Fix some issues with context handling at deployment time

.github/workflows/lint_code.yaml

@@ -59,8 +59,10 @@ jobs:
           python-version: 3.11
       - name: Install hatch
         run: pip install hatch
-      - name: Print Ruff version
-        run: hatch run lint:ruff --version
+      - name: Print package versions
+        run: |
+          hatch run lint:ruff --version
+          hatch run lint:black --version
       - name: Lint Python
         run: hatch run lint:all
 

data_safe_haven/README.md

@@ -29,7 +29,6 @@ Install the following requirements before starting
 > dsh deploy shm
 ```
 
-You will be prompted for various settings.
 Run `dsh deploy shm -h` to see the necessary command line flags and provide them as arguments.
 
 - Add one or more users from a CSV file with columns named (`GivenName`, `Surname`, `Phone`, `Email`, `CountryCode`).
@@ -40,13 +39,20 @@ Run `dsh deploy shm -h` to see the necessary command line flags and provide them
 > dsh admin add-users <my CSV users file>
 ```
 
-- Next deploy the infrastructure for one or more Secure Research Environments (SREs) [approx 30 minutes]:
+- Create the configuration for one or more Secure Research Environments (SREs).
+
+```console
+> dsh config show --file config.yaml
+> vim config.yaml
+> dsh config upload config.yaml
+```
+
+- Next deploy the infrastructure  [approx 30 minutes]:
 
 ```console
 > dsh deploy sre <SRE name>
 ```
 
-You will be prompted for various settings.
 Run `dsh deploy sre -h` to see the necessary command line flags and provide them as arguments.
 
 - Next add one or more existing users to your SRE

data_safe_haven/administration/users/user_handler.py

@@ -71,7 +71,7 @@ def get_usernames(self) -> dict[str, list[str]]:
         usernames = {}
         usernames["Azure AD"] = self.get_usernames_azure_ad()
         usernames["Domain controller"] = self.get_usernames_domain_controller()
-        for sre_name in self.config.sres.keys():
+        for sre_name in self.config.sre_names:
             usernames[f"SRE {sre_name}"] = self.get_usernames_guacamole(sre_name)
         return usernames
 

data_safe_haven/commands/config.py

@@ -41,8 +41,17 @@ def upload(
 
 
 @config_command_group.command()
-def show() -> None:
+def show(
+    file: Annotated[
+        Optional[Path],  # noqa: UP007
+        typer.Option(help="File path to write configuration template to."),
+    ] = None
+) -> None:
     """Print the configuration for the selected Data Safe Haven context"""
     context = ContextSettings.from_file().assert_context()
     config = Config.from_remote(context)
-    print(config.to_yaml())
+    if file:
+        with open(file, "w") as outfile:
+            outfile.write(config.to_yaml())
+    else:
+        print(config.to_yaml())

data_safe_haven/commands/deploy.py

@@ -10,6 +10,7 @@
 from data_safe_haven.functions import bcrypt_salt, password
 from data_safe_haven.infrastructure import SHMStackManager, SREStackManager
 from data_safe_haven.provisioning import SHMProvisioningManager, SREProvisioningManager
+from data_safe_haven.utility import LoggingSingleton
 
 deploy_command_group = typer.Typer()
 
@@ -99,12 +100,17 @@ def sre(
     ] = None,
 ) -> None:
     """Deploy a Secure Research Environment"""
+    logger = LoggingSingleton()
     context = ContextSettings.from_file().assert_context()
     config = Config.from_remote(context)
-
     sre_name = config.sanitise_sre_name(name)
 
     try:
+        # Exit if SRE name is not recognised
+        if sre_name not in config.sre_names:
+            logger.fatal(f"Could not find configuration details for SRE '{sre_name}'.")
+            raise typer.Exit(1)
+
         # Load GraphAPI as this may require user-interaction that is not possible as
         # part of a Pulumi declarative command
         graph_api = GraphApi(

data_safe_haven/config/config.py

@@ -10,15 +10,12 @@
 from pydantic import (
     BaseModel,
     Field,
-    FieldSerializationInfo,
     ValidationError,
-    field_serializer,
     field_validator,
 )
 from yaml import YAMLError
 
 from data_safe_haven import __version__
-from data_safe_haven.config.context_settings import Context
 from data_safe_haven.exceptions import (
     DataSafeHavenConfigError,
     DataSafeHavenParameterError,
@@ -44,6 +41,8 @@
     TimeZone,
 )
 
+from .context_settings import Context
+
 
 class ConfigSectionAzure(BaseModel, validate_assignment=True):
     admin_group_id: Guid = Field(..., exclude=True)
@@ -155,7 +154,7 @@ class ConfigSectionSRE(BaseModel, validate_assignment=True):
     data_provider_ip_addresses: list[IpAddress] = Field(
         ..., default_factory=list[IpAddress]
     )
-    index: int = Field(..., ge=0)
+    index: int = Field(..., ge=1, le=256)
     remote_desktop: ConfigSubsectionRemoteDesktopOpts = Field(
         ..., default_factory=ConfigSubsectionRemoteDesktopOpts
     )
@@ -168,20 +167,13 @@ class ConfigSectionSRE(BaseModel, validate_assignment=True):
     @field_validator("databases")
     @classmethod
     def all_databases_must_be_unique(
-        cls, v: list[DatabaseSystem]
+        cls, v: list[DatabaseSystem | str]
     ) -> list[DatabaseSystem]:
-        if len(v) != len(set(v)):
+        v_ = [DatabaseSystem(d) for d in v]
+        if len(v_) != len(set(v_)):
             msg = "all databases must be unique"
             raise ValueError(msg)
-        return v
-
-    @field_serializer("software_packages")
-    def software_packages_serializer(
-        self,
-        packages: SoftwarePackageCategory,
-        info: FieldSerializationInfo,  # noqa: ARG002
-    ) -> str:
-        return packages.value
+        return v_
 
     def update(
         self,
@@ -260,6 +252,17 @@ def __init__(self, context: Context, **kwargs: dict[Any, Any]):
         tags = ConfigSectionTags(context)
         super().__init__(context=context, tags=tags, **kwargs)
 
+    @field_validator("sres")
+    @classmethod
+    def all_sre_indices_must_be_unique(
+        cls, v: dict[str, ConfigSectionSRE]
+    ) -> dict[str, ConfigSectionSRE]:
+        indices = [s.index for s in v.values()]
+        if len(indices) != len(set(indices)):
+            msg = "all SRE indices must be unique"
+            raise ValueError(msg)
+        return v
+
     @property
     def work_directory(self) -> Path:
         return self.context.work_directory
@@ -276,9 +279,15 @@ def pulumi_encryption_key(self) -> KeyVaultKey:
 
     @property
     def pulumi_encryption_key_version(self) -> str:
+        """ID for the Pulumi encryption key"""
         key_id: str = self.pulumi_encryption_key.id
         return key_id.split("/")[-1]
 
+    @property
+    def sre_names(self) -> list[str]:
+        """Names of all SREs"""
+        return list(self.sres.keys())
+
     def is_complete(self, *, require_sres: bool) -> bool:
         if require_sres:
             if not self.sres:
@@ -293,11 +302,16 @@ def sanitise_sre_name(name: str) -> str:
 
     def sre(self, name: str) -> ConfigSectionSRE:
         """Return the config entry for this SRE, raising an exception if it does not exist"""
-        if name not in self.sres.keys():
+        if name not in self.sre_names:
             msg = f"SRE {name} does not exist"
             raise DataSafeHavenConfigError(msg)
         return self.sres[name]
 
+    def remove_sre(self, name: str) -> None:
+        """Remove SRE config section by name"""
+        if name in self.sre_names:
+            del self.sres[name]
+
     def add_stack(self, name: str, path: Path) -> None:
         """Add a Pulumi stack file to config"""
         if self.pulumi:
@@ -336,6 +350,19 @@ def template(cls, context: Context) -> Config:
                 fqdn="TRE domain name",
                 timezone="Timezone",
             ),
+            sres={
+                "example": ConfigSectionSRE.model_construct(
+                    databases=["List of database systems to enable"],
+                    data_provider_ip_addresses=["Data provider IP addresses"],
+                    remote_desktop=ConfigSubsectionRemoteDesktopOpts.model_construct(
+                        allow_copy="Whether to allow copying text out of the environment",
+                        allow_paste="Whether to allow pasting text into the environment",
+                    ),
+                    workspace_skus=["Azure VM SKUs"],
+                    research_user_ip_addresses=["Research user IP addresses"],
+                    software_packages=SoftwarePackageCategory.ANY,
+                )
+            },
         )
 
     @classmethod
@@ -356,7 +383,7 @@ def from_yaml(cls, context: Context, config_yaml: str) -> Config:
             config_dict[section]["context"] = context
 
         try:
-            return Config.model_validate(config_dict)
+            return Config.model_validate(config_dict, strict=True)
         except ValidationError as exc:
             msg = f"Could not load configuration.\n{exc}"
             raise DataSafeHavenParameterError(msg) from exc
@@ -373,7 +400,7 @@ def from_remote(cls, context: Context) -> Config:
         return Config.from_yaml(context, config_yaml)
 
     def to_yaml(self) -> str:
-        return yaml.dump(self.model_dump(), indent=2)
+        return yaml.dump(self.model_dump(mode="json"), indent=2)
 
     def upload(self) -> None:
         """Upload config to Azure storage"""

data_safe_haven/external/api/azure_cli.py

@@ -68,10 +68,11 @@ def confirm(self) -> None:
             return None
 
         account = self.account
-        self.logger.info(
-            f"name: {account.name} (id: {account.id_}\ntenant: {account.tenant_id})"
-        )
-        if not typer.confirm("Is this the Azure account you expect?\n"):
+        self.logger.info(f"Azure user: {account.name} ({account.id_})")
+        self.logger.info(f"Azure tenant ID: {account.tenant_id})")
+        if not self.logger.confirm(
+            "Is this the Azure account you expect?", default_to_yes=False
+        ):
             self.logger.error(
                 "Please use `az login` to connect to the correct Azure CLI account"
             )

data_safe_haven/infrastructure/stacks/declarative_sre.py

@@ -90,7 +90,7 @@ def run(self) -> None:
                 shm_networking_resource_group_name=self.pulumi_opts.require(
                     "shm-networking-resource_group_name"
                 ),
-                sre_index=self.cfg.sres[self.sre_name].index,
+                sre_index=self.cfg.sre(self.sre_name).index,
             ),
             tags=self.cfg.tags.model_dump(),
         )
@@ -124,11 +124,11 @@ def run(self) -> None:
                     "shm-networking-virtual_network_name"
                 ),
                 shm_zone_name=self.cfg.shm.fqdn,
-                sre_index=self.cfg.sres[self.sre_name].index,
+                sre_index=self.cfg.sre(self.sre_name).index,
                 sre_name=self.sre_name,
-                user_public_ip_ranges=self.cfg.sres[
+                user_public_ip_ranges=self.cfg.sre(
                     self.sre_name
-                ].research_user_ip_addresses,
+                ).research_user_ip_addresses,
             ),
             tags=self.cfg.tags.model_dump(),
         )
@@ -148,7 +148,7 @@ def run(self) -> None:
                 resource_group_name=self.pulumi_opts.require(
                     "shm-monitoring-resource_group_name"
                 ),
-                sre_index=self.cfg.sres[self.sre_name].index,
+                sre_index=self.cfg.sre(self.sre_name).index,
                 timezone=self.cfg.shm.timezone,
             ),
             tags=self.cfg.tags.model_dump(),
@@ -162,9 +162,9 @@ def run(self) -> None:
                 admin_email_address=self.cfg.shm.admin_email_address,
                 admin_group_id=self.cfg.azure.admin_group_id,
                 admin_ip_addresses=self.cfg.shm.admin_ip_addresses,
-                data_provider_ip_addresses=self.cfg.sres[
+                data_provider_ip_addresses=self.cfg.sre(
                     self.sre_name
-                ].data_provider_ip_addresses,
+                ).data_provider_ip_addresses,
                 dns_record=networking.shm_ns_record,
                 dns_server_admin_password=dns.password_admin,
                 location=self.cfg.azure.location,
@@ -204,8 +204,8 @@ def run(self) -> None:
                 aad_application_fqdn=networking.sre_fqdn,
                 aad_auth_token=self.graph_api_token,
                 aad_tenant_id=self.cfg.shm.aad_tenant_id,
-                allow_copy=self.cfg.sres[self.sre_name].remote_desktop.allow_copy,
-                allow_paste=self.cfg.sres[self.sre_name].remote_desktop.allow_paste,
+                allow_copy=self.cfg.sre(self.sre_name).remote_desktop.allow_copy,
+                allow_paste=self.cfg.sre(self.sre_name).remote_desktop.allow_paste,
                 database_password=data.password_user_database_admin,
                 dns_server_ip=dns.ip_address,
                 ldap_bind_dn=ldap_bind_dn,
@@ -260,7 +260,7 @@ def run(self) -> None:
                 subscription_name=self.cfg.context.subscription_name,
                 virtual_network_resource_group=networking.resource_group,
                 virtual_network=networking.virtual_network,
-                vm_details=list(enumerate(self.cfg.sres[self.sre_name].workspace_skus)),
+                vm_details=list(enumerate(self.cfg.sre(self.sre_name).workspace_skus)),
             ),
             tags=self.cfg.tags.model_dump(),
         )
@@ -271,7 +271,7 @@ def run(self) -> None:
             self.stack_name,
             SREUserServicesProps(
                 database_service_admin_password=data.password_database_service_admin,
-                databases=self.cfg.sres[self.sre_name].databases,
+                databases=self.cfg.sre(self.sre_name).databases,
                 dns_resource_group_name=dns.resource_group.name,
                 dns_server_ip=dns.ip_address,
                 domain_netbios_name=self.pulumi_opts.require(
@@ -288,7 +288,7 @@ def run(self) -> None:
                 location=self.cfg.azure.location,
                 networking_resource_group_name=networking.resource_group.name,
                 nexus_admin_password=data.password_nexus_admin,
-                software_packages=self.cfg.sres[self.sre_name].software_packages,
+                software_packages=self.cfg.sre(self.sre_name).software_packages,
                 sre_fqdn=networking.sre_fqdn,
                 sre_private_dns_zone_id=networking.sre_private_dns_zone_id,
                 storage_account_key=data.storage_account_data_configuration_key,

tests_/commands/test_config.py

@@ -6,18 +6,20 @@ def test_template(self, runner):
         result = runner.invoke(config_command_group, ["template"])
         assert result.exit_code == 0
         assert "subscription_id: Azure subscription ID" in result.stdout
-        assert "sres: {}" in result.stdout
+        assert "shm:" in result.stdout
+        assert "sres:" in result.stdout
 
     def test_template_file(self, runner, tmp_path):
-        template_file = (tmp_path / "template.yaml").absolute()
+        template_file = (tmp_path / "template_create.yaml").absolute()
         result = runner.invoke(
             config_command_group, ["template", "--file", str(template_file)]
         )
         assert result.exit_code == 0
         with open(template_file) as f:
             template_text = f.read()
         assert "subscription_id: Azure subscription ID" in template_text
-        assert "sres: {}" in template_text
+        assert "shm:" in template_text
+        assert "sres:" in template_text
 
 
 class TestUpload:
@@ -41,3 +43,15 @@ def test_show(self, runner, config_yaml, mock_download_blob):  # noqa: ARG002
         result = runner.invoke(config_command_group, ["show"])
         assert result.exit_code == 0
         assert config_yaml in result.stdout
+
+    def test_show_file(
+        self, runner, config_yaml, mock_download_blob, tmp_path  # noqa: ARG002
+    ):
+        template_file = (tmp_path / "template_show.yaml").absolute()
+        result = runner.invoke(
+            config_command_group, ["show", "--file", str(template_file)]
+        )
+        assert result.exit_code == 0
+        with open(template_file) as f:
+            template_text = f.read()
+        assert config_yaml in template_text