Index

A

abort_multipart_upload() (S3Manager method) add_versioned_table_methods() (in module biodm.components.table) admin() (KeycloakManager method) admin_required() (in module biodm.utils.security) AdminController (class in biodm.components.controllers.admincontroller) adopt_controller() (Api method) aobject (class in biodm.utils.utils) Api (class in biodm.api) ApiComponent (class in biodm.component) ApiManager (class in biodm.component)

ApiService (class in biodm.component) app (ApiComponent attribute) AppsV1Api (K8sManager property) async_database_url() (DatabaseManager static method) AsyncDBError auth_header() (UserInfo static method) auth_url() (KeycloakManager method) authenticate() (K8sManager method) authenticated() (RootController method) AuthenticationMiddleware (class in biodm.utils.security)

B

Base (class in biodm.components.table) BDMarshmallowPlugin (class in biodm.utils.apispec) BDOpenApiConverter (class in biodm.utils.apispec) biodm module biodm.api module biodm.basics module biodm.basics.k8scontroller module biodm.basics.rootcontroller module biodm.component module biodm.components module biodm.components.controllers module biodm.components.controllers.admincontroller module biodm.components.controllers.controller module biodm.components.controllers.resourcecontroller module biodm.components.controllers.s3controller module biodm.components.k8smanifest module biodm.components.services module biodm.components.services.dbservice module biodm.components.services.k8service module biodm.components.services.kcservice module biodm.components.services.s3service module biodm.components.table module biodm.config module biodm.error module biodm.exceptions module biodm.managers module biodm.managers.dbmanager module

biodm.managers.k8smanager module biodm.managers.kcmanager module biodm.managers.s3manager module biodm.routing module biodm.schemas module biodm.schemas.error module biodm.schemas.group module biodm.schemas.listgroup module biodm.schemas.refresh module biodm.schemas.upload module biodm.schemas.user module biodm.scope module biodm.tables module biodm.tables.asso module biodm.tables.group module biodm.tables.history module biodm.tables.listgroup module biodm.tables.upload module biodm.tables.upload_part module biodm.tables.user module biodm.utils module biodm.utils.apispec module biodm.utils.biodm module biodm.utils.security module biodm.utils.sqla module biodm.utils.utils module

C

change_namespace() (K8sManager method) check_allowed_nested() (UnaryEntityService method) check_hash() (in module biodm.utils.utils) children (Group attribute) classproperty (class in biodm.utils.utils) clone() (Base method) coalesce_dicts() (in module biodm.utils.utils) col() (Base class method) colinfo() (Base class method) complete_multipart() (S3Controller method) (S3Service method) complete_multipart_upload() (S3Manager method) CompositeEntityService (class in biodm.components.services.dbservice) CompositeInsert (class in biodm.utils.sqla) content (History attribute) Controller (class in biodm.components.controllers.controller)

controllers (Api attribute) CoreV1Api (K8sManager property) create() (EntityController method) (ResourceController method) create_custom_resource() (K8sManager method) create_deployment() (K8sManager method) create_group() (KeycloakManager method) create_ingress() (K8sManager method) create_multipart_upload() (S3Manager method) create_presigned_download_url() (S3Manager method) create_service() (K8sManager method) create_upload_part() (S3Manager method) create_user() (KeycloakManager method) csplit_esc() (in module biodm.utils.utils) ctrl (Base attribute) CustomObjectsApi (K8sManager property)

D

DatabaseManager (class in biodm.managers.dbmanager) DatabaseService (class in biodm.components.services.dbservice) DataError db (Api attribute) DBError dbpath() (KCGroupService static method) DEBUG (Scope attribute) decode_token() (KeycloakManager method) (UserInfo method) delayed (CompositeInsert attribute) DELETE (HttpMethod attribute) delete() (ApiService method) (EntityController method) (KCGroupService method) (KCUserService method) (ResourceController method) (UnaryEntityService method)

delete_custom_object() (K8sManager method) delete_group() (KeycloakManager method) delete_user() (KeycloakManager method) deploy_managers() (Api method) detail (RequestError attribute) dispatch() (HistoryMiddleware method) (RequireAuthMiddleware method) (TimeoutMiddleware method) display_name (UserInfo property) dl_count (S3File attribute) download (Permission attribute) download() (S3Controller method) (S3Service method) dump_group() (UserSchema method) dyn_relationships() (Base class method)

E

email (User attribute) emited_at (S3File attribute) enabled_verbs (Permission property) endpoint (ApiManager property) (DatabaseManager property) (History attribute) (K8sManager property) (KeycloakManager property) (S3Manager property)

EndpointError EntityController (class in biodm.components.controllers.controller) Error (class in biodm.error) ErrorSchema (class in biodm.schemas.error) etag (UploadPart attribute) extension (S3File attribute)

F

FailedCreate FailedDelete FailedRead FailedUpdate field (Permission attribute) filename (S3File attribute) FileNotUploadedError

FileTooLargeError FileUploadCompleteError filter() (ApiService method) (EntityController method) (ResourceController method) (UnaryEntityService method) firstName (User attribute) form (UploadPart attribute)

G

gen_cond() (UnaryEntityService method) gen_key() (S3Service method) gen_manifest() (K8sManifest method) gen_schema() (in module biodm.utils.biodm) gen_upload_form() (S3Service method) gen_upsert_holder() (UnaryEntityService method) GET (HttpMethod attribute) get_custom_resource_params() (K8sManager static method) get_group() (KeycloakManager method) get_group_by_name() (KeycloakManager method) get_group_by_path() (KeycloakManager method) get_groups() (KeycloakManager method) get_max_id() (in module biodm.utils.sqla) get_name_in_manifest() (K8sManager static method)

get_user_by_username() (KeycloakManager method) get_user_groups() (KeycloakManager method) get_users() (KeycloakManager method) getattr_in_session() (UnaryEntityService method) gettattr_unbound() (in module biodm.utils.biodm) Group (class in biodm.tables.group) group_required (PermissionLookupTables attribute) group_required() (in module biodm.utils.security) group_user_add() (KeycloakManager method) GroupController (class in biodm.basics) groups (ListGroup attribute) (User attribute) (UserInfo property) GroupSchema (class in biodm.schemas.group)

H

handshake() (RootController method) has_composite_pk_with_leading_id_sqlite (Base attribute) has_default() (Base class method)

has_submitter_username (Base attribute) History (class in biodm.tables.history) HistoryMiddleware (class in biodm.api) HttpMethod (class in biodm.components.controllers.controller)

I

id (Group attribute) (ListGroup attribute) (Upload attribute) (User attribute) ImplementionError in_session() (DatabaseManager static method) info (UserInfo property) init_db() (DatabaseManager method) instance_info() (K8sController method)

InvalidCollectionMethod is_admin (UserInfo property) is_authenticated (UserInfo property) is_autoincrement() (Base class method) is_empty() (CompositeInsert method) is_permission (Base attribute) is_strict_versioned (Base attribute) is_versioned (Base attribute) item (CompositeInsert attribute)

J

json_bytes() (in module biodm.utils.utils)

json_response() (in module biodm.utils.utils)

K

k8 (Api attribute) k8() (K8Service method) k8s (K8sController property) K8sController (class in biodm.basics.k8scontroller) K8Service (class in biodm.components.services.k8service) K8sManager (class in biodm.managers.k8smanager) K8sManifest (class in biodm.components.k8smanifest) kc (Api attribute) (UserInfo attribute) kc() (KCService method)

KCGroupService (class in biodm.components.services.kcservice) kcpath() (KCGroupService static method) KCService (class in biodm.components.services.kcservice) KCUserService (class in biodm.components.services.kcservice) key (S3File attribute) key_fields (S3Service property) key_salt (S3File attribute) keycloak_admin (UserInfo property) keycloak_sync() (RootController method) KeycloakManager (class in biodm.managers.kcmanager) KeycloakUnavailableError

L

last_max_id (Base attribute) lastName (User attribute) list_custom_object() (K8sManager method) list_deployments() (K8sManager method) list_instances() (K8sController method) list_multipart_parts() (S3Manager method) list_pods() (K8sManager method) list_services_ports() (K8sManager method) ListGroup (class in biodm.tables.listgroup)

ListGroupSchema (class in biodm.schemas.listgroup) live() (RootController static method) log() (K8sManager method) logger (Api attribute) (ApiComponent attribute) login() (RootController method) login_required (PermissionLookupTables attribute) login_required() (in module biodm.utils.security) logout() (RootController method)

M

ManagerError manifest (K8Service attribute) ManifestError manifests (K8sController attribute) metadata (Base attribute) method (History attribute) MissingDB MissingService module biodm biodm.api biodm.basics biodm.basics.k8scontroller biodm.basics.rootcontroller biodm.component biodm.components biodm.components.controllers biodm.components.controllers.admincontroller biodm.components.controllers.controller biodm.components.controllers.resourcecontroller biodm.components.controllers.s3controller biodm.components.k8smanifest biodm.components.services biodm.components.services.dbservice biodm.components.services.k8service biodm.components.services.kcservice biodm.components.services.s3service biodm.components.table biodm.config biodm.error biodm.exceptions biodm.managers biodm.managers.dbmanager biodm.managers.k8smanager biodm.managers.kcmanager biodm.managers.s3manager biodm.routing biodm.schemas biodm.schemas.error biodm.schemas.group biodm.schemas.listgroup biodm.schemas.refresh biodm.schemas.upload biodm.schemas.user biodm.scope biodm.tables biodm.tables.asso biodm.tables.group biodm.tables.history biodm.tables.listgroup biodm.tables.upload biodm.tables.upload_part biodm.tables.user biodm.utils biodm.utils.apispec biodm.utils.biodm biodm.utils.security biodm.utils.sqla biodm.utils.utils

N

namespace (K8sManifest attribute)

nested (CompositeInsert attribute) NetworkingV1Api (K8sManager property)

O

onerror() (in module biodm.error) onstart() (Api method) op (Operator attribute) openapi_schema() (Controller method) (RootController method) openid (KeycloakManager property) Operator (class in biodm.utils.sqla) opts (ErrorSchema attribute) (GroupSchema attribute) (ListGroupSchema attribute) (PartsEtagSchema attribute) (RefreshSchema attribute) (Schema attribute) (UploadPartSchema attribute) (UploadSchema attribute) (UserSchema attribute)

overload_docstring() (in module biodm.components.controllers.resourcecontroller)

P

parent (Group attribute) parent_path (Group attribute) part_number (UploadPart attribute) PartialIndex partition() (in module biodm.utils.utils) parts (Upload attribute) PartsEtagSchema (class in biodm.schemas.upload) PATCH (HttpMethod attribute) path (Group attribute) PayloadEmptyError PayloadJSONDecodingError Permission (class in biodm.utils.security) permission_relationships (CompositeEntityService property) PermissionLookupTables (class in biodm.utils.security) permissions (PermissionLookupTables attribute)

pk() (Base method) populate_ids_sqlite() (DatabaseService method) POST (HttpMethod attribute) post_upload_callback (S3Service attribute) PostgresUnavailableError prefix (K8sController property) (ResourceController property) process_apispec_docstrings() (in module biodm.utils.apispec) PROD (Scope attribute) propagates_to (Permission attribute) PublicRoute (class in biodm.routing) PUT (HttpMethod attribute) Python Enhancement Proposals PEP 405 PEP 621

Q

qp_id (ResourceController property)

QueryError

R

raw_permissions (PermissionLookupTables attribute) read (Permission attribute) read() (ApiService method) (EntityController method) (ResourceController method) (UnaryEntityService method) read_deployment() (K8sManager method) read_ingress() (K8sManager method) read_nested() (ResourceController method) (UnaryEntityService method) read_or_create() (KCGroupService method) (KCService method) (KCUserService method) read_service_status() (K8sManager method) ready (S3File attribute) redeem_code_for_token() (KeycloakManager method) refresh() (RootController method) RefreshSchema (class in biodm.schemas.refresh) register_runtime_schema() (in module biodm.utils.apispec) registry (Base attribute) relationships() (Base method)

release() (ApiService method) (EntityController method) (ResourceController method) (S3Service method) (UnaryEntityService method) ReleaseVersionError remove_empty() (in module biodm.utils.utils) remove_skip_values() (Schema method) replace_docstrings_pattern() (in module biodm.utils.apispec) replace_method_docstrings() (ResourceController static method) RequestError RequireAuthMiddleware (class in biodm.routing) required() (Base method) ResourceController (class in biodm.components.controllers.resourcecontroller) response (Error property) RootController (class in biodm.basics.rootcontroller) Route (class in biodm.routing) routes() (Controller method) (K8sController method) (ResourceController method) (RootController method) (S3Controller method)

S

s3 (Api attribute) s3() (S3Service method) s3_uploadId (Upload attribute) S3Controller (class in biodm.components.controllers.s3controller) S3File (class in biodm.components.table) S3Manager (class in biodm.managers.s3manager) S3Service (class in biodm.components.services.s3service) sa_error (DBError attribute) Schema (class in biodm.utils.biodm) schema (EntityController attribute) schema2jsonschema() (BDOpenApiConverter method) schema2parameters() (BDOpenApiConverter method) schema_helper() (BDMarshmallowPlugin method) SchemaError Scope (class in biodm.scope)

serialize() (EntityController class method) server_endpoint (Api property) session() (DatabaseManager method) setup_permissions() (PermissionLookupTables class method) size (S3File attribute) sqlite_declare_strrev() (DatabaseManager static method) stmt_to_dict() (in module biodm.utils.sqla) StrictVersioned (class in biodm.components.table) svc (Base attribute) (S3Controller attribute) swagger_ui_page() (RootController method) syn_ack() (RootController method) sync() (KCService method) sync_all() (KCGroupService method) (KCService method) (KCUserService method)

T

table (DatabaseService attribute) (K8sManifest attribute) takeout_unallowed_nested() (UnaryEntityService method) target_table() (Base class method) TEST (Scope attribute) TimeoutMiddleware (class in biodm.api)

timestamp (History attribute) to_it() (in module biodm.utils.utils) to_stmt() (UpsertStmtValuesHolder method) token (UserInfo attribute) TokenDecodingError touch() (in module biodm.utils.utils) turn_to_transient() (Schema method)

U

UnaryEntityService (class in biodm.components.services.dbservice) UnauthorizedError unevalled_all() (in module biodm.utils.utils) unevalled_or() (in module biodm.utils.utils) update() (EntityController method) (ResourceController method) update_group() (KeycloakManager method) update_runtime_schema() (in module biodm.utils.apispec) update_user() (KeycloakManager method) UpdateVersionedError Upload (class in biodm.tables.upload) upload (S3File attribute) (UploadPart attribute)

upload_id (S3File attribute) (UploadPart attribute) UploadPart (class in biodm.tables.upload_part) UploadPartSchema (class in biodm.schemas.upload) UploadSchema (class in biodm.schemas.upload) UpsertStmtValuesHolder (class in biodm.utils.sqla) User (class in biodm.tables.user) user_username (History attribute) UserController (class in biodm.basics) UserInfo (class in biodm.utils.security) username (User attribute) users (Group attribute) UserSchema (class in biodm.schemas.user) utcnow() (in module biodm.utils.utils)

V

validate() (EntityController class method) validated_at (S3File attribute) value (ValuedOperator attribute)

ValuedOperator (class in biodm.utils.sqla) verbs (Permission attribute) version (Versioned attribute) Versioned (class in biodm.components.table)

W

wait_deployment() (K8sManager method) wait_ingress() (K8sManager method) walk_relationships() (PermissionLookupTables static method) write (Permission attribute)

write() (ApiService method) (CompositeEntityService method) (KCGroupService method) (KCUserService method) (UnaryEntityService method)