the first commit

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)