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Alok Saldanha
2019-08-27 16:14:10 -04:00
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[flake8]
max-line-length = 95

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.DS_Store
__pycache__
*.pyc
run.sh
.cellxgene-gateway

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[settings]
line_length=88
multi_line_output=3
include_trailing_comma=True
force_grid_wrap=0
use_parentheses=True

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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]

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Apache License
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# 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

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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.

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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.
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

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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.
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

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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.
class CellxgeneException(Exception):
def __init__(self, message, http_status):
Exception.__init__(self)
self.message = message
self.http_status = http_status

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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.
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>"

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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.
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")

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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.
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 []

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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.
# 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)

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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.
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

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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.
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,
)

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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.
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()

6
requirements.txt Normal file
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cellxgene
flask
flask_api
psutil
requests

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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

25
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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.
*/
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%;
}

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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.
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

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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.
-->
<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>

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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.
-->
<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>

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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.
-->
<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>

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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.
-->
<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>

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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.
-->
<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>

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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.
from datetime import datetime
def current_time_stamp():
now = datetime.now()
timestamp = datetime.timestamp(now)
return timestamp