Preparing for 0.2.3 release

Grst master

.github/workflows/pr-checks.yaml

@@ -0,0 +1,49 @@
+# Tests that run on every PR
+
+name: Pull Request Checks
+
+on: [push, pull_request]
+
+jobs:
+  black:
+    runs-on: ubuntu-18.04
+    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 -l 79 . --check
+  # This job is copied over from `deploy.yaml`
+  run-tests:
+    runs-on: ubuntu-18.04
+    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 "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          python setup.py install
+
+      - name: Run tests
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate cellxgene-gateway
+          python -m unittest discover tests
+          bash <(curl -s https://codecov.io/bash)

.gitignore

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

.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 +1,21 @@
+# 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

README.md

@@ -30,7 +30,7 @@ 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 +39,7 @@ 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
 ```
 
 
@@ -48,9 +48,6 @@ wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc
 ```bash
 export CELLXGENE_DATA=../cellxgene_data  # change this directory if you put data in a different place.
 export CELLXGENE_LOCATION=`which cellxgene`
-export GATEWAY_HOST=localhost:5005
-export GATEWAY_PROTOCOL=http
-export GATEWAY_IP=127.0.0.1
 ```
 
 3. Now, execute the cellxgene gateway:
@@ -63,12 +60,24 @@ Here's what the environment variables mean:
 
 * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`
 * `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
-* `GATEWAY_HOST` - the hostname and port that the gateway will run on, typically `localhost:5005` if running locally
-* `GATEWAY_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.
-* `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions
+
 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_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
 * `GATEWAY_ENABLE_UPLOAD` - Set to `true` or `1` to enable HTTP uploads. This is not recommended for a public server.
+* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
+* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
+
+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.
 
@@ -112,8 +121,18 @@ 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
 ```

cellxgene_gateway/__init__.py

@@ -6,3 +6,5 @@
 # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
+
+__version__ = "0.2.3"

cellxgene_gateway/backend_cache.py

@@ -13,7 +13,7 @@ from threading import Thread
 from flask_api import status
 
 from cellxgene_gateway import env
-from cellxgene_gateway.cache_entry import CacheEntry
+from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.subprocess_backend import SubprocessBackend
 
@@ -22,8 +22,10 @@ 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 +35,14 @@ class BackendCache:
         contents = self.entry_list
         return [c.port for c in contents]
 
-    def check_entry(self, dataset):
+    def check_entry(self, key):
         contents = self.entry_list
         matches = [
             c
             for c in contents
-            if c.dataset == dataset and c.status != "terminated"
+            if c.key.dataset == key.dataset
+            and c.key.annotation_file == key.annotation_file
+            and c.status != CacheEntryStatus.terminated
         ]
 
         if len(matches) == 0:
@@ -51,13 +55,14 @@ class BackendCache:
                 "Found " + str(len(matches)) + " for " + dataset,
             )
 
-    def create_entry(self, dataset, file_path, scripts):
+    def create_entry(self, key, scripts):
         port = 8000
         existing_ports = self.get_ports()
+
         while (port in existing_ports) or is_port_in_use(port):
             port += 1
 
-        entry = CacheEntry.for_dataset(dataset, file_path, port)
+        entry = CacheEntry.for_key(key, port)
 
         background_thread = Thread(
             target=process_backend.launch,

cellxgene_gateway/cache_entry.py

@@ -6,34 +6,46 @@
 # 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 datetime
 import logging
+from flask.helpers import url_for
+from flask.wrappers import Response
 
-from flask import make_response, request
+import psutil
+from enum import Enum
+from flask import make_response, render_template, request
 from requests import get, post, put
+import re
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
+from cellxgene_gateway.flask_util import querystring
 from cellxgene_gateway.util import current_time_stamp
 
+
+class CacheEntryStatus(Enum):
+    loaded = "loaded"
+    loading = "loading"
+    error = "error"
+    terminated = "terminated"
+
+
 class CacheEntry:
     def __init__(
         self,
         pid,
-        dataset,
-        file_path,
+        key,
         port,
         launchtime,
         timestamp,
-        status,
+        status: CacheEntryStatus,
         message,
         all_output,
         stderr,
         http_status,
     ):
         self.pid = pid
-        self.dataset = dataset
-        self.file_path = file_path
+        self.key = key
         self.port = port
         self.launchtime = launchtime
         self.timestamp = timestamp
@@ -44,15 +56,15 @@ class CacheEntry:
         self.http_status = http_status
 
     @classmethod
-    def for_dataset(cls, dataset, file_path, port):
+    def for_key(cls, key, port):
+
         return cls(
             None,
-            dataset,
-            file_path,
+            key,
             port,
             current_time_stamp(),
             current_time_stamp(),
-            "loading",
+            CacheEntryStatus.loading,
             None,
             None,
             None,
@@ -61,13 +73,13 @@ class CacheEntry:
 
     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:
@@ -77,10 +89,12 @@ 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:
@@ -89,49 +103,83 @@ class CacheEntry:
             terminated.append(p.pid)
             p.terminate()
             psutil.wait_procs([p], callback=on_terminate)
-            logging.getLogger("cellxgene_gateway").info(f"terminated {terminated}")
-        self.status = "terminated"
+            logging.getLogger("cellxgene_gateway").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.gateway_basepath()}static/",
+                cellxgene_content,
+            )
+            .replace("http://fonts.gstatic.com", "https://fonts.gstatic.com")
+            .replace(self.cellxgene_basepath(), self.gateway_basepath())
+        )
+        return gateway_content
+
+    def gateway_basepath(self):
+        return url_for("do_view", path=self.key.pathpart) + "/"
+
+    def cellxgene_basepath(self):
+        return f"http://127.0.0.1:{self.port}"
 
     def serve_content(self, path):
-        dataset = self.dataset
-
-        gateway_basepath = (
-            f"{env.gateway_protocol}://{env.gateway_host}/view/{dataset}/"
-        )
-        subpath = path[len(dataset) :]  # noqa: E203
+        gateway_basepath = self.gateway_basepath()
+        subpath = path[len(self.key.pathpart) :]  # noqa: E203
 
         if len(subpath) == 0:
-            r = make_response(f"Redirect to {gateway_basepath}\n", 301)
-            r.headers["location"] = gateway_basepath
+            r = make_response(f"Redirect to {gateway_basepath}\n", 302)
+            r.headers["location"] = gateway_basepath + querystring()
             return r
-
-        port = self.port
-        cellxgene_basepath = f"http://127.0.0.1:{port}"
+        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,
+            )
 
         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",
+        ]
+        for h in copy_headers:
+            if h in request.headers:
+                headers[h] = request.headers[h]
 
-        if "accept" in request.headers:
-            headers["accept"] = request.headers["accept"]
-        if "user-agent" in request.headers:
-            headers["user-agent"] = request.headers["user-agent"]
-        if "content-type" in request.headers:
-            headers["content-type"] = request.headers["content-type"]
+        full_path = self.cellxgene_basepath() + subpath + querystring()
 
         if request.method in ["GET", "HEAD", "OPTIONS"]:
-            cellxgene_response = get(
-                cellxgene_basepath + subpath, headers=headers
-            )
+            cellxgene_response = get(full_path, headers=headers)
         elif request.method == "PUT":
             cellxgene_response = put(
-                cellxgene_basepath + subpath,
+                full_path,
                 headers=headers,
-                data=request.data.decode(),
+                data=request.data,
             )
         elif request.method == "POST":
             cellxgene_response = post(
-                cellxgene_basepath + subpath,
+                full_path,
                 headers=headers,
-                data=request.data.decode(),
+                data=request.data,
             )
         else:
             raise CellxgeneException(
@@ -139,17 +187,21 @@ class CacheEntry:
             )
         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)
+            gateway_content = self.rewrite_text_content(
+                cellxgene_response.content.decode()
+            )
         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,
-            {"Content-Type": content_type},
+            resp_headers,
         )
 
         return gateway_response

cellxgene_gateway/cache_key.py

@@ -0,0 +1,23 @@
+# 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.
+
+# There are three kinds of CacheKey:
+# 1) somedir/dataset.h5ad: a dataset
+#    in this case, pathpart == dataset == 'somedir/dataset.h5ad'
+# 2) somedir/dataset_annotations/my_annotations.csv : an actual annotaitons file.
+#    in this case, pathpart == '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'
+
+
+class CacheKey:
+    def __init__(self, pathpart, dataset, annotation_file):
+        self.pathpart = pathpart
+        self.dataset = dataset
+        self.annotation_file = annotation_file

cellxgene_gateway/dir_util.py

@@ -52,43 +52,12 @@ def create_dir(parent_path, dir_name):
         os.mkdir(full_path)
 
 
-def recurse_dir(path):
-    if not os.path.exists(path):
-        raise CellxgeneException(
-            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
-        )
-
-    def make_entry(el):
-        full_path = os.path.join(path, el)
-        if os.path.isfile(full_path):
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "file",
-            }
-        elif os.path.isdir(full_path):
-            return {
-                "path": full_path,
-                "name": el,
-                "type": "directory",
-                "children": recurse_dir(full_path),
-            }
-        else:
-            raise CellxgeneException(
-                "Given path is neither file nor directory.",
-                status.HTTP_400_BAD_REQUEST,
-            )
-
-    return [make_entry(x) for x in os.listdir(path)]
+annotations_suffix = "_annotations"
 
 
-def render_entries(entries):
-    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
+def make_h5ad(el):
+    return el[: -len(annotations_suffix)] + ".h5ad"
 
 
-def render_entry(entry):
-    if entry["type"] == "file":
-        url = 'view' + '/' + entry['path'].lstrip("/")
-        return f"<li> <a href='{ url}'>{entry['name']}</a></li>"
-    elif entry["type"] == "directory":
-        return f"<li>{entry['name']}{render_entries(entry['children'])}</li>"
+def make_annotations(el):
+    return el[:-5] + annotations_suffix

cellxgene_gateway/env.py

@@ -7,32 +7,71 @@
 # 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 os
+import socket
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA")
-gateway_host = os.environ.get("GATEWAY_HOST")
-gateway_protocol = os.environ.get("GATEWAY_PROTOCOL")
-ip = os.environ.get("GATEWAY_IP")
+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")
+)
+ip = os.environ.get("GATEWAY_IP", "127.0.0.1")
 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_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [
+    "true",
+    "1",
+]
+enable_annotations = os.environ.get(
+    "GATEWAY_ENABLE_ANNOTATIONS", ""
+).lower() in [
+    "true",
+    "1",
+]
+enable_backed_mode = os.environ.get(
+    "GATEWAY_ENABLE_BACKED_MODE", ""
+).lower() in [
+    "true",
+    "1",
+]
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
     "CELLXGENE_DATA": cellxgene_data,
-    "GATEWAY_HOST": gateway_host,
-    "GATEWAY_PROTOCOL": gateway_protocol,
-    "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_ENABLE_ANNOTATIONS": enable_annotations,
+    "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
+    "CELLXGENE_ARGS": cellxgene_args,
+    "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(
@@ -47,11 +86,12 @@ def validate():
 
         export CELLXGENE_LOCATION=~/anaconda/envs/cellxgene-dev/bin/cellxgene
         export CELLXGENE_DATA=../cellxgene_data
-        export GATEWAY_HOST=localhost:5005
-        export GATEWAY_PROTOCOL=http
-        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

@@ -7,13 +7,14 @@
 # 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 cellxgene_gateway import env
+
 
 def get_extra_scripts():
     # can be array of script tags to inject on every page, e.g. for google analytics could be
     # ['https://www.googletagmanager.com/gtag/js?id=UA-123456-2',
-    #  f"{env.gateway_protocol}://{env.gateway_host}/static/js/google_ua.js"]
+    #  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)

cellxgene_gateway/filecrawl.py

@@ -0,0 +1,121 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+import os
+from cellxgene_gateway import env
+from cellxgene_gateway.dir_util import (
+    make_h5ad,
+    make_annotations,
+    annotations_suffix,
+)
+from flask import url_for
+
+
+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 = sorted(os.listdir(path))
+
+    def is_h5ad(el):
+        return el.endswith(".h5ad") and os.path.isfile(os.path.join(path, el))
+
+    h5ad_entries = [x for x in all_entries if is_h5ad(x)]
+    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 sorted(os.listdir(full_path))
+                if x.endswith(".csv")
+                and os.path.isfile(os.path.join(full_path, x))
+            ]
+        return [
+            {
+                "name": "new",
+                "class": "new",
+                "path": full_path.replace(env.cellxgene_data, ""),
+            }
+        ] + entries
+
+    def make_entry(el):
+        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 all_entries]
+
+
+def render_entries(entries):
+    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
+
+
+def get_url(entry):
+    return url_for("do_view", path=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:
+        return ""

cellxgene_gateway/flask_util.py

@@ -0,0 +1,15 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+from flask import request
+
+
+def querystring():
+    qs = request.query_string.decode()
+    return f"?{qs}" if len(qs) > 0 else ""

cellxgene_gateway/gateway.py

@@ -7,15 +7,16 @@
 # 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 datetime
-import os
-import logging
-from threading import Thread, Lock
 import json
+import logging
+
+# import BaseHTTPServer
+import os
+from threading import Lock, Thread
 
 from flask import (
     Flask,
+    make_response,
     redirect,
     render_template,
     request,
@@ -23,21 +24,49 @@ from flask import (
     url_for,
 )
 from flask_api import status
-from werkzeug import secure_filename
-
+from werkzeug.utils import secure_filename
+from werkzeug.middleware.proxy_fix import ProxyFix
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache
+from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import create_dir, recurse_dir, render_entries, is_subdir
+from cellxgene_gateway.dir_util import create_dir, is_subdir
 from cellxgene_gateway.extra_scripts import get_extra_scripts
-from cellxgene_gateway.path_util import get_dataset, get_file_path
+from cellxgene_gateway.filecrawl import recurse_dir, render_entries
+from cellxgene_gateway.path_util import get_key
 from cellxgene_gateway.process_exception import ProcessException
 from cellxgene_gateway.prune_process_cache import PruneProcessCache
 from cellxgene_gateway.util import current_time_stamp
 
 app = Flask(__name__)
+
+
+def _force_https(app):
+    def wrapper(environ, start_response):
+        environ["wsgi.url_scheme"] = env.external_protocol
+        return app(environ, start_response)
+
+    return wrapper
+
+
+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,
+    )
+
 cache = BackendCache()
-location = f"{env.gateway_protocol}://{env.gateway_host}"
 
 
 @app.errorhandler(CellxgeneException)
@@ -73,7 +102,8 @@ def handle_invalid_process(error):
             http_status=error.http_status,
             stdout=error.stdout,
             stderr=error.stderr,
-            dataset=error.dataset,
+            dataset=error.key.dataset,
+            annotation_file=error.key.annotation_file,
         ),
         error.http_status,
     )
@@ -104,12 +134,13 @@ def index():
         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)
+    return redirect(url_for("index"), code=302)
 
 
 def make_subdir():
@@ -118,22 +149,26 @@ def make_subdir():
 
     create_dir(parent_path, dir_name)
 
-    return redirect(location, code=302)
+    return redirect(url_for("index"), 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 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))
+                        os.path.join(
+                            full_upload_path, secure_filename(f.filename)
+                        )
                     )
-                    return redirect("/filecrawl.html", code=302)
+                    return redirect(url_for("filecrawl"), code=302)
                 else:
                     raise CellxgeneException(
                         "Uploaded file must be in anndata (.h5ad) format.",
@@ -149,46 +184,82 @@ def upload_file():
             "Invalid directory.", status.HTTP_400_BAD_REQUEST
         )
 
-    return redirect(env.location, code=302)
+    return redirect(url_for("index"), 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.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"]
+    )
+
+
+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.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,
+        )
+    )
+    return set_no_cache(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()
+
+
 @app.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
 def do_view(path):
-    dataset = get_dataset(path)
-    file_path = get_file_path(dataset)
+    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(dataset)
+        match = cache.check_entry(key)
         if match is None:
             uascripts = get_extra_scripts()
-            match = cache.create_entry(dataset, file_path, uascripts)
+            match = cache.create_entry(key, uascripts)
 
     match.timestamp = current_time_stamp()
 
-    if match.status == "loaded":
+    if (
+        match.status == CacheEntryStatus.loaded
+        or match.status == CacheEntryStatus.loading
+    ):
         return match.serve_content(path)
-    elif match.status == "loading":
-        launch_time = datetime.datetime.fromtimestamp(match.launchtime)
-        return render_template(
-            "loading.html", launchtime=launch_time, all_output=match.all_output
-        )
-    elif match.status == "error":
+    elif match.status == CacheEntryStatus.error:
         raise ProcessException.from_cache_entry(match)
 
 
@@ -196,35 +267,59 @@ def do_view(path):
 def do_GET_status():
     return render_template("cache_status.html", entry_list=cache.entry_list)
 
+
 @app.route("/cache_status.json", methods=["GET"])
 def do_GET_status_json():
-    return json.dumps({'launchtime':app.launchtime,
-    'entry_list':[{
-        'dataset': entry.dataset,
-        'launchtime': entry.launchtime,
-        'last_access': entry.timestamp,
-        'status': entry.status
-    } for entry in cache.entry_list]})
+    return json.dumps(
+        {
+            "launchtime": app.launchtime,
+            "entry_list": [
+                {
+                    "dataset": entry.key.dataset,
+                    "annotation_file": entry.key.annotation_file,
+                    "launchtime": entry.launchtime,
+                    "last_access": entry.timestamp,
+                    "status": entry.status,
+                }
+                for entry in cache.entry_list
+            ],
+        }
+    )
+
 
 @app.route("/relaunch/<path:path>", methods=["GET"])
 def do_relaunch(path):
-    dataset = get_dataset(path)
-    match = cache.check_entry(dataset)
+    key = get_key(path)
+    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
-    return redirect(url_for("do_view", path=path), code=302)
+    qs = request.query_string.decode()
+    return redirect(
+        url_for("do_view", path=path) + (f"?{qs}" if len(qs) > 0 else ""),
+        code=302,
+    )
+
 
 @app.route("/terminate/<path:path>", methods=["GET"])
 def do_terminate(path):
-    dataset = get_dataset(path)
-    match = cache.check_entry(dataset)
+    key = get_key(path)
+    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
     return redirect(url_for("do_GET_status"), code=302)
 
 
+@app.route("/metadata/ip_address", methods=["GET"])
+def ip_address():
+    resp = make_response(env.ip)
+    return set_no_cache(resp)
+
+
 def main():
-    logging.basicConfig(level=logging.INFO, format='%(asctime)s:%(name)s:%(levelname)s:%(message)s')
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
+    )
     env.validate()
     pruner = PruneProcessCache(cache)
 
@@ -232,7 +327,7 @@ def main():
     background_thread.start()
 
     app.launchtime = current_time_stamp()
-    app.run(host="0.0.0.0", port=5005, debug=False)
+    app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
 
 
 if __name__ == "__main__":

cellxgene_gateway/path_util.py

@@ -12,30 +12,51 @@ import os
 from flask_api import status
 
 from cellxgene_gateway import env
+from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
+from cellxgene_gateway.dir_util import make_h5ad
 
 
-def get_dataset(path):
+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:
-        get_file_path(trimmed)
-        return trimmed
+        # 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/my_annotations.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:
-        split = os.path.split(trimmed)
-        return get_dataset(split[0])
+        pass
+    split = os.path.split(trimmed)
+    return get_key(split[0])
 
 
-def validate_path(file_path):
+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
@@ -43,7 +64,44 @@ def validate_path(file_path):
     return
 
 
-def get_file_path(dataset):
+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_path(file_path)
+    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/process_exception.py

@@ -9,13 +9,13 @@
 
 
 class ProcessException(Exception):
-    def __init__(self, message, stdout, stderr, http_status, dataset):
+    def __init__(self, message, stdout, stderr, http_status, key):
         Exception.__init__(self)
         self.message = message
         self.stdout = stdout
         self.stderr = stderr
         self.http_status = http_status
-        self.dataset = dataset
+        self.key = key
 
     @classmethod
     def from_cache_entry(cls, cache_entry):
@@ -24,5 +24,5 @@ class ProcessException(Exception):
             cache_entry.all_output,
             cache_entry.stderr,
             cache_entry.http_status,
-            cache_entry.dataset,
+            cache_entry.key,
         )

cellxgene_gateway/prune_process_cache.py

@@ -7,16 +7,19 @@
 # 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 import env
+from cellxgene_gateway import util
+
+logger = logging.getLogger(__name__)
 
-from cellxgene_gateway.util import current_time_stamp
-from cellxgene_gateway.env import ttl
 
 class PruneProcessCache:
     def __init__(self, cache):
         self.cache = cache
-        self.expire_seconds = (3600 if ttl is None else int(ttl))
+        self.expire_seconds = 3600 if env.ttl is None else int(env.ttl)
 
     def __call__(self):
         while True:
@@ -24,18 +27,26 @@ class PruneProcessCache:
             self.prune()
 
     def prune(self):
-        timestamp = current_time_stamp()
+        timestamp = util.current_time_stamp()
         cutoff = timestamp - self.expire_seconds
-        def prunable(p):
-            return p.timestamp < cutoff and p.pid != None
-        processes_to_delete = [p for p in self.cache.entry_list if  prunable(p)]
-        processes_to_keep = [p for p in self.cache.entry_list if not prunable(p)]
-        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.dataset})")
+                logger.info(
+                    f"pruning process {process.pid} ({process.key.dataset})"
+                )
                 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.dataset})"
+                )

cellxgene_gateway/static/js/annotation.js

@@ -0,0 +1,19 @@
+// neandertal javascript
+const new_annotation_callback = (() =>{
+    const suffix = `.csv`;
+    return (e) => {
+        e.preventDefault();
+        const el = $(e.target);
+        const href = el.attr('href');
+        const base = prompt(`Name your annotations collection\nnote: the suffix "${suffix}" will be appended`);
+        if (base !== null && base.length > 0) {
+            if (/^[0-9a-zA-Z_]+$/.test(base)) {
+                window.location = `${href}/${base}${suffix}`;
+            } else {
+                alert("Error: name must match ^[0-9a-zA-Z_]+$\nthat is, only numbers, letters and underscore are allowed")
+            }
+        }
+        return false;
+    }
+})()
+

cellxgene_gateway/subprocess_backend.py

@@ -11,7 +11,14 @@ import logging
 import subprocess
 
 from flask_api import status
-
+from cellxgene_gateway.cache_entry import CacheEntryStatus
+from cellxgene_gateway.dir_util import make_annotations
+from cellxgene_gateway.path_util import get_annotation_file_path, get_file_path
+from cellxgene_gateway.env import (
+    enable_annotations,
+    enable_backed_mode,
+    cellxgene_args,
+)
 from cellxgene_gateway.process_exception import ProcessException
 
 
@@ -19,13 +26,29 @@ class SubprocessBackend:
     def __init__(self):
         pass
 
-    def create_cmd(self, cellxgene_loc, file_path, port, scripts):
+    def create_cmd(
+        self, cellxgene_loc, file_path, port, scripts, annotation_file_path
+    ):
+        if enable_annotations and not annotation_file_path is None:
+            if annotation_file_path == "":
+                extra_args = (
+                    f" --annotations-dir {make_annotations(file_path)}"
+                )
+            else:
+                extra_args = f" --annotations-file {annotation_file_path}"
+        else:
+            extra_args = " --disable-annotations"
+        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)
             + " --host 127.0.0.1"
+            + extra_args
         )
 
         for s in scripts:
@@ -36,7 +59,11 @@ class SubprocessBackend:
     def launch(self, cellxgene_loc, scripts, cache_entry):
 
         cmd = self.create_cmd(
-            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
+            cellxgene_loc,
+            get_file_path(cache_entry.key),
+            cache_entry.port,
+            scripts,
+            get_annotation_file_path(cache_entry.key),
         )
         logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
         process = subprocess.Popen(
@@ -59,7 +86,7 @@ class SubprocessBackend:
                     message = "Cellxgene failed to launch dataset."
                     http_status = status.HTTP_500_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)

cellxgene_gateway/templates/cache_status.html

@@ -29,6 +29,7 @@
           <tr>
                <th>PID</th>
                <th>dataset</th>
+               <th>annotation_file</th>
                <th>port</th>
                <th>launchtime</th>
                <th>last access</th>
@@ -42,16 +43,17 @@
 	{% for entry in entry_list %}
           <tr>
                <td>{{ entry.pid }}</td>
-               <td><a href="{{ url_for('do_view', path=entry.dataset) }}">{{ entry.dataset }}</a></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.status.name }}</td>
                <td>{{ entry.message }}</td>
                <td>{{ entry.http_status }}</td>
                <td>
-                 {% if entry.status == 'loaded' %}
-                   <a href="{{ url_for('do_terminate', path=entry.dataset) }}"> terminate </a>
+                 {% if entry.status.name == 'loaded' %}
+                   <a href="{{ url_for('do_terminate', path=entry.key.pathpart) }}"> terminate </a>
                  {% endif %}
                </td>
           </tr>

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

@@ -16,19 +16,36 @@
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
 	{% for script in extra_scripts %}
 	<script src="{{ script }}"></script>
-	{% endfor %}
+     {% endfor %}
+     <script src="{{ url_for('static', filename='js/annotation.js') }}"></script>
      <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 - FILE CRAWLER</h3>
+          {% if path %}
+          <h3>Cellxgene Gateway - {{ path }}</h3>
+          {% else %}
+          <h3>Cellxgene Gateway - FILE CRAWLER</h3>
+          {% endif %}
      </header>
-     <br>
 
      <h4>Please click on a dataset to view it in Cellxgene Server.</h4>
 
-     <br>
      {{ rendered_html|safe }}
-
+     <p>
+          Navigation:
+     <ul>
+     {% if path %}
+     <li><a href="{{ url_for('filecrawl') }}">top level</a></li>
+     {% else %}
+     {% endif %}
+     <li><a href="{{ url_for('index') }}">homepage</a></li>
+     </ul>
+     </p>
+     <script>
+          $(() => {
+               $("a.new").click(new_annotation_callback);
+          })
+     </script>
 </body>
 </html>

cellxgene_gateway/templates/index.html

@@ -35,12 +35,12 @@
 		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>
 	

cellxgene_gateway/templates/loading.html

@@ -35,18 +35,22 @@
           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>
      <script>
+          var count = 0;
           window.setInterval(function(){
                var dots = document.getElementById('dots');
                dots.textContent = dots.textContent + '.';
+               if (count++ > 5) {
+                    window.location.reload();
+               }
           }, 1000);
      </script>
 </body>

cellxgene_gateway/templates/process_error.html

@@ -39,10 +39,10 @@
           <li><a href="{{url_for('do_relaunch', path=dataset)}}">
                     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>

environment.yml

@@ -1,4 +1,4 @@
-name: cellxgene-dev
+name: cellxgene-gateway
 channels:
 - conda-forge
 dependencies:
@@ -6,6 +6,8 @@ dependencies:
 - requests
 - flask
 - psutil
+- black
+- pip
 - pip:
   - flask-api
-  - cellxgene
+  - cellxgene>=0.15

requirements.txt

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

run.sh.example

@@ -1,8 +1,5 @@
 export CELLXGENE_LOCATION=$(pwd)/.cellxgene-gateway/bin/cellxgene
 export CELLXGENE_DATA=../cellxgene_data
-export DEPLOYMENT_ENV=dev
-export GATEWAY_HOST=localhost:5005
-export GATEWAY_PROTOCOL=http
 export GATEWAY_IP=127.0.0.1
 
 #Once these are set, you run like a normal Flask app

setup.cfg

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

setup.py

@@ -1,5 +1,25 @@
 import os
-from setuptools import setup
+import codecs
+from setuptools import find_packages, setup
+import sys
+
+if sys.version_info < (3, 6):
+    sys.exit("Sorry, Python < 3.6 is not supported")
+
+
+def read(rel_path):
+    here = os.path.abspath(os.path.dirname(__file__))
+    with codecs.open(os.path.join(here, rel_path), "r") as fp:
+        return fp.read()
+
+
+def get_version(rel_path):
+    for line in read(rel_path).splitlines():
+        if line.startswith("__version__"):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
 
 
 def parse_requirements():
@@ -10,17 +30,22 @@ def parse_requirements():
     return reqs
 
 
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
 install_reqs = parse_requirements()
 
 setup(
     # mandatory
     name="cellxgene-gateway",
     # mandatory
-    version="0.1",
+    version=get_version("cellxgene_gateway/__init__.py"),
     # mandatory
     author="Niket Patel, Yohann Potier, Alok Saldanha",
     author_email="alok.saldanha@novartis.com",
     description=("Cellxgene Gateway"),
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     license="MIT",
     keywords="visualization, genomics",
     url="http://github.com/Novartis/cellxgene-gateway",
@@ -28,13 +53,16 @@ setup(
     package_data={
         "cellxgene_gateway": [
             "static/css/homepagestyle.css",
+            "static/js/annotation.js",
             "static/nibr.ico",
-            "templates/*.html"
-    ]},
-    data_files=[('', ['Readme.md', 'LICENSE.txt'])],
+            "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",
 )

tests/test_cache_entry.py

@@ -0,0 +1,37 @@
+import unittest
+from flask import Flask
+from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
+from cellxgene_gateway.cache_key import CacheKey
+from cellxgene_gateway.gateway import app
+
+key = CacheKey("czi/pbmc3k.h5ad", "pbmc3k.h5ad", "tmp.csv")
+
+
+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 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):
+        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):
+        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)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_dir_util.py

@@ -1,38 +1,49 @@
 import unittest
 from unittest.mock import MagicMock, patch
-from cellxgene_gateway.dir_util import render_entry
+from cellxgene_gateway.filecrawl 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",
-            }
+            "path": "/somepath/",
+            "name": "entry",
+            "type": "file",
+            "annotations": [],
+            "children": [],
+        }
         rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
+        self.assertIn("view/somepath", rendered)
+
     def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
         entry = {
-                "path": "/somepath",
-                "name": "entry",
-                "type": "file",
-            }
+            "path": "/somepath",
+            "name": "entry",
+            "type": "file",
+            "annotations": [],
+            "children": [],
+        }
         rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
+        self.assertIn("view/somepath", rendered)
+
     def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
         entry = {
-                "path": "somepath/",
-                "name": "entry",
-                "type": "file",
-            }
+            "path": "somepath/",
+            "name": "entry",
+            "type": "file",
+            "annotations": [],
+            "children": [],
+        }
         rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
+        self.assertIn("view/somepath", rendered)
+
     def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
         entry = {
-                "path": "somepath",
-                "name": "entry",
-                "type": "file",
-            }
+            "path": "somepath",
+            "name": "entry",
+            "type": "file",
+            "annotations": [],
+            "children": [],
+        }
         rendered = render_entry(entry)
-        self.assertIn('view/somepath', rendered)
-        
+        self.assertIn("view/somepath", rendered)

tests/test_extra_scripts.py

@@ -1,23 +1,26 @@
 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()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_filecrawl.py

@@ -0,0 +1,46 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from cellxgene_gateway.filecrawl 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",
+            "annotations": [],
+        }
+        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",
+            "annotations": [],
+        }
+        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",
+            "annotations": [],
+        }
+        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",
+            "annotations": [],
+        }
+        rendered = render_entry(entry)
+        self.assertIn("view/somepath", rendered)

tests/test_prune_process_cache.py

@@ -1,13 +1,15 @@
 import unittest
 from unittest.mock import MagicMock, patch
-from cellxgene_gateway.cache_entry import CacheEntry
+
 from cellxgene_gateway.backend_cache import BackendCache
+from cellxgene_gateway.cache_entry import CacheEntry
+
 
 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.ttl", 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
 
@@ -22,5 +24,6 @@ class TestPruneProcessCache(unittest.TestCase):
         self.assertEqual(len(cache.entry_list), 1)
         self.assertEqual(cache.entry_list[0], new)
 
-if __name__ == '__main__':
-    unittest.main()
+
+if __name__ == "__main__":
+    unittest.main()