diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d95c4620d281693da9e69143c06db82e5796ac14..c2d071662c26322d44ed98e6e164c523edcae5af 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -57,7 +57,7 @@ mypy:
tags: [ docker ]
stage: linting
script:
- - pip install mypy types-PyYAML types-jsonschema types-requests types-setuptools types-lxml types-python-dateutil
+ - pip install mypy types-PyYAML types-jsonschema types-requests types-setuptools types-lxml types-python-dateutil pytest
- make mypy
allow_failure: true
diff --git a/Makefile b/Makefile
index eb767dd4053a2b232d425126358cfb0fd23ffb1c..21ea40ac8a6eb34032aba75c089e278fa354a6f5 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,7 @@ lint:
.PHONY: lint
mypy:
- mypy src/linkahead
+ mypy src/linkahead/common unittests
.PHONY: mypy
unittest:
diff --git a/setup.py b/setup.py
index 8a9276d0205fef49d59b7c41b70d21312b074642..27f305c28c70dccdbf1a27fd5a2a4aa9e153f006 100755
--- a/setup.py
+++ b/setup.py
@@ -193,7 +193,7 @@ def setup_package():
tests_require=["pytest", "pytest-cov", "coverage>=4.4.2",
"jsonschema>=4.4.0"],
package_data={
- 'linkahead': ['cert/indiscale.ca.crt', 'schema-pycaosdb-ini.yml'],
+ 'linkahead': ['py.typed', 'cert/indiscale.ca.crt', 'schema-pycaosdb-ini.yml'],
},
scripts=[
"src/linkahead/utils/caosdb_admin.py",
diff --git a/src/linkahead/common/datatype.py b/src/linkahead/common/datatype.py
index c0c15feca240112f1f8e33a0cd37932151fcd9f0..65e6246c0287f0af07aa604f4bc18ce54615cae2 100644
--- a/src/linkahead/common/datatype.py
+++ b/src/linkahead/common/datatype.py
@@ -24,6 +24,10 @@
#
import re
+import sys
+
+if sys.version_info >= (3, 8):
+ from typing import Literal
from ..exceptions import EmptyUniqueQueryError, QueryNotUniqueError
@@ -34,6 +38,8 @@ DATETIME = "DATETIME"
INTEGER = "INTEGER"
FILE = "FILE"
BOOLEAN = "BOOLEAN"
+if sys.version_info >= (3, 8):
+ DATATYPE = Literal["DOUBLE", "REFERENCE", "TEXT", "DATETIME", "INTEGER", "FILE", "BOOLEAN"]
def LIST(datatype):
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index d7bc7a4767467d84b76534c438d7606d1b4e1c24..1d8e8832a3d215363af5ffcb3139d24cb6c27bc3 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -35,6 +35,7 @@ transactions.
from __future__ import annotations # Can be removed with 3.10.
from __future__ import print_function, unicode_literals
+from enum import Enum
import re
import sys
@@ -46,7 +47,14 @@ from os import listdir
from os.path import isdir
from random import randint
from tempfile import NamedTemporaryFile
-from typing import Any, Optional
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING and sys.version_info > (3, 7):
+ from datetime import datetime
+ from typing import Any, Dict, Optional, Type, Union, List, TextIO, Tuple, Literal
+ from .datatype import DATATYPE
+
from warnings import warn
from lxml import etree
@@ -63,8 +71,16 @@ from ..exceptions import (AmbiguousEntityError, AuthorizationError,
QueryNotUniqueError, TransactionError,
UniqueNamesError, UnqualifiedParentsError,
UnqualifiedPropertiesError)
-from .datatype import (BOOLEAN, DATETIME, DOUBLE, INTEGER, TEXT,
- get_list_datatype, is_list_datatype, is_reference)
+from .datatype import (
+ BOOLEAN,
+ DATETIME,
+ DOUBLE,
+ INTEGER,
+ TEXT,
+ get_list_datatype,
+ is_list_datatype,
+ is_reference,
+)
from .state import State
from .timezone import TimeZone
from .utils import uuid, xml2str
@@ -72,14 +88,14 @@ from .versioning import Version
_ENTITY_URI_SEGMENT = "Entity"
-# importances/inheritance
OBLIGATORY = "OBLIGATORY"
SUGGESTED = "SUGGESTED"
RECOMMENDED = "RECOMMENDED"
FIX = "FIX"
ALL = "ALL"
NONE = "NONE"
-
+if TYPE_CHECKING:
+ INHERITANCE = Literal["OBLIGATORY", "SUGGESTED", "RECOMMENDED", "FIX", "ALL", "NONE"]
SPECIAL_ATTRIBUTES = ["name", "role", "datatype", "description",
"id", "path", "checksum", "size", "value"]
@@ -98,41 +114,50 @@ class Entity:
by the user to control several server-side plug-ins.
"""
- def __init__(self, name=None, id=None, description=None, # @ReservedAssignment
- datatype=None, value=None, **kwargs):
+ def __init__(
+ self,
+ name: Optional[str] = None,
+ id: Optional[int] = None,
+ description: Optional[str] = None, # @ReservedAssignment
+ datatype: Optional[DATATYPE] = None,
+ value=None,
+ **kwargs,
+ ):
+
self.__role = kwargs["role"] if "role" in kwargs else None
- self._checksum = None
+ self._checksum: Optional[str] = None
self._size = None
self._upload = None
# If an entity is used (e.g. as parent), it is wrapped instead of being used directly.
# see Entity._wrap()
- self._wrapped_entity = None
- self._version = None
- self._cuid = None
- self._flags = dict()
+ self._wrapped_entity: Optional[Entity] = None
+ self._version: Optional[Version] = None
+ self._cuid: Optional[str] = None
+ self._flags: Dict[str, str] = dict()
self.__value = None
- self.__datatype = None
- self.datatype = datatype
+ self.__datatype: Optional[DATATYPE] = None
+ self.datatype: Optional[DATATYPE] = datatype
self.value = value
self.messages = Messages()
self.properties = _Properties()
self.parents = _ParentList()
- self.path = None
- self.file = None
- self.unit = None
- self.acl = None
- self.permissions = None
+ self.path: Optional[str] = None
+ self.file: Optional[File] = None
+ self.unit: Optional[str] = None
+ self.acl: Optional[ACL] = None
+ self.permissions: Optional[Permissions] = None
self.is_valid = lambda: False
self.is_deleted = lambda: False
self.name = name
self.description = description
- self.id = id
- self.state = None
+ self.id: Optional[int] = id
+ self.state: Optional[State] = None
def copy(self):
"""
Return a copy of entity.
+ FIXME: This method doesn't have a deep keyword argument.
If deep == True return a deep copy, recursively copying all sub entities.
Standard properties are copied using add_property.
@@ -178,7 +203,7 @@ class Entity:
return self._wrapped_entity.version
@version.setter
- def version(self, version):
+ def version(self, version: Optional[Version]):
self._version = version
@property
@@ -250,14 +275,14 @@ class Entity:
return self._wrapped_entity.description
- @property
- def checksum(self):
- return self._checksum
-
@description.setter
def description(self, new_description):
self.__description = new_description
+ @property
+ def checksum(self):
+ return self._checksum
+
@property
def unit(self):
if self.__unit is not None or self._wrapped_entity is None:
@@ -324,8 +349,15 @@ class Entity:
def pickup(self, new_pickup):
self.__pickup = new_pickup
- def grant(self, realm=None, username=None, role=None,
- permission=None, priority=False, revoke_denial=True):
+ def grant(
+ self,
+ realm: Optional[str] = None,
+ username: Optional[str] = None,
+ role: Optional[str] = None,
+ permission: Optional[str] = None,
+ priority: bool = False,
+ revoke_denial: bool = True,
+ ):
"""Grant a permission to a user or role for this entity.
You must specify either only the username and the realm, or only the
@@ -359,8 +391,15 @@ class Entity:
permission=permission, priority=priority,
revoke_denial=revoke_denial)
- def deny(self, realm=None, username=None, role=None,
- permission=None, priority=False, revoke_grant=True):
+ def deny(
+ self,
+ realm: Optional[str] = None,
+ username: Optional[str] = None,
+ role: Optional[str] = None,
+ permission: Optional[str] = None,
+ priority: bool = False,
+ revoke_grant: bool = True,
+ ):
"""Deny a permission to a user or role for this entity.
You must specify either only the username and the realm, or only the
@@ -412,7 +451,7 @@ class Entity:
permission=permission,
priority=priority)
- def is_permitted(self, permission, role=None):
+ def is_permitted(self, permission: Permission, role: Optional[str] = None):
if role is None:
# pylint: disable=unsupported-membership-test
@@ -420,7 +459,7 @@ class Entity:
else:
self.acl.is_permitted(permission=permission)
- def get_all_messages(self):
+ def get_all_messages(self) -> Messages:
ret = Messages()
ret.append(self.messages)
@@ -519,8 +558,29 @@ class Entity:
return self
- def add_property(self, property=None, value=None, id=None, name=None, description=None, datatype=None,
- unit=None, importance=None, inheritance=None): # @ReservedAssignment
+ def add_property(
+ self,
+ property: Union[int, str, Entity, None] = None,
+ value: Union[
+ int,
+ str,
+ bool,
+ datetime,
+ Entity,
+ List[int],
+ List[str],
+ List[bool],
+ List[Entity],
+ None,
+ ] = None,
+ id: Optional[int] = None,
+ name: Optional[str] = None,
+ description: Optional[str] = None,
+ datatype: Optional[str] = None,
+ unit: Optional[str] = None,
+ importance: Optional[str] = None,
+ inheritance: Union[str, INHERITANCE, None] = None,
+ ) -> Entity: # @ReservedAssignment
"""Add a property to this entity.
The first parameter is meant to identify the property entity either via
@@ -690,7 +750,13 @@ class Entity:
return self
- def add_parent(self, parent=None, id=None, name=None, inheritance=None): # @ReservedAssignment
+ def add_parent(
+ self,
+ parent: Union[Entity, int, str, None] = None,
+ id: Optional[int] = None,
+ name: Optional[str] = None,
+ inheritance: Union[INHERITANCE, str, None] = None,
+ ): # @ReservedAssignment
"""Add a parent to this entity.
Parameters
@@ -704,7 +770,7 @@ class Entity:
name : str
Name of the parent entity. Ignored if `parent is not
none`.
- inheritance : str
+ inheritance : str, INHERITANCE
One of ``obligatory``, ``recommended``, ``suggested``, or ``fix``. Specifies the
minimum importance which parent properties need to have to be inherited by this
entity. If no `inheritance` is given, no properties will be inherited by the child.
@@ -811,7 +877,7 @@ out: bool
return self.parents
- def get_parents_recursively(self, retrieve: bool = True):
+ def get_parents_recursively(self, retrieve: bool = True) -> List[Entity]:
"""Get all ancestors of this entity.
Parameters
@@ -826,12 +892,12 @@ out: List[Entity]
The parents of this Entity
"""
- all_parents = []
+ all_parents: List[Entity] = []
self._get_parent_recursively(all_parents, retrieve=retrieve)
return all_parents
- def _get_parent_recursively(self, all_parents: list, retrieve: bool = True):
+ def _get_parent_recursively(self, all_parents: List[Entity], retrieve: bool = True):
"""Get all ancestors with a little helper.
As a side effect of this method, the ancestors are added to
@@ -862,7 +928,7 @@ out: List[Entity]
all_parents.append(w_parent)
w_parent._get_parent_recursively(all_parents, retrieve=retrieve)
- def get_parent(self, key):
+ def get_parent(self, key: Union[int, Entity, str]) -> Union[Entity, None]:
"""Return the first parent matching the key or None if no match exists.
Parameters
@@ -911,7 +977,7 @@ out: List[Entity]
return self.properties
- def get_property(self, pattern):
+ def get_property(self, pattern: Union[int, str, Entity]) -> Union[Property, None]:
""" Return the first matching property or None.
Parameters
@@ -956,7 +1022,9 @@ out: List[Entity]
return None
- def _get_value_for_selector(self, selector):
+ def _get_value_for_selector(
+ self, selector: Union[str, List[str], Tuple[str]]
+ ) -> Any:
"""return the value described by the selector
A selector is a list or a tuple of strings describing a path in an
@@ -1093,7 +1161,7 @@ out: List[Entity]
return ret
- def get_errors_deep(self, roots=None):
+ def get_errors_deep(self, roots=None) -> List[Tuple[str, List[Entity]]]:
"""Get all error messages of this entity and all sub-entities /
parents / properties.
@@ -1124,7 +1192,12 @@ out: List[Entity]
return False
- def to_xml(self, xml=None, add_properties=ALL, local_serialization=False):
+ def to_xml(
+ self,
+ xml: Optional[etree._Element] = None,
+ add_properties: Optional[INHERITANCE] = ALL,
+ local_serialization: bool = False,
+ ) -> etree._Element:
"""Generate an xml representation of this entity. If the parameter xml
is given, all attributes, parents, properties, and messages of this
entity will be added to it instead of creating a new element.
@@ -1144,7 +1217,6 @@ out: List[Entity]
assert isinstance(xml, etree._Element)
# unwrap wrapped entity
-
if self._wrapped_entity is not None:
xml = self._wrapped_entity.to_xml(xml, add_properties)
@@ -1394,8 +1466,14 @@ out: List[Entity]
return Container().append(self).retrieve(
unique=unique, raise_exception_on_error=raise_exception_on_error, flags=flags)
- def insert(self, raise_exception_on_error=True, unique=True,
- sync=True, strict=False, flags=None):
+ def insert(
+ self,
+ raise_exception_on_error=True,
+ unique=True,
+ sync=True,
+ strict=False,
+ flags: Optional[dict] = None,
+ ):
"""Insert this entity into a LinkAhead server. A successful insertion will
generate a new persistent ID for this entity. This entity can be
identified, retrieved, updated, and deleted via this ID until it has
@@ -1758,14 +1836,20 @@ class Parent(Entity):
def affiliation(self, affiliation):
self.__affiliation = affiliation
- def __init__(self, id=None, name=None, description=None, inheritance=None): # @ReservedAssignment
+ def __init__(
+ self,
+ id: Optional[int] = None,
+ name: Optional[str] = None,
+ description: Optional[str] = None,
+ inheritance: Optional[INHERITANCE] = None,
+ ): # @ReservedAssignment
Entity.__init__(self, id=id, name=name, description=description)
if inheritance is not None:
self.set_flag("inheritance", inheritance)
self.__affiliation = None
- def to_xml(self, xml=None, add_properties=None):
+ def to_xml(self, xml: Optional[etree._Element] = None, add_properties=None):
if xml is None:
xml = etree.Element("Parent")
@@ -1822,13 +1906,20 @@ class Property(Entity):
return super(Property, self).add_parent(parent=parent, id=id, name=name, inheritance=inheritance)
- def __init__(self, name=None, id=None, description=None, datatype=None,
- value=None, unit=None):
+ def __init__(
+ self,
+ name: Optional[str] = None,
+ id: Optional[int] = None,
+ description: Optional[str] = None,
+ datatype: Union[DATATYPE, None] = None,
+ value=None,
+ unit: Optional[str] = None,
+ ):
Entity.__init__(self, id=id, name=name, description=description,
datatype=datatype, value=value, role="Property")
self.unit = unit
- def to_xml(self, xml=None, add_properties=ALL):
+ def to_xml(self, xml: Optional[etree._Element] = None, add_properties=ALL):
if xml is None:
xml = etree.Element("Property")
@@ -1878,13 +1969,19 @@ class Property(Entity):
class Message(object):
- def __init__(self, type=None, code=None, description=None, body=None): # @ReservedAssignment
+ def __init__(
+ self,
+ type: Optional[str] = None,
+ code: Optional[int] = None,
+ description: Optional[str] = None,
+ body: Optional[str] = None,
+ ): # @ReservedAssignment
self.description = description
self.type = type if type is not None else "Info"
self.code = int(code) if code is not None else None
self.body = body
- def to_xml(self, xml=None):
+ def to_xml(self, xml: Optional[etree._Element] = None):
if xml is None:
xml = etree.Element(str(self.type))
@@ -1926,7 +2023,13 @@ class RecordType(Entity):
property=property, id=id, name=name, description=description, datatype=datatype,
value=value, unit=unit, importance=importance, inheritance=inheritance)
- def add_parent(self, parent=None, id=None, name=None, inheritance=OBLIGATORY):
+ def add_parent(
+ self,
+ parent: Union[Entity, int, str, None] = None,
+ id: Optional[int] = None,
+ name: Optional[str] = None,
+ inheritance: Union[INHERITANCE, str, None] = OBLIGATORY,
+ ):
"""Add a parent to this RecordType
Parameters
@@ -1959,11 +2062,21 @@ class RecordType(Entity):
return super().add_parent(parent=parent, id=id, name=name, inheritance=inheritance)
- def __init__(self, name=None, id=None, description=None, datatype=None): # @ReservedAssignment
+ def __init__(
+ self,
+ name: Optional[str] = None,
+ id: Optional[int] = None,
+ description: Optional[str] = None,
+ datatype: Optional[DATATYPE] = None,
+ ): # @ReservedAssignment
Entity.__init__(self, name=name, id=id, description=description,
datatype=datatype, role="RecordType")
- def to_xml(self, xml=None, add_properties=ALL):
+ def to_xml(
+ self,
+ xml: Optional[etree._Element] = None,
+ add_properties: Optional[INHERITANCE] = ALL,
+ ) -> etree._Element:
if xml is None:
xml = etree.Element("RecordType")
@@ -1982,7 +2095,12 @@ class Record(Entity):
property=property, id=id, name=name, description=description, datatype=datatype,
value=value, unit=unit, importance=importance, inheritance=inheritance)
- def __init__(self, name=None, id=None, description=None): # @ReservedAssignment
+ def __init__(
+ self,
+ name: Optional[str] = None,
+ id: Optional[int] = None,
+ description: Optional[str] = None,
+ ): # @ReservedAssignment
Entity.__init__(self, name=name, id=id, description=description,
role="Record")
@@ -2023,9 +2141,17 @@ class File(Record):
"""
- def __init__(self, name=None, id=None, description=None, # @ReservedAssignment
- path=None, file=None, pickup=None, # @ReservedAssignment
- thumbnail=None, from_location=None):
+ def __init__(
+ self,
+ name: Optional[str] = None,
+ id: Optional[int] = None,
+ description: Optional[str] = None, # @ReservedAssignment
+ path: Optional[str] = None,
+ file: Union[str, TextIO, None] = None,
+ pickup: Optional[str] = None, # @ReservedAssignment
+ thumbnail: Optional[str] = None,
+ from_location=None,
+ ):
Record.__init__(self, id=id, name=name, description=description)
self.role = "File"
self.datatype = None
@@ -2046,7 +2172,12 @@ class File(Record):
if self.pickup is None:
self.pickup = from_location
- def to_xml(self, xml=None, add_properties=ALL, local_serialization=False):
+ def to_xml(
+ self,
+ xml: Optional[etree._Element] = None,
+ add_properties: Optional[INHERITANCE] = ALL,
+ local_serialization: bool = False,
+ ):
"""Convert this file to an xml element.
@return: xml element
@@ -2142,6 +2273,7 @@ class File(Record):
class _Properties(list):
+ """FIXME: Add docstring."""
def __init__(self):
list.__init__(self)
@@ -2161,7 +2293,7 @@ class _Properties(list):
if property is not None:
self._importance[property] = importance
- def get_by_name(self, name):
+ def get_by_name(self, name: str) -> Property:
"""Get a property of this list via it's name. Raises a LinkAheadException
if not exactly one property has this name.
@@ -2176,7 +2308,12 @@ class _Properties(list):
return self
- def append(self, property, importance=None, inheritance=None): # @ReservedAssignment
+ def append(
+ self,
+ property: Union[List[Entity], Entity],
+ importance=None,
+ inheritance: Union[str, INHERITANCE, None] = None,
+ ): # @ReservedAssignment
if isinstance(property, list):
for p in property:
self.append(p, importance, inheritance)
@@ -2203,7 +2340,9 @@ class _Properties(list):
return self
- def to_xml(self, add_to_element, add_properties):
+ def to_xml(
+ self, add_to_element: etree._Element, add_properties: Union[str, INHERITANCE]
+ ):
for p in self:
importance = self._importance.get(p)
@@ -2213,7 +2352,7 @@ class _Properties(list):
pelem = p.to_xml(xml=etree.Element("Property"), add_properties=FIX)
if p in self._importance:
- pelem.set("importance", importance)
+ pelem.set("importance", str(importance))
if p in self._inheritance:
pelem.set("flag", "inheritance:" +
@@ -2228,7 +2367,7 @@ class _Properties(list):
return xml2str(xml)
- def _get_entity_by_cuid(self, cuid):
+ def _get_entity_by_cuid(self, cuid: str):
'''
Get the first entity which has the given cuid.
Note: this method is intended for internal use.
@@ -2242,7 +2381,7 @@ class _Properties(list):
return e
raise KeyError("No entity with that cuid in this container.")
- def remove(self, prop):
+ def remove(self, prop: Union[Entity, int]):
if isinstance(prop, Entity):
if prop in self:
list.remove(self, prop)
@@ -2366,7 +2505,7 @@ class _ParentList(list):
return xml2str(xml)
- def remove(self, parent):
+ def remove(self, parent: Union[Entity, int, str]):
if isinstance(parent, Entity):
if parent in self:
list.remove(self, parent)
@@ -2813,7 +2952,7 @@ class Container(list):
return error_list
- def get_entity_by_name(self, name, case_sensitive=True):
+ def get_entity_by_name(self, name: str, case_sensitive: bool = True):
"""Get the first entity which has the given name. Note: If several
entities are in this list which have the same name, this method will
only return the first and ignore the others.
@@ -3071,8 +3210,14 @@ class Container(list):
raise LinkAheadException(
"The server's response didn't contain the expected elements. The configuration of this client might be invalid (especially the url).")
- def _sync(self, container, unique, raise_exception_on_error,
- name_case_sensitive=False, strategy=_basic_sync):
+ def _sync(
+ self,
+ container: Container,
+ unique: bool,
+ raise_exception_on_error: bool,
+ name_case_sensitive: bool = False,
+ strategy=_basic_sync,
+ ):
"""Synchronize this container (C1) with another container (C2).
That is: 1) Synchronize any entity e1 in C1 with the
@@ -3118,13 +3263,18 @@ class Container(list):
self._timestamp = container._timestamp
self._srid = container._srid
- def _calc_sync_dict(self, remote_container, unique,
- raise_exception_on_error, name_case_sensitive):
+ def _calc_sync_dict(
+ self,
+ remote_container: Container,
+ unique: bool,
+ raise_exception_on_error: bool,
+ name_case_sensitive: bool,
+ ):
# self is local, remote_container is remote.
# which is to be synced with which:
# sync_dict[local_entity]=sync_remote_enities
- sync_dict = dict()
+ sync_dict: Dict[Entity, Optional[List[Entity]]] = dict()
# list of remote entities which already have a local equivalent
used_remote_entities = []
@@ -3265,7 +3415,7 @@ class Container(list):
return sync_dict
@staticmethod
- def _find_dependencies_in_container(container):
+ def _find_dependencies_in_container(container: Container):
"""Find elements in a container that are a dependency of another element of the same.
Parameters
@@ -3295,7 +3445,7 @@ class Container(list):
for prop in container_item.get_properties():
prop_dt = prop.datatype
- if is_reference(prop_dt):
+ if prop_dt is not None and is_reference(prop_dt):
# add only if it is a reference, not a simple property
# Step 1: look for prop.value
if prop.value is not None:
@@ -3458,8 +3608,14 @@ class Container(list):
return self
- def retrieve(self, query=None, unique=True,
- raise_exception_on_error=True, sync=True, flags=None):
+ def retrieve(
+ self,
+ query: Union[str, list, None] = None,
+ unique: bool = True,
+ raise_exception_on_error: bool = True,
+ sync: bool = True,
+ flags=None,
+ ):
"""Retrieve all entities in this container identified via their id if
present and via their name otherwise. Any locally already existing
attributes (name, description, ...) will be preserved. Any such
@@ -3747,25 +3903,25 @@ class Container(list):
self._linearize()
# TODO: This is a possible solution for ticket#137
-# retrieved = Container()
-# for entity in self:
-# if entity.is_valid():
-# retrieved.append(entity)
-# if len(retrieved)>0:
-# retrieved = retrieved.retrieve(raise_exception_on_error=False, sync=False)
-# for e_remote in retrieved:
-# if e_remote.id is not None:
-# try:
-# self.get_entity_by_id(e_remote.id).is_valid=e_remote.is_valid
-# continue
-# except KeyError:
-# pass
-# if e_remote.name is not None:
-# try:
-# self.get_entity_by_name(e_remote.name).is_valid=e_remote.is_valid
-# continue
-# except KeyError:
-# pass
+ # retrieved = Container()
+ # for entity in self:
+ # if entity.is_valid():
+ # retrieved.append(entity)
+ # if len(retrieved)>0:
+ # retrieved = retrieved.retrieve(raise_exception_on_error=False, sync=False)
+ # for e_remote in retrieved:
+ # if e_remote.id is not None:
+ # try:
+ # self.get_entity_by_id(e_remote.id).is_valid=e_remote.is_valid
+ # continue
+ # except KeyError:
+ # pass
+ # if e_remote.name is not None:
+ # try:
+ # self.get_entity_by_name(e_remote.name).is_valid=e_remote.is_valid
+ # continue
+ # except KeyError:
+ # pass
for entity in self:
if entity.is_valid():
continue
@@ -3968,7 +4124,15 @@ def get_global_acl():
class ACI():
- def __init__(self, realm, username, role, permission):
+ """FIXME: Add docstring"""
+
+ def __init__(
+ self,
+ realm: Optional[str],
+ username: Optional[str],
+ role: Optional[str],
+ permission: Optional[str],
+ ):
self.role = role
self.username = username
self.realm = realm
@@ -3984,7 +4148,7 @@ class ACI():
def __repr__(self):
return str(self.realm) + ":" + str(self.username) + ":" + str(self.role) + ":" + str(self.permission)
- def add_to_element(self, e):
+ def add_to_element(self, e: etree._Element):
if self.role is not None:
e.set("role", self.role)
else:
@@ -3998,16 +4162,17 @@ class ACI():
class ACL():
+ """FIXME: Add docstring"""
- global_acl = None
+ global_acl: Optional[ACL] = None
- def __init__(self, xml=None):
+ def __init__(self, xml: Optional[etree._Element] = None):
if xml is not None:
self.parse_xml(xml)
else:
self.clear()
- def parse_xml(self, xml):
+ def parse_xml(self, xml: etree._Element):
"""Clear this ACL and parse the xml.
Iterate over the rules in the xml and add each rule to this ACL.
@@ -4016,14 +4181,14 @@ class ACL():
Parameters
----------
- xml : lxml.etree.Element
+ xml : lxml.etree._Element
The xml element containing the ACL rules, i.e. <Grant> and <Deny>
rules.
"""
self.clear()
self._parse_xml(xml)
- def _parse_xml(self, xml):
+ def _parse_xml(self, xml: etree._Element):
"""Parse the xml.
Iterate over the rules in the xml and add each rule to this ACL.
@@ -4032,7 +4197,7 @@ class ACL():
Parameters
----------
- xml : lxml.etree.Element
+ xml : lxml.etree._Element
The xml element containing the ACL rules, i.e. <Grant> and <Deny>
rules.
"""
@@ -4056,7 +4221,7 @@ class ACL():
permission=permission, priority=priority,
revoke_grant=False)
- def combine(self, other):
+ def combine(self, other: ACL):
""" Combine and return new instance."""
result = ACL()
result._grants.update(other._grants)
@@ -4078,15 +4243,15 @@ class ACL():
len(self._priority_denials) + len(self._denials) == 0
def clear(self):
- self._grants = set()
- self._denials = set()
- self._priority_grants = set()
- self._priority_denials = set()
+ self._grants: set[ACI] = set()
+ self._denials: set[ACI] = set()
+ self._priority_grants: set[ACI] = set()
+ self._priority_denials: set[ACI] = set()
- def _get_boolean_priority(self, priority):
+ def _get_boolean_priority(self, priority: Any):
return str(priority).lower() in ["true", "1", "yes", "y"]
- def _remove_item(self, item, priority):
+ def _remove_item(self, item, priority: bool):
try:
self._denials.remove(item)
except KeyError:
@@ -4106,8 +4271,14 @@ class ACL():
except KeyError:
pass
- def revoke_grant(self, username=None, realm=None,
- role=None, permission=None, priority=False):
+ def revoke_grant(
+ self,
+ username: Optional[str] = None,
+ realm: Optional[str] = None,
+ role: Optional[str] = None,
+ permission: Optional[str] = None,
+ priority: Union[bool, str] = False,
+ ):
priority = self._get_boolean_priority(priority)
item = ACI(role=role, username=username,
realm=realm, permission=permission)
@@ -4132,8 +4303,15 @@ class ACL():
if item in self._denials:
self._denials.remove(item)
- def grant(self, permission, username=None, realm=None, role=None,
- priority=False, revoke_denial=True):
+ def grant(
+ self,
+ permission: Optional[str],
+ username: Optional[str] = None,
+ realm: Optional[str] = None,
+ role: Optional[str] = None,
+ priority: bool = False,
+ revoke_denial: bool = True,
+ ):
"""Grant a permission to a user or role.
You must specify either only the username and the realm, or only the
@@ -4174,8 +4352,15 @@ class ACL():
else:
self._grants.add(item)
- def deny(self, username=None, realm=None, role=None,
- permission=None, priority=False, revoke_grant=True):
+ def deny(
+ self,
+ username: Optional[str] = None,
+ realm: Optional[str] = None,
+ role: Optional[str] = None,
+ permission: Optional[str] = None,
+ priority: bool = False,
+ revoke_grant: bool = True,
+ ):
"""Deny a permission to a user or role for this entity.
You must specify either only the username and the realm, or only the
@@ -4216,7 +4401,7 @@ class ACL():
else:
self._denials.add(item)
- def to_xml(self, xml=None):
+ def to_xml(self, xml: Optional[etree._Element] = None):
if xml is None:
xml = etree.Element("EntityACL")
@@ -4246,7 +4431,7 @@ class ACL():
return xml
- def get_acl_for_role(self, role):
+ def get_acl_for_role(self, role: str) -> ACL:
ret = ACL()
for aci in self._grants:
@@ -4292,7 +4477,7 @@ class ACL():
return ret
- def get_permissions_for_user(self, username, realm=None):
+ def get_permissions_for_user(self, username: str, realm: Optional[str] = None):
acl = self.get_acl_for_user(username, realm)
_grants = set()
@@ -4313,7 +4498,7 @@ class ACL():
return ((_grants - _denials) | _priority_grants) - _priority_denials
- def get_permissions_for_role(self, role):
+ def get_permissions_for_role(self, role: str):
acl = self.get_acl_for_role(role)
_grants = set()
@@ -4371,10 +4556,10 @@ class Query():
def getFlag(self, key):
return self.flags.get(key)
- def __init__(self, q):
- self.flags = dict()
+ def __init__(self, q: Union[str, etree._Element]):
+ self.flags: Dict[str, str] = dict()
self.messages = Messages()
- self.cached = None
+ self.cached: Optional[bool] = None
self.etag = None
if isinstance(q, etree._Element):
@@ -4419,8 +4604,13 @@ class Query():
yield next_page
index += page_length
- def execute(self, unique=False, raise_exception_on_error=True, cache=True,
- page_length=None):
+ def execute(
+ self,
+ unique: bool = False,
+ raise_exception_on_error: bool = True,
+ cache: bool = True,
+ page_length: Optional[int] = None,
+ ) -> Union[Container, int]:
"""Execute a query (via a server-requests) and return the results.
Parameters
@@ -4507,8 +4697,14 @@ class Query():
return cresp
-def execute_query(q, unique=False, raise_exception_on_error=True, cache=True,
- flags=None, page_length=None):
+def execute_query(
+ q: str,
+ unique: bool = False,
+ raise_exception_on_error: bool = True,
+ cache: bool = True,
+ flags: Optional[Dict[str, str]] = None,
+ page_length: Optional[int] = None,
+) -> Union[Container, int]:
"""Execute a query (via a server-requests) and return the results.
Parameters
@@ -4600,7 +4796,7 @@ class DropOffBox(list):
class UserInfo():
- def __init__(self, xml):
+ def __init__(self, xml: etree._Element):
self.roles = [role.text for role in xml.findall("Roles/Role")]
self.name = xml.get("username")
self.realm = xml.get("realm")
@@ -4652,7 +4848,7 @@ class Info():
class Permission():
- def __init__(self, name, description=None):
+ def __init__(self, name: str, description: Optional[str] = None):
self.name = name
self.description = description
@@ -4676,13 +4872,13 @@ class Permissions():
known_permissions = None
- def __init__(self, xml):
+ def __init__(self, xml: etree._Element):
self.parse_xml(xml)
def clear(self):
self._perms = set()
- def parse_xml(self, xml):
+ def parse_xml(self, xml: etree._Element):
self.clear()
for e in xml:
@@ -4703,7 +4899,7 @@ class Permissions():
return str(self._perms)
-def parse_xml(xml):
+def parse_xml(xml: Union[str, etree._Element]):
"""parse a string or tree representation of an xml document to a set of
entities (records, recordtypes, properties, or files).
@@ -4712,14 +4908,14 @@ def parse_xml(xml):
"""
if isinstance(xml, etree._Element):
- elem = xml
+ elem: etree._Element = xml
else:
elem = etree.fromstring(xml)
return _parse_single_xml_element(elem)
-def _parse_single_xml_element(elem):
+def _parse_single_xml_element(elem: etree._Element):
classmap = {
'record': Record,
'recordtype': RecordType,
@@ -4773,7 +4969,7 @@ def _parse_single_xml_element(elem):
"code"), description=elem.get("description"), body=elem.text)
-def _evaluate_and_add_error(parent_error, ent):
+def _evaluate_and_add_error(parent_error: TransactionError, ent: Union[Entity, Container]):
"""Evaluate the error message(s) attached to entity and add a
corresponding exception to parent_error.
@@ -4782,7 +4978,7 @@ def _evaluate_and_add_error(parent_error, ent):
parent_error : TransactionError
Parent error to which the new exception will be attached. This
exception will be a direct child.
- ent : Entity
+ ent : Entity or Container
Entity that caused the TransactionError. An exception is
created depending on its error message(s).
@@ -4876,7 +5072,7 @@ def _evaluate_and_add_error(parent_error, ent):
return parent_error
-def raise_errors(arg0):
+def raise_errors(arg0: Union[Entity, QueryTemplate, Container]):
"""Raise a TransactionError depending on the error code(s) inside
Entity, QueryTemplate or Container arg0. More detailed errors may
be attached to the TransactionError depending on the contents of
@@ -4903,7 +5099,7 @@ def raise_errors(arg0):
raise transaction_error
-def delete(ids, raise_exception_on_error=True):
+def delete(ids: Union[List[int], range], raise_exception_on_error=True):
c = Container()
if isinstance(ids, list) or isinstance(ids, range):
diff --git a/src/linkahead/py.typed b/src/linkahead/py.typed
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/linkahead/utils/plantuml.py b/src/linkahead/utils/plantuml.py
index e5432dcebff7bd7aef83d2ad0355b34d82fbf331..19594d6e856e740fe2c58c5128eead31c37485ce 100644
--- a/src/linkahead/utils/plantuml.py
+++ b/src/linkahead/utils/plantuml.py
@@ -409,7 +409,7 @@ def to_graphics(recordtypes: List[db.Entity], filename: str,
raise Exception("An error occured during the execution of "
"plantuml when using the format {}. "
"Is plantuml installed? "
- "You might want to dry a different format.".format(format))
+ "You might want to try a different format.".format(format))
# copy only the final product into the target directory
shutil.copy(os.path.join(td, filename + "." + extension),
output_dirname)
diff --git a/tox.ini b/tox.ini
index 9a862f698573c864921ab9998d1a6a8a07978126..b87f6e8140dbc431d0b190301dbfa1125e4b8ede 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,7 +4,6 @@ skip_missing_interpreters = true
[testenv]
deps = .
- pynose
pytest
pytest-cov
mypy
diff --git a/unittests/test_concrete_property.py b/unittests/test_concrete_property.py
index e70668f02aab12762a342f035a974f708652ae69..32d38bbed553b6b1d162f7e76fb271de38e08b95 100644
--- a/unittests/test_concrete_property.py
+++ b/unittests/test_concrete_property.py
@@ -27,10 +27,20 @@
from linkahead import configure_connection
from linkahead.common.models import _ConcreteProperty
from linkahead.connection.mockup import MockUpServerConnection
+from pytest import raises
# pylint: disable=missing-docstring
-from nose.tools import assert_equal as eq
-from nose.tools import assert_is_not_none as there
-from nose.tools import assert_true as tru
+
+
+def eq(a, b):
+ assert a == b
+
+
+def there(a):
+ assert a is not None
+
+
+def tru(a):
+ assert a
def setup_module():
diff --git a/unittests/test_connection.py b/unittests/test_connection.py
index ca36a71680f8e13ac9114b9ab0bff0b6a96ea4c3..a3a1eff705c64f59baec33088906bdd9a4daa14d 100644
--- a/unittests/test_connection.py
+++ b/unittests/test_connection.py
@@ -39,14 +39,21 @@ from linkahead.connection.mockup import (MockUpResponse, MockUpServerConnection,
from linkahead.connection.utils import make_uri_path, quote, urlencode
from linkahead.exceptions import (ConfigurationError, LoginFailedError,
LinkAheadConnectionError)
-from nose.tools import assert_equal as eq
-from nose.tools import assert_false as falz
-from nose.tools import assert_is_not_none as there
-from nose.tools import assert_raises as raiz
-from nose.tools import assert_true as tru
from pytest import raises
+def eq(a, b):
+ assert a == b
+
+
+def there(a):
+ assert a is not None
+
+
+def tru(a):
+ assert a
+
+
def setup_function(function):
configure_connection(url="http://localhost:8888/some/path",
password_method="plain", username="test",
@@ -74,11 +81,11 @@ def test_urlencode():
eq(urlencode({'key1': 'val1'}), 'key1=val1')
eq(urlencode({'keynoval': None}), 'keynoval=')
eq(urlencode({'kèy': 'välüe'}), 'k%C3%A8y=v%C3%A4l%C3%BCe')
- with raiz(AttributeError):
+ with raises(AttributeError) as exc_info:
urlencode({bytes('asdf', 'utf-8'): 'asdf'})
- with raiz(AttributeError):
+ with raises(AttributeError) as exc_info:
urlencode({'asdf': bytes('asdf', 'utf-8')})
- with raiz(AttributeError):
+ with raises(AttributeError) as exc_info:
urlencode({None: 'asdf'})
@@ -138,10 +145,10 @@ def test_configure_connection_bad_url():
def test_connection_interface():
- with raiz(TypeError) as cm:
+ with raises(TypeError) as cm:
CaosDBServerConnection()
- tru(cm.exception.args[0].startswith(
- "Can't instantiate abstract class CaosDBServerConnection"))
+
+ assert "Can't instantiate abstract class CaosDBServerConnection" in str(cm.value)
tru(hasattr(CaosDBServerConnection, "request"))
tru(hasattr(CaosDBServerConnection.request, "__call__"))
@@ -151,10 +158,10 @@ def test_connection_interface():
def test_use_mockup_implementation():
- with raiz(RuntimeError) as rerr:
+ with raises(RuntimeError) as rerr:
execute_query("FIND Something")
- print(rerr.exception.args[0])
- eq(rerr.exception.args[0],
+ print(str(rerr.value))
+ eq(str(rerr.value),
"No response for this request - GET: Entity?query=FIND%20Something")
@@ -219,9 +226,9 @@ def test_resources_list():
def test_request_basics():
connection = test_init_connection()
tru(hasattr(connection, "request"))
- with raiz(RuntimeError) as cm:
+ with raises(RuntimeError) as cm:
connection.request(method="GET", path="asdf")
- eq(cm.exception.args[0], "No response for this request - GET: asdf")
+ eq(str(cm.value), "No response for this request - GET: asdf")
connection = test_resources_list()
there(connection.request(method="GET", path="asdf"))
diff --git a/unittests/test_connection_utils.py b/unittests/test_connection_utils.py
index 6a95fffa2f5f3dbfb302e035deee2f24fab9acf5..d82cfde07150fa3dd480cfcdd0ae63fd25fdad24 100644
--- a/unittests/test_connection_utils.py
+++ b/unittests/test_connection_utils.py
@@ -25,9 +25,7 @@
# pylint: disable=missing-docstring
from __future__ import unicode_literals, print_function
from pytest import raises
-from nose.tools import (assert_equal as eq, assert_raises as raiz, assert_true
- as tru, assert_is_not_none as there, assert_false as
- falz)
+
from linkahead.exceptions import ConfigurationError, LoginFailedError
from linkahead.connection.utils import parse_auth_token, auth_token_to_cookie
from linkahead.connection.connection import (
@@ -40,6 +38,18 @@ from linkahead.connection.authentication.interface import CredentialsAuthenticat
from linkahead import execute_query
+def eq(a, b):
+ assert a == b
+
+
+def there(a):
+ assert a is not None
+
+
+def tru(a):
+ assert a
+
+
def setup_module():
_reset_config()
diff --git a/unittests/test_exception.py b/unittests/test_exception.py
index 23607f46e1794ff336aa6687403c69f99b851988..1e54edbeec4551712a90115e18b5437398657861 100644
--- a/unittests/test_exception.py
+++ b/unittests/test_exception.py
@@ -21,8 +21,8 @@
import warnings
-from caosdb.exceptions import (CaosDBConnectionError, CaosDBException,
- LinkAheadConnectionError, LinkAheadException)
+from linkahead.exceptions import (CaosDBConnectionError, CaosDBException,
+ LinkAheadConnectionError, LinkAheadException)
# make sure the deprecation is raised
with warnings.catch_warnings(record=True) as w:
diff --git a/unittests/test_file.py b/unittests/test_file.py
index dd974cb176ca69e2ffb065b5de185611e528e815..c1093cdd26b71bd8f1d48e98dd224df956f629f8 100644
--- a/unittests/test_file.py
+++ b/unittests/test_file.py
@@ -25,13 +25,10 @@
from linkahead import File, Record, configure_connection
from linkahead.connection.mockup import MockUpServerConnection
# pylint: disable=missing-docstring
-from nose.tools import assert_equal as eq
-from nose.tools import assert_is_not_none as there
-from nose.tools import assert_true as tru
def setup_module():
- there(File)
+ assert File is not None
configure_connection(url="unittests", username="testuser",
password_method="plain",
password="testpassword", timeout=200,
@@ -39,12 +36,12 @@ def setup_module():
def hat(obj, attr):
- tru(hasattr(obj, attr))
+ assert hasattr(obj, attr)
def test_is_record():
file_ = File()
- tru(isinstance(file_, Record))
+ assert isinstance(file_, Record)
def test_instance_variable():
@@ -57,4 +54,4 @@ def test_instance_variable():
def test_role():
file_ = File()
- eq(file_.role, "File")
+ assert file_.role == "File"
diff --git a/unittests/test_high_level_api.py b/unittests/test_high_level_api.py
index ea5e635eadaa849480de5f3ece10b813a538a1b0..be57e3c747619852c7cec2002eac6928c7d77702 100644
--- a/unittests/test_high_level_api.py
+++ b/unittests/test_high_level_api.py
@@ -23,21 +23,21 @@
# A. Schlemmer, 02/2022
-import caosdb as db
-from caosdb.high_level_api import (convert_to_entity, convert_to_python_object,
- new_high_level_entity)
-from caosdb.high_level_api import (CaosDBPythonUnresolvedParent,
- CaosDBPythonUnresolvedReference,
- CaosDBPythonRecord, CaosDBPythonFile,
- high_level_type_for_standard_type,
- standard_type_for_high_level_type,
- high_level_type_for_role,
- CaosDBPythonEntity)
-from caosdb.apiutils import compare_entities
-
-from caosdb.common.datatype import (is_list_datatype,
- get_list_datatype,
- is_reference)
+import linkahead as db
+from linkahead.high_level_api import (convert_to_entity, convert_to_python_object,
+ new_high_level_entity)
+from linkahead.high_level_api import (CaosDBPythonUnresolvedParent,
+ CaosDBPythonUnresolvedReference,
+ CaosDBPythonRecord, CaosDBPythonFile,
+ high_level_type_for_standard_type,
+ standard_type_for_high_level_type,
+ high_level_type_for_role,
+ CaosDBPythonEntity)
+from linkahead.apiutils import compare_entities
+
+from linkahead.common.datatype import (is_list_datatype,
+ get_list_datatype,
+ is_reference)
import pytest
from lxml import etree
diff --git a/unittests/test_record_type.py b/unittests/test_record_type.py
index 594f9c647997d68cccdcccc56eaab482cd694c74..8741950a31c89088f5b96003d363d5e3db030852 100644
--- a/unittests/test_record_type.py
+++ b/unittests/test_record_type.py
@@ -25,13 +25,10 @@
from linkahead import Entity, RecordType, configure_connection
from linkahead.connection.mockup import MockUpServerConnection
# pylint: disable=missing-docstring
-from nose.tools import assert_equal as eq
-from nose.tools import assert_is_not_none as there
-from nose.tools import assert_true as tru
def setup_module():
- there(RecordType)
+ assert RecordType is not None
configure_connection(url="unittests", username="testuser",
password_method="plain",
password="testpassword", timeout=200,
@@ -39,14 +36,14 @@ def setup_module():
def hat(obj, attr):
- tru(hasattr(obj, attr))
+ assert hasattr(obj, attr)
def test_is_entity():
recty = RecordType()
- tru(isinstance(recty, Entity))
+ assert isinstance(recty, Entity)
def test_role():
recty = RecordType()
- eq(recty.role, "RecordType")
+ assert recty.role == "RecordType"
diff --git a/unittests/test_server_side_scripting.py b/unittests/test_server_side_scripting.py
index 7749af982113c71be1717646e83813ee34c7cff0..a27aefd6eb6ad3ab37a183b6e520935f2b8e8cb3 100644
--- a/unittests/test_server_side_scripting.py
+++ b/unittests/test_server_side_scripting.py
@@ -28,8 +28,9 @@ from unittest.mock import Mock
from linkahead.utils import server_side_scripting as sss
from linkahead.connection.mockup import MockUpServerConnection, MockUpResponse
from linkahead import configure_connection
+from typing import List
-_REMOVE_FILES_AFTERWARDS = []
+_REMOVE_FILES_AFTERWARDS: List[str] = []
def setup_module():