Merge branch 'main' of https://github.com/microsoft/AzureTRE into mar…

…robi/issue3992

.github/scripts/yarn.lock

@@ -774,12 +774,12 @@ brace-expansion@^1.1.7:
     balanced-match "^1.0.0"
     concat-map "0.0.1"
 
-braces@^3.0.2:
-  version "3.0.2"
-  resolved "https://registry.yarnpkg.com/braces/-/braces-3.0.2.tgz#3454e1a462ee8d599e236df336cd9ea4f8afe107"
-  integrity sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==
+braces@^3.0.3:
+  version "3.0.3"
+  resolved "https://registry.yarnpkg.com/braces/-/braces-3.0.3.tgz#490332f40919452272d55a8480adc0c441358789"
+  integrity sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==
   dependencies:
-    fill-range "^7.0.1"
+    fill-range "^7.1.1"
 
 browser-process-hrtime@^1.0.0:
   version "1.0.0"
@@ -1109,10 +1109,10 @@ fb-watchman@^2.0.0:
   dependencies:
     bser "2.1.1"
 
-fill-range@^7.0.1:
-  version "7.0.1"
-  resolved "https://registry.yarnpkg.com/fill-range/-/fill-range-7.0.1.tgz#1919a6a7c75fe38b2c7c77e5198535da9acdda40"
-  integrity sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==
+fill-range@^7.1.1:
+  version "7.1.1"
+  resolved "https://registry.yarnpkg.com/fill-range/-/fill-range-7.1.1.tgz#44265d3cac07e3ea7dc247516380643754a05292"
+  integrity sha512-YsGpe3WHLK8ZYi4tWDg2Jy3ebRz2rXowDxnld4bkQB00cc/1Zw9AWnC0i9ztDJitivtQvaI9KaLyKrc+hBW0yg==
   dependencies:
     to-regex-range "^5.0.1"
 
@@ -2479,9 +2479,9 @@ write-file-atomic@^3.0.0:
     typedarray-to-buffer "^3.1.5"
 
 ws@^7.4.6:
-  version "7.5.9"
-  resolved "https://registry.yarnpkg.com/ws/-/ws-7.5.9.tgz#54fa7db29f4c7cec68b1ddd3a89de099942bb591"
-  integrity sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q==
+  version "7.5.10"
+  resolved "https://registry.yarnpkg.com/ws/-/ws-7.5.10.tgz#58b5c20dc281633f6c19113f39b349bd8bd558d9"
+  integrity sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ==
 
 xml-name-validator@^3.0.0:
   version "3.0.0"

.github/workflows/deploy_tre_reusable.yml

@@ -401,6 +401,8 @@ jobs:
              BUNDLE_DIR: "./templates/workspace_services/ohdsi"}
           - {BUNDLE_TYPE: "workspace_service",
              BUNDLE_DIR: "./templates/workspace_services/azuresql"}
+          - {BUNDLE_TYPE: "workspace_service",
+             BUNDLE_DIR: "./templates/workspace_services/openai"}
           - {BUNDLE_TYPE: "user_resource",
              BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-windowsvm"}
           - {BUNDLE_TYPE: "user_resource",

CHANGELOG.md

@@ -1,22 +1,119 @@
 <!-- markdownlint-disable MD041 -->
-## 0.19.0 (Unreleased)
+## 0.20.0 (Unreleased)
 
 **BREAKING CHANGES & MIGRATIONS**:
 
+FEATURES:
+
+ENHANCEMENTS:
+
+BUG FIXES:
+
+COMPONENTS:
+
+## 0.19.1
+
+**BREAKING CHANGES & MIGRATIONS**:
+* Workspace creation blocked due to Azure API depreciation ([#4095](https://github.com/microsoft/AzureTRE/issues/4095))
+
+ENHANCEMENTS:
+* Update Unrestricted and Airlock Import Review workspaces to be built off the Base workspace 0.19.0 ([#4087](https://github.com/microsoft/AzureTRE/pull/4087))
+* Update Release Docs (part of [#2727](https://github.com/microsoft/AzureTRE/issues/2727))
+* Add info regarding workspace limit into docs ([#3920](https://github.com/microsoft/AzureTRE/issues/3920))
+
+BUG FIXES:
+* Workspace creation blocked due to Azure API depreciation ([#4095](https://github.com/microsoft/AzureTRE/issues/4095))
+
+COMPONENTS:
+| name | version |
+| ----- | ----- |
+| devops | 0.5.2 |
+| core | 0.10.8 |
+| ui | 0.5.28 |
+| tre-service-guacamole-linuxvm | 1.0.3 |
+| tre-service-guacamole-import-reviewvm | 0.2.9 |
+| tre-service-guacamole-export-reviewvm | 0.1.9 |
+| tre-service-guacamole-windowsvm | 1.0.1 |
+| tre-service-guacamole | 0.10.9 |
+| tre-service-databricks | 1.0.4 |
+| tre-service-mlflow | 0.7.9 |
+| tre-service-innereye | 0.6.5 |
+| tre-workspace-service-ohdsi | 0.2.5 |
+| tre-workspace-service-gitea | 1.0.5 |
+| tre-workspace-service-mysql | 1.0.4 |
+| tre-workspace-service-azuresql | 1.0.10 |
+| tre-user-resource-aml-compute-instance | 0.5.7 |
+| tre-service-azureml | 0.8.11 |
+| tre-workspace-service-health | 0.2.6 |
+| tre-workspace-service-openai | 1.0.1 |
+| tre-workspace-airlock-import-review | 0.13.1 |
+| tre-workspace-unrestricted | 0.12.1 |
+| tre-workspace-base | 1.5.7 |
+| tre-shared-service-cyclecloud | 0.6.3 |
+| tre-shared-service-databricks-private-auth | 0.1.6 |
+| tre-shared-service-sonatype-nexus | 3.0.1 |
+| tre-shared-service-admin-vm | 0.4.4 |
+| tre-shared-service-firewall | 1.2.1 |
+| tre-shared-service-gitea | 1.0.3 |
+| tre-shared-service-certs | 0.5.2 |
+| tre-shared-service-airlock-notifier | 1.0.2 |
+
+## 0.19.0
+
 FEATURES:
 * Azure SQL Workspace Service ([#3969](https://github.com/microsoft/AzureTRE/issues/3969))
+* OpenAI Workspace Service ([#3810](https://github.com/microsoft/AzureTRE/issues/3810))
 
 ENHANCEMENTS:
 * Add Case Study Docs ([#1366](https://github.com/microsoft/AzureTRE/issues/1366))
 * Ability to host TRE on a custom domain ([#4014](https://github.com/microsoft/AzureTRE/pull/4014))
 * Remove AppServiceFileAuditLogs diagnostic setting ([#4033](https://github.com/microsoft/AzureTRE/issues/4033))
+* Update to the Airlock Notifier Shared Service ([#3909](https://github.com/microsoft/AzureTRE/issues/3909))
 
 BUG FIXES:
+* Removed 429 Error (Costs API) form presenting in UI ([#3929](https://github.com/microsoft/AzureTRE/issues/3929))
 * Fix numbering issue within `bug_report.md` template ([#4028](https://github.com/microsoft/AzureTRE/pull/4028))
 * Disable public network access to the API App Service ([#3986](https://github.com/microsoft/AzureTRE/issues/3986))
+* Fix Guacamole shared drive always enabled ([#3885](https://github.com/microsoft/AzureTRE/issues/3885))
+* Add Dependabot Security updates for July
 * Update Docs to format emojis properly ([#4027](https://github.com/microsoft/AzureTRE/issues/4027))
+* Update API and Resource Processor opentelemetry versions ([#4052](https://github.com/microsoft/AzureTRE/issues/4052))
+* Fix broken links in new Case Study Docs
+* Update Linux VM to stop screensaver locking out the user ([#4065](https://github.com/microsoft/AzureTRE/issues/4065))
+* Update .NET version on Linux VMs ([#4067](https://github.com/microsoft/AzureTRE/issues/4067))
 
 COMPONENTS:
+| name | version |
+| ----- | ----- |
+| devops | 0.5.1 |
+| core | 0.10.6 |
+| ui | 0.5.28 |
+| tre-service-guacamole-linuxvm | 1.0.2 |
+| tre-service-guacamole-import-reviewvm | 0.2.8 |
+| tre-service-guacamole-export-reviewvm | 0.1.8 |
+| tre-service-guacamole-windowsvm | 1.0.0 |
+| tre-service-guacamole | 0.10.8 |
+| tre-service-databricks | 1.0.3 |
+| tre-service-mlflow | 0.7.8 |
+| tre-service-innereye | 0.6.4 |
+| tre-workspace-service-ohdsi | 0.2.4 |
+| tre-workspace-service-gitea | 1.0.3 |
+| tre-workspace-service-mysql | 1.0.2 |
+| tre-workspace-service-azuresql | 1.0.9 |
+| tre-user-resource-aml-compute-instance | 0.5.7 |
+| tre-service-azureml | 0.8.10 |
+| tre-workspace-service-health | 0.2.5 |
+| tre-workspace-airlock-import-review | 0.12.16 |
+| tre-workspace-unrestricted | 0.11.4 |
+| tre-workspace-base | 1.5.4 |
+| tre-shared-service-cyclecloud | 0.5.5 |
+| tre-shared-service-databricks-private-auth | 0.1.5 |
+| tre-shared-service-sonatype-nexus | 3.0.0 |
+| tre-shared-service-admin-vm | 0.4.3 |
+| tre-shared-service-firewall | 1.2.0 |
+| tre-shared-service-gitea | 1.0.2 |
+| tre-shared-service-certs | 0.5.1 |
+| tre-shared-service-airlock-notifier | 1.0.1 |
 
 ## 0.18.0
 

Makefile

@@ -144,6 +144,13 @@ terraform-deploy:
 	&& . ${MAKEFILE_DIR}/devops/scripts/load_env.sh ${DIR}/.env \
 	&& cd ${DIR}/terraform/ && ./deploy.sh
 
+terraform-upgrade:
+	$(call target_title, "Upgrading ${DIR} with Terraform") \
+	&& . ${MAKEFILE_DIR}/devops/scripts/check_dependencies.sh env \
+	&& . ${MAKEFILE_DIR}/devops/scripts/load_and_validate_env.sh \
+	&& . ${MAKEFILE_DIR}/devops/scripts/load_env.sh ${DIR}/.env \
+	&& cd ${DIR}/terraform/ && ./upgrade.sh
+
 terraform-import:
 	$(call target_title, "Importing ${DIR} with Terraform") \
 	&& . ${MAKEFILE_DIR}/devops/scripts/check_dependencies.sh env \

airlock_processor/_version.py

@@ -1 +1 @@
-__version__ = "0.7.1"
+__version__ = "0.7.2"

airlock_processor/requirements.txt

@@ -2,7 +2,7 @@
 azure-core==1.30.0
 azure-functions==1.17.0
 azure-storage-blob==12.19.0
-azure-identity==1.14.1
+azure-identity==1.16.1
 azure-mgmt-storage==21.1.0
 azure-mgmt-resource==23.0.1
 pydantic==1.10.13

api_app/_version.py

@@ -1 +1 @@
-__version__ = "0.18.9"
+__version__ = "0.19.2"

api_app/api/routes/api.py

@@ -24,7 +24,7 @@
     {"name": "workspaces", "description": " **Workspace Owners and Researchers** can view their own workspaces"},
     {"name": "workspace services", "description": "**Workspace Owners** administer workspace services, **Workspace Owners and Researchers** can view services in the workspaces they belong to"},
     {"name": "user resources", "description": "**Researchers** administer and can view their own researchers, **Workspace Owners** can view/update/delete all user resources in their workspaces"},
-    {"name": "shared services", "description": "**TRE administratiors** administer shared services"},
+    {"name": "shared services", "description": "**TRE administratiors** administer shared services"}
 ]
 
 # Root

api_app/api/routes/workspaces.py

@@ -21,6 +21,7 @@
 from models.schemas.workspace_service import WorkspaceServiceInCreate, WorkspaceServicesInList, WorkspaceServiceInResponse
 from models.schemas.resource import ResourceHistoryInList, ResourcePatch
 from models.schemas.resource_template import ResourceTemplateInformationInList
+from models.schemas.users import UsersInResponse
 from resources import strings
 from services.access_service import AuthConfigValidationError
 from services.authentication import get_current_admin_user, \
@@ -187,6 +188,13 @@ async def invoke_action_on_workspace(response: Response, action: str, user=Depen
     return OperationInResponse(operation=operation)
 
 
+@workspaces_shared_router.get("/workspaces/{workspace_id}/users", response_model=UsersInResponse, name=strings.API_GET_WORKSPACE_USERS)
+async def get_workspace_users(workspace=Depends(get_workspace_by_id_from_path)) -> UsersInResponse:
+    access_service = get_access_service()
+    users = access_service.get_workspace_users(workspace)
+    return UsersInResponse(users=users)
+
+
 # workspace operations
 # This method only returns templates that the authenticated user is authorized to use
 @workspaces_shared_router.get("/workspaces/{workspace_id}/workspace-service-templates", response_model=ResourceTemplateInformationInList, name=strings.API_GET_WORKSPACE_SERVICE_TEMPLATES_IN_WORKSPACE)

api_app/models/domain/authentication.py

@@ -10,6 +10,6 @@
 class User(BaseModel):
     id: str
     name: str
-    email: str
+    email: str = Field(None)
     roles: List[str] = Field([])
     roleAssignments: List[RoleAssignment] = Field([])

api_app/models/schemas/users.py

@@ -0,0 +1,28 @@
+from pydantic import BaseModel, Field
+from typing import List
+
+from models.domain.authentication import User
+
+
+class UsersInResponse(BaseModel):
+    users: List[User] = Field(..., title="Users", description="List of users assigned to the workspace")
+
+    class Config:
+        schema_extra = {
+            "example": {
+                "users": [
+                    {
+                        "id": 1,
+                        "name": "John Doe",
+                        "email": "[email protected]",
+                        "roles": ["WorkspaceOwner", "WorkspaceResearcher"]
+                    },
+                    {
+                        "id": 2,
+                        "name": "Jane Smith",
+                        "email": "[email protected]",
+                        "roles": ["WorkspaceResearcher"]
+                    }
+                ]
+            }
+        }

api_app/requirements.txt

@@ -2,21 +2,21 @@ aiohttp==3.9.4
 azure-core==1.30.0
 azure-cosmos==4.5.1
 azure-eventgrid==4.15.0
-azure-identity==1.14.1
+azure-identity==1.16.1
 azure-mgmt-compute==30.3.0
 azure-mgmt-cosmosdb==9.3.0
 azure-mgmt-costmanagement==4.0.1
 azure-mgmt-resource==23.0.1
 azure-mgmt-storage==21.1.0
-azure-monitor-opentelemetry==1.2.0
+azure-monitor-opentelemetry~=1.6
 azure-servicebus==7.11.3
 azure-storage-blob==12.19.0
 fastapi==0.110.0
 fastapi-utils==0.2.1
 gunicorn==22.0.0
 jsonschema[format_nongpl]==4.19.1
 msal==1.26.0
-opentelemetry.instrumentation.logging==0.44b0
+opentelemetry.instrumentation.logging>=0.44b0
 pandas==2.0.3
 PyJWT==2.8.0
 pytz==2022.7

api_app/resources/strings.py

@@ -15,6 +15,8 @@
 API_UPDATE_WORKSPACE = "Update an existing workspace"
 API_INVOKE_ACTION_ON_WORKSPACE = "Invoke action on a workspace"
 
+API_GET_WORKSPACE_USERS = "Get all users for a workspace"
+
 API_GET_ALL_WORKSPACE_SERVICES = "Get all workspace services for workspace"
 API_GET_WORKSPACE_SERVICE_BY_ID = "Get workspace service by Id"
 API_CREATE_WORKSPACE_SERVICE = "Create a workspace service"