Merge branch 'develop' of github.com:MetaCell/cloud-harness into feat…

…ure/CH-100

.gitignore

@@ -18,4 +18,5 @@ skaffold.yaml
 /deployment.yaml
 .hypothesis
 __pycache__
-.env
+.env
+/.venv

application-templates/webapp/frontend/package.json

@@ -0,0 +1,11 @@
+{
+  "name": "__APP_NAME__",
+  "scripts": {
+    "dev": "vite",
+    "start": "DOMAIN=http://localhost:5000 vite",
+    "start:dev": "DOMAIN=https://test.ch.metacell.us vite",
+    "start:local": "DOMAIN=http://samples.ch vite",
+    "prebuild": "eslint .",
+    "build": "vite build"
+  }
+}

applications/common/server/test-requirements.txt

@@ -5,4 +5,4 @@ Flask-Testing==0.8.0
 psycopg2-binary==2.8.5
 Flask-SQLAlchemy==2.4.3
 SQLAlchemy==1.3.17
-requests==2.21.0
+requests>=2.21.0

applications/jupyterhub/Dockerfile

@@ -1,31 +1,39 @@
 ARG CLOUDHARNESS_BASE
 FROM $CLOUDHARNESS_BASE as base
 
-FROM jupyterhub/k8s-hub:1.1.3
+FROM quay.io/jupyterhub/k8s-hub:3.2.1
 USER root
 
 
 COPY --from=base  libraries/models/requirements.txt /libraries/models/requirements.txt
-RUN pip install -r /libraries/models/requirements.txt
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip install -r /libraries/models/requirements.txt
 COPY --from=base  libraries/cloudharness-common/requirements.txt /libraries/cloudharness-common/requirements.txt
-RUN pip install -r /libraries/cloudharness-common/requirements.txt
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip install -r /libraries/cloudharness-common/requirements.txt
 COPY --from=base  libraries/client/cloudharness_cli/requirements.txt /libraries/client/cloudharness_cli/requirements.txt
-RUN pip install -r /libraries/client/cloudharness_cli/requirements.txt
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip install -r /libraries/client/cloudharness_cli/requirements.txt
 
 COPY --from=base  libraries/models /libraries/models
-RUN pip install -e /libraries/models
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+   pip install -e /libraries/models
 
 COPY --from=base  libraries/cloudharness-common /libraries/cloudharness-common
 COPY --from=base  libraries/client/cloudharness_cli /libraries/client/cloudharness_cli
 
 #
 
-RUN pip install -e /libraries/cloudharness-common
-RUN pip install -e /libraries/client/cloudharness_cli
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+   pip install -e /libraries/cloudharness-common
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+   pip install -e /libraries/client/cloudharness_cli
 
 
 COPY src src
-RUN pip install ./src/harness_jupyter
-RUN pip install ./src/chauthenticator
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip install ./src/harness_jupyter
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip install ./src/chauthenticator
 
 USER jovyan

applications/jupyterhub/README.md

@@ -31,3 +31,14 @@ To support the pre pulling of task images see (https://github.com/MetaCell/cloud
 the template `templates/image-puller/_helpers-daemonset.tpl` has been changed (see line 167 and on)
 
 TODO: remember to implement/revise this code after you have updated/changed the templates of JupyterHub
+
+## How to update
+
+The helm chart is based on the [zero-to-jupyterhub](https://github.com/jupyterhub/zero-to-jupyterhub-k8s/) helm chart.
+
+1. Run update.sh [TAG] # Do not use latest!
+2. Restore from the diff files with EDIT: CLOUDHARNESS. Use update.patch as a reference
+3. 3. Update Dockerfile to use the same base image you see on values.yaml: hub/image
+
+Customize notebook image: quay.io/jupyterhub/k8s-singleuser-sample:[TAG]
+

applications/jupyterhub/deploy/resources/hub/jupyterhub_config.py

@@ -1,58 +1,38 @@
+# load the config object (satisfies linters)
+c = get_config()  # noqa
+
+import glob
 import os
 import re
 import sys
-import logging
 
-from tornado.httpclient import AsyncHTTPClient
-from kubernetes import client
 from jupyterhub.utils import url_path_join
+from kubernetes_asyncio import client
+from tornado.httpclient import AsyncHTTPClient
+
+#CLOUDHARNESS: EDIT START
+import logging
 
 try:
     from harness_jupyter.jupyterhub import harness_hub
     harness_hub() # activates harness hooks on jupyterhub
 except Exception as e:
     logging.error("could not import harness_jupyter", exc_info=True)
-
+# CLOUDHARNESS: EDIT END
 
 # Make sure that modules placed in the same directory as the jupyterhub config are added to the pythonpath
 configuration_directory = os.path.dirname(os.path.realpath(__file__))
 sys.path.insert(0, configuration_directory)
 
 from z2jh import (
     get_config,
-    set_config_if_not_none,
     get_name,
     get_name_env,
     get_secret_value,
+    set_config_if_not_none,
 )
 
 
-print('Base url is', c.JupyterHub.get('base_url', '/'))
-
-# Configure JupyterHub to use the curl backend for making HTTP requests,
-# rather than the pure-python implementations. The default one starts
-# being too slow to make a large number of requests to the proxy API
-# at the rate required.
-AsyncHTTPClient.configure("tornado.curl_httpclient.CurlAsyncHTTPClient")
-
-c.JupyterHub.spawner_class = 'kubespawner.KubeSpawner'
-
-# Connect to a proxy running in a different pod
-c.ConfigurableHTTPProxy.api_url = 'http://{}:{}'.format(os.environ['PROXY_API_SERVICE_HOST'], int(os.environ['PROXY_API_SERVICE_PORT']))
-c.ConfigurableHTTPProxy.should_start = False
-
-# Do not shut down user pods when hub is restarted
-c.JupyterHub.cleanup_servers = False
-
-# Check that the proxy has routes appropriately setup
-c.JupyterHub.last_activity_interval = 60
-
-# Don't wait at all before redirecting a spawning user to the progress page
-c.JupyterHub.tornado_settings = {
-    'slow_spawn_timeout': 0,
-}
-
-
 def camelCaseify(s):
     """convert snake_case to camelCase
 
@@ -173,6 +153,7 @@ def camelCaseify(s):
     ("events_enabled", "events"),
     ("extra_labels", None),
     ("extra_annotations", None),
+    # ("allow_privilege_escalation", None), # Managed manually below
     ("uid", None),
     ("fs_gid", None),
     ("service_account", "serviceAccountName"),
@@ -206,10 +187,19 @@ def camelCaseify(s):
 if image:
     tag = get_config("singleuser.image.tag")
     if tag:
-        image = "{}:{}".format(image, tag)
+        image = f"{image}:{tag}"
 
     c.KubeSpawner.image = image
 
+# allow_privilege_escalation defaults to False in KubeSpawner 2+. Since its a
+# property where None, False, and True all are valid values that users of the
+# Helm chart may want to set, we can't use the set_config_if_not_none helper
+# function as someone may want to override the default False value to None.
+#
+c.KubeSpawner.allow_privilege_escalation = get_config(
+    "singleuser.allowPrivilegeEscalation"
+)
+
 # Combine imagePullSecret.create (single), imagePullSecrets (list), and
 # singleuser.image.pullSecrets (list).
 image_pull_secrets = []
@@ -255,7 +245,7 @@ def camelCaseify(s):
         pass
     else:
         raise ValueError(
-            "Unrecognized value for matchNodePurpose: %r" % match_node_purpose
+            f"Unrecognized value for matchNodePurpose: {match_node_purpose}"
         )
 
 # Combine the common tolerations for user pods with singleuser tolerations
@@ -271,7 +261,7 @@ def camelCaseify(s):
     pvc_name_template = get_config("singleuser.storage.dynamic.pvcNameTemplate")
     c.KubeSpawner.pvc_name_template = pvc_name_template
     volume_name_template = get_config("singleuser.storage.dynamic.volumeNameTemplate")
-    c.KubeSpawner.storage_pvc_ensure = False
+    c.KubeSpawner.storage_pvc_ensure = True
     set_config_if_not_none(
         c.KubeSpawner, "storage_class", "singleuser.storage.dynamic.storageClass"
     )
@@ -354,41 +344,62 @@ def camelCaseify(s):
 )
 
 c.JupyterHub.services = []
+c.JupyterHub.load_roles = []
 
+# jupyterhub-idle-culler's permissions are scoped to what it needs only, see
+# https://github.com/jupyterhub/jupyterhub-idle-culler#permissions.
+#
 if get_config("cull.enabled", False):
+    jupyterhub_idle_culler_role = {
+        "name": "jupyterhub-idle-culler",
+        "scopes": [
+            "list:users",
+            "read:users:activity",
+            "read:servers",
+            "delete:servers",
+            # "admin:users", # dynamically added if --cull-users is passed
+        ],
+        # assign the role to a jupyterhub service, so it gains these permissions
+        "services": ["jupyterhub-idle-culler"],
+    }
+
     cull_cmd = ["python3", "-m", "jupyterhub_idle_culler"]
     base_url = c.JupyterHub.get("base_url", "/")
     cull_cmd.append("--url=http://localhost:8081" + url_path_join(base_url, "hub/api"))
 
     cull_timeout = get_config("cull.timeout")
     if cull_timeout:
-        cull_cmd.append("--timeout=%s" % cull_timeout)
+        cull_cmd.append(f"--timeout={cull_timeout}")
 
     cull_every = get_config("cull.every")
     if cull_every:
-        cull_cmd.append("--cull-every=%s" % cull_every)
+        cull_cmd.append(f"--cull-every={cull_every}")
 
     cull_concurrency = get_config("cull.concurrency")
     if cull_concurrency:
-        cull_cmd.append("--concurrency=%s" % cull_concurrency)
+        cull_cmd.append(f"--concurrency={cull_concurrency}")
 
     if get_config("cull.users"):
         cull_cmd.append("--cull-users")
+        jupyterhub_idle_culler_role["scopes"].append("admin:users")
+
+    if not get_config("cull.adminUsers"):
+        cull_cmd.append("--cull-admin-users=false")
 
     if get_config("cull.removeNamedServers"):
         cull_cmd.append("--remove-named-servers")
 
     cull_max_age = get_config("cull.maxAge")
     if cull_max_age:
-        cull_cmd.append("--max-age=%s" % cull_max_age)
+        cull_cmd.append(f"--max-age={cull_max_age}")
 
     c.JupyterHub.services.append(
         {
-            "name": "cull-idle",
-            "admin": True,
+            "name": "jupyterhub-idle-culler",
             "command": cull_cmd,
         }
     )
+    c.JupyterHub.load_roles.append(jupyterhub_idle_culler_role)
 
 for key, service in get_config("hub.services", {}).items():
     # c.JupyterHub.services is a list of dicts, but
@@ -402,33 +413,52 @@ def camelCaseify(s):
 
     c.JupyterHub.services.append(service)
 
+for key, role in get_config("hub.loadRoles", {}).items():
+    # c.JupyterHub.load_roles is a list of dicts, but
+    # hub.loadRoles is a dict of dicts to make the config mergable
+    role.setdefault("name", key)
+
+    c.JupyterHub.load_roles.append(role)
+
+# respect explicit null command (distinct from unspecified)
+# this avoids relying on KubeSpawner.cmd's default being None
+_unspecified = object()
+specified_cmd = get_config("singleuser.cmd", _unspecified)
+if specified_cmd is not _unspecified:
+    c.Spawner.cmd = specified_cmd
 
-set_config_if_not_none(c.Spawner, "cmd", "singleuser.cmd")
 set_config_if_not_none(c.Spawner, "default_url", "singleuser.defaultUrl")
 
-cloud_metadata = get_config("singleuser.cloudMetadata", {})
+cloud_metadata = get_config("singleuser.cloudMetadata")
 
 if cloud_metadata.get("blockWithIptables") == True:
     # Use iptables to block access to cloud metadata by default
     network_tools_image_name = get_config("singleuser.networkTools.image.name")
     network_tools_image_tag = get_config("singleuser.networkTools.image.tag")
+    network_tools_resources = get_config("singleuser.networkTools.resources")
+    ip = cloud_metadata["ip"]
     ip_block_container = client.V1Container(
         name="block-cloud-metadata",
         image=f"{network_tools_image_name}:{network_tools_image_tag}",
         command=[
             "iptables",
-            "-A",
+            "--append",
             "OUTPUT",
-            "-d",
-            cloud_metadata.get("ip", "169.254.169.254"),
-            "-j",
+            "--protocol",
+            "tcp",
+            "--destination",
+            ip,
+            "--destination-port",
+            "80",
+            "--jump",
             "DROP",
         ],
         security_context=client.V1SecurityContext(
             privileged=True,
             run_as_user=0,
             capabilities=client.V1Capabilities(add=["NET_ADMIN"]),
         ),
+        resources=network_tools_resources,
     )
 
     c.KubeSpawner.init_containers.append(ip_block_container)
@@ -438,17 +468,6 @@ def camelCaseify(s):
     c.JupyterHub.log_level = "DEBUG"
     c.Spawner.debug = True
 
-# load /usr/local/etc/jupyterhub/jupyterhub_config.d config files
-config_dir = "/usr/local/etc/jupyterhub/jupyterhub_config.d"
-if os.path.isdir(config_dir):
-    for file_path in sorted(glob.glob(f"{config_dir}/*.py")):
-        file_name = os.path.basename(file_path)
-        print(f"Loading {config_dir} config: {file_name}")
-        with open(file_path) as f:
-            file_content = f.read()
-        # compiling makes debugging easier: https://stackoverflow.com/a/437857
-        exec(compile(source=file_content, filename=file_name, mode="exec"))
-
 # load potentially seeded secrets
 #
 # NOTE: ConfigurableHTTPProxy.auth_token is set through an environment variable
@@ -471,11 +490,24 @@ def camelCaseify(s):
         cfg.pop("keys", None)
     c[app].update(cfg)
 
+
+# load /usr/local/etc/jupyterhub/jupyterhub_config.d config files
+config_dir = "/usr/local/etc/jupyterhub/jupyterhub_config.d"
+if os.path.isdir(config_dir):
+    for file_path in sorted(glob.glob(f"{config_dir}/*.py")):
+        file_name = os.path.basename(file_path)
+        print(f"Loading {config_dir} config: {file_name}")
+        with open(file_path) as f:
+            file_content = f.read()
+        # compiling makes debugging easier: https://stackoverflow.com/a/437857
+        exec(compile(source=file_content, filename=file_name, mode="exec"))
+
 # execute hub.extraConfig entries
 for key, config_py in sorted(get_config("hub.extraConfig", {}).items()):
-    print("Loading extra config: %s" % key)
+    print(f"Loading extra config: {key}")
     exec(config_py)
 
+# CLOUDHARNESS: EDIT START
 # Allow switching authenticators easily
 auth_type = get_config('hub.config.JupyterHub.authenticator_class')
 email_domain = 'local'
@@ -504,6 +536,7 @@ def camelCaseify(s):
     c.Authenticator.auto_login = True
     c.OAuthenticator.client_id = client_id
     c.OAuthenticator.client_secret = client_secret
+    c.OAuthenticator.allow_all = True
 
     c.GenericOAuthenticator.login_service = "CH"
     c.GenericOAuthenticator.username_key = "email"
@@ -525,4 +558,6 @@ def camelCaseify(s):
 c.apps = get_config('apps')
 c.registry = get_config('registry')
 c.domain = get_config('root.domain')
-c.namespace = get_config('root.namespace')
+c.namespace = get_config('root.namespace')
+# CLOUDHARNESS: EDIT END
+