgene_gateway/items/s3/s3item_source.py

@@ -7,9 +7,11 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-from os.path import basename, dirname, join
+import os
+from os.path import basename, dirname
 from typing import List
 
+import flask
 import s3fs
 
 from cellxgene_gateway import dir_util
@@ -18,6 +20,10 @@ from cellxgene_gateway.items.item_source import ItemSource, LookupResult
 from cellxgene_gateway.items.s3.s3item import S3Item
 
 
+def truthy(val: str):
+    return val.lower() in ["true", "1"]
+
+
 class S3ItemSource(ItemSource):
     def __init__(
         self,
@@ -28,7 +34,10 @@ class S3ItemSource(ItemSource):
         annotation_file_suffix=".csv",
     ):
         self._name = name
-        self.s3 = s3fs.S3FileSystem()
+        enable_cache = os.environ.get("S3_ENABLE_LISTINGS_CACHE", "false").lower()
+        assert enable_cache in ["0", "1", "false", "true"]
+        self.use_listings_cache = truthy(enable_cache)
+        self.s3 = s3fs.S3FileSystem(use_listings_cache=self.use_listings_cache)
         if bucket.startswith("s3://"):
             raise Exception(
                 f"Bucket name should not include s3:// prefix, got {bucket}"
@@ -38,8 +47,11 @@ class S3ItemSource(ItemSource):
         self.annotation_dir_suffix = annotation_dir_suffix
         self.annotation_file_suffix = annotation_file_suffix
 
-    def url(self, path):
+    def url(self, key):
-        return "s3://" + join(self.bucket, path)
+        return "s3://" + self.bucket + "/" + key
+
+    def remove_bucket(self, filepath):
+        return filepath[len(self.bucket) :].lstrip("/")
 
     @property
     def name(self):
@@ -61,49 +73,54 @@ class S3ItemSource(ItemSource):
         return self.convert_h5ad_key_to_annotation(item.descriptor)
 
     def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory()
+        item_tree = self.scan_directory("" if filter is None else filter)
         return item_tree
 
-    def scan_directory(self, subpath="") -> dict:
+    @property
-        url = self.url(subpath)
+    def refresh(self):
+        return (
+            truthy(flask.request.args.get("refresh", default="false"))
+            or not self.use_listings_cache
+        )
+
+    def scan_directory(self, directory_key="") -> dict:
+        url = self.url(directory_key)
 
         if not self.s3.exists(url):
             raise Exception(f"S3 url '{url}' does not exist.")
 
         s3key_map = dict(
-            (filepath[len(self.bucket) :].lstrip("/"), "s3://" + filepath)
+            (self.remove_bucket(filepath), "s3://" + filepath)
-            for filepath in sorted(self.s3.ls(url))
+            for filepath in sorted(self.s3.ls(url, refresh=self.refresh))
         )
 
         def is_annotation_dir(dir_s3key):
             return (
                 dir_s3key.endswith(self.annotation_dir_suffix)
-                and self.convert_annotation_key_to_h5ad(dir_s3key) in h5ad_paths
+                and self.convert_annotation_key_to_h5ad(dir_s3key) in h5ad_keys
             )
 
-        h5ad_paths = [
+        h5ad_keys = [
             filepath
             for filepath, item_url in s3key_map.items()
             if self.is_h5ad_url(item_url)
         ]
 
-        subdirs = [
+        subdir_keys = [
             filepath
             for filepath, item_url in s3key_map.items()
             if self.s3.isdir(item_url) and not is_annotation_dir(filepath)
         ]
 
-        items = [
+        items = [self.make_s3item_from_key(basename(key), key) for key in h5ad_keys]
-            self.make_s3item_from_key(filename, join(subpath, filename))
-            for filename in h5ad_paths
-        ]
         branches = None
-        if len(subdirs) > 0:
+        if len(subdir_keys) > 0:
+            branches = [self.scan_directory(key) for key in subdir_keys]
             branches = [
-                self.scan_directory(join(subpath, subdir)) for subdir in subdirs
+                branch for branch in branches if branch.items or branch.branches
             ]
 
-        return ItemTree(subpath, items, branches)
+        return ItemTree(directory_key, items, branches)
 
     def create_annotation(self, item: S3Item, name: str) -> S3Item:
         annotation = self.make_s3item_from_key(
@@ -115,6 +132,9 @@ class S3ItemSource(ItemSource):
     def update(self, item: S3Item) -> None:
         pass
 
+    def is_authorized(self, descriptor):
+        return True
+
     def lookup_item(self, descriptor):
         full_path = self.url(descriptor)
         if self.is_h5ad_url(full_path):
@@ -163,11 +183,13 @@ class S3ItemSource(ItemSource):
         if self.s3.isdir(annotations_fullpath):
             return [
                 self.make_s3item_from_key(
-                    annotation, join(annotations_subpath, annotation), True
+                    basename(annotation), self.remove_bucket(annotation), True
+                )
+                for annotation in sorted(
+                    self.s3.ls(annotations_fullpath, refresh=self.refresh)
                 )
-                for annotation in sorted(self.s3.ls(annotations_fullpath))
                 if annotation.endswith(self.annotation_file_suffix)
-                and self.s3.isfile(join(annotations_fullpath, annotation))
+                and self.s3.isfile("s3://" + annotation)
             ]
         else:
             return None

cellxgene_gateway/path_util.py

@@ -1,41 +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 os
-
-from flask_api import status
-
-from cellxgene_gateway.cache_key import CacheKey
-from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import make_h5ad
-
-
-def validate_exists(file_path):
-    if not os.path.exists(file_path):
-        raise CellxgeneException(
-            "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
-        )
-
-
-def validate_is_file(file_path):
-    validate_exists(file_path)
-    if not os.path.isfile(file_path):
-        raise CellxgeneException(
-            "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST
-        )
-    return
-
-
-def validate_is_dir(file_path):
-    validate_exists(file_path)
-    if not os.path.isdir(file_path):
-        raise CellxgeneException(
-            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
-        )
-    return

cellxgene_gateway/prune_process_cache.py

@@ -18,7 +18,7 @@ logger = logging.getLogger(__name__)
 class PruneProcessCache:
     def __init__(self, cache):
         self.cache = cache
-        self.expire_seconds = 3600 if env.ttl is None else int(env.ttl)
+        self.expire_seconds = env.expire_seconds
 
     def __call__(self):
         while True:
@@ -39,9 +39,9 @@ class PruneProcessCache:
 
         for process in processes_to_delete:
             try:
-                logger.info(f"pruning process {process.pid} ({process.key.dataset})")
+                logger.info(f"pruning process {process.pid} ({process.key.descriptor})")
                 self.cache.prune(process)
             except Exception:
                 logger.exception(
-                    "failed to prune process {process.pid} ({process.dataset})"
+                    "failed to prune process {process.pid} ({process.key.descriptor})"
                 )

cellxgene_gateway/subprocess_backend.py

@@ -9,14 +9,15 @@
 
 import logging
 import subprocess
-
+from http import HTTPStatus
-from flask_api import status
 
 from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.dir_util import make_annotations
 from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode
 from cellxgene_gateway.process_exception import ProcessException
 
+logger = logging.getLogger(__name__)
+
 
 class SubprocessBackend:
     def __init__(self):
@@ -28,8 +29,11 @@ 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:
@@ -55,7 +59,7 @@ class SubprocessBackend:
             scripts,
             cache_entry.key.annotation_file_path,
         )
-        logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
+        logger.info(f"launching {cmd}")
         process = subprocess.Popen(
             [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
         )
@@ -71,10 +75,10 @@ class SubprocessBackend:
                     or "Could not open file" in stderr
                 ):
                     message = "File was invalid."
-                    http_status = status.HTTP_400_BAD_REQUEST
+                    http_status = HTTPStatus.BAD_REQUEST
                 else:
                     message = "Cellxgene failed to launch dataset."
-                    http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
+                    http_status = HTTPStatus.INTERNAL_SERVER_ERROR
 
                 cache_entry.status = CacheEntryStatus.error
                 cache_entry.set_error(message, stderr, http_status)
@@ -84,5 +88,6 @@ class SubprocessBackend:
                 cache_entry.append_output(output)
 
         cache_entry.set_loaded(process.pid)
-
+        for output in process.communicate():
-        return
+            logger.debug(f"cellxgene:{output}")
+        logger.info(f"exiting {cmd}")

cellxgene_gateway/templates/cache_status.html

@@ -75,7 +75,9 @@
                     const el = $(this);
                     const ts = el.text();
                     const dt = new Date(parseInt(ts * 1000));
-                    el.html(`${dt.toISOString()}<br>(${ts})`);
+                    el.prepend(`${dt.toISOString()}<br>(`);
+                    el.append(')');
+
                });
           })
      </script>

env_example

@@ -0,0 +1,3 @@
+export CELLXGENE_LOCATION=$(pwd)/.venv/bin/cellxgene
+export CELLXGENE_DATA=../cellxgene_data
+export GATEWAY_IP=127.0.0.1

environment.yml

@@ -2,13 +2,16 @@ name: cellxgene-gateway
 channels:
 - conda-forge
 dependencies:
-- python=3.7
+- python=3.11
 - requests
 - flask
 - psutil
 - black
+- twine
+- isort
 - coverage
 - pip
 - pip:
-  - flask-api
+  - pre_commit
-  - cellxgene>=0.15
+  - werkzeug
+  - cellxgene

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

@@ -1,5 +1,5 @@
-cellxgene>=0.15
+cellxgene
 flask
-flask_api
+werkzeug
 psutil
 requests

run.sh.example

@@ -1,6 +0,0 @@
-export CELLXGENE_LOCATION=$(pwd)/.cellxgene-gateway/bin/cellxgene
-export CELLXGENE_DATA=../cellxgene_data
-export GATEWAY_IP=127.0.0.1
-
-#Once these are set, you run like a normal Flask app
-cellxgene-gateway

start_flask.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
+#
+# PREREQUISITES:
+# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
+# - Virtual environment activated
+# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
+#
+# USAGE:
+# ./start_gunicorn.sh
+
+# Exit on error
+set -e
+
+# Get the directory where this script is located
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+
+# Source environment variables
+echo "Loading environment variables..."
+if [ -f "$SCRIPT_DIR/.env" ]; then
+    source "$SCRIPT_DIR/.env"
+else
+    echo "Error: .env file not found at $SCRIPT_DIR/.env"
+    echo "Please create it with required environment variables"
+    exit 1
+fi
+
+# Verify required environment variables
+if [ -z "$CELLXGENE_LOCATION" ]; then
+    echo "Error: CELLXGENE_LOCATION not set"
+    exit 1
+fi
+
+if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
+    echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
+    exit 1
+fi
+
+exec cellxgene-gateway

start_gunicorn.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
+#
+# PREREQUISITES:
+# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
+# - Virtual environment activated
+# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
+#
+# USAGE:
+# ./start_gunicorn.sh
+
+# Exit on error
+set -e
+
+# Get the directory where this script is located
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# Source environment variables
+echo "Loading environment variables..."
+if [ -f "$SCRIPT_DIR/.env" ]; then
+    source "$SCRIPT_DIR/.env"
+else
+    echo "Error: .env file not found at $SCRIPT_DIR/.env"
+    echo "Please create it with required environment variables"
+    exit 1
+fi
+
+# Verify required environment variables
+if [ -z "$CELLXGENE_LOCATION" ]; then
+    echo "Error: CELLXGENE_LOCATION not set"
+    exit 1
+fi
+
+if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
+    echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
+    exit 1
+fi
+
+# Gunicorn configuration
+# WARNING: Multi-worker mode has cache synchronization issues (see plans/002-shared-cache-implementation.md)
+# Each worker maintains its own in-memory cache, causing 404s for static assets when different
+# workers handle requests for the same dataset. Use GUNICORN_WORKERS=1 until shared cache is implemented.
+WORKERS=${GUNICORN_WORKERS:-1}
+BIND=${GATEWAY_IP:-0.0.0.0}:${GATEWAY_PORT:-5005}
+TIMEOUT=${GUNICORN_TIMEOUT:-120}
+WORKER_CLASS=${GUNICORN_WORKER_CLASS:-sync}
+KEEPALIVE=${GUNICORN_KEEPALIVE:-5}
+LOG_LEVEL=${GUNICORN_LOG_LEVEL:-info}
+
+# Production optimization: enable backed mode to reduce memory usage
+export GATEWAY_ENABLE_BACKED_MODE=${GATEWAY_ENABLE_BACKED_MODE:-true}
+
+# Check if gunicorn is installed
+if ! command -v gunicorn &> /dev/null; then
+    echo "Error: gunicorn not found. Install with: pip install gunicorn"
+    exit 1
+fi
+
+# Display configuration
+echo "Starting Cellxgene Gateway with Gunicorn..."
+echo "Configuration:"
+echo "  Data source: ${CELLXGENE_DATA:-$CELLXGENE_BUCKET}"
+echo "  Binding to: $BIND"
+echo "  Workers: $WORKERS"
+echo "  Worker class: $WORKER_CLASS"
+echo "  Timeout: ${TIMEOUT}s"
+echo "  Keepalive: ${KEEPALIVE}s"
+echo "  Log level: $LOG_LEVEL"
+echo "  Backed mode: ${GATEWAY_ENABLE_BACKED_MODE}"
+echo ""
+
+cd "$SCRIPT_DIR"
+
+# Start Gunicorn with optimized settings
+# Additional options you can add via environment variables:
+# - GUNICORN_MAX_REQUESTS: Restart worker after N requests (prevents memory leaks)
+# - GUNICORN_MAX_REQUESTS_JITTER: Add randomness to max-requests
+exec gunicorn cellxgene_gateway.gateway:app \
+    --workers "$WORKERS" \
+    --worker-class "$WORKER_CLASS" \
+    --bind "$BIND" \
+    --timeout "$TIMEOUT" \
+    --keep-alive "$KEEPALIVE" \
+    --access-logfile - \
+    --error-logfile - \
+    --log-level "$LOG_LEVEL" \
+    --preload \
+    ${GUNICORN_MAX_REQUESTS:+--max-requests "$GUNICORN_MAX_REQUESTS"} \
+    ${GUNICORN_MAX_REQUESTS_JITTER:+--max-requests-jitter "$GUNICORN_MAX_REQUESTS_JITTER"} \
+    "$@"

start_uwsgi.sh

@@ -0,0 +1,89 @@
+#!/bin/bash
+
+# start_uwsgi.sh - Start Cellxgene Gateway with uWSGI
+#
+# PREREQUISITES:
+# - uWSGI installed (pip install uwsgi)
+# - Virtual environment activated
+# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
+#
+# USAGE:
+# ./start_uwsgi.sh
+
+# Exit on error
+set -e
+
+# Get the directory where this script is located
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# Source environment variables
+echo "Loading environment variables..."
+if [ -f "$SCRIPT_DIR/.env" ]; then
+    source "$SCRIPT_DIR/.env"
+else
+    echo "Error: .env file not found at $SCRIPT_DIR/.env"
+    echo "Please create it with required environment variables"
+    exit 1
+fi
+
+# Verify required environment variables
+if [ -z "$CELLXGENE_LOCATION" ]; then
+    echo "Error: CELLXGENE_LOCATION not set"
+    exit 1
+fi
+
+if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
+    echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
+    exit 1
+fi
+
+# uWSGI configuration
+# WARNING: Multi-worker mode has cache synchronization issues (see plans/002-shared-cache-implementation.md)
+# Each worker maintains its own in-memory cache, causing 404s for static assets when different
+# workers handle requests for the same dataset. Use UWSGI_WORKERS=1 until shared cache is implemented.
+WORKERS=${UWSGI_WORKERS:-1}
+HOST=${GATEWAY_IP:-0.0.0.0}
+PORT=${GATEWAY_PORT:-5005}
+TIMEOUT=${UWSGI_TIMEOUT:-120}
+THREADS=${UWSGI_THREADS:-1}
+
+# Production optimization: enable backed mode to reduce memory usage
+export GATEWAY_ENABLE_BACKED_MODE=${GATEWAY_ENABLE_BACKED_MODE:-true}
+
+# Check if uwsgi is installed
+if ! command -v uwsgi &> /dev/null; then
+    echo "Error: uwsgi not found. Install with: pip install uwsgi"
+    exit 1
+else
+    # Display configuration
+    echo "Starting Cellxgene Gateway with uWSGI..."
+    echo "Configuration:"
+    echo "  Data source: ${CELLXGENE_DATA:-$CELLXGENE_BUCKET}"
+    echo "  Binding to: $HOST:$PORT"
+    echo "  Workers: $WORKERS"
+    echo "  Threads: $THREADS"
+    echo "  Timeout: ${TIMEOUT}s"
+    echo "  Backed mode: ${GATEWAY_ENABLE_BACKED_MODE}"
+    echo ""
+
+    cd "$SCRIPT_DIR"
+
+    # Start uWSGI with optimized settings
+    # Additional options you can add via environment variables:
+    # - UWSGI_MAX_REQUESTS: Restart worker after N requests (prevents memory leaks)
+    exec uwsgi \
+        --http "$HOST:$PORT" \
+        --module cellxgene_gateway.gateway:app \
+        --workers "$WORKERS" \
+        --threads "$THREADS" \
+        --harakiri "$TIMEOUT" \
+        --master \
+        --enable-threads \
+        --single-interpreter \
+        --need-app \
+        --die-on-term \
+        --log-x-forwarded-for \
+        ${UWSGI_MAX_REQUESTS:+--max-requests "$UWSGI_MAX_REQUESTS"} \
+        "$@"
+fi
+

tests/items/file/test_fileitem_source.py

@@ -1,10 +1,31 @@
 import tempfile
 import unittest
+from unittest.mock import patch
 
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
 
 
+def stub_join(path):
+    path.join = lambda x, y: x + "/" + y
+
+
 class TestFileItemSource(unittest.TestCase):
+    @patch("os.path")
+    @patch("os.listdir")
+    def test_list_items_GIVEN_no_subpath_THEN_checks_dir(self, listdir, path):
+        stub_join(path)
+        source = FileItemSource("/tmp/unittest", "local")
+        source.list_items()
+        path.exists.assert_called_once_with("/tmp/unittest/")
+
+    @patch("os.path")
+    @patch("os.listdir")
+    def test_list_items_GIVEN_subpath_THEN_checks_subpath(self, listdir, path):
+        stub_join(path)
+        source = FileItemSource("/tmp/unittest", "local")
+        source.list_items("foo")
+        path.exists.assert_called_once_with("/tmp/unittest/foo")
+
     def test_make_fileitem_from_path_GIVEN_annotation_file_THEN_name_lacks_csv(
         self,
     ):

tests/items/s3/test_s3item_source.py

@@ -0,0 +1,184 @@
+import unittest
+import os
+import shutil
+import tempfile
+
+from unittest.mock import MagicMock, Mock, patch
+
+from cellxgene_gateway.items.item import ItemType
+from cellxgene_gateway.items.s3.s3item import S3Item
+from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
+from cellxgene_gateway.gateway import app
+
+
+class TestScanDirectory(unittest.TestCase):
+    def setUp(self):
+
+        self.app = app
+
+    def tearDown(self):
+        pass
+
+    @patch("s3fs.S3FileSystem")
+    def test_GIVEN_invalid_bucket_THEN_throws_error(self, s3func):
+        class S3Mock:
+            def exists(path):
+                if path in ["s3://my-bucket/"]:
+                    return False
+
+        s3func.return_value = S3Mock
+        source = S3ItemSource("my-bucket")
+        with self.assertRaises(Exception) as context:
+            source.scan_directory()
+        self.assertEqual(
+            "S3 url 's3://my-bucket/' does not exist.",
+            str(context.exception),
+        )
+
+    @patch("s3fs.S3FileSystem")
+    def test__GIVEN_multilevel_bucket_THEN_properly_recurses_suburls(self, s3func):
+
+        class S3Mock:
+            def exists(path):
+                if path in [
+                    "s3://my-bucket/",
+                    "s3://my-bucket/pbmc3k.h5ad",
+                    "s3://my-bucket/lvl1",
+                    "s3://my-bucket/lvl1/pbmc3k_l1.h5ad",
+                    "s3://my-bucket/lvl1/lvl2",
+                    "s3://my-bucket/lvl1/lvl2/pbmc3k_l2.h5ad",
+                ]:
+                    return True
+                raise Exception("exists called with " + path)
+
+            def ls(path, refresh):
+                assert refresh == True
+                if path == "s3://my-bucket/":
+                    return [
+                        "my-bucket/lvl1",
+                        "my-bucket/pbmc3k.h5ad",
+                        "my-bucket/pbmc3k_annotations",
+                    ]
+                elif path == "s3://my-bucket/pbmc3k_annotations":
+                    return ["my-bucket/pbmc3k_annotations/annot.csv"]
+                elif path == "s3://my-bucket/lvl1":
+                    return ["my-bucket/lvl1/lvl2", "my-bucket/lvl1/pbmc3k_l1.h5ad"]
+                elif path == "s3://my-bucket/lvl1/lvl2":
+                    return ["my-bucket/lvl1/lvl2/pbmc3k_l2.h5ad"]
+
+                raise Exception("ls called with " + path)
+
+            def isdir(path):
+                if path in [
+                    "s3://my-bucket/lvl1",
+                    "s3://my-bucket/pbmc3k_annotations",
+                    "s3://my-bucket/lvl1/lvl2",
+                ]:
+                    return True
+                if path in [
+                    "s3://my-bucket/pbmc3k.h5ad",
+                    "s3://my-bucket/lvl1/pbmc3k_l1.h5ad",
+                    "s3://my-bucket/lvl1/pbmc3k_l1_annotations",
+                    "s3://my-bucket/lvl1/lvl2/pbmc3k_l2.h5ad",
+                    "s3://my-bucket/lvl1/lvl2/pbmc3k_l2_annotations",
+                ]:
+                    return False
+                raise Exception("isdir called with " + path)
+
+            def isfile(path):
+                if path in ["s3://my-bucket/pbmc3k_annotations/annot.csv"]:
+                    return True
+                if path in ["s3://my-bucket/pbmc3k_annotations"]:
+                    return False
+                raise Exception("isfile called with " + path)
+
+        s3func.return_value = S3Mock
+        source = S3ItemSource("my-bucket")
+        with self.app.test_request_context(query_string="refresh=true") as test_context:
+            tree = source.scan_directory()
+
+        def s3item_compare(i1, i2, msg=""):
+            self.assertEqual(i1.name, i2.name, "name equals")
+            self.assertEqual(i1.type, i2.type, "type equals")
+            self.assertEqual(i1.s3key, i2.s3key, "s3key equals")
+            if i1.annotations is None:
+                self.assertEqual(i1.annotations, i2.annotations, "annotations equals")
+            else:
+                self.assertEqual(
+                    len(i1.annotations),
+                    len(i2.annotations),
+                    "annotations length equals",
+                )
+                for a1, a2 in zip(i1.annotations, i2.annotations):
+                    self.assertEqual(a1, a2)
+            return True
+
+        self.addTypeEqualityFunc(S3Item, s3item_compare)
+
+        def assertTree(t, descriptor, items):
+            self.assertEqual(t.descriptor, descriptor)
+            self.assertEqual(len(t.items), len(items))
+            for i1, i2 in zip(t.items, items):
+                self.assertEqual(i1, i2)
+
+        assertTree(
+            tree,
+            "",
+            [
+                S3Item(
+                    "pbmc3k.h5ad",
+                    name="pbmc3k.h5ad",
+                    type=ItemType.h5ad,
+                    annotations=[
+                        S3Item(
+                            "pbmc3k_annotations/annot.csv",
+                            name="annot.csv",
+                            type=ItemType.annotation,
+                        )
+                    ],
+                )
+            ],
+        )
+        self.assertEqual(len(tree.branches), 1)
+        lvl1 = tree.branches[0]
+        assertTree(
+            lvl1,
+            "lvl1",
+            [
+                S3Item(
+                    "lvl1/pbmc3k_l1.h5ad",
+                    name="pbmc3k_l1.h5ad",
+                    type=ItemType.h5ad,
+                    annotations=None,
+                )
+            ],
+        )
+        self.assertEqual(len(lvl1.branches), 1)
+        lvl2 = lvl1.branches[0]
+        assertTree(
+            lvl2,
+            "lvl1/lvl2",
+            [
+                S3Item(
+                    "lvl1/lvl2/pbmc3k_l2.h5ad",
+                    name="pbmc3k_l2.h5ad",
+                    type=ItemType.h5ad,
+                    annotations=None,
+                )
+            ],
+        )
+        self.assertEqual(lvl2.branches, None)
+
+
+class TestListItems(unittest.TestCase):
+    def test_GIVEN_filter_THEN_pass_filter_into_scan_directory(self):
+        source = S3ItemSource("my-bucket")
+        source.scan_directory = MagicMock()
+        tree = source.list_items("some-filter")
+        source.scan_directory.assert_called_once_with("some-filter")
+
+    def test_GIVEN_no_filter_THEN_pass_empty_string_into_scan_directory(self):
+        source = S3ItemSource("my-bucket")
+        source.scan_directory = MagicMock()
+        tree = source.list_items()
+        source.scan_directory.assert_called_once_with("")

tests/test_backend_cache.py

@@ -0,0 +1,28 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from cellxgene_gateway.backend_cache import is_port_in_use
+
+
+class TestIsPortInUse(unittest.TestCase):
+    @patch("socket.socket")
+    def test_GIVEN_free_port_THEN_returns_true(self, socketMock):
+        connectMock = socketMock()
+        connectMock.connect_ex.return_value = 0
+        connectMock.__enter__.return_value = connectMock
+        self.assertEqual(is_port_in_use(123), True)
+        self.assertTrue(connectMock.__enter__.calledOnce)
+        self.assertTrue(connectMock.__exit__.calledOnce)
+        self.assertTrue(connectMock.connect_ex.calledOnceWith("a"))
+        self.assertTrue(socketMock.calledOnceWith("a"))
+
+    @patch("socket.socket")
+    def test_GIVEN_used_port_THEN_returns_false(self, socketMock):
+        connectMock = socketMock()
+        connectMock.__enter__.return_value = connectMock
+        connectMock.connect_ex.return_value = 1
+        self.assertTrue(connectMock.__enter__.calledOnce)
+        self.assertTrue(connectMock.__exit__.calledOnce)
+        self.assertTrue(connectMock.connect_ex.calledOnceWith("a"))
+        self.assertTrue(socketMock.calledOnceWith("a"))
+        self.assertEqual(is_port_in_use(123), False)

tests/test_cache_entry.py

@@ -1,14 +1,16 @@
 import unittest
+import tempfile
+import os
+import shutil
 
 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 import app
+from cellxgene_gateway.items.item import ItemType
 from cellxgene_gateway.items.file.fileitem import FileItem
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-from cellxgene_gateway.items.item import ItemType
+from cellxgene_gateway.gateway import app
 
 key = CacheKey(
     FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
@@ -23,6 +25,9 @@ class TestRenderEntry(unittest.TestCase):
         self.app_context.push()
         self.client = self.app.test_client()
 
+    def tearDown(self):
+        self.app_context.pop()
+
     def test_GIVEN_key_and_port_THEN_returns_loading_CacheEntry(self):
         entry = CacheEntry.for_key("some-key", 1)
         self.assertEqual(entry.status, CacheEntryStatus.loading)

tests/test_dir_util.py

@@ -0,0 +1,35 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from cellxgene_gateway.dir_util import ensure_dir_exists, make_annotations, make_h5ad
+
+
+class TestMakeH5ad(unittest.TestCase):
+    def test_GIVEN_annotation_dir_THEN_returns_h5ad(self):
+        self.assertEqual(make_h5ad("pbmc_annotations"), "pbmc.h5ad")
+
+
+class TestMakeAnnotations(unittest.TestCase):
+    def test_GIVEN_h5ad_THEN_returns_annotations(self):
+        self.assertEqual(make_annotations("pbmc.h5ad"), "pbmc_annotations")
+
+
+class TestMakeAnnotations(unittest.TestCase):
+    def test_GIVEN_h5ad_THEN_returns_annotations(self):
+        self.assertEqual(make_annotations("pbmc.h5ad"), "pbmc_annotations")
+
+
+class TestEnsureDirExists(unittest.TestCase):
+    @patch("os.path.exists")
+    @patch("os.makedirs")
+    def test_GIVEN_existing_THEN_does_not_call_makedir(self, makedirsMock, existsMock):
+        existsMock.return_value = True
+        ensure_dir_exists("/foo")
+        makedirsMock.assert_not_called()
+
+    @patch("os.path.exists")
+    @patch("os.makedirs")
+    def test_GIVEN_not_existing_THEN_calls_makedir(self, makedirsMock, existsMock):
+        existsMock.return_value = False
+        ensure_dir_exists("/foo")
+        makedirsMock.assert_called_once_with("/foo")

tests/test_extra_scripts.py

@@ -21,6 +21,15 @@ class TestExtraScripts(unittest.TestCase):
     def test_GIVEN_empty_string_THEN_returns_empty_array(self):
         self.assertEqual(get_extra_scripts(), [])
 
+    @patch("cellxgene_gateway.env.extra_scripts", new="'asdf'")
+    def test_GIVEN_bare_string_THEN_throws_Exception(self):
+        with self.assertRaises(Exception) as context:
+            self.assertEqual(get_extra_scripts(), [])
+        self.assertEqual(
+            'Error parsing GATEWAY_EXTRA_SCRIPTS, expected JSON array e.g. ["https://example.com/path/to/script.js"]',
+            str(context.exception),
+        )
+
 
 if __name__ == "__main__":
     unittest.main()

tests/test_filecrawl.py

@@ -1,31 +1,170 @@
+import os
+import shutil
+import tempfile
 import unittest
-from unittest.mock import MagicMock, patch
+from collections import defaultdict
+from unittest.mock import patch
 
-from cellxgene_gateway.filecrawl import render_item
+from cellxgene_gateway.filecrawl import (
+    render_item,
+    render_item_source,
+    render_item_tree,
+)
 from cellxgene_gateway.items.file.fileitem import FileItem
 from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-from cellxgene_gateway.items.item import ItemType
+from cellxgene_gateway.items.item import ItemTree, ItemType
+from cellxgene_gateway.gateway import app
 
 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 setUp(self):
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
     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):
+
+    def setUp(self):
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @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):
+    @patch("cellxgene_gateway.items.file.fileitem_source.FileItemSource")
+    def test_GIVEN_some_filter_THEN_includes_filterpart_in_heading(self, item_source):
+        item_source.name = "FakeSource"
+        item_source.list_items.return_value = ItemTree("rootdir", [], [])
+        rendered = render_item_source(item_source, "some_filter")
+        self.assertEqual(
+            rendered,
+            "<h6><a href='/filecrawl.html?source=FakeSource'>FakeSource</a>:some_filter</h6><li><a href='/filecrawl/rootdir?source=FakeSource'>rootdir</a><ul></ul></li>",
+        )
+
+
+class TestRenderItemTree(unittest.TestCase):
+    def setUp(self):
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @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_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>"
+            "<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_gateway_status_json.py

@@ -0,0 +1,54 @@
+import json
+import unittest
+from types import SimpleNamespace
+
+from cellxgene_gateway.gateway import do_GET_status_json, app, cache
+from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
+
+
+class TestGatewayStatusJson(unittest.TestCase):
+    def test_do_GET_status_json_returns_expected_structure(self):
+        # Create a minimal fake key with required attributes
+        h5ad_item = SimpleNamespace(descriptor="somedir/dataset.h5ad")
+        key = SimpleNamespace(
+            h5ad_item=h5ad_item,
+            annotation_descriptor="somedir/dataset_annotations/foo.csv",
+        )
+
+        # Create a CacheEntry with known launchtime/timestamp/status
+        entry = CacheEntry(
+            None,
+            key,
+            8000,
+            111,
+            222,
+            CacheEntryStatus.loaded,
+            None,
+            None,
+            None,
+            None,
+        )
+
+        # Install into the gateway cache and set app launchtime
+        cache.entry_list = [entry]
+        app.extensions.setdefault("cellxgene_gateway", {})["launchtime"] = "LAUNCH_TIME"
+
+        rv = do_GET_status_json()
+
+        data = json.loads(rv)
+        # top-level launchtime comes from app.extensions
+        self.assertEqual("LAUNCH_TIME", data["launchtime"])
+
+        self.assertIn("entry_list", data)
+        self.assertEqual(1, len(data["entry_list"]))
+
+        e = data["entry_list"][0]
+        self.assertEqual("somedir/dataset.h5ad", e["dataset"])
+        self.assertEqual("somedir/dataset_annotations/foo.csv", e["annotation_file"])
+        self.assertEqual("loaded", e["status"])
+        self.assertEqual(111, e["launchtime"])
+        self.assertEqual(222, e["last_access"])
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_prune_process_cache.py

@@ -1,13 +1,21 @@
 import unittest
-from unittest.mock import MagicMock, patch
+from unittest.mock import patch, seal
 
 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
+from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+from cellxgene_gateway.items.item import ItemType
+
+key = CacheKey(
+    FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+    FileItemSource("/tmp", "local"),
+)
 
 
 class TestPruneProcessCache(unittest.TestCase):
     @patch("cellxgene_gateway.util.current_time_stamp", new=lambda: 0)
-    @patch("cellxgene_gateway.env.ttl", new="10")
+    @patch("cellxgene_gateway.env.expire_seconds", new=10)
     @patch("cellxgene_gateway.cache_entry.CacheEntry")
     @patch("cellxgene_gateway.cache_entry.CacheEntry")
     def test_GIVEN_one_old_one_new_THEN_prune_old(self, old, new):
@@ -15,14 +23,23 @@ class TestPruneProcessCache(unittest.TestCase):
 
         cache = BackendCache()
         old.timestamp = -100
+        old.foo = 12
+        old.pid = 1
+        old.key = key
+        old.terminate.return_value = None
+        seal(old)
+        new.key = key
         cache.entry_list.append(old)
         new.timestamp = -5
+        seal(new)
         cache.entry_list.append(new)
         self.assertEqual(len(cache.entry_list), 2)
         ppc = PruneProcessCache(cache)
         ppc.prune()
         self.assertEqual(len(cache.entry_list), 1)
         self.assertEqual(cache.entry_list[0], new)
+        self.assertEqual(cache.entry_list[0], new)
+        self.assertTrue(old.terminate.called)
 
 
 if __name__ == "__main__":

tests/test_subprocess_backend.py

@@ -0,0 +1,77 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from cellxgene_gateway.cache_entry import CacheEntry
+from cellxgene_gateway.cache_key import CacheKey
+from cellxgene_gateway.items.file.fileitem import FileItem
+from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+from cellxgene_gateway.items.item import ItemType
+from cellxgene_gateway.process_exception import ProcessException
+
+
+class TestSubprocessBackend(unittest.TestCase):
+    @patch("subprocess.Popen")
+    def test_launch_GIVEN_no_stdout_THEN_throw_ProcessException(self, popen):
+        subprocess = MagicMock()
+        subprocess.stdout.readline().decode.return_value = ""
+        subprocess.stderr.read().decode.return_value = "An unexpected error"
+        popen.return_value = subprocess
+
+        key = CacheKey(
+            FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+            FileItemSource("/tmp", "local"),
+        )
+        entry = CacheEntry.for_key(key, 8000)
+        from cellxgene_gateway.subprocess_backend import SubprocessBackend
+
+        backend = SubprocessBackend()
+        cellxgene_loc = "/some/cellxgene"
+        scripts = ["http://example.com/script.js", "http://example.com/script2.js"]
+
+        with self.assertRaises(ProcessException) as context:
+            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 --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,
+        )