CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

• New setup extra test which installs the dependencies for testing.
• The Container class has a new member function filter which is based o _filter_entity_list.
• The Entity properties _cuid and _flags are now available for read-only access as cuid and flags, respectively.

Changed

Deprecated

Removed

• Support for Python 3.8

Fixed

• #73 Entity.to_xml now detects potentially infinite recursion and prevents an error
• #89 to_xml does not add noscript or TransactionBenchmark tags anymore
• #103 authentication/interface/on_response() does not overwrite auth_token if new value is None
• #119 The diff returned by compare_entities now uses id instead of name as key if either property does not have a name
• #87 XMLSyntaxError messages when parsing (incomplete) responses in case of certain connection timeouts. The diff returned by compare_entities now uses id instead of name as key if either property does not have a name
• #127 pylinkahead.ini now supports None and tuples as values for the timeout keyword

Security

Documentation

[0.16.0] - 2024-11-13

Added

• ParentList and PropertyList now have a filter function that allows to select a subset of the contained elements by ID and/or name.
• Official support for Python 3.13
• Added arguments to describe_diff that allow customizing the labels for the 'old' and the 'new' diffs.
• Optional realm argument for linkahead_admin.py set_user_password which defaults to None, i.e., the server's default realm.

Changed

• compare_entities is now case insensitive with respect to property and recordtype names
• _ParentList is now called ParentList
• _Properties is now called PropertyList
• ParentList.remove is now case insensitive when a name is used.

Deprecated

• the use of the arguments old_entity and new_entity in compare_entities is now deprecated. Please use entity0 and entity1 respectively instead.

Fixed

• gitlab.indiscale.com#200 linkahead_admin.py prints reasonable error messages when users or roles don't exist.

[0.15.1] - 2024-08-21

Deprecated

• connection.get_username. Use la.Info().user_info.name instead.

Fixed

• #128 Assign datetime.date or datetime.datetime values to DATETIME properties.

Documentation

• Added docstrings for linkahead.models.Info and linkahead.models.UserInfo.

[0.15.0] - 2024-07-09

Added

• Support for Python 3.12
• The linkahead module now opts into type checking and supports mypy.
• #112 Entity.update_acl now supports optional **kwargs that are passed to the Entity.update method that is called internally, thus allowing, e.g., updating the ACL despite possible naming collisions with unique=False.
• a role argument for get_entity_by_name and get_entity_by_id

Changed

• Using environment variable PYLINKAHEADINI instead of PYCAOSDBINI.

Removed

• Support for Python 3.7

Fixed

• #104 Selecting parts of a Container with a slice used to return a list object instead of a Container, removing all useful methods of the Container class. This has been fixed and using a slice such as [:2] now returns a new Container.
• #120 Unwanted subproperties in reference properties.

Documentation

• Added documentation and a tutorial example for the usage of the page_length argument of execute_query.

[0.14.0] - 2024-02-20

Added

• utils.merge_entities now has a merge_id_with_resolved_entity keyword which allows to identify property values with each other in case that one is an id and the other is an Entity with this id. Default is False, so no change to the default behavior.
• apiutils.escape_quoted_text for escaping text in queries.

Changed

• cached_query() now also caches uniqueness related exceptions.

[0.13.2] - 2023-12-15

Fixed

• #113 Container could fail to delete when there were reference properties.
• HTTP status 431 (Headers too long) now also raises an URI too long exception.

[0.13.1] - 2023-10-11

Fixed

• no Error when no configuration file is used Issue

[0.13.0] - 2023-10-10

Added

• New page_length parameter for caosdb.execute_query and caosdb.Query.execute. See docstrings for more details.
• Entity.remove_value_from_property function that removes a given value from a property and optionally removes the property if it is empty afterwards.

Changed

• _Messages is now Messages and inherits from list instead of dict
• Message.__init__ signature changed and type defaults to "Info" now.
• Message.__eq__ changed. Equality is equality of type, code, and description now.
• Rename from CaosDB to LinkAhead. For proper migration, follow the instructions in migration_to_linkahead.md and check the documentation at docs.indiscale.com.

Deprecated

• The API of Messages has been simplified and some ways to interact with messages have been deprecated. Warnings are raised correspondingly.
• Message.get_code. Use the code property instead.

Fixed

• Detection for cyclic references when converting entites using the high level API.

[0.12.0] - 2023-06-02

Added

• Added location argument to src/caosdb/utils/checkFileSystemConsistency.py
• Entity getters: get_entity_by_<name/id/path>
• Cached versions of entity getters and of execute_query (cached_query)

Deprecated

• getOriginUrlIn, getDiffIn, getBranchIn, getCommitIn (formerly apiutils) have been moved to caosdb.utils.git_utils

Fixed

• Fixed src/caosdb/utils/checkFileSystemConsistency.py

Documentation

• #83 - Improved documentation on adding REFERENCE properties, both in the docstring of Entity.add_property and in the data-insertion tutorial.

[0.11.2] - 2023-03-14

Fixed

• root logger is no longer used to create warnings. Fixes undesired output in stderr

[0.11.1] - 2023-03-07

(Florian Spreckelsen)

Changed

• Renamed caosdb.common.models._Parents to caosdb.common.models._ParentList.

Fixed

• caosdb-pylib#90: Entity.get_parents_recursively() did not work for unretrieved parents.

[0.11.0] - 2023-01-19

(Florian Spreckelsen)

Added

• apiutils.EntityMergeConflictError class for unresesolvable merge conflicts when merging two entities
• Re-introduced support for Python 3.7

Changed

• apiutils.merge_entities now raises an EntityMergeConflictError in case of unresolvable merge conflicts.

Fixed

• #82 Merging an entity with properties with missing datatype leads to Exception - The correct exception is raised in case of a missing LIST datatype.

Documentation

• Fixed {action}_entity_permissions help line.

[0.10.0] - 2022-11-14

(Florian Spreckelsen)

Added

• HTTP connections are allowed additionally to HTTPS connections.
• Dependency on the requests package.
• Dependency on the python-dateutil package.
• Connection.https_proxy and Connection.http_proxy option of the pycaosdb.ini and the https_proxy and http_proxy parameter of the configure_connection function. See the documentation of the latter for more information. Note that the HTTP_PROXY and HTTPS_PROXY environment variables are respected as well, unless overridden programmatically.
• apiutils.empty_diff function that returns True if the diffs of two entities found with the compare_entitis function are empty, False otherwise.

Changed

• apiutils.compare_entities now has an optional compare_referenced_records argument to compare referenced Entities recursively (fomerly, only the referenced Python objects would be compared). The default is False to recover the original behavior.
• apiutils.merge_entities now has an optional merge_references_with_empty_diffs argument that determines whether a merge of two entities will be performed if they reference identical records (w.r.t th above empty_diff function). Formerly this would have caused a merge conflict if the referenced record(s) were identical, but stored in different Python objects.
• apiutils.merge_entities now has an optional force argument (defaults to False, i.e., the old behavior) which determines whether in case of merge conflicts errors will be raised or the properties and attributes of entity A will be overwritten by entity B.

Deprecated

• Connection.socket_proxy option of the pycaosdb.ini. Please use Connection.https_proxy or Connection.http_proxy instead. The deprecated option will be removed with the next minor release.

Fixed

• handling of special attributes (name, id, ...) in apiutils.empty_diff

[0.9.0] - 2022-10-24

(Florian Spreckelsen)

Added

• Add TimeZone class and parse the server's time zone in the Info response.

Fixed

• #141 (closed) password_method = unauthenticated not allowed by schema
• Set PyYAML dependency back to PyYaml>=5.4.1 (from 6.0) for better compatibility with docker-compose

Documentation

• Added curator role permissions example to code gallery

[0.8.0] - 2022-07-12

(Timm Fitschen)

Removed

• Support for Python 3.6 and Python 3.7

Fixed

• read() of MockupResponse returns now an appropriate type on modern systems
• caosdb-server#142 Can't create users with dots in their user names

[0.7.4] - 2022-05-31

(Florian Spreckelsen)

Fixed

• #64 Use Dict[] and List[] from typing for type hinting instead of dict[] and list[] for compatibility with Python<3.9.

[0.7.3] - 2022-05-03

(Henrik tom Wörden)

Added

• New function in apiutils that copies an Entity.
• New EXPERIMENTAL module high_level_api which is a completely refactored version of the old high_level_api from apiutils. Please see the included documentation for details.
• to_graphics now has no_shadow option.

Changed

• Added additional customization options to the plantuml module.
• The to_graphics function in the plantuml module uses a temporary directory now for creating the output files.

Fixed

• #75 (closed), #103 (closed) Fixed JSON schema to allow more sections, and correct requirements for password method.

[0.7.2] - 2022-03-25

(Timm Fitschen)

Deprecated

• In module caosdb.apiutils:
  • CaosDBPythonEntity class
  • convert_to_entity function
  • convert_to_python_object function

Fixed

• caosdb-pylib#106 Parsing Error in class caosdb.common.models.ACL. This may lead to the unintentional revocation of permissions for some users or roles during updates. However, no additional permissions are being granted.

Documentation

[0.7.1] - 2022-03-11

(Daniel Hornung)

Documentation

• timeout option in example pycaosdb.ini

[0.7.0] - 2022-01-21

Added

• Function in administration that generates passwords that comply with the rules.

Fixed

• #90 (closed) compare_entities function in apiutils does not check units
• #94 (closed) some special properties were not checked in compare_entities

Security

[0.6.1] - 2021-12-03

Fixed

• #50 keyring can be used as password input method again

• #81 (closed) compare_entities from apiutils does not compare entity values

[0.6.0] - 2021-10-19

Added

• It is possible now to supply a password for caosdb_admin on the command line and also activate the user directly using "-c".

• Added examples for complex data models to documentation
• extended apiutils with resolve_reference(Property)
• is_reference function for Properties
• function retrieve_substructure that recursively adds connected entities.

Changed

• Retrievals of entities where the class does not match the entity role raise a ValueError now. See here for more information. Updating a role is now being done by setting the Entity.role to the new role (as string).
• Entity.add_property and Entity.add_parent do not accept **kwargs-style keywords anymore. Formerly known keywords have been refactored into named parameters.
• #35 Loggers now use the name of the unit where they are called instead of a static name

Deprecated

• id_query(ids) in apiutils (to be removed with >=0.5.4)
• The whole yamlapi with the following functions (to be removed with >=0.5.4):
  • append_sublist
  • kv_to_xml
  • dict_to_xml
  • yaml_to_xml
  • process
  • yaml_file_to_xml
  • insert_yaml_file

Fixed

• #60 (closed) Unintuitive behavior of Entity.role after a Entity(id).retrieve() Originally the role was None. The correct role is present now.
• #53 (closed) Documentation of inheritance
• #38 (closed) Dependencies in chunk-deletion of containers

Security

[0.5.2] - 2021-06-03

Added

• Entity State support (experimental, no StateModel support yet). See the caosdb.State class for more information.
• etag property for the caosdb.Query class. The etag allows to debug the caching and to decide whether the server has changed between queries.
• function _read_config_files to read pycaosdb.ini files from different paths.

Changed

• Updated error-handling tutorial in documentation to reflect the new error classes

Fixed

• #45 (moved) - test_config_ini_via_envvar

Security

[0.5.1] - 2021-02-12

Fixed

• #43 (closed) - Error with execute_query when server doesn't support query caching.

[0.5.0] - 2021-02-11

Added

• New exceptions HTTPForbiddenException and HTTPResourceNotFoundException for HTTP 403 and 404 errors, respectively.
• BadQueryError, EmptyUniqueQueryError, and QueryNotUniqueError for bad (unique) queries.
• Added cache paramter to execute_query and Query.execute which indicates whether server may use the cache for the query execution.
• Added cached property to the Query class which indicates whether the server used the cache for the execution of the last query.
• Documentation moved from wiki to this repository and enhanced.

Changed

• Renaming of URITooLongException to HTTPURITooLongError.
• Raising of entity exceptions and transaction errors. Whenever any transaction fails, a TransactionError is raised. If one ore more entities caused that failure, corresponding entity errors are attached as direct and indirect children of the TransactionError. They can be accessed via the get_errors (direct children) and get_all_errors (direct and indirect children) methods; the causing entities are accessed by get_entities and get_all_entities. The has_error method can be used to check whether a TransactionError was caused by a specific EntityError.
• Unique queries will now result in EmptyUniqueQueryError or QueryNotUniqueError if no or more than one possible candidate is found, respectively.

Removed

• Dynamic exception type EntityMultiError.
• get_something functions from all error object in exceptions.py
• AmbiguityException

[0.4.1] - 2021-02-10

Added

• Versioning support (experimental). The version db.Version class can represents particular entity versions and also the complete history of an entity.
• Automated documentation builds: make doc

Fixed

• deepcopy of _Messages objects

[0.4.0] - 2020-07-17##

Added

• [Entity|Container].get_property_values for deeply nested references, e.g. from results of SELECT queries.
• two new password_methods for the pycaosdb.ini and the configure_connection function: unauthenticated for staying unauthenticated (and using the anonymous user) and auth_token. If password_method == "auth_token" the auth_token option is required as well.
• Empty string support (See caosdb-server#33 (closed))

Changed

• get_property method also accepts instances of properties now, e.g. record.get_property(Property(name="length"))
• the value of properties is parsed to python types (int, float, boolean) when setting the value with the setter and when the datatype changes. Before this change, the value was parsed to python types only when parsing an xml and only for int and float.

Deprecated

• Setting the auth_token option without setting the password_method to auth_token. This affects both the pycaosdb.ini and the configure_connection function. During the deprecation phase it will be assumed that password_method is auth_token if the the auth_token is set.

Fixed

• Replaced deprecated Logger.warn() method.

[0.3.0] - 2020-04-24##

Added

• apiutils.apply_to_ids -- a helper which applies a function to all ids which are used by an entity (own entity, parents, properties, references etc.).

Fixed

• import bugs in apiutils

[0.2.4] - 2020-04-23

Added

• An auth_token parameter for caosdb.configure_connection(...). This parameter accepts a plain text auth token (which can only be issued by the CaosDB Server). Under the hood, auth tokens are stored plain, instead of urlencoded now.
• New type of exception: ConfigurationException for misconfigurations.
• Some unit tests, mainly for the caosdb.connection.authentication module
• Advanced setup.py for easy versioning and publication as pypi repository.
• caosdb.apiutils has new functions id_query and retrieve_entities_with_ids
• New exception: EntityDoesNotExistError
• RELEASE_GUIDELINES.md with release instructions.
• More documentation and tests.

Changed

• pytest is the new preferred unit test frame work.
• If a password is specified in the configuration even though the password_method is not set to plain, a warning is logged.
• Under the hood, the password of from a pass or keyring call is not stored anymore. Instead the password is requested each time a login is necessary.
• Always load system default CA repository into the ssl context.
• Datatypes are now in caosdb.common.datatype (though still available in the main caosdb namespace).
• Logging to stdout is now more configurable.

Deprecated

• Unit test frame work: Nose should not be used anymore. Please use pytest instead.

Fixed

• #1 (closed) - Problems with pass as a credentials provider
• #3 (closed) - Python client does login before the first request to circumvent problems with anonymous role.
• Many other fixes

[0.1.0] - 2018-10-09

Tag v0.1 - Commit 6fc0dcaa

Added

• everything