Release/0.7.0 to dev

.dockerignore

@@ -2,4 +2,5 @@
 /deployment
 .gitignore
 /.vscode
-.pytest_cache
+.pytest_cache
+/cloud-harness

applications/accounts-api/backend/accounts_api/services/user_service.py

@@ -12,21 +12,25 @@ class UserNotFound(Exception): pass
 class UserNotAuthorized(Exception): pass
 
 
-def get_user(userid: str) -> User:
+def get_user(username_or_id: str) -> User:
+    client = AuthClient()
     try:
-        client = AuthClient()
-        kc_user = client.get_user(userid)
+
+        kc_user = client.get_user(username_or_id)
+
     except KeycloakGetError as e:
         if e.response_code == 404:
-            raise UserNotFound(userid)
+            raise UserNotFound(username_or_id)
         raise Exception("Unhandled Keycloak exception") from e
+    except IndexError:
+        raise UserNotFound(username_or_id)
     except KeycloakError as e:
         raise Exception("Unhandled Keycloak exception") from e
 
     user = map_user(kc_user)
     try:
         current_user = client.get_current_user()
-        if not current_user or current_user['id'] != userid:
+        if not current_user or current_user['username'] != username_or_id:
             user.email = None
     except:  # user not provided
         log.error("Error checking user", exc_info=True)
@@ -78,7 +82,7 @@ def update_user(userid, user: User):
 
     try:
         current_user = client.get_current_user()
-        if current_user['id'] != userid != user.id:
+        if current_user['id'] != user.id:
             raise UserNotAuthorized
         admin_client = client.get_admin_client()
         updated_user = {

applications/jupyterhub/src/osb_jupyter/osb_jupyter/jupyterhub.py

@@ -1,11 +1,9 @@
-import sys
-
-import yaml
 from jupyterhub.user import User
 from kubespawner.spawner import KubeSpawner
 
 from cloudharness.auth import AuthClient
 from cloudharness import log
+from cloudharness import applications
 
 
 def affinity_spec(key, value):
@@ -72,28 +70,37 @@ def workspace_volume_is_legacy(workspace_id):
         if not [v for v in self.volumes if v['name'] == volume_name]:
             self.volumes.append(ws_pvc)
 
-        workspace_owner = get_from_cookie('workspaceOwner')
+        app_user = get_app_user(self.user)
+
 
         # Add labels to use for affinity
+        clean_username = "".join(c for c in app_user.username if c.isalnum())
         labels = {
             'workspace': str(workspace_id),
-            'user': self.user.name
+            'username': clean_username,
+            'user': str(self.user.id),
         }
 
+        appname = self.image.split('/')[-1].split(':')[0]
+
         self.common_labels = labels
         self.extra_labels = labels
         self.storage_class = f'{self.config["namespace"]}-nfs-client'
+
         if not user_volume_is_legacy(self.user.id):
             # User pod affinity is by default added by cloudharness
             self.pod_affinity_required = []
-
+
+        workspace = get_workspace(workspace_id, get_from_cookie("accessToken"))
         write_access = has_user_write_access(
-            workspace_id, self.user, workspace_owner)
+            workspace, self.user, app_user=app_user)
+
         if workspace_volume_is_legacy(workspace_id):
             # Pods with write access must be on the same node
             self.pod_affinity_required.append(affinity_spec('workspace', workspace_id))
         from pprint import pprint
         pprint(self.volumes)
+        self.pod_name = f'ws-{clean_username}-{workspace_id}-{appname}'
         if not [v for v in self.volume_mounts if v['name'] == volume_name]:
             self.volume_mounts.append({
                 'name': volume_name,
@@ -104,10 +111,28 @@ def workspace_volume_is_legacy(workspace_id):
         log.error('Change pod manifest failed due to an error.', exc_info=True)
 
 
+def get_app_user(user: User):
+    auth_client = AuthClient()
+    kc_user = auth_client.get_user(user.name)
+    return kc_user
+
+def has_user_write_access(workspace, user: User, app_user=None):
+    print('Checking access, name:', user.name, "workspace:", workspace["id"])
 
-def has_user_write_access(workspace_id, user: User, workspace_owner: str):
-    print('name:', user.name, workspace_owner)
+
+    workspace_owner = workspace["user"]["id"]
+    print("Workspace owner", workspace_owner, "-", workspace["user"]["username"])
+
     if workspace_owner == user.name:
         return True
     auth_client = AuthClient()
-    return auth_client.user_has_realm_role(user.name, 'administrator')
+    return auth_client.user_has_realm_role(app_user.id, 'administrator')
+
+def get_workspace(workspace_id, token, workspace_base_url=None):
+    if workspace_base_url is None:
+        workspace_conf: applications.ApplicationConfiguration = applications.get_configuration('workspaces')
+        workspace_base_url = workspace_conf.get_service_address()
+    import requests
+    workspace = requests.get(f"{workspace_base_url}/api/workspace/{workspace_id}", headers={"Authorization": f"Bearer {token}"}).json()
+
+    return workspace

applications/netpyne/Dockerfile

@@ -2,7 +2,7 @@ FROM node:13.14 as jsbuild
 ENV REPO=https://github.com/MetaCell/NetPyNE-UI.git
 ENV BRANCH_TAG=osb2-dev
 ENV FOLDER=netpyne
-RUN echo "no-cache 2023-1-9"
+RUN echo "no-cache 2023-3-15b"
 RUN git clone $REPO -b $BRANCH_TAG $FOLDER
 RUN rm -Rf .git
 
@@ -13,9 +13,8 @@ RUN yarn install  --network-timeout 1000000000
 RUN yarn build-dev
 
 
-RUN mv node_modules/@metacell .
-RUN rm -Rf node_modules/*
-RUN mv @metacell node_modules
+RUN mv node_modules/@metacell . && rm -Rf node_modules/* && mv @metacell node_modules
+
 
 ###
 FROM jupyter/base-notebook:hub-1.4.2
@@ -52,7 +51,7 @@ RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
 RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
 RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
 
-RUN python utilities/install.py --npm-skip --netpyne $NETPYNE_CORE_BRANCH_TAG --workspace= 
+RUN python utilities/install.py --npm-skip --netpyne $NETPYNE_CORE_BRANCH_TAG
 
 
 
@@ -70,12 +69,14 @@ COPY overrides/hub/jupyter_notebook_config.py /etc/jupyter/jupyter_notebook_conf
 RUN rm -f ~/.jupyter/*.json
 RUN chown $NB_UID .
 RUN chown $NB_UID /opt
-RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
+RUN rm -Rf workspace
+# RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
 USER $NB_UID
 
 # sym link workspace pvc to $FOLDER
 RUN mkdir -p /opt/workspace
 RUN mkdir -p /opt/user
+
 RUN ln -s /opt/workspace workspace
 
 ENV NEURON_HOME=/opt/conda

applications/nfsserver/deploy/values-dev.yaml

@@ -0,0 +1,2 @@
+nfs:
+  useDNS: true

applications/nfsserver/deploy/values.yaml

@@ -0,0 +1,4 @@
+
+# nfs server pvc disk size (/exports)
+server:
+  diskSize: 20Gi

applications/osb-portal/deploy/values.yaml

@@ -1,5 +1,5 @@
 harness:
-  subdomain: www
+  subdomain: app
   secured: false
   deployment:
     auto: true