Merge pull request #102 from Novartis/reenable-codecov

reenable-codecov

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+branch = True
+source = cellxgene_gateway
+
+[report]
+exclude_lines =
+    if self.debug:
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True
+omit =
+    tests/*

.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

@@ -0,0 +1,91 @@
+# Tests that run on every PR
+
+name: Pull Request Checks
+
+on: [push, pull_request]
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        name: Checkout repository
+
+      - uses: actions/setup-python@v2
+        name: Setup Python
+        with:
+          python-version: 3.9
+
+      - name: Install black
+        run: |
+          python -m pip install --upgrade pip
+          pip install black
+      - name: Run black
+        run: |
+          black . --check
+  # This job is copied over from `deploy.yaml`
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      # See: https://github.com/marketplace/actions/setup-conda
+      - uses: s-weigand/setup-conda@v1
+        with:
+          conda-channels: "conda-forge"
+
+      - name: Build environment
+        run: |
+          conda env create -f environment.yml
+          eval "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          python setup.py install
+          pip install -r requirements-test.txt
+
+      - name: Run tests
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          coverage run -m unittest discover tests
+
+      - name: Check coverage
+        run: |
+          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 HTML report
+        uses: actions/upload-artifact@v4
+        with:
+          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

.gitignore

@@ -55,6 +55,7 @@ htmlcov/
 .nox/
 .coverage
 .coverage.*
+htmlcov
 .cache
 nosetests.xml
 coverage.xml
@@ -136,3 +137,6 @@ dmypy.json
 .pyre/
 
 # End of https://www.gitignore.io/api/python
+
+*.patch
+.vscode

.pre-commit-config.yaml

@@ -7,14 +7,7 @@ repos:
       language: system
       types: [python]
       stages: [commit]
-    - id: flake8
-      name: flake8
-      language: system
-      entry: flake8
-      types: [python]
-      stages: [commit]
     - id: black
-      language_version: python3.6+
       name: black
       language: system
       entry: black

.travis.yml

@@ -0,0 +1,41 @@
+# This is necessary for nxviz as matplotlib is involved.
+# before_script:
+#   - "export DISPLAY=:99.0"
+#   - "sh -e /etc/init.d/xvfb start"
+#   - sleep 5 # give xvfb some time to start
+
+language: python
+matrix:
+  include:
+    - python: 3.5 # we don't actually use this
+      env: PYTHON_VERSION=3.7
+
+install:
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda config --add channels conda-forge
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # Install Python, py.test, and required packages.
+  - conda env create -f environment.yml
+  - source activate cellxgene-gateway
+  - python setup.py install
+
+script:
+  # Your test script goes here
+  - black -l 79 . --check
+  - python -m unittest discover tests
+
+after_success:
+  - bash <(curl -s https://codecov.io/bash)
+
+notifications:
+  email: true

Changelog.md

@@ -0,0 +1,108 @@
+# 0.4.2
+
+* update package name
+
+# 0.4.1
+
+* Fix UnicodeDecodeError when viewing compressed datasets
+* Fix WSGI server initialization by extracting data source setup
+* Fix AttributeError by storing ItemSource objects in default_item_source
+* Delay itemsource initialization until first request is served
+* Set default_item_source and start pruner thread
+* Added start scripts for flask, gunicorn and uwsgi
+* Made pruner a daemon thread
+* Updated start scripts to run in subshells
+* Fixed bug in status.json
+
+# 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
+
+# 0.2.2
+
+  * Fixed bug with annotations (missing annotation.js asset)
+
+# 0.2.1
+
+  * Minor fixes to enable cellxgene 0.16.0
+  * Added CELLXGENE_ARGS to enable passing additional arguments to cellxgene
+  * added metadata/ip_address endpoint
+
+# 0.2.0
+
+Incrementing minor version since the changes for 0.15 are breaking, and we may want to release bugfixes from 0.1.0 branch.
+
+# 0.1.1
+
+Added support for cellxgene 0.15

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
@@ -30,7 +32,7 @@ Note: you may need to downgrade h5py with `pip install h5py==2.9.0` due to an [i
 ### Option 2: Install from PyPI
 
 ```bash
-# NOT YET DONE, COMING! STAY TUNED
+pip install cellxgene-gateway
 ```
 
 ## Running cellxgene gateway
@@ -39,7 +41,7 @@ Note: you may need to downgrade h5py with `pip install h5py==2.9.0` due to an [i
 
 ```bash
 mkdir ../cellxgene_data
-wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
+wget https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
 ```
 
 
@@ -59,17 +61,76 @@ cellxgene-gateway
 Here's what the environment variables mean:
 
 * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`
+
+At least one of the following is required:
 * `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
+* `CELLXGENE_BUCKET` - an s3 bucket that can contain keys with `.h5ad` data files, e.g. `my-cellxgene-data-bucket`
+Cellxgene Gateway is designed to make it easy to add additional data sources, please see the source code for gateway.py and the ItemSource interface in items/item_source.py
+
 Optional environment variables:
+* `CELLXGENE_ARGS` - catch-all variable that can be used to pass additional command line args to cellxgene server
 * `EXTERNAL_HOST` - the hostname and port from the perspective of the web browser, typically `localhost:5005` if running locally. Defaults to "localhost:{GATEWAY_PORT}"
 * `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_UPLOAD` - Set to `true` or `1` to enable HTTP uploads. This is not recommended for a public server.
+* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations 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
+* `PROXY_FIX_PROTO` - Number of upstream proxies setting X-Forwarded-Proto
+* `PROXY_FIX_HOST` - Number of upstream proxies setting X-Forwarded-Host
+* `PROXY_FIX_PORT` - Number of upstream proxies setting X-Forwarded-Port
+* `PROXY_FIX_PREFIX` - Number of upstream proxies setting X-Forwarded-Prefix
 
 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:
@@ -110,26 +171,70 @@ python setup.py develop
 
 For convenience, the code repo includes a `run.sh.example` shell script to run the gateway.
 
+4. Install pre-commit hooks
+
+```bash
+conda install -c conda-forge pre-commit
+pre-commit install
+```
+
+
 ## Running Tests
 
+[![Build Status](https://travis-ci.org/Novartis/cellxgene-gateway.svg?branch=master)](https://travis-ci.org/Novartis/cellxgene-gateway)
+
 ```bash
     python -m unittest discover tests
 ```
 
+## Code Coverage
+```bash
+    coverage run -m unittest discover tests
+    coverage html
+```
+
 ## Running Linters
 
 pip install isort flake8 black
 
 ```bash
-isort -rc .
-flake8 .
-black -l 79 .
+isort -rc . # rc means recursive, and was deprecated in dev version of isort
+black .
 ```
 
 # Getting Help
 
 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

@@ -6,3 +6,5 @@
 # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
+
+__version__ = "0.4.2"

cellxgene_gateway/backend_cache.py

@@ -8,12 +8,13 @@
 # the specific language governing permissions and limitations under the License.
 
 import time
+from http import HTTPStatus
 from threading import Thread
-
-from flask_api import status
+from typing import List
 
 from cellxgene_gateway import env
-from cellxgene_gateway.cache_entry import CacheEntry
+from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
+from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.subprocess_backend import SubprocessBackend
 
@@ -22,8 +23,10 @@ process_backend = SubprocessBackend()
 
 def is_port_in_use(port):
     import socket
+
     with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-        return s.connect_ex(('localhost', port)) == 0
+        return s.connect_ex(("localhost", port)) == 0
+
 
 class BackendCache:
     def __init__(self):
@@ -33,12 +36,14 @@ class BackendCache:
         contents = self.entry_list
         return [c.port for c in contents]
 
-    def check_entry(self, key):
+    def check_path(self, source, path):
         contents = self.entry_list
         matches = [
             c
             for c in contents
-            if c.key.dataset == key.dataset and c.key.annotation_file == key.annotation_file and c.status != "terminated"
+            if c.key.source.name == source.name
+            and path.startswith(c.key.descriptor)
+            and c.status != CacheEntryStatus.terminated
         ]
 
         if len(matches) == 0:
@@ -47,11 +52,29 @@ class BackendCache:
             return matches[0]
         else:
             raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
-                "Found " + str(len(matches)) + " for " + dataset,
+                HTTPStatus.INTERNAL_SERVER_ERROR,
+                "Found " + str(len(matches)) + " for " + path,
             )
 
-    def create_entry(self, key, scripts):
+    def check_entry(self, key):
+        contents = self.entry_list
+        matches = [
+            c
+            for c in contents
+            if c.key.equals(key) and c.status != CacheEntryStatus.terminated
+        ]
+
+        if len(matches) == 0:
+            return None
+        elif len(matches) == 1:
+            return matches[0]
+        else:
+            raise CellxgeneException(
+                HTTPStatus.INTERNAL_SERVER_ERROR,
+                "Found " + str(len(matches)) + " for " + key.dataset,
+            )
+
+    def create_entry(self, key: CacheKey, scripts: List[str]):
         port = 8000
         existing_ports = self.get_ports()
 

cellxgene_gateway/cache_entry.py

@@ -6,17 +6,30 @@
 # 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 psutil
-import logging
 import datetime
+import logging
+import re
+from enum import Enum
 
-from flask import make_response, request, render_template
+import psutil
+from flask import make_response, render_template, request
+from flask.wrappers import Response
 from requests import get, post, put
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.util import current_time_stamp
 from cellxgene_gateway.flask_util import querystring
+from cellxgene_gateway.util import current_time_stamp
+
+logger = logging.getLogger(__name__)
+
+
+class CacheEntryStatus(Enum):
+    loaded = "loaded"
+    loading = "loading"
+    error = "error"
+    terminated = "terminated"
+
 
 class CacheEntry:
     def __init__(
@@ -26,7 +39,7 @@ class CacheEntry:
         port,
         launchtime,
         timestamp,
-        status,
+        status: CacheEntryStatus,
         message,
         all_output,
         stderr,
@@ -45,29 +58,32 @@ class CacheEntry:
 
     @classmethod
     def for_key(cls, key, port):
-
         return cls(
             None,
             key,
             port,
             current_time_stamp(),
             current_time_stamp(),
-            "loading",
+            CacheEntryStatus.loading,
             None,
             None,
             None,
             None,
         )
 
+    @property
+    def source_name(self):
+        return self.key.source_name
+
     def set_loaded(self, pid):
         self.pid = pid
-        self.status = "loaded"
+        self.status = CacheEntryStatus.loaded
 
     def set_error(self, message, stderr, http_status):
         self.message = message
         self.stderr = stderr
         self.http_status = http_status
-        self.status = "error"
+        self.status = CacheEntryStatus.error
 
     def append_output(self, output):
         if self.all_output == None:
@@ -77,101 +93,118 @@ class CacheEntry:
 
     def terminate(self):
         pid = self.pid
-        if pid != None and self.status != "terminated":
+        if pid != None and self.status != CacheEntryStatus.terminated:
             terminated = []
+
             def on_terminate(p):
                 terminated.append(p.pid)
+
             p = psutil.Process(pid)
             children = p.children()
             for child in children:
                 child.terminate()
             psutil.wait_procs(children, callback=on_terminate)
-            terminated.append(p.pid)
-            p.terminate()
-            psutil.wait_procs([p], callback=on_terminate)
-            logging.getLogger("cellxgene_gateway").info(f"terminated {terminated}")
-        self.status = "terminated"
+            # the parent process may automatically die once its children have --
+            try:
+                p.terminate()
+                psutil.wait_procs([p], callback=on_terminate)
+            except psutil.NoSuchProcess:
+                pass
+
+            logger.info(f"terminated {terminated}")
+        self.status = CacheEntryStatus.terminated
+
+    def rewrite_text_content(self, cellxgene_content):
+        # for v0.16.0 compatibility, see issue #24
+        gateway_content = (
+            re.sub(
+                '(="|\()/static/',
+                f"\\1{self.key.gateway_basepath()}static/",
+                cellxgene_content,
+            )
+            .replace("http://fonts.gstatic.com", "https://fonts.gstatic.com")
+            .replace(self.cellxgene_basepath(), self.key.gateway_basepath())
+        )
+        return gateway_content
+
+    def cellxgene_basepath(self):
+        return f"http://127.0.0.1:{self.port}"
 
     def serve_content(self, path):
-        gateway_basepath = (
-            f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
-        )
-        subpath = path[len(self.key.pathpart) :]  # noqa: E203
-            
+        gateway_basepath = self.key.gateway_basepath()
+        subpath = path[len(self.key.descriptor) :]  # noqa: E203
         if len(subpath) == 0:
-            r = make_response(f"Redirect to {gateway_basepath}\n", 301)
-            r.headers["location"] = gateway_basepath+querystring()
+            r = make_response(f"Redirect to {gateway_basepath}\n", 302)
+            r.headers["location"] = gateway_basepath + querystring()
             return r
-        elif self.status == "loading":
+        elif self.status == CacheEntryStatus.loading:
             launch_time = datetime.datetime.fromtimestamp(self.launchtime)
             return render_template(
-                "loading.html", launchtime=launch_time, all_output=self.all_output
+                "loading.html",
+                launchtime=launch_time,
+                all_output=self.all_output,
             )
 
-        port = self.port
-        cellxgene_basepath = f"http://127.0.0.1:{port}"
         headers = {}
         copy_headers = [
-            'accept',
-            'accept-encoding',
-            'accept-language',
-            'cache-control',
-            'connection',
-            'content-length',
-            'content-type',
-            'cookie',
-            'host',
-            'origin',
-            'pragma',
-            'referer',
-            'sec-fetch-mode',
-            'sec-fetch-site',
-            'user-agent'
+            "accept",
+            # "accept-encoding" - removed: let requests library handle compression/decompression
+            "accept-language",
+            "cache-control",
+            "connection",
+            "content-length",
+            "content-type",
+            "cookie",
+            "host",
+            "origin",
+            "pragma",
+            "referer",
+            "sec-fetch-mode",
+            "sec-fetch-site",
+            "user-agent",
         ]
         for h in copy_headers:
             if h in request.headers:
                 headers[h] = request.headers[h]
 
-        full_path = cellxgene_basepath + subpath + querystring()
+        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"]:
-            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:
-            cellxgene_content = cellxgene_response.content.decode()
-            gateway_content = cellxgene_content.replace(
-                "http://fonts.gstatic.com", "https://fonts.gstatic.com"
-            ).replace(cellxgene_basepath, gateway_basepath)
-        else:
-            gateway_content = cellxgene_response.content
-
-        resp_headers = {}
-        for h in copy_headers:
-            if h in cellxgene_response.headers:
-                resp_headers[h] = cellxgene_response.headers[h]
-
-        gateway_response = make_response(
-            gateway_content,
-            cellxgene_response.status_code,
-            resp_headers,
-        )
+            resp_headers = {}
+            for h in copy_headers:
+                if h in cellxgene_response.headers:
+                    resp_headers[h] = cellxgene_response.headers[h]
 
+            gateway_response = make_response(
+                gateway_content,
+                cellxgene_response.status_code,
+                resp_headers,
+            )
+        finally:
+            if cellxgene_response is not None:
+                cellxgene_response.close()
         return gateway_response

cellxgene_gateway/cache_key.py

@@ -7,23 +7,75 @@
 # 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 import env
-from cellxgene_gateway.cellxgene_exception import CellxgeneException
-
 # There are three kinds of CacheKey:
 # 1) somedir/dataset.h5ad: a dataset
-#    in this case, pathpart == dataset == 'somedir/dataset.h5ad'
-# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
-#    in this case, pathpart == 'dataset_annotations/saldaal1-T5HMVBNV.csv', dataset == 'somedir/dataset.h5ad'
+#    in this case, descriptor == dataset == 'somedir/dataset.h5ad'
+# 2) somedir/dataset_annotations/my_annotations.csv : an actual annotations file.
+#    in this case, descriptor == 'somedir/dataset_annotations/my_annotations.csv', dataset == 'somedir/dataset.h5ad'
 # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
-#    in this case, pathpart == 'dataset_annotations', dataset == 'somedir/dataset.h5ad'
+#    in this case, descriptor == 'somedir/dataset_annotations', dataset == 'somedir/dataset.h5ad'
+
+from cellxgene_gateway import flask_util
+from cellxgene_gateway.items.item import Item
+from cellxgene_gateway.items.item_source import ItemSource, LookupResult
+
 
 class CacheKey:
-    def __init__(self, pathpart, dataset, annotation_file):
-        self.pathpart = pathpart
-        self.dataset = dataset
-        self.annotation_file = annotation_file
+    @property
+    def descriptor(self):
+        if self.annotation_item is None:
+            return self.h5ad_item.descriptor
+        else:
+            return self.annotation_item.descriptor
+
+    @property
+    def file_path(self):
+        return self.source.get_local_path(self.h5ad_item)
+
+    @property
+    def annotation_file_path(self):
+        if self.annotation_item is None:
+            return None
+        else:
+            return self.source.get_local_path(self.annotation_item)
+
+    def relaunch_url(self):
+        return flask_util.relaunch_url(self.descriptor, self.source_name)
+
+    def gateway_basepath(self):
+        return self.view_url + "/"
+
+    @property
+    def view_url(self):
+        return flask_util.view_url(self.descriptor, self.source_name)
+
+    @property
+    def source_name(self):
+        return self.source.name
+
+    @property
+    def annotation_descriptor(self):
+        if self.annotation_item is None:
+            return None
+        else:
+            return self.annotation_item.descriptor
+
+    def equals(self, other):
+        return (
+            (self.source.name == other.source.name)
+            and (self.h5ad_item.descriptor == other.h5ad_item.descriptor)
+            and (self.annotation_descriptor == other.annotation_descriptor)
+        )
+
+    def __init__(
+        self, h5ad_item: Item, source: ItemSource, annotation_item: Item = None
+    ):
+        assert h5ad_item is not None
+        assert source is not None
+        self.h5ad_item = h5ad_item
+        self.annotation_item = annotation_item
+        self.source = source
+
+    @classmethod
+    def for_lookup(cls, source: ItemSource, lookup: LookupResult):
+        return CacheKey(lookup.h5ad_item, source, lookup.annotation_item)

cellxgene_gateway/dir_util.py

@@ -9,50 +9,21 @@
 
 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)
+annotations_suffix = "_annotations"
+h5ad_suffix = ".h5ad"
 
 
-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'
 def make_h5ad(el):
-    return el[:-len(annotations_suffix)]+'.h5ad'
+    return el[: -len(annotations_suffix)] + h5ad_suffix
+
+
 def make_annotations(el):
-    return el[:-5]+annotations_suffix
+    return el[:-5] + annotations_suffix
+
+
+def ensure_dir_exists(file_path):
+    if not os.path.exists(file_path):
+        os.makedirs(file_path)

cellxgene_gateway/env.py

@@ -7,37 +7,65 @@
 # 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 logging
-import socket
+import os
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
-cellxgene_data = os.environ.get("CELLXGENE_DATA")
+cellxgene_data = os.environ.get("CELLXGENE_DATA", "")
+cellxgene_args = os.environ.get("CELLXGENE_ARGS", None)
 gateway_port = int(os.environ.get("GATEWAY_PORT", "5005"))
-external_host = os.environ.get("EXTERNAL_HOST", os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"))
-external_protocol = os.environ.get("EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http"))
+external_host = os.environ.get(
+    "EXTERNAL_HOST",
+    os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"),
+)
+external_protocol = os.environ.get(
+    "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")
-enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
-enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in ['true', '1']
+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",
+]
+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,
-    "CELLXGENE_DATA": cellxgene_data,
-    "GATEWAY_IP": ip,
 }
 
+proxy_fix_for = int(os.environ.get("PROXY_FIX_FOR", "0"))
+proxy_fix_proto = int(os.environ.get("PROXY_FIX_PROTO", "0"))
+proxy_fix_host = int(os.environ.get("PROXY_FIX_HOST", "0"))
+proxy_fix_port = int(os.environ.get("PROXY_FIX_PORT", "0"))
+proxy_fix_prefix = int(os.environ.get("PROXY_FIX_PREFIX", "0"))
+
 optional_env_vars = {
     "EXTERNAL_HOST": external_host,
     "EXTERNAL_PROTOCOL": external_protocol,
+    "GATEWAY_IP": ip,
     "GATEWAY_PORT": gateway_port,
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
-    "GATEWAY_TTL": ttl,
-    "GATEWAY_ENABLE_UPLOAD": enable_upload,
+    "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,
+    "PROXY_FIX_PROTO": proxy_fix_proto,
+    "PROXY_FIX_HOST": proxy_fix_host,
+    "PROXY_FIX_PORT": proxy_fix_port,
+    "PROXY_FIX_PREFIX": proxy_fix_prefix,
 }
 
+
 def validate():
     if not all(env_vars.values()):
         raise ValueError(
@@ -52,9 +80,12 @@ def validate():
 
         export CELLXGENE_LOCATION=~/anaconda/envs/cellxgene-dev/bin/cellxgene
         export CELLXGENE_DATA=../cellxgene_data
-        export GATEWAY_IP=127.0.0.1
     """
         )
     else:
-        logging.getLogger("cellxgene_gateway").info(f"Got required env: {env_vars}", )
-        logging.getLogger("cellxgene_gateway").info(f"Got optional env: {optional_env_vars}")
+        logging.getLogger("cellxgene_gateway").info(
+            f"Got required env: {env_vars}",
+        )
+        logging.getLogger("cellxgene_gateway").info(
+            f"Got optional env: {optional_env_vars}"
+        )

cellxgene_gateway/extra_scripts.py

@@ -7,8 +7,10 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-from cellxgene_gateway import env
 from json import loads
+from json.decoder import JSONDecodeError
+
+from cellxgene_gateway import env
 
 
 def get_extra_scripts():
@@ -16,4 +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

@@ -7,78 +7,62 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-import os
-from cellxgene_gateway import env
-from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
+import html
+import urllib.parse
 
-def recurse_dir(path):
-    if not os.path.exists(path):
-        raise CellxgeneException(
-            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
-        )
-
-    all_entries = os.listdir(path)
-    def is_h5ad(el):
-        return el.endswith('.h5ad') and os.path.isfile(os.path.join(path, el))
-    h5ad_entries = [x for x in all_entries if is_h5ad(x)]
-    annotation_dir_entries = [x for x in all_entries if x.endswith(annotations_suffix) and make_h5ad(x) in h5ad_entries]
-    def list_annotations(el):
-        full_path = os.path.join(path, el)
-        if not os.path.isdir(full_path):
-            entries = []
-        else:
-            entries = [{
-                "name": x[:-13] if (len(x) > 13 and x[-13] in ['-','_']) else (
-                    x[:-4] if x.endswith('.csv') else x),
-                "path": os.path.join(full_path, x).replace(env.cellxgene_data, ""),
-            } for x in os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
-        return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
-
-    def make_entry(el):
-        full_path = os.path.join(path, el)
-        if el in h5ad_entries:
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "file",
-                "annotations": list_annotations(make_annotations(el)),
-            }
-        elif os.path.isdir(full_path) and el not in annotation_dir_entries:
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "directory",
-                "children": recurse_dir(full_path),
-            }
-        else:
-            return {
-                "path": full_path,
-                "name": el,
-                "type": "neither",
-            }
-
-    return [make_entry(x) for x in os.listdir(path)]
+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_entries(entries):
-    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
-
-def get_url(entry):
-    return f"/view/{ entry['path'].lstrip('/') }"
-def get_class(entry):
-    return f" class='{entry['class']}'" if 'class' in entry else ''
-
-def render_annotations(entry):
-    if len(entry['annotations']) > 0:
-        return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'{get_class(a)}>{a['name']}</a>" for a in entry['annotations']])
-    else:
-        return ''
-
-def render_entry(entry):
-    if entry["type"] == "file":
-        return f"<li> <a href='{ get_url(entry) }'>{entry['name']}</a> {render_annotations(entry)}</li>"
-    elif entry["type"] == "directory":
-        url = f"/filecrawl/{entry['path'].lstrip('/')}"
-        return f"<li><a href='{url}'>{entry['name']}</a>{render_entries(entry['children'])}</li>"
-    else:
+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>"]
+
+    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 []
+    )
+    return "| annotations: " + ", ".join(new_annotation + annotations)
+
+
+def render_item(item, item_source):
+    item_string = f"<li> <a href='{ CacheKey(item, item_source).view_url }/'>{item.name}</a> {render_annotations(item, item_source)}</li>"
+    return item_string
+
+
+def render_item_tree(item_tree, item_source):
+    items = (
+        "\n".join([render_item(i, item_source) for i in item_tree.items])
+        if item_tree.items
+        else ""
+    )
+    branches = (
+        "\n".join([render_item_tree(b, item_source) for b in item_tree.branches])
+        if item_tree.branches
+        else ""
+    )
+    html = "<ul>" + items + branches + "</ul>"
+    if item_tree.descriptor:
+        descriptor = item_tree.descriptor.lstrip("/")
+        url = f"/filecrawl/{descriptor}?source={item_source.name}"
+        name = descriptor.rsplit("/", 1)[-1]
+        return f"<li><a href='{url}'>{name}</a>{html}</li>"
+    else:
+        return html
+
+
+def render_item_source(item_source, filter=None):
+    item_tree = item_source.list_items(filter)
+    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/flask_util.py

@@ -7,8 +7,27 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-from flask import request
+from flask import request, url_for
+
 
 def querystring():
     qs = request.query_string.decode()
-    return f'?{qs}' if len(qs) > 0 else ''
+    return f"?{qs}" if len(qs) > 0 else ""
+
+
+include_source_in_url = False
+
+
+def url(endpoint, descriptor, source_name):
+    if include_source_in_url:
+        return url_for(endpoint, source_name=source_name, path=descriptor)
+    else:
+        return url_for(endpoint, path=descriptor)
+
+
+def view_url(descriptor, source_name):
+    return url("do_view", descriptor, source_name)
+
+
+def relaunch_url(descriptor, source_name):
+    return url("do_relaunch", descriptor, source_name)

cellxgene_gateway/gateway.py

@@ -6,52 +6,164 @@
 # 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 os
-import logging
-from threading import Thread, Lock
 import json
+import logging
+import os
+import urllib.parse
+from threading import Lock, Thread
 
 from flask import (
     Flask,
-    redirect,
     make_response,
+    redirect,
     render_template,
     request,
     send_from_directory,
     url_for,
 )
-from flask_api import status
-from werkzeug.utils import secure_filename
+from werkzeug.middleware.proxy_fix import ProxyFix
 
-from cellxgene_gateway import env
+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.filecrawl import recurse_dir, render_entries
 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
-from cellxgene_gateway.path_util import get_key
 
 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
+    or env.proxy_fix_proto > 0
+    or env.proxy_fix_host > 0
+    or env.proxy_fix_port > 0
+    or env.proxy_fix_prefix > 0
+):
+    app.wsgi_app = ProxyFix(
+        app.wsgi_app,
+        x_for=env.proxy_fix_for,
+        x_proto=env.proxy_fix_proto,
+        x_host=env.proxy_fix_host,
+        x_port=env.proxy_fix_port,
+        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()
-location = f"{env.external_protocol}://{env.external_host}"
+
+
+# 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 (
@@ -66,7 +178,6 @@ def handle_invalid_usage(error):
 
 @app.errorhandler(ProcessException)
 def handle_invalid_process(error):
-
     message = []
 
     message.append(error.message)
@@ -82,8 +193,8 @@ def handle_invalid_process(error):
             http_status=error.http_status,
             stdout=error.stdout,
             stderr=error.stderr,
-            dataset=error.key.dataset,
-            annotation_file=error.key.annotation_file,
+            relaunch_url=error.key.relaunch_url(),
+            annotation_file=error.key.annotation_descriptor,
         ),
         error.http_status,
     )
@@ -100,167 +211,196 @@ def favicon():
 
 @app.route("/")
 def index():
-    users = [
-        name
-        for name in os.listdir(env.cellxgene_data)
-        if os.path.isdir(os.path.join(env.cellxgene_data, name))
-    ]
     return render_template(
         "index.html",
         ip=env.ip,
         cellxgene_data=env.cellxgene_data,
         extra_scripts=get_extra_scripts(),
-        users=users,
-        enable_upload=env.enable_upload,
     )
 
-def make_user():
-    dir_name = request.form["directory"]
-
-    create_dir(env.cellxgene_data, dir_name)
-
-    return redirect(location, code=302)
-
-
-def make_subdir():
-    parent_path = os.path.join(env.cellxgene_data, request.form["usernames"])
-    dir_name = request.form["directory"]
-
-    create_dir(parent_path, dir_name)
-
-    return redirect(location, code=302)
-
-
-def upload_file():
-    upload_dir = request.form["path"]
-
-    full_upload_path = os.path.join(env.cellxgene_data, upload_dir)
-    if is_subdir(full_upload_path, env.cellxgene_data) and os.path.isdir(full_upload_path):
-        if request.method == "POST":
-            if "file" in request.files:
-                f = request.files["file"]
-                if f and f.filename.endswith(".h5ad"):
-                    f.save(
-                        os.path.join(full_upload_path, secure_filename(f.filename))
-                    )
-                    return redirect("/filecrawl.html", code=302)
-                else:
-                    raise CellxgeneException(
-                        "Uploaded file must be in anndata (.h5ad) format.",
-                        status.HTTP_400_BAD_REQUEST,
-                    )
-            else:
-                raise CellxgeneException(
-                    "A file must be chosen to upload.",
-                    status.HTTP_400_BAD_REQUEST,
-                )
-    else:
-        raise CellxgeneException(
-            "Invalid directory.", status.HTTP_400_BAD_REQUEST
-        )
-
-    return redirect(location, code=302)
-
-
-if env.enable_upload:
-    app.add_url_rule('/make_user', 'make_user', make_user, methods=["POST"])
-    app.add_url_rule('/make_subdir', 'make_subdir', make_subdir, methods=["POST"])
-    app.add_url_rule('/upload_file', 'upload_file', upload_file, methods=["POST"])
 
 @app.route("/filecrawl.html")
-def filecrawl():
-    entries = recurse_dir(env.cellxgene_data)
-    rendered_html = render_entries(entries)
-    resp = make_response(render_template(
-        "filecrawl.html",
-        extra_scripts=get_extra_scripts(),
-        rendered_html=rendered_html,
-    ))
-    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'
+@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
 
-@app.route("/filecrawl/<path:path>")
-def do_filecrawl(path):
-    filecrawl_path = os.path.join(env.cellxgene_data, path)
-    if not os.path.isdir(filecrawl_path):
-        raise CellxgeneException(
-            "Path is not directory: " + filecrawl_path, status.HTTP_400_BAD_REQUEST
-        )
-    entries = recurse_dir(filecrawl_path)
-    rendered_html = render_entries(entries)
-    return render_template(
-        "filecrawl.html",
-        extra_scripts=get_extra_scripts(),
-        rendered_html=rendered_html,
-        path=path,
-    )
 
 entry_lock = Lock()
+
+
+def matching_source(source_name):
+    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:
+        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):
-    key = get_key(path)
-    print(f"view path={path}, dataset={key.dataset}, annotation_file= {key.annotation_file}, key={key.pathpart}")
-    with entry_lock:
-        match = cache.check_entry(key)
-        if match is None:
-            uascripts = get_extra_scripts()
-            match = cache.create_entry(key, uascripts)
+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 == "loaded" or match.status == "loading":
-        return match.serve_content(path)
-    elif match.status == "error":
+    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)
+    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():
-    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]})
+    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.extensions.get("cellxgene_gateway", {}).get("launchtime"),
+            "entry_list": [map_entry(entry) for entry in cache.entry_list],
+        }
+    )
+
+
+def get_cache_key(path):
+    if request.args.get("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_key(path)
+    key = get_cache_key(path)
     match = cache.check_entry(key)
     if not match is None:
         match.terminate()
-    qs = request.query_string.decode()
-    return redirect(url_for("do_view", path=path) + (f'?{qs}' if len(qs) > 0 else ''), code=302)
+    return redirect(
+        key.view_url,
+        code=302,
+    )
+
 
 @app.route("/terminate/<path:path>", methods=["GET"])
 def do_terminate(path):
-    key = get_key(path)
+    key = get_cache_key(path)
     match = cache.check_entry(key)
     if not match is None:
         match.terminate()
     return redirect(url_for("do_GET_status"), code=302)
 
 
-def main():
-    logging.basicConfig(level=logging.INFO, format='%(asctime)s:%(name)s:%(levelname)s:%(message)s')
-    env.validate()
-    pruner = PruneProcessCache(cache)
+@app.route("/metadata/ip_address", methods=["GET"])
+def ip_address():
+    resp = make_response(env.ip)
+    return set_no_cache(resp)
 
-    background_thread = Thread(target=pruner)
+
+def start_pruner_thread():
+    pruner = PruneProcessCache(cache)
+    # Run the pruner as a daemon thread so it won't block interpreter
+    # 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():
+    """CLI entry point for Flask development server."""
+    launch()
+
+
 if __name__ == "__main__":
     main()

cellxgene_gateway/items/file/fileitem.py

@@ -0,0 +1,28 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+import os
+
+from cellxgene_gateway.items.item import Item
+
+
+class FileItem(Item):
+    """e.g. FileItem(subpath = subpath, name = filename, type = ItemType.h5ad)
+
+    The Item superclass expects a 'name' and 'type'.
+    """
+
+    def __init__(self, subpath: str, ext: str = "", *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.subpath = subpath
+        self.ext = ext
+
+    @property
+    def descriptor(self) -> str:
+        return os.path.join(self.subpath, self.name + self.ext).strip("/")

cellxgene_gateway/items/file/fileitem_source.py

@@ -0,0 +1,214 @@
+# 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 typing import List
+
+from cellxgene_gateway import dir_util
+from cellxgene_gateway.items.file.fileitem import FileItem
+from cellxgene_gateway.items.item import ItemTree, ItemType
+from cellxgene_gateway.items.item_source import ItemSource, LookupResult
+
+
+class FileItemSource(ItemSource):
+    def __init__(
+        self,
+        base_path,
+        name=None,
+        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)
+
+    def convert_annotation_path_to_h5ad(self, path):
+        return path[: -len(self.annotation_dir_suffix)] + self.h5ad_suffix
+
+    def convert_h5ad_path_to_annotation(self, path):
+        return path[: -len(self.h5ad_suffix)] + self.annotation_dir_suffix
+
+    def get_local_path(self, item: FileItem) -> str:
+        return os.path.join(self.base_path, item.descriptor)
+
+    def get_annotations_subpath(self, item) -> str:
+        return self.convert_h5ad_path_to_annotation(item.descriptor)
+
+    def list_items(self, filter: str = None) -> ItemTree:
+        item_tree = self.scan_directory("" if filter is None else filter)
+
+        """def get_items(dir):
+            if dir.branches:
+                return [*dir.items, *[item for subdir in dir.branches for item in get_items(subdir)]]
+            else:
+                return dir.items
+
+        return get_items(self.item_tree)"""
+
+        return item_tree
+
+    def scan_directory(self, subpath: str = "") -> ItemTree:
+        base_path = os.path.join(self.base_path, subpath)
+
+        if not os.path.exists(base_path):
+            raise Exception(f"Path for local files '{base_path}' does not exist.")
+
+        filepath_map = dict(
+            (filepath, os.path.join(base_path, filepath))
+            for filepath in sorted(os.listdir(base_path))
+        )
+
+        def is_annotation_dir(dir):
+            return (
+                dir.endswith(self.annotation_dir_suffix)
+                and self.convert_annotation_path_to_h5ad(dir) in h5ad_paths
+            )
+
+        h5ad_paths = [
+            filepath
+            for filepath, full_path in filepath_map.items()
+            if self.is_h5ad_file(full_path)
+        ]
+
+        subdirs = [
+            filepath
+            for filepath, full_path in filepath_map.items()
+            if os.path.isdir(full_path) and not is_annotation_dir(filepath)
+        ]
+
+        items = [
+            self.make_fileitem_from_path(filename, subpath) for filename in h5ad_paths
+        ]
+        branches = None
+        if len(subdirs) > 0:
+            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)
+
+    def create_annotation(self, item: FileItem, name: str) -> FileItem:
+        annotation = self.make_fileitem_from_path(
+            name, self.get_annotations_subpath(item), is_annotation=True
+        )
+        item.annotations = (item.annotations or []).append(annotation)
+        return annotation
+
+    def update(self, item: FileItem) -> None:
+        pass
+
+    def full_path(self, p):
+        return os.path.join(self.base_path, p)
+
+    def lookup_item(self, descriptor):
+        full_path = self.full_path(descriptor)
+        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):
+            annotation_item = self.shallowitem_from_descriptor(descriptor, True)
+            h5ad_descriptor = self.convert_annotation_path_to_h5ad(
+                annotation_item.subpath
+            )
+            item = self.lookup_item(h5ad_descriptor)
+            if item is not None:
+                dir_util.ensure_dir_exists(self.full_path(annotation_item.subpath))
+                return LookupResult(item, annotation_item)
+        else:
+            item = self.lookup_item(descriptor)
+            if item is not None:
+                return LookupResult(item)
+
+    def shallowitem_from_descriptor(self, descriptor, is_annotation=False):
+        filename = os.path.basename(descriptor)
+        subpath = os.path.dirname(descriptor)
+        return self.make_fileitem_from_path(
+            filename,
+            subpath,
+            is_annotation,
+            True,
+        )
+
+    def make_fileitem_from_path(
+        self, filename, subpath, is_annotation=False, is_shallow=False
+    ) -> FileItem:
+        if is_annotation and filename.endswith(self.annotation_file_suffix):
+            name = filename[: -len(self.annotation_file_suffix)]
+            ext = self.annotation_file_suffix
+        else:
+            name = filename
+            ext = ""
+        item = FileItem(
+            subpath=subpath,
+            name=name,
+            ext=ext,
+            type=ItemType.annotation if is_annotation else ItemType.h5ad,
+        )
+
+        if not is_annotation and not is_shallow:
+            annotations = self.make_annotations_for_fileitem(item)
+            item.annotations = annotations
+
+        return item
+
+    def make_annotations_for_fileitem(self, item: FileItem) -> List[FileItem]:
+        annotations_subpath = self.get_annotations_subpath(item)
+        annotations_fullpath = self.full_path(annotations_subpath)
+        if os.path.isdir(annotations_fullpath):
+            sorted_files = sorted(os.listdir(annotations_fullpath))
+            annotation_files = [
+                self.make_fileitem_from_path(annotation, annotations_subpath, True)
+                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.py

@@ -0,0 +1,41 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+from abc import ABC, abstractmethod
+from enum import Enum
+from typing import List
+
+
+class ItemType(Enum):
+    annotation = "annotation"
+    h5ad = "h5ad"
+
+
+class Item(ABC):
+    def __init__(self, name: str, type: ItemType, annotations: List["Item"] = None):
+        self.name = name
+        self.type = type
+        self.annotations = annotations
+
+    @property
+    @abstractmethod
+    def descriptor(self):
+        raise Exception('"descriptor" not implemented')
+
+
+class ItemTree:
+    def __init__(
+        self,
+        descriptor: str,
+        items: List[Item] = None,
+        branches: List["ItemTree"] = None,
+    ):
+        self.descriptor = descriptor
+        self.items = items
+        self.branches = branches

cellxgene_gateway/items/item_source.py

@@ -0,0 +1,54 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+from abc import ABC, abstractmethod
+from typing import List
+
+from cellxgene_gateway.items.item import Item
+
+
+class LookupResult:
+    def __init__(self, h5ad_item: Item, annotation_item: Item = None):
+        self.h5ad_item = h5ad_item
+        self.annotation_item = annotation_item
+
+
+class ItemSource(ABC):
+    @abstractmethod
+    def list_items(self, filter: str = None) -> List[Item]:
+        raise Exception('"list_items" unimplemented')
+
+    @abstractmethod
+    def get_local_path(self, item: Item) -> str:
+        raise Exception('"local_path" unimplemented')
+
+    @abstractmethod
+    def get_annotations_subpath(self, item) -> str:
+        raise Exception('"annotations_path" unimplemented')
+
+    @abstractmethod
+    def create_annotation(self, item: Item, name: str) -> Item:
+        raise Exception('"annotation" unimplemented')
+
+    @abstractmethod
+    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')
+
+    @property
+    @abstractmethod
+    def name(self):
+        pass

cellxgene_gateway/items/s3/s3item.py

@@ -0,0 +1,27 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+import os
+
+from cellxgene_gateway.items.item import Item
+
+
+class S3Item(Item):
+    """e.g. FileItem(subpath = subpath, name = filename, type = ItemType.h5ad)
+
+    The Item superclass expects a 'name' and 'type'.
+    """
+
+    def __init__(self, s3key: str, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.s3key = s3key
+
+    @property
+    def descriptor(self) -> str:
+        return self.s3key

cellxgene_gateway/items/s3/s3item_source.py

@@ -0,0 +1,195 @@
+# 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 os.path import basename, dirname
+from typing import List
+
+import flask
+import s3fs
+
+from cellxgene_gateway import dir_util
+from cellxgene_gateway.items.item import ItemTree, ItemType
+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,
+        bucket,
+        name=None,
+        h5ad_suffix=dir_util.h5ad_suffix,
+        annotation_dir_suffix=dir_util.annotations_suffix,
+        annotation_file_suffix=".csv",
+    ):
+        self._name = name
+        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}"
+            )
+        self.bucket = bucket
+        self.h5ad_suffix = h5ad_suffix
+        self.annotation_dir_suffix = annotation_dir_suffix
+        self.annotation_file_suffix = annotation_file_suffix
+
+    def url(self, key):
+        return "s3://" + self.bucket + "/" + key
+
+    def remove_bucket(self, filepath):
+        return filepath[len(self.bucket) :].lstrip("/")
+
+    @property
+    def name(self):
+        return self._name or f"Items:{self.url('')}"
+
+    def is_h5ad_url(self, s3url: str) -> bool:
+        return s3url.endswith(self.h5ad_suffix) and self.s3.exists(s3url)
+
+    def convert_annotation_key_to_h5ad(self, s3key):
+        return s3key[: -len(self.annotation_dir_suffix)] + self.h5ad_suffix
+
+    def convert_h5ad_key_to_annotation(self, s3key):
+        return s3key[: -len(self.h5ad_suffix)] + self.annotation_dir_suffix
+
+    def get_local_path(self, item: S3Item) -> str:
+        return self.url(item.descriptor)
+
+    def get_annotations_subpath(self, item) -> str:
+        return self.convert_h5ad_key_to_annotation(item.descriptor)
+
+    def list_items(self, filter: str = None) -> ItemTree:
+        item_tree = self.scan_directory("" if filter is None else filter)
+        return item_tree
+
+    @property
+    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(
+            (self.remove_bucket(filepath), "s3://" + filepath)
+            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_keys
+            )
+
+        h5ad_keys = [
+            filepath
+            for filepath, item_url in s3key_map.items()
+            if self.is_h5ad_url(item_url)
+        ]
+
+        subdir_keys = [
+            filepath
+            for filepath, item_url in s3key_map.items()
+            if self.s3.isdir(item_url) and not is_annotation_dir(filepath)
+        ]
+
+        items = [self.make_s3item_from_key(basename(key), key) for key in h5ad_keys]
+        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)
+
+    def create_annotation(self, item: S3Item, name: str) -> S3Item:
+        annotation = self.make_s3item_from_key(
+            name, self.get_annotations_subpath(item), is_annotation=True
+        )
+        item.annotations = (item.annotations or []).append(annotation)
+        return annotation
+
+    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):
+            return self.shallowitem_from_descriptor(descriptor)
+
+    def lookup(self, indescriptor: str) -> LookupResult:
+        descriptor = indescriptor.strip("/")
+        if descriptor.endswith(self.annotation_file_suffix):
+            annotation_item = self.shallowitem_from_descriptor(descriptor, True)
+            if not self.s3.exists(self.url(annotation_item.s3key)):
+                with self.s3.open(self.url(annotation_item.s3key), "w") as f:
+                    f.write("")
+            h5ad_descriptor = self.convert_annotation_key_to_h5ad(
+                dirname(annotation_item.s3key)
+            )
+            item = self.shallowitem_from_descriptor(h5ad_descriptor)
+            return LookupResult(item, annotation_item)
+        else:
+            item = self.lookup_item(descriptor)
+            if item is not None:
+                return LookupResult(item)
+
+    def shallowitem_from_descriptor(self, descriptor, is_annotation=False):
+        return self.make_s3item_from_key(
+            basename(descriptor), descriptor, is_annotation, True
+        )
+
+    def make_s3item_from_key(
+        self, name, s3key, is_annotation=False, is_shallow=False
+    ) -> S3Item:
+        item = S3Item(
+            s3key=s3key,
+            name=name,
+            type=ItemType.annotation if is_annotation else ItemType.h5ad,
+        )
+
+        if not is_annotation and not is_shallow:
+            annotations = self.make_annotations_for_fileitem(item)
+            item.annotations = annotations
+
+        return item
+
+    def make_annotations_for_fileitem(self, item: S3Item) -> List[S3Item]:
+        annotations_subpath = self.get_annotations_subpath(item)
+        annotations_fullpath = self.url(annotations_subpath)
+        if self.s3.isdir(annotations_fullpath):
+            return [
+                self.make_s3item_from_key(
+                    basename(annotation), self.remove_bucket(annotation), True
+                )
+                for annotation in sorted(
+                    self.s3.ls(annotations_fullpath, refresh=self.refresh)
+                )
+                if annotation.endswith(self.annotation_file_suffix)
+                and self.s3.isfile("s3://" + annotation)
+            ]
+        else:
+            return None

cellxgene_gateway/path_util.py

@@ -1,95 +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 import env
-from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import make_h5ad
-from cellxgene_gateway.cache_key import CacheKey
-
-def get_key(path):
-    if path == "/" or path == "":
-        raise CellxgeneException(
-            "No matching dataset found.", status.HTTP_404_NOT_FOUND
-        )
-
-    trimmed = path[:-1] if path[-1] == "/" else path
-    try:
-        # valid paths come in three forms:
-        if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
-            # 1) somedir/dataset.h5ad: a dataset
-            return CacheKey(trimmed, trimmed, None)
-        elif trimmed.endswith('.csv'):
-
-            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
-            annotations_dir = os.path.split(trimmed)[0]
-            dataset = make_h5ad(annotations_dir)
-            if data_file_exists(dataset):
-                data_dir_ensure(annotations_dir)
-                return CacheKey(trimmed, dataset, trimmed)
-        elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
-            # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
-            dataset = make_h5ad(trimmed)
-            if data_file_exists(dataset):
-                return CacheKey(trimmed, dataset, '')
-    except CellxgeneException:
-        pass
-    split = os.path.split(trimmed)
-    return get_key(split[0])
-
-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
-
-def data_file_exists(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_is_file(file_path)
-    return True
-def data_dir_exists(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_is_dir(file_path)
-    return True
-def data_dir_ensure(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    if not os.path.exists(file_path):
-        os.makedirs(file_path)
-
-def get_file_path(key):
-    dataset = key.dataset
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_is_file(file_path)
-    return file_path
-
-def get_annotation_file_path(key):
-    if key.annotation_file is None:
-        return None
-    if key.annotation_file == '':
-        return ''
-    file_path = os.path.join(env.cellxgene_data, key.annotation_file)
-    return file_path

cellxgene_gateway/prune_process_cache.py

@@ -7,17 +7,18 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-import time
 import logging
+import time
 
-from cellxgene_gateway.util import current_time_stamp
-from cellxgene_gateway.env import ttl
+from cellxgene_gateway import env, util
+
+logger = logging.getLogger(__name__)
 
 
 class PruneProcessCache:
     def __init__(self, cache):
         self.cache = cache
-        self.expire_seconds = (3600 if ttl is None else int(ttl))
+        self.expire_seconds = env.expire_seconds
 
     def __call__(self):
         while True:
@@ -25,16 +26,22 @@ class PruneProcessCache:
             self.prune()
 
     def prune(self):
-        timestamp = current_time_stamp()
+        timestamp = util.current_time_stamp()
         cutoff = timestamp - self.expire_seconds
-        processes_to_delete = [p for p in self.cache.entry_list if  p.timestamp < cutoff]
-        processes_to_keep = [p for p in self.cache.entry_list if not p.timestamp < cutoff]
-        logger = logging.getLogger("cellxgene_gateway")
-        logger.debug(f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}")
-        
+        processes_to_delete = [p for p in self.cache.entry_list if p.timestamp < cutoff]
+        processes_to_keep = [
+            p for p in self.cache.entry_list if not p.timestamp < cutoff
+        ]
+
+        logger.debug(
+            f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}, pruning {processes_to_delete}"
+        )
+
         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})")
+                logger.exception(
+                    "failed to prune process {process.pid} ({process.key.descriptor})"
+                )

cellxgene_gateway/static/js/annotation.js

@@ -1,4 +1,5 @@
 // neandertal javascript
+// Annotations only work with file itemsources at the moment. If they work with others in the future we may need to revisit this.
 const new_annotation_callback = (() =>{
     const suffix = `.csv`;
     return (e) => {

cellxgene_gateway/subprocess_backend.py

@@ -9,12 +9,15 @@
 
 import logging
 import subprocess
+from http import HTTPStatus
 
-from flask_api import status
-from cellxgene_gateway.env import enable_annotations
-from cellxgene_gateway.process_exception import ProcessException
+from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.dir_util import make_annotations
-from cellxgene_gateway.path_util import get_file_path, get_annotation_file_path
+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):
@@ -22,19 +25,25 @@ class SubprocessBackend:
 
     def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
         if enable_annotations and not annotation_file_path is None:
-            annotation_args_prefix = " --experimental-annotations"
             if annotation_file_path == "":
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
+                extra_args = f" --annotations-dir {make_annotations(file_path)}"
             else:
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
+                extra_args = f" --annotations-file {annotation_file_path}"
+                gene_sets_file_path = annotation_file_path[:-4] + "_gene_sets.csv"
+                extra_args += f" --gene-sets-file {gene_sets_file_path}"
         else:
-            annotation_args = ""
+            extra_args = " --disable-annotations"
+            extra_args += " --disable-gene-sets-save"
+        if enable_backed_mode:
+            extra_args += " --backed"
+        if not cellxgene_args is None:
+            extra_args += f" {cellxgene_args}"
+
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
-            + " --port "
-            + str(port)
+            + f" --port {port}"
             + " --host 127.0.0.1"
-            + annotation_args
+            + extra_args
         )
 
         for s in scripts:
@@ -43,11 +52,14 @@ class SubprocessBackend:
         return cmd
 
     def launch(self, cellxgene_loc, scripts, cache_entry):
-
         cmd = self.create_cmd(
-            cellxgene_loc, get_file_path(cache_entry.key), cache_entry.port, scripts, get_annotation_file_path(cache_entry.key)
+            cellxgene_loc,
+            cache_entry.key.file_path,
+            cache_entry.port,
+            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
         )
@@ -63,12 +75,12 @@ 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 = "error"
+                cache_entry.status = CacheEntryStatus.error
                 cache_entry.set_error(message, stderr, http_status)
 
                 raise ProcessException.from_cache_entry(cache_entry)
@@ -76,5 +88,6 @@ class SubprocessBackend:
                 cache_entry.append_output(output)
 
         cache_entry.set_loaded(process.pid)
-
-        return
+        for output in process.communicate():
+            logger.debug(f"cellxgene:{output}")
+        logger.info(f"exiting {cmd}")

cellxgene_gateway/templates/cache_status.html

@@ -10,65 +10,77 @@
 -->
 
 <html>
+
 <head>
      <title>Cellxgene Gateway - FILE CRAWLER</title>
      <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
-	{% for script in extra_scripts %}
-	<script src="{{ script }}"></script>
-	{% endfor %}
-     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+     {% for script in extra_scripts %}
+     <script src="{{ script }}"></script>
+     {% endfor %}
+     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css"
+          integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
 </head>
+
 <body>
      <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
-       <h3>Cellxgene Gateway - Cache Status</h3>
+          <h3>Cellxgene Gateway - Cache Status</h3>
      </header>
      <br>
      <table class="table">
           <thead>
-          <tr>
-               <th>PID</th>
-               <th>dataset</th>
-               <th>annotation_file</th>
-               <th>port</th>
-               <th>launchtime</th>
-               <th>last access</th>
-               <th>status</th>
-               <th>message</th>
-               <th>http_status</th>
-               <th>actions</th>
-          </tr>
-     </thead>
-     <tbody>
-	{% for entry in entry_list %}
-          <tr>
-               <td>{{ entry.pid }}</td>
-               <td><a href="{{ url_for('do_view', path=entry.key.pathpart) }}">{{ entry.key.dataset }}</a></td>
-               <td>{{ entry.key.annotation_file }}</td>
-               <td>{{ entry.port }}</td>
-               <td class="timestamp">{{ entry.launchtime }}</td>
-               <td class="timestamp">{{ entry.timestamp }}</td>
-               <td>{{ entry.status }}</td>
-               <td>{{ entry.message }}</td>
-               <td>{{ entry.http_status }}</td>
-               <td>
-                 {% if entry.status == 'loaded' %}
-                   <a href="{{ url_for('do_terminate', path=entry.key.pathpart) }}"> terminate </a>
-                 {% endif %}
-               </td>
-          </tr>
-     {% endfor %}
-     </tbody>
+               <tr>
+                    <th>PID</th>
+                    <th>dataset</th>
+                    <th>annotation_file</th>
+                    <th>source</th>
+                    <th>port</th>
+                    <th>launchtime</th>
+                    <th>last access</th>
+                    <th>status</th>
+                    <th>message</th>
+                    <th>http_status</th>
+                    <th>actions</th>
+               </tr>
+          </thead>
+          <tbody>
+               {% for entry in entry_list %}
+               <tr>
+                    <td>{{ entry.pid }}</td>
+                    <td><a
+                              href="{{ entry.key.view_url }}">{{ entry.key.h5ad_item.descriptor }}</a>
+                    </td>
+                    <td>{{ entry.key.annotation_descriptor }}</td>
+                    <td>{{ entry.source_name }}</td>
+                    <td>{{ entry.port }}</td>
+                    <td class="timestamp">{{ entry.launchtime }}</td>
+                    <td class="timestamp">{{ entry.timestamp }}</td>
+                    <td>{{ entry.status.name }}</td>
+                    <td>{{ entry.message }}</td>
+                    <td>{{ entry.http_status }}</td>
+                    <td>
+                         {% if entry.status.name == 'loaded' %}
+                         <a
+                              href="{{ url_for('do_terminate', path=entry.key.descriptor, source_name=entry.key.source_name) }}">
+                              terminate </a>
+                         {% endif %}
+                    </td>
+               </tr>
+               {% endfor %}
+          </tbody>
      </table>
      <script>
           $(() => {
-               $(".timestamp").each(function(){
+               $(".timestamp").each(function () {
                     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>
 </body>
-</html>
+
+</html>

cellxgene_gateway/templates/cellxgene_error.html

@@ -28,11 +28,11 @@
           
      <h4>{{ message }}</h4>
 
-     <a href="/filecrawl.html">
+     <a href="{{ url_for('filecrawl') }}">
           Please click here to be redirected to the file directory.
      </a>
      <br>
-     <a href="/">
+     <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="/filecrawl.html">top level</a></li>
+     <li><a href="{{ url_for('filecrawl') }}">top level</a></li>
      {% else %}
      {% endif %}
-     <li><a href="/">homepage</a></li>
+     <li><a href="{{ url_for('index') }}">homepage</a></li>
      </ul>
      </p>
      <script>

cellxgene_gateway/templates/index.html

@@ -35,56 +35,15 @@
 		Links:	
 	</h1>
 	<div class="list-group" style="width:50%;padding-left:65px">
-	  <a href="/filecrawl.html" 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="/cache_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>
 	
-	{% if enable_upload %}
-	<br>
-	<h1 style="padding-left:35px">
-		How To Upload Data via HTTP:
-	</h1>
-	<ol style="padding-left:85px;">
-		<li>
-			Create a folder for your Username: 
-		</li>
-		<br>
-		<form action="{{ url_for('make_user') }}" method="post">
-		    Username <input type="text" name="directory">
-		    <input type="submit" value="Create">
-		</form>
-		<li>
-			Create a subdirectory under the selected Folder: 
-		</li>		
-		<br>
-		<form action="{{ url_for('make_subdir') }}" method="post">
-			<select name="usernames" id="usernames">
-				{% for user in users %}
-					<option value="{{ user }}">{{ user }}</option>
-				{% endfor %}
-			</select>
-			<br>
-			Subdirectory Name <input type="text" name="directory">
-		    <input type="submit" value="Create">
-		</form>
-		<li>Choose a folder to copy your data to, then upload your data file (must be in .h5ad format).</li>
-		<br>
-		<form action="{{ url_for('upload_file') }}" method="post" enctype="multipart/form-data">
-		Type in the name of the directory and subdirectory you wish to upload to, i.e. "USER/cells". <input type="text" name="path">
-		<br>
-		File: <input type="file" name="file"><br>
-		<input style="position:relative; top:10px;" type="submit" value="Upload">
-		</form>
-		<br>
-		<li>Take a look at your data using the file crawler link above</li>
-	</ol>
-	{% endif %}
-
 	<br>
 
 	<h1 style="padding-left:35px">

cellxgene_gateway/templates/loading.html

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

cellxgene_gateway/templates/process_error.html

@@ -36,13 +36,13 @@
 <h4>Options</h4>
      Please choose one of the following, or use the back button:
      <ul>
-          <li><a href="{{url_for('do_relaunch', path=dataset)}}">
+          <li><a href="{{ relaunch_url }}">
                     Attempt to relaunch the cellxgene server.
                </a></li>
-          <li><a href="/filecrawl.html">
+          <li><a href="{{ url_for('filecrawl') }}">
                Return to the file directory.
           </a></li>
-          <li><a href="/">
+          <li><a href="{{ url_for('index') }}">
                Return to the homepage.
           </a></li>
      </ul>

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-dev.yml

@@ -1,11 +0,0 @@
-name: cellxgene-dev
-channels:
-- conda-forge
-dependencies:
-- python=3.7
-- requests
-- flask
-- psutil
-- pip:
-  - flask-api
-  - cellxgene==0.14.1

environment.yml

@@ -0,0 +1,17 @@
+name: cellxgene-gateway
+channels:
+- conda-forge
+dependencies:
+- python=3.11
+- requests
+- flask
+- psutil
+- black
+- twine
+- isort
+- coverage
+- pip
+- pip:
+  - pre_commit
+  - 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-test.txt

@@ -0,0 +1 @@
+freezegun~=1.5.5

requirements.txt

@@ -1,5 +1,5 @@
-cellxgene==0.14.1
+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

setup.py

@@ -1,13 +1,36 @@
+import codecs
 import os
-from setuptools import setup
+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__))
+    with codecs.open(os.path.join(here, rel_path), "r") as fp:
+        return fp.read()
+
+
+def get_version(rel_path):
+    for line in read(rel_path).splitlines():
+        if line.startswith("__version__"):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
+
 
 def parse_requirements():
     reqs = []
     with open("requirements.txt", "r") as f:
-        for l in f.readlines():
-            reqs.append(l.strip("\n"))
+        for line in f.readlines():
+            reqs.append(line.strip("\n"))
     return reqs
 
+
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
@@ -15,9 +38,9 @@ install_reqs = parse_requirements()
 
 setup(
     # mandatory
-    name="cellxgene-gateway",
+    name="cellxgene_gateway",
     # mandatory
-    version="0.1.0",
+    version=get_version("cellxgene_gateway/__init__.py"),
     # mandatory
     author="Niket Patel, Yohann Potier, Alok Saldanha",
     author_email="alok.saldanha@novartis.com",
@@ -27,18 +50,20 @@ setup(
     license="MIT",
     keywords="visualization, genomics",
     url="http://github.com/Novartis/cellxgene-gateway",
-    packages=["cellxgene_gateway"],
+    packages=find_packages(),
     package_data={
         "cellxgene_gateway": [
             "static/css/homepagestyle.css",
+            "static/js/annotation.js",
             "static/nibr.ico",
-            "templates/*.html"
-    ]},
-    data_files=[('', ['README.md', 'LICENSE'])],
+            "templates/*.html",
+        ]
+    },
+    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',
+    python_requires=">=3.6",
 )

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

@@ -0,0 +1,43 @@
+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,
+    ):
+        source = FileItemSource(tempfile.gettempdir(), "local")
+        item = source.make_fileitem_from_path(
+            "customanno.csv", "someh5ad_annotations", True
+        )
+        self.assertEqual(item.name, "customanno")
+        self.assertEqual(item.descriptor, "someh5ad_annotations/customanno.csv")
+
+    def test_make_fileitem_from_path_GIVEN_h5ad_file_THEN_returns_name(self):
+        source = FileItemSource(tempfile.gettempdir(), "local")
+        item = source.make_fileitem_from_path("someanalysis.h5ad", "studydir")
+        self.assertEqual(item.name, "someanalysis.h5ad")
+        self.assertEqual(item.descriptor, "studydir/someanalysis.h5ad")

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 +1,362 @@
+import unittest
+from http import HTTPStatus
+from unittest.mock import MagicMock, Mock, patch, call
+from freezegun import freeze_time
+
+from cellxgene_gateway.backend_cache import BackendCache, is_port_in_use
+from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
+from cellxgene_gateway.cache_key import CacheKey
+from cellxgene_gateway.cellxgene_exception import CellxgeneException
+
+
+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)
+
+
+class TestBackendCacheInit(unittest.TestCase):
+    def test_GIVEN_new_backend_cache_THEN_entry_list_is_empty(self):
+        """BackendCache should initialize with an empty entry list."""
+        cache = BackendCache()
+        self.assertEqual(cache.entry_list, [])
+
+
+class TestBackendCacheGetPorts(unittest.TestCase):
+    def test_GIVEN_empty_cache_THEN_get_ports_returns_empty_list(self):
+        """get_ports should return empty list when no entries exist."""
+        cache = BackendCache()
+        ports = cache.get_ports()
+        self.assertEqual(ports, [])
+
+    def test_GIVEN_cache_with_entries_THEN_get_ports_returns_all_ports(self):
+        """get_ports should return list of all ports from entries."""
+        cache = BackendCache()
+
+        # Create mock entries with different ports
+        entry1 = Mock()
+        entry1.port = 8000
+        entry2 = Mock()
+        entry2.port = 8001
+        entry3 = Mock()
+        entry3.port = 8002
+
+        cache.entry_list = [entry1, entry2, entry3]
+
+        ports = cache.get_ports()
+        self.assertEqual(ports, [8000, 8001, 8002])
+
+    def test_GIVEN_single_entry_THEN_get_ports_returns_single_port(self):
+        """get_ports should correctly handle a single entry."""
+        cache = BackendCache()
+        entry = Mock()
+        entry.port = 9000
+
+        cache.entry_list = [entry]
+
+        ports = cache.get_ports()
+        self.assertEqual(ports, [9000])
+
+
+class TestBackendCacheCheckPath(unittest.TestCase):
+    def setUp(self):
+        self.cache = BackendCache()
+
+    def test_GIVEN_no_matching_path_THEN_check_path_returns_none(self):
+        """check_path should return None when no entries match the path."""
+        source = Mock()
+        source.name = "test_source"
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.loaded
+        cache_entry.key = Mock()
+        cache_entry.key.source.name = "other_source"
+        cache_entry.key.descriptor = "/some/path"
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_path(source, "/test/path")
+        self.assertIsNone(result)
+
+    def test_GIVEN_terminated_entry_THEN_check_path_ignores_it(self):
+        """check_path should ignore entries with terminated status."""
+        source = Mock()
+        source.name = "test_source"
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.terminated
+        cache_entry.key = Mock()
+        cache_entry.key.source.name = "test_source"
+        cache_entry.key.descriptor = "/data"
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_path(source, "/data/file.txt")
+        self.assertIsNone(result)
+
+    def test_GIVEN_single_matching_entry_THEN_check_path_returns_it(self):
+        """check_path should return the matching entry when exactly one matches."""
+        source = Mock()
+        source.name = "test_source"
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.loaded
+        cache_entry.key = Mock()
+        cache_entry.key.source.name = "test_source"
+        cache_entry.key.descriptor = "/data"
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_path(source, "/data/file.txt")
+        self.assertIs(result, cache_entry)
+
+    def test_GIVEN_path_that_does_not_start_with_descriptor_THEN_check_path_returns_none(
+        self,
+    ):
+        """check_path should return None if path doesn't start with descriptor."""
+        source = Mock()
+        source.name = "test_source"
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.loaded
+        cache_entry.key = Mock()
+        cache_entry.key.source.name = "test_source"
+        cache_entry.key.descriptor = "/data"
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_path(source, "/other/file.txt")
+        self.assertIsNone(result)
+
+    def test_GIVEN_multiple_matching_entries_THEN_check_path_raises_exception(self):
+        """check_path should raise exception when multiple entries match."""
+        source = Mock()
+        source.name = "test_source"
+
+        cache_entry1 = Mock()
+        cache_entry1.status = CacheEntryStatus.loaded
+        cache_entry1.key = Mock()
+        cache_entry1.key.source.name = "test_source"
+        cache_entry1.key.descriptor = "/data"
+
+        cache_entry2 = Mock()
+        cache_entry2.status = CacheEntryStatus.loaded
+        cache_entry2.key = Mock()
+        cache_entry2.key.source.name = "test_source"
+        cache_entry2.key.descriptor = "/data"
+
+        self.cache.entry_list = [cache_entry1, cache_entry2]
+
+        with self.assertRaises(CellxgeneException) as context:
+            self.cache.check_path(source, "/data/file.txt")
+
+        # The CellxgeneException is raised with HTTPStatus as first arg and message as second
+        self.assertEqual(context.exception.message, HTTPStatus.INTERNAL_SERVER_ERROR)
+        self.assertIn("Found 2", context.exception.http_status)
+
+    def test_GIVEN_mixed_entries_THEN_check_path_returns_only_matching_active_entry(
+        self,
+    ):
+        """check_path should correctly filter by source, path, and status."""
+        source = Mock()
+        source.name = "target_source"
+
+        # Terminated entry - should be ignored
+        terminated_entry = Mock()
+        terminated_entry.status = CacheEntryStatus.terminated
+        terminated_entry.key = Mock()
+        terminated_entry.key.source.name = "target_source"
+        terminated_entry.key.descriptor = "/data"
+
+        # Different source - should be ignored
+        other_source_entry = Mock()
+        other_source_entry.status = CacheEntryStatus.loaded
+        other_source_entry.key = Mock()
+        other_source_entry.key.source.name = "other_source"
+        other_source_entry.key.descriptor = "/data"
+
+        # Matching entry - should be returned
+        matching_entry = Mock()
+        matching_entry.status = CacheEntryStatus.loaded
+        matching_entry.key = Mock()
+        matching_entry.key.source.name = "target_source"
+        matching_entry.key.descriptor = "/data"
+
+        self.cache.entry_list = [terminated_entry, other_source_entry, matching_entry]
+
+        result = self.cache.check_path(source, "/data/file.txt")
+        self.assertIs(result, matching_entry)
+
+
+class TestBackendCacheCheckEntry(unittest.TestCase):
+    def setUp(self):
+        self.cache = BackendCache()
+
+    def test_GIVEN_no_matching_entry_THEN_check_entry_returns_none(self):
+        """check_entry should return None when no entries match the key."""
+        key = Mock()
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.loaded
+        cache_entry.key = Mock()
+        cache_entry.key.equals.return_value = False
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_entry(key)
+        self.assertIsNone(result)
+
+    def test_GIVEN_terminated_entry_THEN_check_entry_ignores_it(self):
+        """check_entry should ignore entries with terminated status."""
+        key = Mock()
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.terminated
+        cache_entry.key = Mock()
+        cache_entry.key.equals.return_value = True
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_entry(key)
+        self.assertIsNone(result)
+
+    def test_GIVEN_single_matching_entry_THEN_check_entry_returns_it(self):
+        """check_entry should return the matching entry when exactly one matches."""
+        key = Mock()
+
+        cache_entry = Mock()
+        cache_entry.status = CacheEntryStatus.loaded
+        cache_entry.key = Mock()
+        cache_entry.key.equals.return_value = True
+
+        self.cache.entry_list = [cache_entry]
+
+        result = self.cache.check_entry(key)
+        self.assertIs(result, cache_entry)
+
+    def test_GIVEN_multiple_matching_entries_THEN_check_entry_raises_exception(self):
+        """check_entry should raise exception when multiple entries match."""
+        key = Mock()
+        key.dataset = "test_dataset"
+
+        cache_entry1 = Mock()
+        cache_entry1.status = CacheEntryStatus.loaded
+        cache_entry1.key = Mock()
+        cache_entry1.key.equals.return_value = True
+
+        cache_entry2 = Mock()
+        cache_entry2.status = CacheEntryStatus.loaded
+        cache_entry2.key = Mock()
+        cache_entry2.key.equals.return_value = True
+
+        self.cache.entry_list = [cache_entry1, cache_entry2]
+
+        with self.assertRaises(CellxgeneException) as context:
+            self.cache.check_entry(key)
+
+        # The CellxgeneException is raised with HTTPStatus as first arg and message as second
+        self.assertEqual(context.exception.message, HTTPStatus.INTERNAL_SERVER_ERROR)
+        self.assertIn("Found 2", context.exception.http_status)
+
+    def test_GIVEN_mixed_entries_THEN_check_entry_returns_only_matching_active_entry(
+        self,
+    ):
+        """check_entry should correctly filter by key equality and status."""
+        key = Mock()
+
+        # Terminated entry - should be ignored
+        terminated_entry = Mock()
+        terminated_entry.status = CacheEntryStatus.terminated
+        terminated_entry.key = Mock()
+        terminated_entry.key.equals.return_value = True
+
+        # Non-matching entry - should be ignored
+        non_matching_entry = Mock()
+        non_matching_entry.status = CacheEntryStatus.loaded
+        non_matching_entry.key = Mock()
+        non_matching_entry.key.equals.return_value = False
+
+        # Matching entry - should be returned
+        matching_entry = Mock()
+        matching_entry.status = CacheEntryStatus.loaded
+        matching_entry.key = Mock()
+        matching_entry.key.equals.return_value = True
+
+        self.cache.entry_list = [terminated_entry, non_matching_entry, matching_entry]
+
+        result = self.cache.check_entry(key)
+        self.assertIs(result, matching_entry)
+
+
+class TestBackendCachePrune(unittest.TestCase):
+    def test_GIVEN_entry_in_cache_THEN_prune_removes_it(self):
+        """prune should remove the entry from the cache."""
+        cache = BackendCache()
+
+        entry_mock = Mock()
+        cache.entry_list = [entry_mock]
+
+        cache.prune(entry_mock)
+
+        self.assertEqual(len(cache.entry_list), 0)
+        self.assertNotIn(entry_mock, cache.entry_list)
+
+    def test_GIVEN_entry_in_cache_THEN_prune_terminates_it(self):
+        """prune should call terminate on the entry."""
+        cache = BackendCache()
+
+        entry_mock = Mock()
+        cache.entry_list = [entry_mock]
+
+        cache.prune(entry_mock)
+
+        entry_mock.terminate.assert_called_once()
+
+    def test_GIVEN_multiple_entries_THEN_prune_removes_only_target_entry(self):
+        """prune should only remove the specified entry, not others."""
+        cache = BackendCache()
+
+        entry1 = Mock()
+        entry2 = Mock()
+        entry3 = Mock()
+
+        cache.entry_list = [entry1, entry2, entry3]
+
+        cache.prune(entry2)
+
+        self.assertEqual(len(cache.entry_list), 2)
+        self.assertIn(entry1, cache.entry_list)
+        self.assertNotIn(entry2, cache.entry_list)
+        self.assertIn(entry3, cache.entry_list)
+
+        # Verify only entry2 was terminated
+        entry1.terminate.assert_not_called()
+        entry2.terminate.assert_called_once()
+        entry3.terminate.assert_not_called()
+
+    def test_GIVEN_empty_cache_THEN_prune_raises_value_error(self):
+        """prune should raise ValueError if entry is not in cache."""
+        cache = BackendCache()
+
+        entry_mock = Mock()
+
+        with self.assertRaises(ValueError):
+            cache.prune(entry_mock)

tests/test_cache_entry.py

@@ -0,0 +1,69 @@
+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.items.item import ItemType
+from cellxgene_gateway.items.file.fileitem import FileItem
+from cellxgene_gateway.items.file.fileitem_source import FileItemSource
+from cellxgene_gateway.gateway import app
+
+key = CacheKey(
+    FileItem("/czi/", name="pbmc3k.h5ad", type=ItemType.h5ad),
+    FileItemSource("/tmp", "local"),
+)
+
+
+class TestRenderEntry(unittest.TestCase):
+    def setUp(self):
+        self.app = app
+        self.app_context = self.app.test_request_context()
+        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)
+
+    def test_GIVEN_absolute_static_url_THEN_include_path(self):
+        flask_util.include_source_in_url = False
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            "src:url(/static/assets/"
+        )
+        expected = "src:url(/view/czi/pbmc3k.h5ad/static/assets/"
+        self.assertEqual(actual, expected)
+
+    def test_GIVEN_absolute_src_THEN_include_path(self):
+        flask_util.include_source_in_url = False
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            '<link rel="shortcut icon" href="/static/assets/favicon.ico">'
+        )
+        expected = '<link rel="shortcut icon" href="/view/czi/pbmc3k.h5ad/static/assets/favicon.ico">'
+        self.assertEqual(actual, expected)
+
+    def test_GIVEN_absolute_static_url_include_source_THEN_include_path(self):
+        flask_util.include_source_in_url = True
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            "src:url(/static/assets/"
+        )
+        expected = "src:url(/source/local/view/czi/pbmc3k.h5ad/static/assets/"
+        self.assertEqual(actual, expected)
+
+    def test_GIVEN_absolute_src_include_source_THEN_include_path(self):
+        flask_util.include_source_in_url = True
+        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
+            '<link rel="shortcut icon" href="/static/assets/favicon.ico">'
+        )
+        expected = '<link rel="shortcut icon" href="/source/local/view/czi/pbmc3k.h5ad/static/assets/favicon.ico">'
+        self.assertEqual(actual, expected)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_dir_util.py

@@ -1,38 +1,35 @@
 import unittest
 from unittest.mock import MagicMock, patch
-from cellxgene_gateway.dir_util import render_entry
 
-class TestRenderEntry(unittest.TestCase):
-    def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
-        entry = {
-                "path": "/somepath/",
-                "name": "entry",
-                "type": "file",
-            }
-        rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
-    def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
-        entry = {
-                "path": "/somepath",
-                "name": "entry",
-                "type": "file",
-            }
-        rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
-    def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
-        entry = {
-                "path": "somepath/",
-                "name": "entry",
-                "type": "file",
-            }
-        rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
-    def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
-        entry = {
-                "path": "somepath",
-                "name": "entry",
-                "type": "file",
-            }
-        rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
-        
+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

@@ -1,23 +1,35 @@
 import unittest
 from unittest.mock import MagicMock, patch
+
 from cellxgene_gateway.extra_scripts import get_extra_scripts
 
+
 class TestExtraScripts(unittest.TestCase):
-    @patch('cellxgene_gateway.env.extra_scripts', new='["abc","def"]')
+    @patch("cellxgene_gateway.env.extra_scripts", new='["abc","def"]')
     def test_GIVEN_two_scripts_THEN_returns_two_strings(self):
-        self.assertEqual(get_extra_scripts(), ['abc', 'def'])
+        self.assertEqual(get_extra_scripts(), ["abc", "def"])
 
-    @patch('cellxgene_gateway.env.extra_scripts', new='["abc", "def"]')
+    @patch("cellxgene_gateway.env.extra_scripts", new='["abc", "def"]')
     def test_GIVEN_two_scripts_space_THEN_returns_two_strings(self):
-        self.assertEqual(get_extra_scripts(), ['abc', 'def'])
+        self.assertEqual(get_extra_scripts(), ["abc", "def"])
 
-    @patch('cellxgene_gateway.env.extra_scripts', new=None)
+    @patch("cellxgene_gateway.env.extra_scripts", new=None)
     def test_GIVEN_none_THEN_returns_empty_array(self):
         self.assertEqual(get_extra_scripts(), [])
 
-    @patch('cellxgene_gateway.env.extra_scripts', new='[]')
+    @patch("cellxgene_gateway.env.extra_scripts", new="[]")
     def test_GIVEN_empty_string_THEN_returns_empty_array(self):
         self.assertEqual(get_extra_scripts(), [])
 
-if __name__ == '__main__':
-    unittest.main()
+    @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

@@ -0,0 +1,170 @@
+import os
+import shutil
+import tempfile
+import unittest
+from collections import defaultdict
+from unittest.mock import patch
+
+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 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 = make_entry(subpath="/somepath/")
+        rendered = render_item(entry, source)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
+
+    def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
+        entry = make_entry(subpath="/somepath")
+        rendered = render_item(entry, source)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
+
+    def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
+        entry = make_entry(subpath="somepath/")
+        rendered = render_item(entry, source)
+        self.assertIn("view/somepath/entry.h5ad/'", rendered)
+
+    def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
+        entry = make_entry(subpath="somepath")
+        rendered = render_item(entry, source)
+        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

@@ -1,26 +1,46 @@
 import unittest
-from unittest.mock import MagicMock, patch
-from cellxgene_gateway.cache_entry import CacheEntry
+from unittest.mock import patch, seal
+
 from cellxgene_gateway.backend_cache import BackendCache
+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.cache_entry.CacheEntry')
-    @patch('cellxgene_gateway.cache_entry.CacheEntry')
+    @patch("cellxgene_gateway.util.current_time_stamp", new=lambda: 0)
+    @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):
         from cellxgene_gateway.prune_process_cache import PruneProcessCache
 
         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__':
-    unittest.main()
+
+if __name__ == "__main__":
+    unittest.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,
+        )