#9 only prune entries that have a pid

Readme.md

@@ -48,6 +48,9 @@ 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:
@@ -60,11 +63,10 @@ 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:
-* `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.
 

cellxgene_gateway/backend_cache.py

@@ -33,12 +33,12 @@ class BackendCache:
         contents = self.entry_list
         return [c.port for c in contents]
 
-    def check_entry(self, key):
+    def check_entry(self, dataset):
         contents = self.entry_list
         matches = [
             c
             for c in contents
-            if c.key.dataset == key.dataset and c.key.annotation_file == key.annotation_file and c.status != "terminated"
+            if c.dataset == dataset and c.status != "terminated"
         ]
 
         if len(matches) == 0:
@@ -51,14 +51,13 @@ class BackendCache:
                 "Found " + str(len(matches)) + " for " + dataset,
             )
 
-    def create_entry(self, key, scripts):
+    def create_entry(self, dataset, file_path, scripts):
         port = 8000
         existing_ports = self.get_ports()
-
         while (port in existing_ports) or is_port_in_use(port):
             port += 1
 
-        entry = CacheEntry.for_key(key, port)
+        entry = CacheEntry.for_dataset(dataset, file_path, port)
 
         background_thread = Thread(
             target=process_backend.launch,

cellxgene_gateway/cache_entry.py

@@ -8,21 +8,20 @@
 # the specific language governing permissions and limitations under the License.
 import psutil
 import logging
-import datetime
 
-from flask import make_response, request, render_template
+from flask import make_response, request
 from requests import get, post, put
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.util import current_time_stamp
-from cellxgene_gateway.flask_util import querystring
 
 class CacheEntry:
     def __init__(
         self,
         pid,
-        key,
+        dataset,
+        file_path,
         port,
         launchtime,
         timestamp,
@@ -33,7 +32,8 @@ class CacheEntry:
         http_status,
     ):
         self.pid = pid
-        self.key = key
+        self.dataset = dataset
+        self.file_path = file_path
         self.port = port
         self.launchtime = launchtime
         self.timestamp = timestamp
@@ -44,11 +44,11 @@ class CacheEntry:
         self.http_status = http_status
 
     @classmethod
-    def for_key(cls, key, port):
-
+    def for_dataset(cls, dataset, file_path, port):
         return cls(
             None,
-            key,
+            dataset,
+            file_path,
             port,
             current_time_stamp(),
             current_time_stamp(),
@@ -93,62 +93,45 @@ class CacheEntry:
         self.status = "terminated"
 
     def serve_content(self, path):
+        dataset = self.dataset
+
         gateway_basepath = (
-            f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
+            f"{env.gateway_protocol}://{env.gateway_host}/view/{dataset}/"
         )
-        subpath = path[len(self.key.pathpart) :]  # noqa: E203
-            
+        subpath = path[len(dataset) :]  # noqa: E203
+
         if len(subpath) == 0:
             r = make_response(f"Redirect to {gateway_basepath}\n", 301)
-            r.headers["location"] = gateway_basepath+querystring()
+            r.headers["location"] = gateway_basepath
             return r
-        elif self.status == "loading":
-            launch_time = datetime.datetime.fromtimestamp(self.launchtime)
-            return render_template(
-                "loading.html", launchtime=launch_time, all_output=self.all_output
-            )
 
         port = self.port
         cellxgene_basepath = f"http://127.0.0.1:{port}"
-        headers = {}
-        copy_headers = [
-            'accept',
-            'accept-encoding',
-            'accept-language',
-            'cache-control',
-            'connection',
-            'content-length',
-            'content-type',
-            'cookie',
-            'host',
-            'origin',
-            'pragma',
-            'referer',
-            'sec-fetch-mode',
-            'sec-fetch-site',
-            'user-agent'
-        ]
-        for h in copy_headers:
-            if h in request.headers:
-                headers[h] = request.headers[h]
 
-        full_path = cellxgene_basepath + subpath + querystring()
+        headers = {}
+
+        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"]
 
         if request.method in ["GET", "HEAD", "OPTIONS"]:
             cellxgene_response = get(
-                full_path, headers=headers
+                cellxgene_basepath + subpath, headers=headers
             )
         elif request.method == "PUT":
             cellxgene_response = put(
-                full_path,
+                cellxgene_basepath + subpath,
                 headers=headers,
-                data=request.data,
+                data=request.data.decode(),
             )
         elif request.method == "POST":
             cellxgene_response = post(
-                full_path,
+                cellxgene_basepath + subpath,
                 headers=headers,
-                data=request.data,
+                data=request.data.decode(),
             )
         else:
             raise CellxgeneException(
@@ -163,15 +146,10 @@ class CacheEntry:
         else:
             gateway_content = cellxgene_response.content
 
-        resp_headers = {}
-        for h in copy_headers:
-            if h in cellxgene_response.headers:
-                resp_headers[h] = cellxgene_response.headers[h]
-
         gateway_response = make_response(
             gateway_content,
             cellxgene_response.status_code,
-            resp_headers,
+            {"Content-Type": content_type},
         )
 
         return gateway_response

cellxgene_gateway/cache_key.py

@@ -1,29 +0,0 @@
-# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
-# under the Apache License, Version 2.0 (the "License"); you may not use
-# this file except in compliance with the License. You may obtain a copy
-# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
-# required by applicable law or agreed to in writing, software distributed
-# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
-# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
-# the specific language governing permissions and limitations under the License.
-
-import os
-
-from flask_api import status
-
-from cellxgene_gateway import env
-from cellxgene_gateway.cellxgene_exception import CellxgeneException
-
-# There are three kinds of CacheKey:
-# 1) somedir/dataset.h5ad: a dataset
-#    in this case, pathpart == dataset == 'somedir/dataset.h5ad'
-# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
-#    in this case, pathpart == 'dataset_annotations/saldaal1-T5HMVBNV.csv', dataset == 'somedir/dataset.h5ad'
-# 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

@@ -51,8 +51,44 @@ def create_dir(parent_path, dir_name):
     else:
         os.mkdir(full_path)
 
-annotations_suffix = '_annotations'
-def make_h5ad(el):
-    return el[:-len(annotations_suffix)]+'.h5ad'
-def make_annotations(el):
-    return el[:-5]+annotations_suffix
+
+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":
+        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>"

cellxgene_gateway/env.py

@@ -9,33 +9,28 @@
 
 import os
 import logging
-import socket
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA")
-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"))
+gateway_host = os.environ.get("GATEWAY_HOST")
+gateway_protocol = os.environ.get("GATEWAY_PROTOCOL")
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
 enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
-enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in ['true', '1']
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
     "CELLXGENE_DATA": cellxgene_data,
+    "GATEWAY_HOST": gateway_host,
+    "GATEWAY_PROTOCOL": gateway_protocol,
     "GATEWAY_IP": ip,
 }
 
 optional_env_vars = {
-    "EXTERNAL_HOST": external_host,
-    "EXTERNAL_PROTOCOL": external_protocol,
-    "GATEWAY_PORT": gateway_port,
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
     "GATEWAY_TTL": ttl,
     "GATEWAY_ENABLE_UPLOAD": enable_upload,
-    "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
 }
 
 def validate():
@@ -52,6 +47,8 @@ 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
     """
         )

cellxgene_gateway/extra_scripts.py

@@ -14,6 +14,6 @@ from json import loads
 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.external_protocol}://{env.external_host}/static/js/google_ua.js"]
+    #  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 [] if env.extra_scripts is None else loads(env.extra_scripts)

cellxgene_gateway/filecrawl.py

@@ -1,75 +0,0 @@
-import os
-from cellxgene_gateway import env
-from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
-
-def recurse_dir(path):
-    if not os.path.exists(path):
-        raise CellxgeneException(
-            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
-        )
-
-    all_entries = os.listdir(path)
-    def is_h5ad(el):
-        return el.endswith('.h5ad') and os.path.isfile(os.path.join(path, el))
-    h5ad_entries = [x for x in all_entries if is_h5ad(x)]
-    annotation_dir_entries = [x for x in all_entries if x.endswith(annotations_suffix) and make_h5ad(x) in h5ad_entries]
-    def list_annotations(el):
-        full_path = os.path.join(path, el)
-        if not os.path.isdir(full_path):
-            entries = []
-        else:
-            entries = [{
-                "name": x[:-13] if (len(x) > 13 and x[-13] in ['-','_']) else (
-                    x[:-4] if x.endswith('.csv') else x),
-                "path": os.path.join(full_path, x).replace(env.cellxgene_data, ""),
-            } for x in os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
-        return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
-
-    def make_entry(el):
-        full_path = os.path.join(path, el)
-        if el in h5ad_entries:
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "file",
-                "annotations": list_annotations(make_annotations(el)),
-            }
-        elif os.path.isdir(full_path) and el not in annotation_dir_entries:
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "directory",
-                "children": recurse_dir(full_path),
-            }
-        else:
-            return {
-                "path": full_path,
-                "name": el,
-                "type": "neither",
-            }
-
-    return [make_entry(x) for x in os.listdir(path)]
-
-
-def render_entries(entries):
-    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
-
-def get_url(entry):
-    return f"/view/{ entry['path'].lstrip('/') }"
-def get_class(entry):
-    return f" class='{entry['class']}'" if 'class' in entry else ''
-
-def render_annotations(entry):
-    if len(entry['annotations']) > 0:
-        return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'{get_class(a)}>{a['name']}</a>" for a in entry['annotations']])
-    else:
-        return ''
-
-def render_entry(entry):
-    if entry["type"] == "file":
-        return f"<li> <a href='{ get_url(entry) }'>{entry['name']}</a> {render_annotations(entry)}</li>"
-    elif entry["type"] == "directory":
-        url = f"/filecrawl/{entry['path'].lstrip('/')}"
-        return f"<li><a href='{url}'>{entry['name']}</a>{render_entries(entry['children'])}</li>"
-    else:
-        return ""

cellxgene_gateway/flask_util.py

@@ -1,5 +0,0 @@
-from flask import request
-
-def querystring():
-    qs = request.query_string.decode()
-    return f'?{qs}' if len(qs) > 0 else ''

cellxgene_gateway/gateway.py

@@ -8,6 +8,7 @@
 # the specific language governing permissions and limitations under the License.
 
 # import BaseHTTPServer
+import datetime
 import os
 import logging
 from threading import Thread, Lock
@@ -16,37 +17,27 @@ import json
 from flask import (
     Flask,
     redirect,
-    make_response,
     render_template,
     request,
     send_from_directory,
     url_for,
 )
 from flask_api import status
-from werkzeug.utils import secure_filename
+from werkzeug import secure_filename
 
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import create_dir, is_subdir
-from cellxgene_gateway.filecrawl import recurse_dir, render_entries
+from cellxgene_gateway.dir_util import create_dir, recurse_dir, render_entries, 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.process_exception import ProcessException
 from cellxgene_gateway.prune_process_cache import PruneProcessCache
 from cellxgene_gateway.util import current_time_stamp
-from cellxgene_gateway.path_util import get_key
 
 app = Flask(__name__)
-
-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)
-
 cache = BackendCache()
-location = f"{env.external_protocol}://{env.external_host}"
+location = f"{env.gateway_protocol}://{env.gateway_host}"
 
 
 @app.errorhandler(CellxgeneException)
@@ -82,8 +73,7 @@ def handle_invalid_process(error):
             http_status=error.http_status,
             stdout=error.stdout,
             stderr=error.stderr,
-            dataset=error.key.dataset,
-            annotation_file=error.key.annotation_file,
+            dataset=error.dataset,
         ),
         error.http_status,
     )
@@ -159,7 +149,7 @@ def upload_file():
             "Invalid directory.", status.HTTP_400_BAD_REQUEST
         )
 
-    return redirect(location, code=302)
+    return redirect(env.location, code=302)
 
 
 if env.enable_upload:
@@ -169,50 +159,35 @@ if env.enable_upload:
 
 @app.route("/filecrawl.html")
 def filecrawl():
-    entries = recurse_dir(env.cellxgene_data)
-    rendered_html = render_entries(entries)
-    resp = make_response(render_template(
-        "filecrawl.html",
-        extra_scripts=get_extra_scripts(),
-        rendered_html=rendered_html,
-    ))
-    resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
-    resp.headers["Pragma"] = "no-cache"
-    resp.headers["Expires"] = "0"
-    resp.headers['Cache-Control'] = 'public, max-age=0'
-    return resp
 
-@app.route("/filecrawl/<path:path>")
-def do_filecrawl(path):
-    filecrawl_path = os.path.join(env.cellxgene_data, path)
-    if not os.path.isdir(filecrawl_path):
-        raise CellxgeneException(
-            "Path is not directory: " + filecrawl_path, status.HTTP_400_BAD_REQUEST
-        )
-    entries = recurse_dir(filecrawl_path)
+    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,
-        path=path,
     )
 
 entry_lock = Lock()
 @app.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
 def do_view(path):
-    key = get_key(path)
-    print(f"view path={path}, dataset={key.dataset}, annotation_file= {key.annotation_file}, key={key.pathpart}")
+    dataset = get_dataset(path)
+    file_path = get_file_path(dataset)
     with entry_lock:
-        match = cache.check_entry(key)
+        match = cache.check_entry(dataset)
         if match is None:
             uascripts = get_extra_scripts()
-            match = cache.create_entry(key, uascripts)
+            match = cache.create_entry(dataset, file_path, uascripts)
 
     match.timestamp = current_time_stamp()
 
-    if match.status == "loaded" or match.status == "loading":
+    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_cache_entry(match)
 
@@ -225,8 +200,7 @@ def do_GET_status():
 def do_GET_status_json():
     return json.dumps({'launchtime':app.launchtime,
     'entry_list':[{
-        'dataset': entry.key.dataset,
-        'annotation_file': entry.key.annotation_file,
+        'dataset': entry.dataset,
         'launchtime': entry.launchtime,
         'last_access': entry.timestamp,
         'status': entry.status
@@ -234,17 +208,16 @@ def do_GET_status_json():
 
 @app.route("/relaunch/<path:path>", methods=["GET"])
 def do_relaunch(path):
-    key = get_key(path)
-    match = cache.check_entry(key)
+    dataset = get_dataset(path)
+    match = cache.check_entry(dataset)
     if not match is None:
         match.terminate()
-    qs = request.query_string.decode()
-    return redirect(url_for("do_view", path=path) + (f'?{qs}' if len(qs) > 0 else ''), code=302)
+    return redirect(url_for("do_view", path=path), code=302)
 
 @app.route("/terminate/<path:path>", methods=["GET"])
 def do_terminate(path):
-    key = get_key(path)
-    match = cache.check_entry(key)
+    dataset = get_dataset(path)
+    match = cache.check_entry(dataset)
     if not match is None:
         match.terminate()
     return redirect(url_for("do_GET_status"), code=302)
@@ -259,7 +232,7 @@ def main():
     background_thread.start()
 
     app.launchtime = current_time_stamp()
-    app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
+    app.run(host="0.0.0.0", port=5005, debug=False)
 
 
 if __name__ == "__main__":

cellxgene_gateway/path_util.py

@@ -13,83 +13,37 @@ from flask_api import status
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import make_h5ad
-from cellxgene_gateway.cache_key import CacheKey
 
-def get_key(path):
+
+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:
-        # valid paths come in three forms:
-        if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
-            # 1) somedir/dataset.h5ad: a dataset
-            return CacheKey(trimmed, trimmed, None)
-        elif trimmed.endswith('.csv'):
-
-            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
-            annotations_dir = os.path.split(trimmed)[0]
-            dataset = make_h5ad(annotations_dir)
-            if data_file_exists(dataset):
-                data_dir_ensure(annotations_dir)
-                return CacheKey(trimmed, dataset, trimmed)
-        elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
-            # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
-            dataset = make_h5ad(trimmed)
-            if data_file_exists(dataset):
-                return CacheKey(trimmed, dataset, '')
+        get_file_path(trimmed)
+        return trimmed
     except CellxgeneException:
-        pass
-    split = os.path.split(trimmed)
-    return get_key(split[0])
+        split = os.path.split(trimmed)
+        return get_dataset(split[0])
 
-def validate_exists(file_path):
+
+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
         )
-
-def validate_is_file(file_path):
-    validate_exists(file_path)
     if not os.path.isfile(file_path):
         raise CellxgeneException(
             "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST
         )
     return
-def validate_is_dir(file_path):
-    validate_exists(file_path)
-    if not os.path.isdir(file_path):
-        raise CellxgeneException(
-            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
-        )
-    return
 
-def data_file_exists(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_is_file(file_path)
-    return True
-def data_dir_exists(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_is_dir(file_path)
-    return True
-def data_dir_ensure(dataset):
-    file_path = os.path.join(env.cellxgene_data, dataset)
-    if not os.path.exists(file_path):
-        os.makedirs(file_path)
 
-def get_file_path(key):
-    dataset = key.dataset
+def get_file_path(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)
+    validate_path(file_path)
     return file_path

cellxgene_gateway/process_exception.py

@@ -15,7 +15,7 @@ class ProcessException(Exception):
         self.stdout = stdout
         self.stderr = stderr
         self.http_status = http_status
-        self.key = key
+        self.dataset = dataset
 
     @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.key,
+            cache_entry.dataset,
         )

cellxgene_gateway/prune_process_cache.py

@@ -13,7 +13,6 @@ import logging
 from cellxgene_gateway.util import current_time_stamp
 from cellxgene_gateway.env import ttl
 
-
 class PruneProcessCache:
     def __init__(self, cache):
         self.cache = cache
@@ -27,14 +26,16 @@ class PruneProcessCache:
     def prune(self):
         timestamp = current_time_stamp()
         cutoff = timestamp - self.expire_seconds
-        processes_to_delete = [p for p in self.cache.entry_list if  p.timestamp < cutoff]
-        processes_to_keep = [p for p in self.cache.entry_list if not p.timestamp < cutoff]
+        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}")
         
         for process in processes_to_delete:
             try:
-                logger.info(f"pruning process {process.pid} ({process.key.dataset})")
+                logger.info(f"pruning process {process.pid} ({process.dataset})")
                 self.cache.prune(process)
             except Exception:
                 logger.exception("failed to prune process {process.pid} ({process.dataset})")

cellxgene_gateway/static/js/annotation.js

@@ -1,19 +0,0 @@
-// 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

@@ -11,30 +11,21 @@ import logging
 import subprocess
 
 from flask_api import status
-from cellxgene_gateway.env import enable_annotations
+
 from cellxgene_gateway.process_exception import ProcessException
-from cellxgene_gateway.dir_util import make_annotations
-from cellxgene_gateway.path_util import get_file_path, get_annotation_file_path
+
 
 class SubprocessBackend:
     def __init__(self):
         pass
 
-    def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
-        if enable_annotations and not annotation_file_path is None:
-            annotation_args_prefix = " --experimental-annotations"
-            if annotation_file_path == "":
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
-            else:
-                annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
-        else:
-            annotation_args = ""
+    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"
-            + annotation_args
         )
 
         for s in scripts:
@@ -45,7 +36,7 @@ class SubprocessBackend:
     def launch(self, cellxgene_loc, scripts, cache_entry):
 
         cmd = self.create_cmd(
-            cellxgene_loc, get_file_path(cache_entry.key), cache_entry.port, scripts, get_annotation_file_path(cache_entry.key)
+            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
         )
         logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
         process = subprocess.Popen(

cellxgene_gateway/templates/cache_status.html

@@ -29,7 +29,6 @@
           <tr>
                <th>PID</th>
                <th>dataset</th>
-               <th>annotation_file</th>
                <th>port</th>
                <th>launchtime</th>
                <th>last access</th>
@@ -43,8 +42,7 @@
 	{% for entry in entry_list %}
           <tr>
                <td>{{ entry.pid }}</td>
-               <td><a href="{{ url_for('do_view', path=entry.key.pathpart) }}">{{ entry.key.dataset }}</a></td>
-               <td>{{ entry.key.annotation_file }}</td>
+               <td><a href="{{ url_for('do_view', path=entry.dataset) }}">{{ entry.dataset }}</a></td>
                <td>{{ entry.port }}</td>
                <td class="timestamp">{{ entry.launchtime }}</td>
                <td class="timestamp">{{ entry.timestamp }}</td>
@@ -53,7 +51,7 @@
                <td>{{ entry.http_status }}</td>
                <td>
                  {% if entry.status == 'loaded' %}
-                   <a href="{{ url_for('do_terminate', path=entry.key.pathpart) }}"> terminate </a>
+                   <a href="{{ url_for('do_terminate', path=entry.dataset) }}"> terminate </a>
                  {% endif %}
                </td>
           </tr>

cellxgene_gateway/templates/filecrawl.html

@@ -16,36 +16,19 @@
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
 	{% for script in extra_scripts %}
 	<script src="{{ script }}"></script>
-     {% endfor %}
-     <script src="{{ url_for('static', filename='js/annotation.js') }}"></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">
-          {% if path %}
-          <h3>Cellxgene Gateway - {{ path }}</h3>
-          {% else %}
-          <h3>Cellxgene Gateway - FILE CRAWLER</h3>
-          {% endif %}
+       <h3>Cellxgene Gateway - FILE CRAWLER</h3>
      </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="/filecrawl.html">top level</a></li>
-     {% else %}
-     {% endif %}
-     <li><a href="/">homepage</a></li>
-     </ul>
-     </p>
-     <script>
-          $(() => {
-               $("a.new").click(new_annotation_callback);
-          })
-     </script>
+
 </body>
 </html>

cellxgene_gateway/templates/loading.html

@@ -44,13 +44,9 @@
      </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>

run.sh.example

@@ -1,5 +1,8 @@
 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