the first commit

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 95

.gitignore

@@ -0,0 +1,5 @@
+.DS_Store
+__pycache__
+*.pyc
+run.sh
+.cellxgene-gateway

.isort.cfg

@@ -0,0 +1,6 @@
+[settings]
+line_length=88
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+use_parentheses=True

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+repos:
+-   repo: local
+    hooks:
+    - id: isort
+      name: isort
+      entry: isort
+      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
+      types: [python]
+      stages: [commit]
+    - id: pytest
+      name: pytest
+      language: system
+      entry: pytest
+      types: [python]
+      pass_filenames: false
+      always_run: true
+      stages: [push]

LICENSE.txt

@@ -0,0 +1,201 @@
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+   limitations under the License.

Readme.md

@@ -0,0 +1,72 @@
+# Overview #
+
+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.
+
+# Running locally #
+
+Before running the gateway, make sure you can run the Cellxgene Server from CZI, and that you have a folder with h5ad files ready to view.
+
+The first step is to set up an environment and install requirements:
+```
+# create an environment for packages
+python -m venv .cellxgene-gateway
+source .cellxgene-gateway/bin/activate
+# install requirements
+pip install -r requirements.txt
+```
+Then copy run.sh.example to run.sh and edit
+```
+cp run.sh.example run.sh
+```
+
+`run.sh` defines various environment variables, you probably only need to edit CELLXGENE_LOCATION and CELLXGENE_DATA:
+
+* DEPLOYMENT_ENV - expects 'dev', 'tst' or 'prd'
+* 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.
+
+Finally, execute run.sh:
+```
+source run.sh
+```
+
+# Customization #
+
+The current paradigm for customization is to modify files during a build or deployment phase:
+
+* To modify CSS or JS on particular gateway pages, overwrite or append to the templates
+* To add script tags such as for user analytics to all pages, overwrite the extra_scripts.py file.
+  * these scripts will also be run on the pages served by cellxgene server via the --scripts parameter
+  * See https://github.com/chanzuckerberg/cellxgene/pull/680 for details on --scripts parameter
+
+Currently we use a build.sh that copies the gateway to a "build" directory before modifying with sed and the like.
+
+# Development #
+
+## Running Linters ##
+
+pip install isort flake8 black
+
+```
+isort -rc .
+```
+
+```
+flake8 .
+```
+
+```
+black .
+```
+
+# Getting Help #
+
+If you need help for any reason, please make a github ticket. One of the contributors should help you out.
+
+# Contributors #
+
+* Niket Patel - https://github.com/NiketPatel9
+* Alok Saldanha - https://github.com/alokito
+* Yohann Potier - https://github.com/ypotier

__init__.py

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+# 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.
+

backend_cache.py

@@ -0,0 +1,62 @@
+# 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 time
+from threading import Thread
+
+from flask_api import status
+
+import env
+from cache_entry import CacheEntry
+from cellxgene_exception import CellxgeneException
+from subprocess_backend import SubprocessBackend
+
+process_backend = SubprocessBackend()
+
+
+class BackendCache:
+    def __init__(self):
+        self.entry_list = []
+
+    def get_ports(self):
+        contents = self.entry_list
+        return [c.port for c in contents]
+
+    def check_entry(self, dataset):
+        contents = self.entry_list
+        matches = [c for c in contents if c.dataset == dataset]
+
+        if len(matches) == 0:
+            return None
+        elif len(matches) == 1:
+            return matches[0]
+        else:
+            raise CellxgeneException(
+                status.HTTP_500_INTERNAL_SERVER_ERROR,
+                "Found " + str(len(matches)) + " for " + dataset,
+            )
+
+    def create_entry(self, dataset, file_path, scripts):
+        port = 8000
+        existing_ports = self.get_ports()
+        while port in existing_ports:
+            port += 1
+
+        entry = CacheEntry.for_dataset(dataset, file_path, port)
+
+        background_thread = Thread(
+            target=process_backend.launch, args=(env.cellxgene_location, scripts, entry)
+        )
+        background_thread.start()
+
+        self.entry_list.append(entry)
+
+        time.sleep(1)  # Automatic refresh is too fast, needs a second to pause
+
+        return entry

cache_entry.py

@@ -0,0 +1,108 @@
+# 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 Response, request
+from requests import get
+
+import env
+from util import current_time_stamp
+
+
+class CacheEntry:
+    def __init__(
+        self,
+        pid,
+        dataset,
+        file_path,
+        port,
+        launchtime,
+        timestamp,
+        status,
+        message,
+        all_output,
+        stderr,
+        http_status,
+    ):
+        self.pid = pid
+        self.dataset = dataset
+        self.file_path = file_path
+        self.port = port
+        self.launchtime = launchtime
+        self.timestamp = timestamp
+        self.status = status
+        self.message = message
+        self.all_output = all_output
+        self.stderr = stderr
+        self.http_status = http_status
+
+    @classmethod
+    def for_dataset(cls, dataset, file_path, port):
+        return cls(
+            "",
+            dataset,
+            file_path,
+            port,
+            current_time_stamp(),
+            current_time_stamp(),
+            "loading",
+            "",
+            "",
+            "",
+            "",
+        )
+
+    def set_loaded(self, pid):
+        self.pid = pid
+        self.status = "loaded"
+
+    def set_error(self, message, stderr, http_status):
+        self.message = message
+        self.stderr = stderr
+        self.http_status = http_status
+        self.status = "error"
+
+    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
+
+        if len(subpath) == 0:
+            r = Response(f"Redirect to {gateway_basepath}\n", status=301)
+            r.headers["location"] = gateway_basepath
+            return r
+
+        port = self.port
+        cellxgene_basepath = f"http://127.0.0.1:{port}"
+
+        headers = (
+            {"accept": request.headers["accept"]} if "accept" in request.headers else {}
+        )
+
+        cellxgene_response = get(cellxgene_basepath + subpath, headers=headers)
+
+        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
+
+        gateway_response = Response(
+            gateway_content, status=cellxgene_response.status_code
+        )
+
+        gateway_response.headers["content-type"] = content_type
+
+        return gateway_response

cellxgene_exception.py

@@ -0,0 +1,14 @@
+# 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.
+
+class CellxgeneException(Exception):
+    def __init__(self, message, http_status):
+        Exception.__init__(self)
+        self.message = message
+        self.http_status = http_status

dir_util.py

@@ -0,0 +1,91 @@
+# 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
+
+import env
+from cellxgene_exception import CellxgeneException
+
+
+def is_subdir(full_path, parent_path):
+    subdir = os.path.realpath(full_path)
+    parent = os.path.realpath(parent_path)
+    return subdir.startswith(parent)
+
+
+def create_dir(parent_path, dir_name):
+    full_path = os.path.join(parent_path, dir_name)
+
+    if "/" in dir_name:
+        raise CellxgeneException(
+            "Please have no slashes in the intended directory.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not os.path.exists(parent_path):
+        raise CellxgeneException(
+            "The selected User directory does not exist.", status.HTTP_400_BAD_REQUEST
+        )
+    elif os.path.exists(full_path):
+        raise CellxgeneException(
+            "The provided subdirectory already exists within Directory.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not is_subdir(full_path, parent_path):
+        raise CellxgeneException(
+            "The directory must be a subdirectory of the parent path.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not os.path.isdir(parent_path):
+        raise CellxgeneException(
+            "The parent is not a directory.", status.HTTP_400_BAD_REQUEST
+        )
+    else:
+        os.mkdir(full_path)
+
+
+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)]
+
+
+def render_entries(entries):
+    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
+
+
+def render_entry(entry):
+    if entry["type"] == "file":
+        return f"<li> <a target='_blank' href='view{entry['path']}'>{entry['name']}</a></li>"
+    elif entry["type"] == "directory":
+        return f"<li>{entry['name']}{render_entries(entry['children'])}</li>"

env.py

@@ -0,0 +1,17 @@
+# 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
+
+deployment_env = os.environ.get("DEPLOYMENT_ENV")
+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")

extra_scripts.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.
+
+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"]
+    # where google_ua.js is a script you add to the static/js folder prior to deployment.
+    return []

gateway.py

@@ -0,0 +1,173 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+# import BaseHTTPServer
+import datetime
+import os
+from threading import Thread
+
+from flask import Flask, redirect, render_template, request, send_from_directory
+from flask_api import status
+from werkzeug import secure_filename
+
+import env
+from backend_cache import BackendCache
+from cellxgene_exception import CellxgeneException
+from dir_util import create_dir, recurse_dir, render_entries
+from extra_scripts import get_extra_scripts
+from path_util import get_dataset, get_file_path
+from process_exception import ProcessException
+from prune_process_cache import PruneProcessCache
+from util import current_time_stamp
+
+app = Flask(__name__)
+cache = BackendCache()
+location = f"{env.gateway_protocol}://{env.gateway_host}"
+
+
+@app.errorhandler(CellxgeneException)
+def handle_invalid_usage(error):
+
+    message = f"{error.http_status} Error : {error.message}"
+
+    return (
+        render_template(
+            "cellxgene_error.html", extra_scripts=get_extra_scripts(), message=message
+        ),
+        error.http_status,
+    )
+
+
+@app.errorhandler(ProcessException)
+def handle_invalid_process(error):
+
+    message = []
+
+    message.append(error.message)
+    message.append(f"{error.http_status} Error.")
+    message.append(f"Stdout: {error.stdout}")
+    message.append(f"Stderr: {error.stderr}")
+
+    return (
+        render_template(
+            "process_error.html", extra_scripts=get_extra_scripts(), message=message
+        ),
+        error.http_status,
+    )
+
+
+@app.route("/favicon.ico")
+def favicon():
+    return send_from_directory(
+        os.path.join(app.root_path, "static"),
+        "nibr.ico",
+        mimetype="image/vnd.microsof.icon",
+    )
+
+
+@app.route("/")
+def index():
+    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,
+    )
+
+
+@app.route("/make_user", methods=["POST"])
+def make_user():
+    dir_name = request.form["directory"]
+
+    create_dir(env.cellxgene_data, dir_name)
+
+    return redirect(location, code=302)
+
+
+@app.route("/make_subdir", methods=["POST"])
+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)
+
+
+@app.route("/upload_file", methods=["POST"])
+def upload_file():
+    upload_dir = request.form["path"]
+
+    full_upload_path = env.cellxgene_data + "/" + upload_dir
+    if 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(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(env.location, code=302)
+
+
+@app.route("/filecrawl.html")
+def filecrawl():
+
+    entries = recurse_dir(env.cellxgene_data)
+    rendered_html = render_entries(entries)
+    return render_template(
+        "filecrawl.html", extra_scripts=get_extra_scripts(), rendered_html=rendered_html
+    )
+
+
+@app.route("/view/<path:path>")
+def do_GET(path):
+
+    dataset = get_dataset(path)
+    file_path = get_file_path(dataset)
+    match = cache.check_entry(dataset)
+    if match is None:
+        uascripts = get_extra_scripts()
+        match = cache.create_entry(dataset, file_path, uascripts)
+
+    match.timestamp = current_time_stamp()
+
+    if match.status == "loaded":
+        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":
+        raise ProcessException.from_pid_object(match)
+
+
+if __name__ == "__main__":
+    background_thread = Thread(target=PruneProcessCache(cache))
+    background_thread.start()
+
+    app.run(host="0.0.0.0", port=5005, debug=False)

path_util.py

@@ -0,0 +1,49 @@
+# 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
+
+import env
+from cellxgene_exception import CellxgeneException
+
+
+def get_dataset(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
+    except CellxgeneException:
+        split = os.path.split(trimmed)
+        return get_dataset(split[0])
+
+
+def validate_path(file_path):
+    if not os.path.exists(file_path):
+        raise CellxgeneException(
+            "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
+        )
+    if not os.path.isfile(file_path):
+        raise CellxgeneException(
+            "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST
+        )
+    return
+
+
+def get_file_path(dataset):
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    validate_path(file_path)
+    return file_path

process_exception.py

@@ -0,0 +1,25 @@
+# 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.
+
+class ProcessException(Exception):
+    def __init__(self, message, stdout, stderr, http_status):
+        Exception.__init__(self)
+        self.message = message
+        self.stdout = stdout
+        self.stderr = stderr
+        self.http_status = http_status
+
+    @classmethod
+    def from_pid_object(cls, pid_object):
+        return cls(
+            pid_object.message,
+            pid_object.all_output,
+            pid_object.stderr,
+            pid_object.http_status,
+        )

prune_process_cache.py

@@ -0,0 +1,39 @@
+# 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 time
+
+import psutil
+
+from util import current_time_stamp
+
+
+class PruneProcessCache:
+    def __init__(self, cache):
+        self.cache = cache
+
+    def __call__(self):
+        while True:
+            time.sleep(60)
+
+            timestamp = current_time_stamp()
+
+            processes_to_delete = []
+            for p in self.cache.entry_list:
+                if timestamp - p.timestamp > 3600:
+                    processes_to_delete.append(p)
+                    processes_to_delete
+
+            for process in processes_to_delete:
+                self.cache.entry_list.remove(process)
+                pid = process.pid
+                p = psutil.Process(pid)
+                p.terminate()
+                p = psutil.Process(pid + 2)
+                p.terminate()

requirements.txt

@@ -0,0 +1,6 @@
+cellxgene
+flask
+flask_api
+psutil
+requests
+

run.sh.example

@@ -0,0 +1,9 @@
+export CELLXGENE_LOCATION=/path/to/cellxgene
+export CELLXGENE_DATA=/path/to/datasets
+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
+python gateway.py

static/css/homepagestyle.css

@@ -0,0 +1,25 @@
+/*
+ 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.
+*/
+
+pre {
+    display: block;
+    padding: 8.5px;
+    margin: 0 0 9px;
+    font-size: 6px;
+    line-height: 1.385;
+    color: #333333;
+    word-break: break-all;
+    word-wrap: break-word;
+    background-color: #f5f5f5;
+    border: 1px solid #cccccc;
+    border-radius: 3px;
+    width: 80%;
+}

subprocess_backend.py

@@ -0,0 +1,71 @@
+# 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 logging
+import subprocess
+
+from flask_api import status
+
+from process_exception import ProcessException
+
+
+class SubprocessBackend:
+    def __init__(self):
+        pass
+
+    def create_cmd(self, cellxgene_loc, file_path, port, scripts):
+
+        cmd = (
+            f"yes | {cellxgene_loc} launch {file_path}"
+            + " --port "
+            + str(port)
+            + " --host 127.0.0.1"
+        )
+
+        for s in scripts:
+            cmd += f" --scripts {s}"
+
+        return cmd
+
+    def launch(self, cellxgene_loc, scripts, cache_entry):
+
+        cmd = self.create_cmd(
+            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
+        )
+        logging.getLogger("werkzeug").info(f"launching {cmd}")
+        process = subprocess.Popen(
+            [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
+        )
+
+        while True:
+            output = process.stdout.readline().decode()
+            if output == "[cellxgene] Type CTRL-C at any time to exit.\n":
+                break
+            elif output == "":
+                stderr = process.stderr.read().decode()
+                if (
+                    "Error while loading file" in stderr
+                    or "Could not open file" in stderr
+                ):
+                    message = "File was invalid."
+                    http_status = status.HTTP_400_BAD_REQUEST
+                else:
+                    message = "Cellxgene failed to launch dataset."
+                    http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
+
+                cache_entry.status = "error"
+                cache_entry.set_error(message, stderr, http_status)
+
+                raise ProcessException.from_pid_object(cache_entry)
+            else:
+                cache_entry.all_output += output
+
+        cache_entry.set_loaded(process.pid)
+
+        return

templates/cellxgene_error.html

@@ -0,0 +1,40 @@
+<!--
+ 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.
+-->
+
+<html>
+<head>
+     <title>Cellxgene Gateway - Error</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">
+</head>
+<body>
+     <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
+       <h3>Cellxgene Gateway - Error</h3>
+     </header>
+     <br>
+     <div style="margin-left:20px">
+          
+     <h4>{{ message }}</h4>
+
+     <a href="/filecrawl.html">
+          Please click here to be redirected to the file directory.
+     </a>
+     <br>
+     <a href="/">
+          Please click here to return to the homepage.
+     </a>
+     </div>
+</body>
+</html>

templates/filecrawl.html

@@ -0,0 +1,34 @@
+<!--
+ 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.
+-->
+
+<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">
+</head>
+<body>
+     <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
+       <h3>Cellxgene Gateway - FILE CRAWLER</h3>
+     </header>
+     <br>
+
+     <h4>Please wait until a dataset is done loading before trying to launch a different one</h4>
+
+     <br>
+     {{ rendered_html|safe }}
+
+</body>
+</html>

templates/index.html

@@ -0,0 +1,123 @@
+<!--
+ 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.
+-->
+
+<html>
+<head>
+	<title>Cellxgene Gateway</title>
+	<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
+	<link rel="stylesheet" href="{{ url_for('static', filename='css/homepagestyle.css') }}">
+	<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">
+	<style>
+		li {
+			font-size: 20px;
+		}
+	</style>
+</head>
+<body>
+	<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
+	  <h3>Cellxgene Gateway - HOME</h3>
+	</header>
+	<br>
+
+	<h1 style="padding-left:35px">
+		Links:	
+	</h1>
+	<div class="list-group" style="width:50%;padding-left:65px">
+	  <a target="_blank" href="/filecrawl.html" class="list-group-item list-group-item-action">
+		  <u>File Crawler: Allows you to view all uploaded data.</u></a>
+		  
+	</div>
+
+	<br>
+
+	<h1 style="padding-left:35px">
+		How To Upload Data:	
+	</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>
+
+
+	<br>
+
+	<h1 style="padding-left:35px">
+		How To Upload Data via SSH and SCP (Linux):	
+	</h1>
+	<ol style="padding-left:85px;">
+		<li>
+			Confirm that your ssh key has been properly added. Running the following command should connect you to the server:
+		</li>
+		<pre>ssh ec2-user@{{ ip }}</pre>	
+		<li>
+			Prepare your data on your own machine. They should be in a common folder called 'USER' and should look <br>similar to the following structure:  
+		</li>
+		<pre>- USER
+    - hpc.h5ad
+    - pbmc3k.h5ad</pre>	
+		<li>Copy your data to the server (replace USER with your username):</li>
+		<pre>ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/'
+ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/DATA/'
+scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/</pre>	
+		<li>Take a look at your data using the file crawler link above</li>
+	</ol>	
+
+	<br>
+	<br>
+
+	<script>
+	if (NIBRIam && NIBRIam.NIBR521 !== undefined) {
+		var usernames = document.getElementById("usernames")
+		var options = usernames.options
+				
+		for (i = 0; i < options.length; i++) { 
+			if (options[i].value.toLowerCase() == currentUser.toLowerCase()) {
+				options[i].setAttribute("selected", "selected")
+			}
+		}
+	}
+	</script>
+</body>
+</html>

templates/loading.html

@@ -0,0 +1,53 @@
+<!--
+ 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.
+-->
+
+<html>
+<head>
+     <title>Cellxgene Gateway - Loading</title>
+     <link rel="icon" type="image/png" href="nibr.png">
+	<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+
+     <meta http-equiv="refresh" content="5">
+</head>
+<body>
+     <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
+       <h3>Cellxgene Gateway - Loading<span id='dots'></span></h3>
+     </header>
+
+     <br>
+     <div style="margin-left:20px">
+     
+     <br>     
+     <h4>Output:</h4>
+     <pre>{{ all_output }}</pre>
+     <p>
+          Launch Time: <span id="launch_time"> {{ launchtime.isoformat(' ') }} </span>
+     </p>
+     <p>
+          The page will refresh shortly.
+     </p>
+
+     <a href="/filecrawl.html">
+          Please click here to be redirected to the file directory.
+     </a>
+     <br>
+     <a href="/">
+          Please click here to return to the homepage.
+     </a>
+     </div>
+     <script>
+          window.setInterval(function(){
+               var dots = document.getElementById('dots');
+               dots.textContent = dots.textContent + '.';
+          }, 1000);
+     </script>
+</body>
+</html>

templates/process_error.html

@@ -0,0 +1,43 @@
+<!--
+ 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.
+-->
+
+<html>
+<head>
+     <title>Cellxgene Gateway - Process Error</title>
+     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
+     <link rel="icon" type="image/png" href="nibr.png">
+	{% 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 - Process Error</h3>
+     </header>
+     <br>
+     <div style="margin-left:20px">
+          
+     <h4>{{ message[0] }}</h4>
+     <h4>{{ message[1] }}</h4>
+     <h4>{{ message[2] }}</h4>
+     <h4>{{ message[3] }}</h4>
+
+     <a href="/filecrawl.html">
+          Please click here to be redirected to the file directory.
+     </a>
+     <br>
+     <a href="/">
+          Please click here to return to the homepage.
+     </a>
+     </div>
+</body>
+</html>

util.py

@@ -0,0 +1,16 @@
+# 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 datetime import datetime
+
+
+def current_time_stamp():
+    now = datetime.now()
+    timestamp = datetime.timestamp(now)
+    return timestamp