' + + '' + + _("Hide Search Matches") + + "
" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/advanced_use.html b/advanced_use.html new file mode 100644 index 0000000..6a3916f --- /dev/null +++ b/advanced_use.html @@ -0,0 +1,122 @@ + + + + + + +TODO:
+This section describes how to implement a server that goes beyond the standard functionalities provided by
+BioDM.
Bases: Starlette
Main Server class.
+Sets up and holds managers + OpenAPI schema generator
Instanciates CORE_CONTROLLERS and passed controllers +- Sets up routes
adds our middlewares
listens on events
Adopts controllers, and their associated routes.
+Conditionally deploy managers. Each manager connects to an external service. +Appart from the DB, managers are optional, with respect to config population.
+Bases: BaseHTTPMiddleware
Logins in authenticated user requests in History.
+Bases: BaseHTTPMiddleware
Emit timeout signals.
+Bases: ResourceController
Group Controller.
+Bases: ResourceController
User Controller.
+Bases: ResourceController
Kubernetes Instances Controller.
+Deploys K8s Instance.
+Instance info.
+List running K8s Instances.
+Routes for k8s instances management
+schema (bool) – when called from schema generation, defaults to False
+starlette.routing.Mount
+Bases: Controller
Bundles Routes located at the root of the app i.e. ‘/’.
+ + +Login handshake function.
+Syn_Ack url
+str
+Liveness endpoint.
+Login endpoint.
+Generates openapi schema.
+Controller routes.
+We get an authorization code that we redeem to keycloak for a token. +This way the client_secret remains hidden to the user.
+Bases: object
Abstract API component, refrencing main server class and its loggger.
+app (class:biodm.Api) – Reference to running server class.
+Bases: ApiComponent
Manager base class. +A manager represents an external service dependency. +It holds a connection object and relevant primitives for data state change.
+External service endpoint.
+Bases: ApiComponent
Service base class. +A Service acts as a translation layer between a controller receiving a request +and managers executing data state change.
+Bases: ResourceController
Class for admin managed entities, i.e. KC User/Groups/Projects.
+READ require an admin token based on read_public flag
CREATE/UPDATE/DELETE require an admin token
Controller base class.
+Bases: ApiComponent
Controller Base class: An APP Component exposing a set of routes mapped to method +endpoints including openapi schema generation for that given set.
+Generates openapi schema for this controllers’ routes.
+starlette: https://www.starlette.io/schemas/
doctrings: https://apispec.readthedocs.io/en/stable/
status codes: https://restfulapi.net/http-status-codes/
Controller routes.
+Bases: Controller
Also requires CRUD methods implementation for that entity.
+schema (class:marshmallow.schema.Schema) – Entity schema class
+Serialize SQLAlchemy statement execution result to json.
+data (dict, class:biodm.components.Base, List[class:biodm.components.Base]) – some request body
many (bool) – plurality flag, essential to marshmallow
only (Iterable[str]) – Set of fields to restrict serialization on, optional, defaults to None
Check incoming data against class schema and marshall to python dict.
+data (bytes) – some request body
+Marshalled python dict and plurality flag.
+Tuple[(Any | List[Any] | Dict[str, Any] | None), bool]
+Controller
+EntityController
+HttpMethod
+Api Componenents exposing routes. +Also responsible for validation and serialization and openapi schema generation.
+Controller class for Tables acting as a Resource.
+Bases: EntityController
Class for controllers exposing routes constituting a ressource.
+Implements and exposes routes under a prefix named as the resource pluralized +that act as a standard REST-to-CRUD interface.
+Creates associated entity.
+Does “UPSERTS” behind the hood. +If you’d prefer to avoid the case of having an entity being created with parts of its +primary key you should flag said parts with dump_only=True in your marshmallow schemas.
+request (Request) – incomming request
+created object in JSON form
+Response
+Delete resource.
+request (Request) – incomming request
+Deletion confirmation ‘Deleted.’
+Response
+Returns all resources, accepting a querystring filter.
+Computes route path prefix from entity name.
+Put primary key in queryparam form.
+Fetch associated entity matching id in the path.
+request (Request) – incomming request
+JSON reprentation of the object
+Response
+Call read, with attribute and serializes with child resource controller.
+Releases a new version for a versioned resource.
+child_routes: from children classes calling super().__init__().
+Relevant doc: +- https://restfulapi.net/http-methods/
+UPDATE. Essentially calling create, as it perorm upserts.
+request (Request) – incomming request
+updated object in JSON form
+Response
+Decorator to allow for docstring overloading.
+To apply on a “c-like” preprocessor on controllers subclasses. +Targeted at the REST-to-CRUD mapped endpoints in order to do a per-entity schema documentation.
+Necessary because docstring inheritance is managed a little bit weirdly +behind the hood in python and depending on the version the .__doc__ attribute of a +member function is not editable - Not the case as of python 3.11.2.
+Relevant SO posts: +- https://stackoverflow.com/questions/38125271/extending-or-overwriting-a-docstring-when-composing-classes +- https://stackoverflow.com/questions/1782843/python-decorator-handling-docstrings
+f (Callable) – The method we overload the docstrings of
+Bases: ResourceController
Controller for entities involving file management leveraging an S3Service.
+Returns boto3 presigned download URL with a redirect header.
+Add an endpoint for successful file uploads and direct download.
+Uppon receival, update entity status in the DB.
+Base
+Permission
+S3File
+Versioned
+Database service: Translates requests data into SQLA statements and execute.
+Bases: UnaryEntityService
Special case for Composite Entities (i.e. containing nested entities attributes).
+CREATE, Handle list and single case.
+Get permissions relationships by computing the difference of between instanciation time +and runtime, since those get populated later in Base.setup_permissions().
+Bases: ApiService
DB Service class: manages database transactions for entities. +Holds atomic database statement execution functions.
+Bases: DatabaseService
Generic Service class for non-composite entities.
+CREATE one or many rows. data: schema validation result.
+Does UPSERTS behind the hood, hence this method is also called on UPDATE
Perform write permission check according to input data
READ rows filted on query parameters.
+Generates (pk_1 == pk_1.type.python_type(val_1)) & (pk_2 == …) …). +Without evaluating at runtime, so it can be plugged in a where condition.
+pk_val (List[Any]) – Primary key values
+CNF Clause
+Any
+Handle SQLite autoincrement for composite primary key. +Which is a handy feature for a versioned entity. So we fetch the current max id in a +separate request and prepopulate the dicts. This is not the most performant, but sqlite +support is for testing purposes mostly.
+READ: fetch one ORM mapped object from value(s) of its primary key.
+pk_val (List[Any]) – entity primary key values in order
fields (List[str], optional) – fields to restrict the query on, defaults to None
SQLAlchemy ORM item
+Read nested collection from an entity.
+Internal translation layer from controller endpoints to managers.
+Bases: CompositeEntityService
Manages kubernetes instances.
+Submits manifest to kubernetes cluster before inserting into DB.
+Bases: KCService
Create entities on Keycloak Side before passing to parent class for DB.
+DELETE Group from DB then from Keycloak.
+READ group from keycloak, create if not found.
+data (Dict[str, Any]) – Group data
+Bases: CompositeEntityService
Abstract class for local keycloak entities.
+Return KCManager instance.
+Try to read from DB, create on keycloak side if not present. +Populate ‘id’ - Keycloak UUID in string form - in data.
+Bases: KCService
CREATE entities on Keycloak, before inserting in DB.
+DELETE User from DB then from keycloak.
+READ entry from Database, CREATE it if not found.
+data (Dict[str, Any]) – Entry object representation
groups (List[str], optional) – User groups, defaults to None
group_ids (List[str], optional) – User groups ids, defaults to None
User id
+str
+Bases: UnaryEntityService
Class that manages AWS S3 bucket transactions. +Automatically associated with files entities which in principle should be unary.
+SQLAlchemy tables convenience Parent classes: +- Declarative Base +- File entity +- Permission setup logic
+Bases: DeclarativeBase, AsyncAttrs
Base class for ORM declarative Tables.
+svc (DatabaseService) – Enable entity - service linkage
ctrl (ResourceController) – Enable entity - controller linkage -> Resources tables only
raw_permissions (Dict) – Stores rules for user defined permissions on hierarchical entities
permissions (Dict) – Stores processed permissions with hierarchical linkage.
Return columns object from name.
+Return column and associated python type for conditions.
+Refers to the _schema.MetaData collection that will be used
+for new _schema.Table objects.
See also
+ +Return primary key names.
+Refers to the _orm.registry in use where new
+_orm.Mapper objects will be associated.
Return table relationships.
+After tables have been added to Base, and before you initialize DB +you shall call this method to factor in changes.
+children hold parent id
Set ref for Children controller
Has to be done after all tables have been declared.
+Currently assumes straight composition: +i.e. You cannot flag an o2m with the same target in two different parent classes.
+Return target table of a property.
+Bases: object
Holds permissions for a given entity’s attributes.
+Bases: object
Class to use in order to have a file managed on S3 bucket associated to this table +Defaults internal fields that are expected by S3Service.
+Bases: object
Versioned entity parent class.
+Populates id/version primary_key fields
Enable release functionalities
Error event handler.
+Relevant documentation: https://restfulapi.net/http-status-codes/
+Bases: RuntimeError
Raised when DB related errors are catched.
+Bases: RequestError
Could not create record.
+Bases: RequestError
Raised when a delete operation is not successful.
+Bases: RequestError
Requested record doesn’t exist.
+Bases: RequestError
Raised when an update operation is not successful.
+Bases: RuntimeError
Raised when a wrong use of components is detected.
+Bases: RequestError
Raised when a unit method is accesed as a collection.
+Bases: RuntimeError
Raised when Keycloak failed to initialize.
+Bases: RequestError
Raised when a request requiring a manifest id fails to find it in instance.
+Bases: RequestError
DB access attempted with no manager attached to the service.
+Bases: RuntimeError
Raised when a controller expects a service that is not present.
+Bases: RequestError
Raised when a method expecting entity primary key receives a partial index.
+Bases: RuntimeError
Raised when a route expecting a payload, is reached without one.
+Bases: RuntimeError
Raised when payload data failed to be parsed in JSON format.
+Bases: RuntimeError
Raised when input data can not be coerced into an entity.
+Bases: RuntimeError
Raised when Postgres failed to initialize.
+Bases: RuntimeError
Raised when faulty schema pattern is detected.
+Bases: RequestError
Raised when token decoding failed.
+Bases: RequestError
Raised when a request on a group restricted route is sent by an unauthorized user.
+AsyncDBErrorDBError
+FailedCreateFailedDeleteFailedReadFailedUpdateImplementionErrorInvalidCollectionMethodKeycloakUnavailableErrorManifestErrorMissingDBMissingServicePartialIndexPayloadEmptyErrorPayloadJSONDecodingErrorPayloadValidationErrorPostgresUnavailableErrorRequestError
+SchemaErrorTokenDecodingErrorUnauthorizedErrorScope
+BioDM framework.
+Bases: ApiManager
Manages DB side query execution.
+Adds a matching async driver to a database url.
+External service endpoint.
+Session object is either passed as an argument (from nested obj creation) or a new context +manager is opened. This decorator guarantees exactly 1 session per request.
+Also performs serialization within a sync session:
+Avoids errors in case serializing acceses a lazy attribute
All functions applying this decorator should pass down some **kwargs
Drop all tables and create them.
+Opens and yields a new AsyncSession.
+Custom string revese function for SQLite backend.
+K8sManagerK8sManager.AppsV1ApiK8sManager.CoreV1ApiK8sManager.CustomObjectsApiK8sManager.NetworkingV1ApiK8sManager.authenticate()K8sManager.change_namespace()K8sManager.create_custom_resource()K8sManager.create_deployment()K8sManager.create_ingress()K8sManager.create_service()K8sManager.delete_custom_object()K8sManager.endpointK8sManager.get_custom_resource_params()K8sManager.get_name_in_manifest()K8sManager.list_custom_object()K8sManager.list_deployments()K8sManager.list_pods()K8sManager.list_services_ports()K8sManager.log()K8sManager.read_deployment()K8sManager.read_ingress()K8sManager.read_service_status()KeycloakManagerKeycloakManager.adminKeycloakManager.auth_url()KeycloakManager.create_group()KeycloakManager.create_user()KeycloakManager.decode_token()KeycloakManager.delete_group()KeycloakManager.delete_user()KeycloakManager.endpointKeycloakManager.get_group()KeycloakManager.get_group_by_name()KeycloakManager.get_group_by_path()KeycloakManager.get_user_by_username()KeycloakManager.get_user_groups()KeycloakManager.group_user_add()KeycloakManager.openidKeycloakManager.redeem_code_for_token()KeycloakManager.update_group()KeycloakManager.update_user()I/O with external services.
+Bases: ApiManager
Small util wrapper around kubernetes python client API.
+K8_HOST Address of the kubernetes cluster. +K8_TOKEN Token of the authorized serviceaccount. +K8_CERT Path to kubernetes cluster root certificate +K8_NAMESPACE Active namespace
+The client exposes several APIs: +- https://github.com/kubernetes-client/python/blob/a6d44ff625b5e8d8ad380a70245d40fa3d5472b2/kubernetes/README.md?plain=1 +Each api has access to a subset of the ressources.
+AppsV1 kubernetes api
+CoreV1 kubernetes api
+NetworkingV1 kubernetes api
+NetworkingV1 kubernetes api
+Set configuration with the credentials and certificate
+Change active namespace
+Create a custom resource.
+Create a deployment
+Create an ingress
+Create a service
+External service endpoint.
+Try to find and return metadata.name field from a manifest
+List all deployments.
+List all pods.
+List all service ports in use, support selectors.
+Conditional print
+Bases: ApiManager
Manages a service account connection and an admin connection. +Use the first to authenticate tokens and the second to manage the realm.
+Admin connection.
+Authentication URL.
+Create group.
+Decode token.
+Delete group with this id.
+Delete user with this id.
+External service endpoint.
+Add user with user_id to group with group_id.
+Service account connection.
+Code for token.
+Update group.
+Update user.
+Bases: ApiManager
Manages requests with an S3 storage instance.
+Generate a presigned URL to share an S3 object
+object_name – string
+Presigned URL as string.
+Generates a presigned url + form fiels to upload a given file on s3 bucket.
+Relevant links: +- https://boto3.amazonaws.com/v1/documentation/api/latest/guide/s3-presigned-urls.html +- https://github.com/minio/minio/issues/19811#issue-2317920163
+External service endpoint.
+Bases: Schema
Schema for Keycloak Groups. id field is purposefully left out as we manage it internally.
+Bases: Schema
K8Instance Schema.
+Bases: Schema
Bases: Schema
Schema for Keycloak Users. id field is purposefully left out as we manage it internally.
+Internally managed tables.
+UserInfoUserInfo.KeycloakManagerUserInfo.KeycloakManager.adminUserInfo.KeycloakManager.auth_url()UserInfo.KeycloakManager.create_group()UserInfo.KeycloakManager.create_user()UserInfo.KeycloakManager.decode_token()UserInfo.KeycloakManager.delete_group()UserInfo.KeycloakManager.delete_user()UserInfo.KeycloakManager.endpointUserInfo.KeycloakManager.get_group()UserInfo.KeycloakManager.get_group_by_name()UserInfo.KeycloakManager.get_group_by_path()UserInfo.KeycloakManager.get_user_by_username()UserInfo.KeycloakManager.get_user_groups()UserInfo.KeycloakManager.group_user_add()UserInfo.KeycloakManager.openidUserInfo.KeycloakManager.redeem_code_for_token()UserInfo.KeycloakManager.update_group()UserInfo.KeycloakManager.update_user()UserInfo.auth_header()UserInfo.decode_token()UserInfo.infoUserInfo.kcadmin_required()group_required()login_required()utils.
+Security convenience functions.
+Bases: aobject
Hold user info for a given request.
+If the request contains an authentication header, self.info shall return User Info, else None
+Bases: ApiManager
Manages a service account connection and an admin connection. +Use the first to authenticate tokens and the second to manage the realm.
+Admin connection.
+Authentication URL.
+Create group.
+Decode token.
+Delete group with this id.
+Delete user with this id.
+External service endpoint.
+Add user with user_id to group with group_id.
+Service account connection.
+Code for token.
+Update group.
+Update user.
+Check and return token from headers if present else returns None.
+Decode token.
+group_required special case for admin group.
+Decorator for function expecting groups: decorates a controller CRUD function.
+Docorator for function expecting header ‘Authorization: Bearer <token>’
+Bases: object
Class to hold composite entities statements before insertion.
+item (Insert) – Parent item insert statement
nested (Dict[str, Insert | CompositeInsert | List[Insert] | List[CompositeInsert]]) – Nested items insert statement indexed by attribute name
delayed (Dict[str, Insert | CompositeInsert | List[Insert] | List[CompositeInsert]]) – Nested list of items insert statements indexed by attribute name
Utils.
+Bases: object
Inheriting this class allows you to define an async __init__. +Syntax sugar allowing you to create objects like this await MyClass(params).
+Courtesy of: https://stackoverflow.com/a/45364670/6847689
+Assembles multiple dicts into one. +- Overlapping keys: override value in order.
+Encodes python Dict as utf-8 bytes.
+Formats a Response object and set application/json header.
+Partition a list into two based on condition. +Return list of values checking condition. +If excl_na, values whose truth value is False will be evicted from both lists.
+ls (list) – input list
cond (Callable[[_T], bool]) – Condition
excl_na – Exclude empty flag
Lists of elements separated around condition
+List[_T], List[_T]
+Return identity list/tuple or pack atomic value in a tuple.
+Python version of the unix shell touch function.
+Build (ls[0] and ls[1] … ls[n]) but does not evaluate like all() does.
+Build (ls[0] or ls[1] … ls[n]) but does not evaluate like or() does.
+Support for python==3.10 and below.
+AsyncDBErrorDBErrorFailedCreateFailedDeleteFailedReadFailedUpdateImplementionErrorInvalidCollectionMethodKeycloakUnavailableErrorManifestErrorMissingDBMissingServicePartialIndexPayloadEmptyErrorPayloadJSONDecodingErrorPayloadValidationErrorPostgresUnavailableErrorRequestErrorSchemaErrorTokenDecodingErrorUnauthorizedErrorScopeThis section describes how to use biodm package in order to swiftly deploy a modular
+data management API tailored to your needs.
You also may consult src/example/ toy project, which encapsulates more complex project needs.
Following, we will go in detail about the toolkit and builtins.
+At the core of Data Management means storing collections of files and their associated metadata.
+BioDM is leveraging SQLAlchemy ORM Tables definitions + matching Marshmallow Schemas, specifying
+metadata and relationships, to setup standard RESTful endpoints.
The main server class biodm.Api is a vessel for biodm.components.controllers.Controller
+subinstances.
Each Controller is independently responsible for exposing a set of routes, validating and serializing
+i/o and send incomming Request data to a relevant biodm.component.ApiService subinstance.
Services, are tied to a Table and calling each other in order to parse and adapt
+input data.
+All Services are biodm.components.services.DatabaseService subinstances as their
+primary mission is to faithfully log activity and maintain data integrity.
Finally this internal representation is sent to a biodm.component.managers, each holding communication primities with external micro-services (i.e. DB, S3 bucket, Kubernetes and so on).
BioDM extends Starlette,
+hence its Configuration system works by populating a .env file, preferably sitting in the same directory as the running script.
We invite you to consult config.py +to discover all possible options.
+Functionalities depending on external micro-services are enabled if matching configuration options are provided.
+e.g. Keycloak functionalities shall be activated, if and only if, defaultless config parameters prefixed by KC_ are populated.
+Otherwise, User/Group tables shall still be deployed. However, they will not be synced against a keycloak server.
You may have a look at compose.test.yml file to see how testing containers used in our CI, are deployed with partial configuration in order to test by parts.
Say you or your organization needs to store Datasets, each containing a set of File we will go
+over the following minimal example.
import marshmallow as ma
+from marshmallow import fields as mf
+import sqlalchemy as sa
+from sqlalchemy import orm as sao
+from typing import List
+import uvicorn
+
+import biodm as bd
+from biodm.components.controllers import ResourceController, S3Controller
+
+
+# Tables
+class Dataset(bd.components.Versioned, bd.components.Base):
+ name : sao.Mapped[str] = sa.Column(sa.String(50), nullable=False)
+ description : sao.Mapped[str] = sa.Column(sa.String(500), nullable=False)
+ username_owner: sao.Mapped[int] = sa.Column(sa.ForeignKey("USER.username"), nullable=False)
+ owner : sao.Mapped["User"] = sao.relationship(foreign_keys=[username_owner])
+ files : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset")
+
+class File(bd.components.S3File, bd.components.Base):
+ id = sa.Column(sa.Integer, primary_key=True)
+ id_dataset = sa.Column(sa.ForeignKey("DATASET.id"), nullable=False)
+ dataset: sao.Mapped["Dataset"] = sao.relationship(back_populates="files", single_parent=True, foreign_keys=[id_dataset])
+
+# Schemas
+class DatasetSchema(ma.Schema):
+ id = mf.Integer()
+ version = mf.Integer()
+ name = mf.String(required=True)
+ description = mf.String(required=False)
+ username_owner = mf.String(required=True, load_only=True)
+ owner = mf.Nested("UserSchema")
+ files = mf.List(mf.Nested("FileSchema"))
+
+class FileSchema(ma.Schema):
+ id = mf.Integer()
+ filename = mf.String(required=True)
+ extension = mf.String(required=True)
+ url = mf.String( dump_only=True)
+ ready = mf.Bool( dump_only=True)
+ id_dataset = mf.Integer(required=True, load_only=True)
+ dataset = mf.Nested("DatasetSchema")
+
+# Controllers
+class DatasetController(ResourceController):
+ def __init__(self, app) -> None:
+ super().__init__(app=app)
+
+class FileController(S3Controller):
+ def __init__(self, app) -> None:
+ super().__init__(app=app)
+
+# Server
+def main():
+ return bd.Api(debug=True, controllers=[DatasetController, FileController],)
+
+if __name__ == "__main__":
+ uvicorn.run(
+ f"{__name__}:main", factory=True,
+ host=bd.config.SERVER_HOST, port=bd.config.SERVER_PORT,
+ loop="uvloop", log_level="debug", access_log=False
+ )
+Note
+Dataset has no declared primary_key fields, because it inherits from Versioned that populate
+[id, version] as primary key. To see what this enables, see also User Manual.
Warning
+It is currently not possible to apply Versioned and S3File on the same table. This is
+planned for v0.5.0 release.
Warning
+SQLite doesn’t support [partial|] autoincrement for a composite primary key. +In the case of a versioned entity, this is explicitely handled by fetching the max index for +newly created objects. Overall it is advised to avoid composite primary key for sqlite.
+Note
+Notice that File Table declarative Class inherits from S3File component and is
+paired with an S3Controller. Those two classes are automatically handling extra fields
+that can be seen on FileSchema and extra routes.
+For other tables, if you’re only interested about standard functionalities, you should stick with Base and ResourceController.
Note
+For file management this demo requires an s3 compatible storage service.
+To quickly deploy micro-services dependencies for testing purposes, refer to
+Development environment.
The following variables have to be provided.
+S3_ENDPOINT_URL=
+S3_BUCKET_NAME=
+S3_ACCESS_KEY_ID=
+S3_SECRET_ACCESS_KEY=
+Running this script deploys a server:
++++
+- +
Responding on standard RESTful routes (see User Manual) for:
++++
+- +
Instance tables: Dataset, File
++
+- +
Serving pre-signed PUT/GET URLs for direct file upload/download.
- +
Core tables: User, Group
++
+- +
Keycloak not being enabled, those tables are managed locally.
- +
Internally managing core tables:
++++
+- +
ListGroup, History
In order to protect your data, BioDM provides two structures of permissions.
Those are requiring a keycloak service running and the following variables to
+be provided in a .env file at the same level as your demo.py script.
KC_HOST=
+KC_REALM=
+KC_PUBLIC_KEY=
+KC_ADMIN=
+KC_ADMIN_PASSWORD=
+KC_CLIENT_ID=
+KC_CLIENT_SECRET=
+biodm.utils.security module contains three decorators that are meant to be used
+on Controller endpoints in order to apply static permissions directly within the codebase.
@token_required()
Protects the endpoint demanding incomming requests to by signed with a valid Keycloak JW Token
@group_required(groups=[gname_1,... gname_n])
Like token_required, and assesses that requesting User is part of one of those groups.
@admin_required()
group_required special case, requesting User must be part of admin group.
On our example, this is how you could apply those on DatasetController:
+from biodm.utils.security import group_required, admin_required
+
+class DatasetController(bdc.ResourceController):
+ def __init__(self, app) -> None:
+ super().__init__(app=app)
+ self.create = group_required(self.create, ['my_team'])
+ self.update = group_required(self.update, ['my_team'])
+ self.delete = admin_required(self.delete)
+Here we restricted the creation and updating of datasets to my_team, deletion is admin
+priviledge and reading data is left public.
In case you would also like to document your API endpoints, you may use those decorators in
+combination with @overload_docstrings, made to overload docstrings of controller methods:
from biodm.utils.security import group_required, admin_required
+
+class DatasetController(bdc.ResourceController):
+ def __init__(self, app) -> None:
+ super().__init__(app=app)
+
+ @group_required(['my_team'])
+ @overload_docstring
+ async def create(**kwargs):
+ """
+ requestBody:
+ description: payload.
+ required: true
+ content:
+ application/json:
+ schema: DatasetSchema
+ responses:
+ 201:
+ description: Create Dataset.
+ examples: |
+ # TODO:
+ {"name": "instant_sc_1234", ""}
+ content:
+ application/json:
+ schema: DatasetSchema
+ 204:
+ description: Empty Payload.
+ """
+ ...
+ class TagController(ResourceController):
+ @overload_docstring
+ async def read(**kwargs):
+ """
+ parameters:
+ - in: path
+ name: name
+ description: Tag name
+ responses:
+ 200:
+ description: Found matching Tag.
+ examples: |
+ {"name": "epidemiology"}
+ content:
+ application/json:
+ schema: TagSchema
+ 404:
+ description: Tag not found.
+ """
+ ...
+Warning
+@overload_docstrings returns a wrapper pointing to the parent class method,
+hence if you use the latter variant, be sure to this decorator first even if you do not wish to
+document that endpoint.
Docstrings Guide
+Docstrings are parsed by apispec and shall
+comply with their specification. In particular you have to be precise with parameters,
+and marshmallow schema specifications.
+This is required in order to output specification in OpenAPISchema format,
+which enables support for swagger-ui and the rest of the ecosystem.
Note
+The core patches abstract method documentation at runtime for endpoints that are left
+undocumented. However, if you are using @overload_docstrings ensuring that it works is up
+to you.
If your data management platform is intended to receive data from users external to your
+organisation, BioDM provide tools to let them in control of permissions.
biodm.components.Permission class is designed as an extra SQLAlchemy table argument that let
+you flag composition pattern (i.e. One-to-Many relationships) with the following permissions that
+will be applied recursively for all children of that particular entity:
Read
Write
Download
In our example:
+from biodm.components import Permission
+
+
+class Dataset(bd.components.Base):
+ id : sao.Mapped[int] = sa.Column(sa.Integer, primary_key=True)
+ ...
+ files : sao.Mapped[List["File"]] = sao.relationship(back_populates="dataset")
+
+ __permissions__ = (
+ Permission(files, write=True, read=False, download=True),
+ )
+The latter enables File permissions at the Dataset level.
In other words it lets you define for a top level entity who is allowed to interact +with a nested collection and its elements.
+Note
+Those permissions will be taken into account when directly accessing /files API routes.
|
+
|
+
| + | + |
|
+ + |
| + | + |
|
+ + |
| + | + |
| + | + |
| + | + |
| + | + |
|
+
|
+
| + |
| + | + |
| + | + |
| + |
Recommended: PEP 405 Create virtual environment
python3 -m venv venv
+source venv/bin/activate/
+Warning
+using built in python tools such as venv and pip is preferred.
+conda and co. package managers are currently untested.
Using pip and git
pip3 install git+https://github.com/bag-cnag/biodm
+Install with kubernetes functionalities
pip3 install "biodm[kubernetes] @ git+https://github.com/bag-cnag/biodm"
+Build from sources
git clone https://github.com/bag-cnag/biodm
+cd biodm/
+pip3 install -r src/requirements/dev.txt
+pip3 install .
+E.g. for our example project.
+Configuration is done through .env files, thus server has to be run from its immediate directory.
+The one provided at src/example/.env is set on development environment values.
cd src/example/
+python3 app.py
+Install in editable mode
pip3 install -r src/requirements/dev.txt
+pip3 install -e .
+To start all service dependnencies at once and skip individual configuration you may use
+the provided compose.yml. Passing the flag –build it will also build for you an appropriate
+keycloak image with your local certificates in order to serve https:// requests.
docker compose up --build -d
+Default configuration parameters are set on fixed IPs declared in this compose.yml file.
optional - strongly recommended for keycloak -: for testing convenience you +may add those lines to your host table.
+sudo cat >> /etc/hosts <<EOF
+# biodm-dev
+10.10.0.2 postgres.local
+10.10.0.3 keycloak.local
+10.10.0.4 s3bucket.local
+EOF
+It might be a pre-requisite for keycloak as it is quite strict with security protocols. +Definitely something to try if you cannot reach admin UI or your app is unable to fetch any data.
+Swagger-UI This compose file also bundles a Swagger-UI set to discover API routes.
+It is available at http://localhost:9080
Optional: - To personalize defaults, see Individual configuration below.
+- Keycloak comes with a default 3TR realm and appropriate client that has user/group rights.
+- MinIO launches with admin credentials, that are used as ACCESS_KEY.
Database
docker run --name api-db -e POSTGRES_PASSWORD=pass -d postgres:16-bookworm
+docker exec -u postgres api-db createdb biodm
+Keycloak
First you need to build the image yourself according to the documentation:
+cd docker/ && \
+docker build . -t keycloak:22.0_local-certs \
+ -f Dockerfile.keycloak-22.0_local-certs \
+ --build-arg _KC_DB=postgres \
+ --build-arg _KC_DB_USERNAME=postgres \
+ --build-arg _KC_DB_PASSWORD=pass \
+ --build-arg=_KC_HOSTNAME=keycloak.local \
+ --build-arg _KC_DB_URL=jdbc:postgresql://10.10.0.5:5432/keycloak && \
+cd -
+Keycloak also needs a databse:
+docker run --name kc-db -e POSTGRES_PASSWORD=pass -e POSTGRES_DB=keycloak -d postgres:16-bookworm
+docker exec -u postgres biodm-pg createdb keycloak
+Then you may start keycloak itself:
+docker run --name local_keycloak -e KEYCLOAK_USER=admin -e KEYCLOAK_PASSWORD=admin -p 8443:8080 keycloak:22.0.5_local-certs
+Configuration
+Once keycloak is running you need to configure a realm and a client for the app to log in. +Default values are:
+KC_REALM="3TR"
+KC_CLIENT_ID="submission_client"
+Once you’ve created the realm, create the client. Then
++++
+- +
set Access Type to confidential
- +
set Inplicit Flow Enabled to True.
- +
Add Valid Redirect Uri:
++
+- +
dev: http://* and https://*
- +
prod: provide the url of the login callback {SERVER_HOST}/syn_ack.
Note
+Depending on your keycloak version or running instance SERVER_HOST may have to be appended with /auth.
+Then you should provide the server with the SECRET field located in the
+Credentials tab, that appears after you changed access type and the realm public key
+located at {KC_HOST}[auth/]realms/{KC_REALM}/.
To be able to serve as a gateway to administrate keycloak concepts, +the API also needs admin credentials:
+KC_HOST={url}
+KC_CLIENT_SECRET={secret}
+KC_PUBLIC_KEY={public_key}
+KC_ADMIN={admin_id}
+KC_ADMIN_PASSWORD={admin_password}
+Minio
docker run -e MINIO_ROOT_USER=admin \
+ -e MINIO_ROOT_PASSWORD=12345678 \
+ -e MINIO_DEFAULT_BUCKETS=bucketdevel3tropal \
+ -p 9000:9000 \
+ -p 9001:9001 \
+ bitnami/minio:2024-debian-12
+Then visit the administration interface at localhost:9001, +generate a key and populate:
+S3_ENDPOINT_URL={url}
+S3_BUCKET_NAME={bucket_name}
+S3_ACCESS_KEY_ID={access_key_id}
+S3_SECRET_ACCESS_KEY={access_key}
+pre-requisite:
pip3 install -r src/requirements/docs.txt
+Then you may use the following:
+sphinx-apidoc --implicit-namespaces --separate -H "API Reference" -fo docs/biodm/ src/biodm "**/*tests*"
+python3 -m sphinx -b html docs/ docs/build/html
+Unit tests are leveraging an in-memory sqlite database and not testing any feature requiring +deployement of an external service.
+pre-requisite:
pip3 install -r src/requirements/dev.txt
+run tests
Just like example, tests have to be run within their directory.
+cd src/biodm/tests/
+pytest
+cd -
+coverage
cd src/biodm/tests/
+pytest --cov-report term --cov=../
+cd -
+run in a VSCode debugpy session
To run a unit test in a debugging session, you may create the following .vscode/launch.json
+file at the root of this repository. The run and debug tab should now ofer an extra option.
+If you installed sources in editable mode, that allows you to set breakpoints within BioDM codebase.
{
+ "version": "0.2.0",
+ "configurations": [
+ {
+ "name": "BioDM PyTest",
+ "type": "debugpy",
+ "request": "launch",
+ "cwd": "${workspaceFolder}/src/tests/unit",
+ "subProcess": true,
+ "module": "pytest",
+ "python": "/path/to/myvenv/bin/python3",
+ "args": [
+ "-k", "test_basics"
+ ],
+ "justMyCode": false,
+ },
+ ]
+}
+Integration tests are leveraging docker compose and the development environment to simulate
+external services allowing for end to end testing. It is effectively testing the app from
+outside, hence it is not possible to go over BioDM sources with the debugger on such tests.
Integration are split in silos according to their external service dependency:
+Keycloak
docker compose -f compose.test.yml run --build test-keycloak-run
+docker compose -f compose.test.yml down
+S3
docker compose -f compose.test.yml run --build test-s3-run
+docker compose -f compose.test.yml down
+Introduction Presentation: https://www.overleaf.com/read/wxpdnptnkpsy
+Source Code: https://github.com/bag-cnag/biodm
+Documentation: https://bag-cnag.github.io/biodm/
+BioDM is a fast, modular, stateless and asynchronous REST API framework with the following core features:
+Provide standard HTTP REST-to-CRUD endpoints from developper provided entity definitions:
+`SQLAlchemy <https://github.com/sqlalchemy/sqlalchemy/>`_ tables
`marshmallow <https://github.com/marshmallow-code/marshmallow>`_ schemas
Inter-operate services ecosystem:
+Permissions leveraging Keycloak
Storage leveraging S3 protocol
Jobs & Visualization leveraging Kubernetes cluster
-> Act as an API gateway and log relevant data.
+Also sets up essentials:
+Liveness endpoint
Login and token retrieval system
OpenAPI schema generation
pip3 install git+https://github.com/bag-cnag/biodm
+To run the API you will also need an ASGI server, i.e. uvicorn+uvloop by default:
+pip3 install uvicorn,uvloop
+OR
+pip3 install -r src/requirements/dev.txt
+Then you may run our example after populating src/example/.env with your desired configuration:
cd src/example/
+python3 src/example/app.py
+Alternatively, if your goal is simply to run example locally
+you may use the following command beforehand in order to deploy the development stack:
docker compose -f compose.yml up --build -d
+This stack comes with an interactive swagger-ui visitable at http://localhost:9080/
+once the server is running.
Contents:
+ + GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
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+
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+Public License instead of this License. But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
+This section describes how your Users may communicate with the API once it is deployed.
+The examples are demonstrating using curl, but they are free to use any HTTP library out there.
Integration tests located at src/tests/integration are also providing plenty of resources.
OpenAPI schema
curl ${SERVER_ENDPOINT}/schema
+Yields full API schema in JSON form.
+Liveness endpoint
curl ${SERVER_ENDPOINT}/live
+Returns 'live'
Login
curl ${SERVER_ENDPOINT}/login
+Returns a keycloak login url.
+Visiting and authenticating there gives you an authentication JSON Web Token that you shall
+provide in header to hit protected routes, see authenticated next.
curl ${SERVER_ENDPOINT}/login
+Authenticated
export TOKEN=ey....
+curl -S "${SERVER_ENDPOINT}/authenticated"\
+ -H "Authorization: Bearer ${TOKEN}"
+This routes checks token and returns requesting user info: username, groups and projects.
+Syn Ack
This route is the callback login route located at ${SERVER_ENDPOINT}/syn_ack
+and it is not meant to be accessed directly.
For each entity being managed by a ResourceController, the following routes are supported.
Note
+As per REST standard, each entity is accessible under a resource prefix which is the name of the entity in plural form.
URLs end without trailing slashes
In the case of a multi-indexed entity (i.e. composite primary key), {id}
+refers to primary key elements separated by underscore symbol _.
POST
curl -d ${JSON_OBJECT}\
+ ${SERVER_ENDPOINT}/my_resources
+Supports submitting a resource and or a list of resource with nested resources.
+GET
one
+curl ${SERVER_ENDPOINT}/my_resources/{id}
+or all
+curl ${SERVER_ENDPOINT}/my_resources
+PUT
curl -X PUT\
+ -H "Content-Type: application/json"\
+ -d ${UPDATED_JSON_OBJECT}\
+ ${SERVER_ENDPOINT}/my_resources/{id}
+DELETE
curl -X DELETE\
+ ${SERVER_ENDPOINT}/my_resources/{id}
+Group key is its path according to top level groups. Since / is a reserved route character
+it is replaced by double underscore: __ (with no prefix).
E.g. parent__child__grandchild
When a table is inheriting from Versioned e.g Dataset in our demo, associated controller
+exposes an extra route: POST /my_versioned_resources/{id}_{version}/release.
This triggers creation of a new row with a version increment.
+E.g.
+curl -X POST ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release
+OR to pass in an update for the new version.
+curl -d '{"name": "new_name"}' ${SERVER_ENDPOINT}/my_file_resources/{id}_{version}/release
+Note
+At the moment nested collections will remain to ancestries.
+Moreover, you still need to pass explicitely the version.
+In a future version of BioDM it is planned that all actions involving a
+versioned entity default to latest version and that previous versions stay readonly.
+To fetch the whole chain you may use filter on the shared id.
When requesting all resources under a prefix (i.e. GET /my_resources)
+it is possible to filter results by appending a QueryString starting with ?
+and followed by:
field=value pairs, separated by &
Use field=val1,val2,val3 to OR between multiple values
Use nested.field=val to select on a nested attribute field
Use * in a string attribute for wildcards
field.op(value)
Currently only [lt, le, gt, ge] operators are supported for numerical values.
e.g.
+Note
+When querying with curl, don’t forget to escape & symbol or enclose the whole url in quotes, else your scripting language may intepret it as several commands.
Alternatively you may get a resource nested collection like this
+curl ${SERVER_ENDPOINT}/my_resources/{id}/{collection}
+It also supports partial results. i.e. by appending ?fields=f1,...,fn
Files are stored leveraging an S3 bucket instance. Upload and Downloads are requested directly +there through boto3 presigned-urls.
+Upload
On creating a file, the resource will contain a field named upload_form that is a presigned
+PUT request dictionary that you may use to perform direct upload.
The following snippet lets you upload via script:
+import requests
+
+post = {'url': ..., 'fields': ...}
+
+file_path = "/path/to/my_file.ext"
+file_name = "my_file.ext"
+
+with open(file_path, 'rb') as f:
+ files = {'file': (file_name, f)}
+ http_response = requests.post(
+ post['url'],
+ data=post['fields'],
+ files=files,
+ verify=True,
+ allow_redirects=True)
+ assert http_response.status_code == 201
+Download
Calling GET /my_file_resources will only return associated metadata
To download a file use the following endpoint.
+curl ${SERVER_ENDPOINT}/my_file_resources/{id}/download
+That will return a url to directly download the file via GET request.
+When a Composition/One-to-Many relationship is flagged with permissions as described in
+Fine: Dynamic user owned permissions a new field perm_{relationship_name} is available for that resource.
E.g. Dataset resource in our example, would have an extra field perm_files.
A Permission is holding a ListGroup object for each enabled verbs. +ListGroup being a routeless core table, allowing to manage lists of groups.
+E.g. In our example, CREATE/READ/DOWNLOAD are enabled, +hence a JSON representation of a dataset with its permissions looks like this:
+{
+ "name": "ds_test",
+ "owner": {
+ "username": "my_dataset_owner"
+ },
+ "perm_files": {
+ "write": {
+ "groups": [
+ {"name": "genomics_team"},
+ {"name": "IT_team"},
+ {"..."}
+ ]
+ },
+ "download": {
+ "groups": [{"..."}]
+ }
+ }
+}
+Note
+Passing a top level group will allow all descending children group for that verb/resource tuple.
Permissions are taken into account if and only if keyclaok functionalities are enabled.
+Without keycloak, no token exchange -> No way of getting back protected data.