mex.backend package

Subpackages

• mex.backend.auxiliary package
  • Submodules
  • mex.backend.auxiliary.ldap module
    • search_persons_or_contact_points_in_ldap()
  • mex.backend.auxiliary.orcid module
    • search_persons_in_orcid()
  • mex.backend.auxiliary.organigram module
    • extracted_organizational_units()
  • mex.backend.auxiliary.primary_source module
    • _fetch_or_insert_primary_source()
    • extracted_primary_source_ldap()
    • extracted_primary_source_orcid()
    • extracted_primary_source_organigram()
    • extracted_primary_source_wikidata()
  • mex.backend.auxiliary.utils module
    • fetch_extracted_item_by_source_identifiers()
  • mex.backend.auxiliary.wikidata module
    • _fetch_or_insert_organization()
    • extracted_organization_rki()
    • search_organizations_in_wikidata()
  • Module contents
• mex.backend.cache package
  • Submodules
  • mex.backend.cache.connector module
    • CacheConnector
      • CacheConnector.__init__()
      • CacheConnector.close()
      • CacheConnector.flush()
      • CacheConnector.get_value()
      • CacheConnector.metrics()
      • CacheConnector.set_value()
    • LocalCache
      • LocalCache.close()
      • LocalCache.flushdb()
      • LocalCache.info()
      • LocalCache.set()
    • ValkeyCache
      • ValkeyCache.__init__()
      • ValkeyCache.close()
      • ValkeyCache.flushdb()
      • ValkeyCache.get()
      • ValkeyCache.info()
      • ValkeyCache.set()
  • Module contents
• mex.backend.extracted package
  • Submodules
  • mex.backend.extracted.helpers module
    • get_extracted_item_from_graph()
    • get_extracted_items_from_graph()
    • search_extracted_items_in_graph()
  • mex.backend.extracted.main module
    • get_extracted_item()
    • search_extracted_items()
  • Module contents
• mex.backend.graph package
  • Submodules
  • mex.backend.graph.connector module
    • GraphConnector
      • GraphConnector.__init__()
      • GraphConnector._check_connectivity_and_authentication()
      • GraphConnector._fetch_extracted_or_rule_items()
      • GraphConnector._init_driver()
      • GraphConnector._run_ingest_in_transaction()
      • GraphConnector._seed_constraints()
      • GraphConnector._seed_data()
      • GraphConnector._seed_indices()
      • GraphConnector.close()
      • GraphConnector.commit()
      • GraphConnector.delete_item()
      • GraphConnector.delete_rule_set()
      • GraphConnector.exists_item()
      • GraphConnector.fetch_extracted_items()
      • GraphConnector.fetch_identities()
      • GraphConnector.fetch_merged_items()
      • GraphConnector.fetch_rule_items()
      • GraphConnector.flush()
      • GraphConnector.ingest_items()
  • mex.backend.graph.exceptions module
    • DeletionFailedError
    • GraphError
      • GraphError.__init__()
      • GraphError.errors()
      • GraphError.is_retryable()
    • InconsistentGraphError
    • IngestionError
    • MultipleResultsFoundError
    • NoResultFoundError
  • mex.backend.graph.models module
    • EdgeExporter
      • EdgeExporter.transform()
    • GraphRel
      • GraphRel.edgeLabel
      • GraphRel.edgeProps
      • GraphRel.nodeLabels
      • GraphRel.nodeProps
    • IngestData
      • IngestData.createRels
      • IngestData.entityType
      • IngestData.identifier
      • IngestData.linkRels
      • IngestData.metadata()
      • IngestData.model_config
      • IngestData.nodeProps
      • IngestData.sort_create_rels()
      • IngestData.sort_link_rels()
      • IngestData.stableTargetId
    • IngestParams
      • IngestParams.all_nested_labels
      • IngestParams.all_referenced_labels
      • IngestParams.delete_node_edges
      • IngestParams.detach_node_edges
      • IngestParams.has_create_rels
      • IngestParams.has_link_rels
      • IngestParams.merged_label
      • IngestParams.model_config
      • IngestParams.node_label
    • MExPrimarySource
      • MExPrimarySource.entityType
      • MExPrimarySource.hadPrimarySource
      • MExPrimarySource.identifier
      • MExPrimarySource.identifierInPrimarySource
      • MExPrimarySource.model_config
      • MExPrimarySource.stableTargetId
    • Result
      • Result.__init__()
      • Result.all()
      • Result.get_update_counters()
      • Result.log_notifications()
      • Result.one()
      • Result.one_or_none()
  • mex.backend.graph.query module
    • Query
      • Query.__init__()
      • Query.render()
    • QueryBuilder
      • QueryBuilder.__init__()
      • QueryBuilder._get_ingest_query_for_entity_type()
      • QueryBuilder.close()
    • render_constraints()
  • mex.backend.graph.transform module
    • _SearchResultReference
      • _SearchResultReference.label
      • _SearchResultReference.position
      • _SearchResultReference.value
    • clean_dict()
    • expand_references_in_search_result()
    • get_error_details_from_neo4j_error()
    • get_graph_rel_id()
    • transform_model_into_ingest_data()
    • validate_ingested_data()
  • Module contents
• mex.backend.identity package
  • Submodules
  • mex.backend.identity.main module
    • assign_identity()
    • fetch_identity()
  • mex.backend.identity.provider module
    • GraphIdentityProvider
      • GraphIdentityProvider.__init__()
      • GraphIdentityProvider.assign()
      • GraphIdentityProvider.close()
      • GraphIdentityProvider.fetch()
      • GraphIdentityProvider.metrics()
  • Module contents
• mex.backend.ingest package
  • Submodules
  • mex.backend.ingest.main module
    • ingest_items()
  • Module contents
• mex.backend.ldap package
  • Submodules
  • mex.backend.ldap.main module
    • get_merged_person_from_login()
  • Module contents
• mex.backend.merged package
  • Submodules
  • mex.backend.merged.helpers module
    • delete_merged_item_from_graph()
    • get_merged_item_from_graph()
    • merge_search_result_item()
    • search_merged_items_in_graph()
  • mex.backend.merged.main module
    • delete_merged_item()
    • get_merged_item()
    • search_merged_items()
  • Module contents
• mex.backend.preview package
  • Submodules
  • mex.backend.preview.main module
    • preview_item()
    • preview_items()
  • Module contents
• mex.backend.rules package
  • Submodules
  • mex.backend.rules.helpers module
    • create_and_get_rule_set()
    • delete_rule_set_from_graph()
    • get_rule_set_from_graph()
    • update_and_get_rule_set()
  • mex.backend.rules.main module
    • create_rule_set()
    • delete_rule_set()
    • get_rule_set()
    • update_rule_set()
  • mex.backend.rules.transform module
    • transform_raw_rules_to_rule_set_response()
  • Module contents
• mex.backend.system package
  • Submodules
  • mex.backend.system.main module
    • check_system_status()
    • get_prometheus_metrics()
  • mex.backend.system.models module
    • GraphStatus
      • GraphStatus.model_config
      • GraphStatus.status
    • SystemStatus
      • SystemStatus.model_config
      • SystemStatus.status
      • SystemStatus.version
  • Module contents
• mex.backend.testing package
  • Submodules
  • mex.backend.testing.ldap module
    • get_merged_person_from_login()
    • search_persons_or_contact_points_in_ldap()
  • mex.backend.testing.main module
  • mex.backend.testing.security module
    • has_write_access_ldap_mocked()
  • mex.backend.testing.system module
    • flush_graph_database()
  • Module contents

Submodules

mex.backend.exceptions module

exception mex.backend.exceptions.BackendError

Bases: MExError

Base backend error that offer details on underlying pydantic errors.

errors() → list[ErrorDetails]

Details about underlying pydantic errors.

is_retryable() → bool

Whether the error is retryable.

class mex.backend.exceptions.DebuggingInfo(*, errors: list[dict[str, Any]], scope: DebuggingScope)

Bases: BaseModel

Debugging information for error responses.

errors: list[dict[str, Any]]

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

scope: DebuggingScope

class mex.backend.exceptions.DebuggingScope(*, http_version: str, method: str, path: str, path_params: dict[str, Any], query_string: str, scheme: str)

Bases: BaseModel

Scope for debugging info of error responses.

http_version: str

method: str

model_config = {'extra': 'ignore'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

path: str

path_params: dict[str, Any]

query_string: str

scheme: str

class mex.backend.exceptions.DetailedError(*args, **kwargs)

Bases: Protocol

Protocol for errors that offer details.

errors() → list[ErrorDetails]

Details about each underlying error.

class mex.backend.exceptions.ErrorResponse(*, message: str, debug: DebuggingInfo)

Bases: BaseModel

Response model for user and system errors.

debug: DebuggingInfo

message: str

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

mex.backend.exceptions.handle_detailed_error(request: Request, exc: Exception) → Response

Handle detailed errors and provide debugging info.

mex.backend.exceptions.handle_uncaught_exception(request: Request, exc: Exception) → Response

Handle uncaught errors and provide debugging info.

mex.backend.fields module

mex.backend.logging module

mex.backend.main module

mex.backend.main.lifespan(_: FastAPI) → AsyncIterator[None]

Async context manager to execute startup and teardown of the FastAPI app.

mex.backend.security module

mex.backend.security.check_header_for_authorization_method(api_key: Annotated[str | None, ~fastapi.params.Depends(dependency=<fastapi.security.api_key.APIKeyHeader object at 0x7ff4fce4e120>, use_cache=True, scope=None)] = None, credentials: HTTPBasicCredentials | None, ~fastapi.params.Depends(dependency=<fastapi.security.http.HTTPBasic object at 0x7ff4fce4e510>, use_cache=True, scope=None)] = None, user_agent: Annotated[str, Header(PydanticUndefined)]='n/a') → None

Check authorization header for API key or credentials.

Raises:

HTTPException if both API key and credentials or none of them are in header. –

Parameters:

• api_key – the API key

• credentials – username and password

• user_agent – user-agent (in case of a web browser starts with “Mozilla/”)

mex.backend.security.has_read_access(api_key: Annotated[str | None, ~fastapi.params.Depends(dependency=<fastapi.security.api_key.APIKeyHeader object at 0x7ff4fce4e120>, use_cache=True, scope=None)] = None, credentials: HTTPBasicCredentials | None, ~fastapi.params.Depends(dependency=<fastapi.security.http.HTTPBasic object at 0x7ff4fce4e510>, use_cache=True, scope=None)] = None, user_agent: Annotated[str, Header(PydanticUndefined)]='n/a') → None

Verify if api key or credentials have read access or write access.

Raises:

HTTPException if no header or provided APIKey/credentials have no read access. –

Parameters:

• api_key – the API key

• credentials – username and password

• user_agent – user-agent (in case of a web browser starts with “Mozilla/”)

Settings:

check credentials in backend_user_database or backend_api_key_database

mex.backend.security.has_write_access(api_key: Annotated[str | None, ~fastapi.params.Depends(dependency=<fastapi.security.api_key.APIKeyHeader object at 0x7ff4fce4e120>, use_cache=True, scope=None)] = None, credentials: HTTPBasicCredentials | None, ~fastapi.params.Depends(dependency=<fastapi.security.http.HTTPBasic object at 0x7ff4fce4e510>, use_cache=True, scope=None)] = None, user_agent: Annotated[str, Header(PydanticUndefined)]='n/a') → None

Verify if provided api key or credentials have write access.

Raises:

HTTPException if no header or provided APIKey/credentials have no write access. –

Parameters:

• api_key – the API key

• credentials – username and password

• user_agent – user-agent (in case of a web browser starts with “Mozilla/”)

Settings:

check credentials in backend_user_database or backend_api_key_database

mex.backend.security.has_write_access_ldap(credentials: ~typing.Annotated[~fastapi.security.http.HTTPBasicCredentials, ~fastapi.params.Depends(dependency=<fastapi.security.http.HTTPBasic object at 0x7ff4fce4e510>, use_cache=True, scope=None)]) → str

Verify if provided credentials have LDAP write access.

Raises:

HTTPException if credentials have no LDAP write access or are missing. –

Parameters:

credentials – username and password

mex.backend.settings module

class mex.backend.settings.BackendSettings(_env_file: Path | str | Sequence[Path | str] | None = PosixPath('.'), _env_file_encoding: str | None = None, _env_nested_delimiter: str | None = None, _secrets_dir: str | Path | None = None, *, pdb: bool = False, MEX_SINK: list[Sink] = [Sink.NDJSON], MEX_ASSETS_DIR: Path = PosixPath('/home/runner/work/mex-backend/mex-backend/assets'), MEX_WORK_DIR: Path = PosixPath('/home/runner/work/mex-backend/mex-backend'), MEX_IDENTITY_PROVIDER: IdentityProvider = IdentityProvider.MEMORY, MEX_BACKEND_API_URL: HttpUrl = HttpUrl('http://localhost:8080/'), MEX_BACKEND_API_KEY: SecretStr = SecretStr('**********'), MEX_BACKEND_API_PARALLELIZATION: int = 1, MEX_BACKEND_API_CHUNK_SIZE: int = 25, MEX_VERIFY_SESSION: bool | AssetsPath = True, MEX_ORGANIGRAM_PATH: AssetsPath = AssetsPath('raw-data/organigram/organizational_units.json'), MEX_PRIMARY_SOURCES_PATH: AssetsPath = AssetsPath('raw-data/primary-sources/primary-sources.json'), MEX_LDAP_URL: SecretStr = SecretStr('**********'), MEX_LDAP_SEARCH_BASE: str = 'dc=ldapmock,dc=local', MEX_WIKI_API_URL: HttpUrl = HttpUrl('http://wikidata/'), MEX_WEB_USER_AGENT: str = 'rki/mex', MEX_ORCID_API_URL: HttpUrl = HttpUrl('https://orcid/'), MEX_BACKEND_HOST: Annotated[str, MinLen(min_length=1), MaxLen(max_length=250)] = 'localhost', MEX_BACKEND_PORT: Annotated[int, Gt(gt=0), Lt(lt=65536)] = 8080, MEX_BACKEND_ROOT_PATH: str = '', MEX_GRAPH_URL: str = 'neo4j://localhost:7687', MEX_GRAPH_NAME: str = 'neo4j', MEX_GRAPH_USER: SecretStr = SecretStr('**********'), MEX_GRAPH_PASSWORD: SecretStr = SecretStr('**********'), MEX_GRAPH_TX_TIMEOUT: int | float = 15.0, MEX_GRAPH_SESSION_TIMEOUT: int | float = 45.0, MEX_BACKEND_API_KEY_DATABASE: APIKeyDatabase = APIKeyDatabase(read=[], write=[]), MEX_BACKEND_API_USER_DATABASE: APIUserDatabase = APIUserDatabase(read={}, write={}), MEX_BACKEND_VALKEY_URL: SecretStr | None = None)

Bases: BaseSettings

Settings definition for the backend server.

backend_api_key_database: APIKeyDatabase

backend_host: str

backend_port: int

backend_root_path: str

backend_user_database: APIUserDatabase

graph_db: str

graph_password: SecretStr

graph_session_timeout: int | float

graph_tx_timeout: int | float

graph_url: str

graph_user: SecretStr

model_config = {'arbitrary_types_allowed': True, 'case_sensitive': False, 'cli_avoid_json': False, 'cli_enforce_required': False, 'cli_exit_on_error': True, 'cli_flag_prefix_char': '-', 'cli_hide_none_type': False, 'cli_ignore_unknown_args': False, 'cli_implicit_flags': False, 'cli_kebab_case': False, 'cli_parse_args': None, 'cli_parse_none_str': None, 'cli_prefix': '', 'cli_prog_name': None, 'cli_shortcuts': None, 'cli_use_class_docs_for_groups': False, 'enable_decoding': True, 'env_file': '.env', 'env_file_encoding': 'utf-8', 'env_ignore_empty': False, 'env_nested_delimiter': '__', 'env_nested_max_split': None, 'env_parse_enums': None, 'env_parse_none_str': None, 'env_prefix': 'mex_', 'extra': 'ignore', 'json_file': None, 'json_file_encoding': None, 'nested_model_default_partial_update': False, 'populate_by_name': True, 'protected_namespaces': ('model_validate', 'model_dump', 'settings_customise_sources'), 'secrets_dir': None, 'toml_file': None, 'validate_assignment': True, 'validate_by_alias': True, 'validate_by_name': True, 'validate_default': True, 'yaml_config_section': None, 'yaml_file': None, 'yaml_file_encoding': None}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

valkey_url: SecretStr | None

mex.backend.types module

class mex.backend.types.APIKey(secret_value: SecretType)

Bases: SecretStr

An API Key used for authenticating and authorizing a client.

class mex.backend.types.APIKeyDatabase(*, read: list[APIKey] = [], write: list[APIKey] = [])

Bases: BaseModel

A lookup from access level to list of allowed APIKeys.

model_config = {'extra': 'ignore', 'populate_by_name': True, 'str_max_length': 100000, 'str_min_length': 1, 'str_strip_whitespace': True, 'use_enum_values': True, 'validate_assignment': True, 'validate_by_alias': True, 'validate_by_name': True, 'validate_default': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

read: list[APIKey]

write: list[APIKey]

class mex.backend.types.APIUserDatabase(*, read: dict[str, APIUserPassword] = {}, write: dict[str, APIUserPassword] = {})

Bases: BaseModel

Database containing usernames and passwords for backend API.

model_config = {'extra': 'ignore', 'populate_by_name': True, 'str_max_length': 100000, 'str_min_length': 1, 'str_strip_whitespace': True, 'use_enum_values': True, 'validate_assignment': True, 'validate_by_alias': True, 'validate_by_name': True, 'validate_default': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

read: dict[str, APIUserPassword]

write: dict[str, APIUserPassword]

class mex.backend.types.APIUserPassword(secret_value: SecretType)

Bases: SecretStr

An API password used for basic authentication along with a username.

class mex.backend.types.AccessLevel(*values)

Bases: Enum

Enum of access level.

READ = 'read'

WRITE = 'write'

class mex.backend.types.DynamicStrEnum(name: str, bases: tuple[type], dct: EnumDict)

Bases: EnumType

Metaclass to dynamically populate an enumeration from a list of strings.

class mex.backend.types.ExtractedType(*values)

Bases: Enum

Enumeration of possible types for extracted items.

EXTRACTED_ACCESS_PLATFORM = 'ExtractedAccessPlatform'

EXTRACTED_ACTIVITY = 'ExtractedActivity'

EXTRACTED_BIBLIOGRAPHIC_RESOURCE = 'ExtractedBibliographicResource'

EXTRACTED_CONSENT = 'ExtractedConsent'

EXTRACTED_CONTACT_POINT = 'ExtractedContactPoint'

EXTRACTED_DISTRIBUTION = 'ExtractedDistribution'

EXTRACTED_ORGANIZATION = 'ExtractedOrganization'

EXTRACTED_ORGANIZATIONAL_UNIT = 'ExtractedOrganizationalUnit'

EXTRACTED_PERSON = 'ExtractedPerson'

EXTRACTED_PRIMARY_SOURCE = 'ExtractedPrimarySource'

EXTRACTED_RESOURCE = 'ExtractedResource'

EXTRACTED_VARIABLE = 'ExtractedVariable'

EXTRACTED_VARIABLE_GROUP = 'ExtractedVariableGroup'

class mex.backend.types.MergedType(*values)

Bases: Enum

Enumeration of possible types for merged items.

MERGED_ACCESS_PLATFORM = 'MergedAccessPlatform'

MERGED_ACTIVITY = 'MergedActivity'

MERGED_BIBLIOGRAPHIC_RESOURCE = 'MergedBibliographicResource'

MERGED_CONSENT = 'MergedConsent'

MERGED_CONTACT_POINT = 'MergedContactPoint'

MERGED_DISTRIBUTION = 'MergedDistribution'

MERGED_ORGANIZATION = 'MergedOrganization'

MERGED_ORGANIZATIONAL_UNIT = 'MergedOrganizationalUnit'

MERGED_PERSON = 'MergedPerson'

MERGED_PRIMARY_SOURCE = 'MergedPrimarySource'

MERGED_RESOURCE = 'MergedResource'

MERGED_VARIABLE = 'MergedVariable'

MERGED_VARIABLE_GROUP = 'MergedVariableGroup'

class mex.backend.types.ReferenceFieldName(*values)

Bases: Enum

Enumeration of possible field names that contain references.

ACCESS_PLATFORM = 'accessPlatform'

ACCESS_SERVICE = 'accessService'

AFFILIATION = 'affiliation'

BELONGS_TO = 'belongsTo'

CONTACT = 'contact'

CONTAINED_BY = 'containedBy'

CONTRIBUTING_UNIT = 'contributingUnit'

CONTRIBUTOR = 'contributor'

CREATOR = 'creator'

DISTRIBUTION = 'distribution'

EDITOR = 'editor'

EDITOR_OF_SERIES = 'editorOfSeries'

EXTERNAL_ASSOCIATE = 'externalAssociate'

EXTERNAL_PARTNER = 'externalPartner'

FUNDER_OR_COMMISSIONER = 'funderOrCommissioner'

HAD_PRIMARY_SOURCE = 'hadPrimarySource'

HAS_DATA_SUBJECT = 'hasDataSubject'

INVOLVED_PERSON = 'involvedPerson'

INVOLVED_UNIT = 'involvedUnit'

IS_PART_OF = 'isPartOf'

IS_PART_OF_ACTIVITY = 'isPartOfActivity'

MEMBER_OF = 'memberOf'

PARENT_UNIT = 'parentUnit'

PUBLICATION = 'publication'

PUBLISHER = 'publisher'

RESPONSIBLE_UNIT = 'responsibleUnit'

STABLE_TARGET_ID = 'stableTargetId'

SUCCEEDS = 'succeeds'

UNIT_IN_CHARGE = 'unitInCharge'

UNIT_OF = 'unitOf'

USED_IN = 'usedIn'

WAS_GENERATED_BY = 'wasGeneratedBy'

Module contents