Merge pull request #6 from uc-cdis/feat/nde_demo

feat(original dockerfile for nde)

jupyter-daids/Dockerfile

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+FROM quay.io/cdis/jupyter-notebook:latest
+
+USER root
+
+# COPY premade notebook 
+RUN mkdir /home/jovyan/daids-notebook
+
+ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIDS_notebook/CHARLIE_demo.ipynb /home/jovyan/daids-notebook/
+ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIDS_notebook/ndh_analysis_functions.py /home/jovyan/daids-notebook/
+
+
+RUN chmod -R 777 /home/jovyan/daids-notebook
+
+USER $NB_UID
+WORKDIR /home/jovyan

jupyter-daids/cull_idle_servers.py

@@ -0,0 +1,367 @@
+#!/usr/bin/env python3
+"""script to monitor and cull idle single-user servers
+
+Caveats:
+
+last_activity is not updated with high frequency,
+so cull timeout should be greater than the sum of:
+
+- single-user websocket ping interval (default: 30s)
+- JupyterHub.last_activity_interval (default: 5 minutes)
+
+You can run this as a service managed by JupyterHub with this in your config::
+
+
+    c.JupyterHub.services = [
+        {
+            'name': 'cull-idle',
+            'admin': True,
+            'command': [sys.executable, 'cull_idle_servers.py', '--timeout=3600'],
+        }
+    ]
+
+Or run it manually by generating an API token and storing it in `JUPYTERHUB_API_TOKEN`:
+
+    export JUPYTERHUB_API_TOKEN=$(jupyterhub token)
+    python3 cull_idle_servers.py [--timeout=900] [--url=http://127.0.0.1:8081/hub/api]
+
+This script uses the same ``--timeout`` and ``--max-age`` values for
+culling users and users' servers.  If you want a different value for
+users and servers, you should add this script to the services list
+twice, just with different ``name``s, different values, and one with
+the ``--cull-users`` option.
+"""
+
+from datetime import datetime, timezone
+from functools import partial
+import json
+import os
+
+try:
+    from urllib.parse import quote
+except ImportError:
+    from urllib import quote
+
+import dateutil.parser
+
+from tornado.gen import coroutine, multi
+from tornado.locks import Semaphore
+from tornado.log import app_log
+from tornado.httpclient import AsyncHTTPClient, HTTPRequest
+from tornado.ioloop import IOLoop, PeriodicCallback
+from tornado.options import define, options, parse_command_line
+
+
+def parse_date(date_string):
+    """Parse a timestamp
+
+    If it doesn't have a timezone, assume utc
+
+    Returned datetime object will always be timezone-aware
+    """
+    dt = dateutil.parser.parse(date_string)
+    if not dt.tzinfo:
+        # assume naïve timestamps are UTC
+        dt = dt.replace(tzinfo=timezone.utc)
+    return dt
+
+
+def format_td(td):
+    """
+    Nicely format a timedelta object
+
+    as HH:MM:SS
+    """
+    if td is None:
+        return "unknown"
+    if isinstance(td, str):
+        return td
+    seconds = int(td.total_seconds())
+    h = seconds // 3600
+    seconds = seconds % 3600
+    m = seconds // 60
+    seconds = seconds % 60
+    return "{h:02}:{m:02}:{seconds:02}".format(h=h, m=m, seconds=seconds)
+
+
+@coroutine
+def cull_idle(url, api_token, inactive_limit, cull_users=False, max_age=0, concurrency=10):
+    """Shutdown idle single-user servers
+
+    If cull_users, inactive *users* will be deleted as well.
+    """
+    auth_header = {
+        'Authorization': 'token %s' % api_token,
+    }
+    req = HTTPRequest(
+        url=url + '/users',
+        headers=auth_header,
+    )
+    now = datetime.now(timezone.utc)
+    client = AsyncHTTPClient()
+
+    if concurrency:
+        semaphore = Semaphore(concurrency)
+        @coroutine
+        def fetch(req):
+            """client.fetch wrapped in a semaphore to limit concurrency"""
+            yield semaphore.acquire()
+            try:
+                return (yield client.fetch(req))
+            finally:
+                yield semaphore.release()
+    else:
+        fetch = client.fetch
+
+    resp = yield fetch(req)
+    users = json.loads(resp.body.decode('utf8', 'replace'))
+    futures = []
+
+    @coroutine
+    def handle_server(user, server_name, server):
+        """Handle (maybe) culling a single server
+
+        Returns True if server is now stopped (user removable),
+        False otherwise.
+        """
+        log_name = user['name']
+        if server_name:
+            log_name = '%s/%s' % (user['name'], server_name)
+        if server.get('pending'):
+            app_log.warning(
+                "Not culling server %s with pending %s",
+                log_name, server['pending'])
+            return False
+
+        # jupyterhub < 0.9 defined 'server.url' once the server was ready
+        # as an *implicit* signal that the server was ready.
+        # 0.9 adds a dedicated, explicit 'ready' field.
+        # By current (0.9) definitions, servers that have no pending
+        # events and are not ready shouldn't be in the model,
+        # but let's check just to be safe.
+
+        if not server.get('ready', bool(server['url'])):
+            app_log.warning(
+                "Not culling not-ready not-pending server %s: %s",
+                log_name, server)
+            return False
+
+        if server.get('started'):
+            age = now - parse_date(server['started'])
+        else:
+            # started may be undefined on jupyterhub < 0.9
+            age = None
+
+        # check last activity
+        # last_activity can be None in 0.9
+        if server['last_activity']:
+            inactive = now - parse_date(server['last_activity'])
+        else:
+            # no activity yet, use start date
+            # last_activity may be None with jupyterhub 0.9,
+            # which introduces the 'started' field which is never None
+            # for running servers
+            inactive = age
+
+        should_cull = (inactive is not None and
+                       inactive.total_seconds() >= inactive_limit)
+        if should_cull:
+            app_log.info(
+                "Culling server %s (inactive for %s)",
+                log_name, format_td(inactive))
+
+        if max_age and not should_cull:
+            # only check started if max_age is specified
+            # so that we can still be compatible with jupyterhub 0.8
+            # which doesn't define the 'started' field
+            if age is not None and age.total_seconds() >= max_age:
+                app_log.info(
+                    "Culling server %s (age: %s, inactive for %s)",
+                    log_name, format_td(age), format_td(inactive))
+                should_cull = True
+
+        if not should_cull:
+            app_log.debug(
+                "Not culling server %s (age: %s, inactive for %s)",
+                log_name, format_td(age), format_td(inactive))
+            return False
+
+        if server_name:
+            # culling a named server
+            delete_url = url + "/users/%s/servers/%s" % (
+                quote(user['name']), quote(server['name'])
+            )
+        else:
+            delete_url = url + '/users/%s/server' % quote(user['name'])
+
+        req = HTTPRequest(
+            url=delete_url, method='DELETE', headers=auth_header,
+        )
+        resp = yield fetch(req)
+        if resp.code == 202:
+            app_log.warning(
+                "Server %s is slow to stop",
+                log_name,
+            )
+            # return False to prevent culling user with pending shutdowns
+            return False
+        return True
+
+    @coroutine
+    def handle_user(user):
+        """Handle one user.
+
+        Create a list of their servers, and async exec them.  Wait for
+        that to be done, and if all servers are stopped, possibly cull
+        the user.
+        """
+        # shutdown servers first.
+        # Hub doesn't allow deleting users with running servers.
+        # jupyterhub 0.9 always provides a 'servers' model.
+        # 0.8 only does this when named servers are enabled.
+        if 'servers' in user:
+            servers = user['servers']
+        else:
+            # jupyterhub < 0.9 without named servers enabled.
+            # create servers dict with one entry for the default server
+            # from the user model.
+            # only if the server is running.
+            servers = {}
+            if user['server']:
+                servers[''] = {
+                    'last_activity': user['last_activity'],
+                    'pending': user['pending'],
+                    'url': user['server'],
+                }
+        server_futures = [
+            handle_server(user, server_name, server)
+            for server_name, server in servers.items()
+        ]
+        results = yield multi(server_futures)
+        if not cull_users:
+            return
+        # some servers are still running, cannot cull users
+        still_alive = len(results) - sum(results)
+        if still_alive:
+            app_log.debug(
+                "Not culling user %s with %i servers still alive",
+                user['name'], still_alive)
+            return False
+
+        should_cull = False
+        if user.get('created'):
+            age = now - parse_date(user['created'])
+        else:
+            # created may be undefined on jupyterhub < 0.9
+            age = None
+
+        # check last activity
+        # last_activity can be None in 0.9
+        if user['last_activity']:
+            inactive = now - parse_date(user['last_activity'])
+        else:
+            # no activity yet, use start date
+            # last_activity may be None with jupyterhub 0.9,
+            # which introduces the 'created' field which is never None
+            inactive = age
+
+        should_cull = (inactive is not None and
+                       inactive.total_seconds() >= inactive_limit)
+        if should_cull:
+            app_log.info(
+                "Culling user %s (inactive for %s)",
+                user['name'], inactive)
+
+        if max_age and not should_cull:
+            # only check created if max_age is specified
+            # so that we can still be compatible with jupyterhub 0.8
+            # which doesn't define the 'started' field
+            if age is not None and age.total_seconds() >= max_age:
+                app_log.info(
+                    "Culling user %s (age: %s, inactive for %s)",
+                    user['name'], format_td(age), format_td(inactive))
+                should_cull = True
+
+        if not should_cull:
+            app_log.debug(
+                "Not culling user %s (created: %s, last active: %s)",
+                user['name'], format_td(age), format_td(inactive))
+            return False
+
+        req = HTTPRequest(
+            url=url + '/users/%s' % user['name'],
+            method='DELETE',
+            headers=auth_header,
+        )
+        yield fetch(req)
+        return True
+
+    for user in users:
+        futures.append((user['name'], handle_user(user)))
+
+    for (name, f) in futures:
+        try:
+            result = yield f
+        except Exception:
+            app_log.exception("Error processing %s", name)
+        else:
+            if result:
+                app_log.debug("Finished culling %s", name)
+
+
+if __name__ == '__main__':
+    define(
+        'url',
+        default=os.environ.get('JUPYTERHUB_API_URL'),
+        help="The JupyterHub API URL",
+    )
+    define('timeout', default=600, help="The idle timeout (in seconds)")
+    define('cull_every', default=0,
+           help="The interval (in seconds) for checking for idle servers to cull")
+    define('max_age', default=0,
+           help="The maximum age (in seconds) of servers that should be culled even if they are active")
+    define('cull_users', default=False,
+           help="""Cull users in addition to servers.
+                This is for use in temporary-user cases such as tmpnb.""",
+           )
+    define('concurrency', default=10,
+           help="""Limit the number of concurrent requests made to the Hub.
+
+                Deleting a lot of users at the same time can slow down the Hub,
+                so limit the number of API requests we have outstanding at any given time.
+                """
+           )
+
+    parse_command_line()
+    if not options.cull_every:
+        options.cull_every = options.timeout // 2
+    api_token = os.environ['JUPYTERHUB_API_TOKEN']
+
+    try:
+        AsyncHTTPClient.configure("tornado.curl_httpclient.CurlAsyncHTTPClient")
+    except ImportError as e:
+        app_log.warning(
+            "Could not load pycurl: %s\n"
+            "pycurl is recommended if you have a large number of users.",
+            e)
+
+    loop = IOLoop.current()
+    cull = partial(
+        cull_idle,
+        url=options.url,
+        api_token=api_token,
+        inactive_limit=options.timeout,
+        cull_users=options.cull_users,
+        max_age=options.max_age,
+        concurrency=options.concurrency,
+    )
+    # schedule first cull immediately
+    # because PeriodicCallback doesn't start until the end of the first interval
+    loop.add_callback(cull)
+    # schedule periodic cull
+    pc = PeriodicCallback(cull, 1e3 * options.cull_every)
+    pc.start()
+    try:
+        loop.start()
+    except KeyboardInterrupt:
+        pass

jupyter-daids/jupyter_notebook_config.py

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+import os
+
+c.NotebookApp.tornado_settings = {
+    'headers': {
+        'Content-Security-Policy':
+        'frame-ancestors self %s' % os.getenv('FRAME_ANCESTORS', '')
+    }
+}