diff --git a/CHANGELOG.md b/CHANGELOG.md
index b65d9c17e4780e91b5983200796dbc6d9ab6ad14..9b1ab4456782b859960e7730e329a7641dede4bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,81 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* Entity State support (experimental, no StateModel support yet). See the `caosdb.State` class for
more information.
+
+### Changed ###
+
+### Deprecated ###
+
+### Removed ###
+
+### Fixed ###
+
+### Security ###
+
+## [0.5.1] - 2021-02-12 ##
+
+### Added ###
+
+### Changed ###
+
+### Deprecated ###
+
+### Removed ###
+
+### Fixed ###
+
+* #43 - Error with `execute_query` when server doesn't support query caching.
+
+### Security ###
+
+## [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.
+
+### Deprecated ###
+
+### Removed ###
+
+* Dynamic exception type `EntityMultiError`.
+* `get_something` functions from all error object in `exceptions.py`
+* `AmbiguityException`
+
+### Fixed ###
+
+### Security ###
+
+## [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.
@@ -81,7 +156,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* import bugs in apiutils
-## [0.2.4] -- 2020-04-23
+## [0.2.4] - 2020-04-23
### Added
diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md
new file mode 100644
index 0000000000000000000000000000000000000000..04e783a7fa31b1d5c3a600a1009c8f040db1620d
--- /dev/null
+++ b/DEPENDENCIES.md
@@ -0,0 +1,6 @@
+* caosdb-server == 0.3
+* Python >= 3.5
+* pip >= 20.0.2
+
+
+Any other dependencies are being installed via pip
diff --git a/README.md b/README.md
index ef26a604905d5140ae9a775065002af35ffe2121..e44702a3a22c28af986d641b5d7e454f915326c8 100644
--- a/README.md
+++ b/README.md
@@ -16,9 +16,9 @@ project](https://gitlab.com/caosdb/caosdb) for more information.
# License
-Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute for
-Dynamics and Self-Organization Göttingen.
-Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+* Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute
+ for Dynamics and Self-Organization Göttingen.
+* Copyright (C) 2020-2021 Indiscale GmbH <info@indiscale.com>
All files in this repository are licensed under a [GNU Affero General Public
License](LICENCE.md) (version 3 or later).
diff --git a/README_SETUP.md b/README_SETUP.md
index 481182d02d4c25acc5c5ed9607a282b22e861448..2db73cfaec2f6aadfc7fa3742892d970d562c946 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -30,6 +30,23 @@ packages you will ever need out of the box. If you prefer, you may also install
After installation, open an Anaconda prompt from the Windows menu and continue in the [Generic
installation](#generic-installation) section.
+#### iOS ####
+
+If there is no Python 3 installed yet, there are two main ways to obtain it: Either get the binary
+package from [python.org](https://www.python.org/downloads/) or, for advanced users, install via [Homebrew](https://brew.sh/). After installation
+from python.org, it is recommended to also update the TLS certificates for Python (this requires
+administrator rights for your user):
+
+```sh
+# Replace this with your Python version number:
+cd /Applications/Python\ 3.9/
+
+# This needs administrator rights:
+sudo ./Install\ Certificates.command
+```
+
+After these steps, you may continue with the [Generic installation](#generic-installation).
+
#### Generic installation ####
To install PyCaosDB locally, use `pip3` (also called `pip` on some systems):
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 02be5c1ad19f6a3a405fb08d62e23dab350ad445..dd6d5af4c43e1eea17c70f29da837c905694fed4 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -16,21 +16,27 @@ guidelines of the CaosDB Project
1. Create a release branch from the dev branch. This prevents further changes
to the code base and a never ending release process. Naming: `release-<VERSION>`
-2. Check all general prerequisites.
+2. Update CHANGELOG.md
-3. Prepare [setup.py](./setup.py): Update the `MAJOR`, `MINOR`, `MICRO`, `PRE`
+3. Check all general prerequisites.
+
+4. Prepare [setup.py](./setup.py): Check the `MAJOR`, `MINOR`, `MICRO`, `PRE`
variables and set `ISRELEASED` to `True`. Use the possibility to issue
pre-release versions for testing.
-4. Merge the release branch into the master branch.
+5. Merge the release branch into the master branch.
-5. Tag the latest commit of the master branch with `v<VERSION>`.
+6. Tag the latest commit of the master branch with `v<VERSION>`.
-6. Delete the release branch.
+7. Delete the release branch.
-7. Remove possibly existing `./dist` directory with old release.
+8. Remove possibly existing `./dist` directory with old release.
-8. Publish the release by executing `./release.sh` with uploads the caosdb
+9. Publish the release by executing `./release.sh` with uploads the caosdb
module to the Python Package Index [pypi.org](https://pypi.org).
-9. Merge the master branch back into the dev branch.
+10. Merge the master branch back into the dev branch.
+
+11. After the merge of master to dev, start a new development version by
+ setting `ISRELEASED` to `False` and by increasing at least the `MIRCO`
+ version in [setup.py](./setup.py)
diff --git a/examples/set_permissions.py b/examples/set_permissions.py
index 8b2b59f10ac033110af846eef0ed90356a09553d..dfc0a1510823a36d963f5d868052abb17b3fe12d 100755
--- a/examples/set_permissions.py
+++ b/examples/set_permissions.py
@@ -51,26 +51,26 @@ out : tuple
try:
human_user = admin._retrieve_user("jane")
_activate_user("jane")
- except db.EntityDoesNotExistError:
+ except db.ResourceNotFoundError:
human_user = admin._insert_user(
"jane", password="Human_Rememberable_Password_1234", status="ACTIVE")
try:
alien_user = admin._retrieve_user("xaxys")
_activate_user("xaxys")
- except db.EntityDoesNotExistError:
+ except db.ResourceNotFoundError:
alien_user = admin._insert_user("xaxys", password="4321_Syxax",
status="ACTIVE")
# At the moment, the return value is only "ok" for successful insertions.
try:
human_role = admin._retrieve_role("human")
- except db.EntityDoesNotExistError:
+ except db.ResourceNotFoundError:
human_role = admin._insert_role("human", "An Earthling.")
try:
alien_role = admin._retrieve_role("alien")
- except db.EntityDoesNotExistError:
+ except db.ResourceNotFoundError:
alien_role = admin._insert_role("alien", "An Extra-terrestrial.")
admin._set_roles("jane", ["human"])
@@ -111,9 +111,11 @@ Returns
out : Container
A container of retrieved entities, the length is given by the parameter count.
"""
- cont = db.execute_query("FIND RECORD Guitar", flags={"P": "0L{n}".format(n=count)})
+ cont = db.execute_query("FIND RECORD Guitar", flags={
+ "P": "0L{n}".format(n=count)})
if len(cont) != count:
- raise db.CaosDBException(msg="Incorrect number of entitities returned.")
+ raise db.CaosDBException(
+ msg="Incorrect number of entitities returned.")
return cont
@@ -138,7 +140,8 @@ general : bool, optional
# Set general permissions
if general:
- grant = admin.PermissionRule(action="grant", permission="RETRIEVE:OWNER")
+ grant = admin.PermissionRule(
+ action="grant", permission="RETRIEVE:OWNER")
deny = admin.PermissionRule(action="deny", permission="RETRIEVE:FILE")
admin._set_permissions(role=role_grant, permission_rules=[grant])
@@ -189,9 +192,12 @@ None
for ent in cont:
ent.retrieve()
print("Successfully retrieved all entities.")
- except db.AuthorizationException:
- print(ent)
- print("Could not retrieve this entity although it should have been possible!")
+ except db.TransactionError as te:
+ if te.has_error(db.AuthorizationError):
+ print(ent)
+ print("Could not retrieve this entity although it should have been possible!")
+ else:
+ raise te
# Switch to user without permissions
db.configure_connection(username=denied_user[0], password=denied_user[1],
@@ -206,8 +212,11 @@ None
denied_all = False
print(ent)
print("Could retrieve this entity although it should not have been possible!")
- except db.AuthorizationException:
- pass
+ except db.TransactionError as te:
+ # Only do something if an error wasn't caused by an
+ # AuthorizationError
+ if not te.has_error(db.AuthorizationError):
+ raise te
if denied_all:
print("Retrieval of all entities was successfully denied.")
diff --git a/release.sh b/release.sh
index a5f3654291743e5ac22fd3b938719e294b3a1e90..1af097f014de6cd9eb3d3e8ba5da34aea0fe1671 100755
--- a/release.sh
+++ b/release.sh
@@ -1,4 +1,4 @@
#!/bin/bash
-rm -r dist/ build/ .eggs/
+rm -rf dist/ build/ .eggs/
python setup.py sdist bdist_wheel
python -m twine upload -s dist/*
diff --git a/setup.py b/setup.py
index 4ab2d7669cc4f6d3f4873c0265da6c8cf06932ba..d491a1d340796b9b4701b307003c3e62e75d6001 100755
--- a/setup.py
+++ b/setup.py
@@ -46,8 +46,8 @@ from setuptools import find_packages, setup
########################################################################
MAJOR = 0
-MINOR = 4
-MICRO = 1
+MINOR = 5
+MICRO = 2
PRE = "" # e.g. rc0, alpha.1, 0.beta-23
ISRELEASED = False
diff --git a/src/caosdb/__init__.py b/src/caosdb/__init__.py
index 7f656e264f9b726ed457f05c2816502a3a135634..b320b8295e2981f99788f141c1a5e8c8952aabce 100644
--- a/src/caosdb/__init__.py
+++ b/src/caosdb/__init__.py
@@ -48,8 +48,8 @@ from caosdb.common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
get_known_permissions, raise_errors)
from caosdb.configuration import configure, get_config
from caosdb.connection.connection import configure_connection, get_connection
-from caosdb.exceptions import *
from caosdb.version import version as __version__
+from caosdb.exceptions import *
# read configuration these files
diff --git a/src/caosdb/apiutils.py b/src/caosdb/apiutils.py
index bd279fcfe5c394b9b5cff787169cff5b9f2d3031..73074efc3057e0548c5abfd56ef3cf1ac9e9bf47 100644
--- a/src/caosdb/apiutils.py
+++ b/src/caosdb/apiutils.py
@@ -34,10 +34,10 @@ from collections.abc import Iterable
from subprocess import call
from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
- REFERENCE, TEXT)
+ REFERENCE, TEXT, is_reference)
from caosdb.common.models import (Container, Entity, File, Property, Query,
Record, RecordType, get_config,
- execute_query, is_reference)
+ execute_query)
def new_record(record_type, name=None, description=None,
@@ -244,6 +244,8 @@ class CaosDBPythonEntity(object):
return (val, False)
elif pr[0:4] == "LIST":
return self._type_converted_list(val, pr)
+ elif isinstance(val, Entity):
+ return (convert_to_python_object(val), False)
else:
return (int(val), True)
diff --git a/src/caosdb/common/administration.py b/src/caosdb/common/administration.py
index e2846ef14d481ec938dd401289f8f0bbbfdc1d06..5b7a098a58463489eec9b827c8baa1c90a580e13 100644
--- a/src/caosdb/common/administration.py
+++ b/src/caosdb/common/administration.py
@@ -30,8 +30,9 @@ from lxml import etree
from caosdb.common.utils import xml2str
from caosdb.connection.connection import get_connection
-from caosdb.exceptions import (AuthorizationException, ClientErrorException,
- EntityDoesNotExistError, ServerConfigurationException)
+from caosdb.exceptions import (HTTPClientError,
+ HTTPForbiddenError,
+ HTTPResourceNotFoundError)
def set_server_property(key, value):
@@ -112,10 +113,10 @@ def _retrieve_user(name, realm=None, **kwargs):
con = get_connection()
try:
return con._http_request(method="GET", path="User/" + (realm + "/" + name if realm is not None else name), **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this user."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
@@ -124,10 +125,10 @@ def _delete_user(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="DELETE", path="User/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to delete this user."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
@@ -150,13 +151,13 @@ def _update_user(name, realm=None, password=None, status=None,
params["entity"] = str(entity)
try:
return con.put_form_data(entity_uri_segment="User/" + (realm + "/" + name if realm is not None else name), params=params, **kwargs).read()
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to update this user."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Entity does not exist."
raise
@@ -179,10 +180,10 @@ def _insert_user(name, password=None, status=None, email=None, entity=None, **kw
params["entity"] = entity
try:
return con.post_form_data(entity_uri_segment="User", params=params, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to insert a new user."
raise e
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "User name is already in use."
@@ -195,10 +196,10 @@ def _insert_role(name, description, **kwargs):
con = get_connection()
try:
return con.post_form_data(entity_uri_segment="Role", params={"role_name": name, "role_description": description}, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to insert a new role."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Role name is already in use. Choose a different name."
raise
@@ -208,10 +209,10 @@ def _update_role(name, description, **kwargs):
con = get_connection()
try:
return con.put_form_data(entity_uri_segment="Role/" + name, params={"role_description": description}, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to update this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -220,10 +221,10 @@ def _retrieve_role(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="GET", path="Role/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -232,10 +233,10 @@ def _delete_role(name, **kwargs):
con = get_connection()
try:
return con._http_request(method="DELETE", path="Role/" + name, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to delete this role."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -249,14 +250,15 @@ def _set_roles(username, roles, realm=None, **kwargs):
body = xml2str(xml)
con = get_connection()
try:
- body = con._http_request(method="PUT", path="UserRoles/" + (realm + "/" + username if realm is not None else username), body=body, **kwargs).read()
- except AuthorizationException as e:
+ body = con._http_request(method="PUT", path="UserRoles/" + (realm + "/" +
+ username if realm is not None else username), body=body, **kwargs).read()
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to set this user's roles."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
- except ClientErrorException as e:
+ except HTTPClientError as e:
if e.status == 409:
e.msg = "Role does not exist."
raise
@@ -272,11 +274,12 @@ def _set_roles(username, roles, realm=None, **kwargs):
def _get_roles(username, realm=None, **kwargs):
con = get_connection()
try:
- body = con._http_request(method="GET", path="UserRoles/" + (realm + "/" + username if realm is not None else username), **kwargs).read()
- except AuthorizationException as e:
+ body = con._http_request(method="GET", path="UserRoles/" + (
+ realm + "/" + username if realm is not None else username), **kwargs).read()
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this user's roles."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "User does not exist."
raise
ret = set()
@@ -316,10 +319,10 @@ Returns
con = get_connection()
try:
return con._http_request(method="PUT", path="PermissionRules/" + role, body=body, **kwargs).read()
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to set this role's permissions."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
@@ -328,10 +331,10 @@ def _get_permissions(role, **kwargs):
con = get_connection()
try:
return PermissionRule._parse_body(con._http_request(method="GET", path="PermissionRules/" + role, **kwargs).read())
- except AuthorizationException as e:
+ except HTTPForbiddenError as e:
e.msg = "You are not permitted to retrieve this role's permissions."
raise
- except EntityDoesNotExistError as e:
+ except HTTPResourceNotFoundError as e:
e.msg = "Role does not exist."
raise
diff --git a/src/caosdb/common/datatype.py b/src/caosdb/common/datatype.py
index 246485c3957462fc98ac83f9d904413ad7518302..eb8c1e4e0088f1924940a104ec3916b9d5d40f99 100644
--- a/src/caosdb/common/datatype.py
+++ b/src/caosdb/common/datatype.py
@@ -25,7 +25,7 @@
import re
-from ..exceptions import AmbiguityException, EntityDoesNotExistError
+from ..exceptions import EmptyUniqueQueryError, QueryNotUniqueError
DOUBLE = "DOUBLE"
REFERENCE = "REFERENCE"
@@ -91,9 +91,9 @@ def get_id_of_datatype(datatype):
Raises
------
- AmbiguityException
+ QueryNotUniqueError
If there are more than one entities with the same name as the datatype.
- EntityDoesNotExistError
+ EmptyUniqueQueryError
If there is no entity with the name of the datatype.
"""
from caosdb import execute_query
@@ -107,11 +107,11 @@ def get_id_of_datatype(datatype):
res = [el for el in res if el.name.lower() == datatype.lower()]
if len(res) > 1:
- raise AmbiguityException(
+ raise QueryNotUniqueError(
"Name {} did not lead to unique result; Missing "
"implementation".format(datatype))
elif len(res) != 1:
- raise EntityDoesNotExistError(
+ raise EmptyUniqueQueryError(
"No RecordType named {}".format(datatype))
return res[0].id
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index c3de01fa133f25144b665f3b6b1f8d683de1e9e1..71955e300ed2751bd2838718c9d310d90027a1c7 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -5,8 +5,9 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Florian Spreckelsen <f.spreckelsen@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
-# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -29,7 +30,6 @@ from __future__ import print_function, unicode_literals
import re
import sys
-import traceback
from builtins import str
from functools import cmp_to_key
from hashlib import sha512
@@ -40,25 +40,28 @@ from sys import hexversion
from tempfile import NamedTemporaryFile
from warnings import warn
-from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
- LIST, REFERENCE, TEXT, is_reference)
+from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, INTEGER, TEXT)
from caosdb.common.versioning import Version
from caosdb.common.state import State
from caosdb.common.utils import uuid, xml2str
from caosdb.configuration import get_config
from caosdb.connection.connection import get_connection
from caosdb.connection.encode import MultipartParam, multipart_encode
-from caosdb.exceptions import (AmbiguityException, AuthorizationException,
- CaosDBException, ConnectionException,
- ConsistencyError, EntityDoesNotExistError,
- EntityError, EntityHasNoDatatypeError,
- TransactionError, UniqueNamesError,
+from caosdb.exceptions import (AmbiguousEntityError,
+ AuthorizationError,
+ CaosDBException, CaosDBConnectionError,
+ ConsistencyError,
+ EmptyUniqueQueryError,
+ EntityDoesNotExistError, EntityError,
+ EntityHasNoDatatypeError,
+ MismatchingEntitiesError,
+ QueryNotUniqueError, TransactionError,
+ UniqueNamesError,
UnqualifiedParentsError,
- UnqualifiedPropertiesError, URITooLongException)
+ UnqualifiedPropertiesError,
+ HTTPURITooLongError)
from lxml import etree
-from .datatype import is_reference
-
_ENTITY_URI_SEGMENT = "Entity"
# importances/inheritance
@@ -639,7 +642,6 @@ class Entity(object):
if not isinstance(selector, (tuple, list)):
selector = [selector]
- val = None
ref = self
# there are some special selectors which can be applied to the
@@ -759,15 +761,14 @@ class Entity(object):
return ret
- def get_errors_deep(self, roots=[]):
+ def get_errors_deep(self, roots=None):
"""Get all error messages of this entity and all sub-entities /
- parents.
-
- / properties.
+ parents / properties.
@return A list of tuples. Tuple index 0 contains the error message
and tuple index 1 contains the tree.
"""
+ roots = [] if roots is None else roots
result_list = list()
ret_self = self.get_errors()
result_list.extend([
@@ -808,8 +809,7 @@ class Entity(object):
xml = etree.Element("Entity")
assert isinstance(xml, etree._Element)
- ''' unwrap wrapped entity '''
-
+ # unwrap wrapped entity
if self._wrapped_entity is not None:
xml = self._wrapped_entity.to_xml(xml, add_properties)
@@ -970,7 +970,7 @@ class Entity(object):
# add VALUE
value = None
- if len(vals):
+ if vals:
# The value[s] have been inside a <Value> tag.
value = vals
elif elem.text is not None and elem.text.strip() != "":
@@ -995,11 +995,20 @@ class Entity(object):
if self.id is None:
c = Container().retrieve(query=self.name, sync=False)
- if len(c == 1):
+ if len(c) == 1:
e = c[0]
+ elif len(c) == 0:
+ ee = EntityDoesNotExistError(
+ "The entity to be updated does not exist on the server.",
+ entity=self
+ )
+ raise TransactionError(ee)
else:
- raise AmbiguityException(
- "Could not determine the desired Entity which is to be updated by its name.")
+ ae = AmbiguousEntityError(
+ "Could not determine the desired Entity which is to be updated by its name.",
+ entity=self
+ )
+ raise TransactionError(ae)
else:
e = Container().retrieve(query=self.id, sync=False)[0]
e.acl = ACL(self.acl.to_xml())
@@ -1038,13 +1047,12 @@ class Entity(object):
if len(c) == 1:
c[0].messages.extend(c.messages)
-
return c[0]
- else:
- raise AmbiguityException("This retrieval was not unique!!!")
- else:
- return Container().append(self).retrieve(
- unique=unique, raise_exception_on_error=raise_exception_on_error, flags=flags)
+
+ raise QueryNotUniqueError("This retrieval was not unique!!!")
+
+ 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):
@@ -1249,8 +1257,8 @@ class QueryTemplate():
self.version = None
self.state = None
- def retrieve(self, strict=True, raise_exception_on_error=True,
- unique=True, sync=True, flags=None):
+ def retrieve(self, raise_exception_on_error=True, unique=True, sync=True,
+ flags=None):
return Container().append(self).retrieve(
raise_exception_on_error=raise_exception_on_error,
@@ -1395,8 +1403,7 @@ class Parent(Entity):
if xml is None:
xml = etree.Element("Parent")
- return super(Parent, self).to_xml(
- xml=xml, add_properties=add_properties)
+ return super().to_xml(xml=xml, add_properties=add_properties)
class _EntityWrapper(object):
@@ -1461,7 +1468,7 @@ class Message(object):
if xml is None:
xml = etree.Element(str(self.type))
- if self.code:
+ if self.code is not None:
xml.set("code", str(self.code))
if self.description:
@@ -1477,7 +1484,7 @@ class Message(object):
def __eq__(self, obj):
if isinstance(obj, Message):
- return self.type == obj.type and self.code == obj.codes
+ return self.type == obj.type and self.code == obj.code
return False
@@ -1500,8 +1507,8 @@ class RecordType(Entity):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(RecordType, self).add_property(
- property=property, value=value, **copy_kwargs)
+ return super().add_property(property=property, value=value,
+ **copy_kwargs)
def add_parent(self, parent=None, **kwargs):
copy_kwargs = kwargs.copy()
@@ -1510,7 +1517,7 @@ class RecordType(Entity):
# set default importance
copy_kwargs['inheritance'] = OBLIGATORY
- return super(RecordType, self).add_parent(parent=parent, **copy_kwargs)
+ return super().add_parent(parent=parent, **copy_kwargs)
def __init__(self, name=None, id=None, description=None, datatype=None): # @ReservedAssignment
Entity.__init__(self, name=name, id=id, description=description,
@@ -1538,7 +1545,7 @@ class Record(Entity):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(Record, self).add_property(
+ return super().add_property(
property=property, value=value, **copy_kwargs)
def __init__(self, name=None, id=None, description=None): # @ReservedAssignment
@@ -1702,7 +1709,7 @@ class File(Record):
# set default importance
copy_kwargs['inheritance'] = FIX
- return super(File, self).add_property(
+ return super().add_property(
property=property, value=value, **copy_kwargs)
@@ -2027,7 +2034,8 @@ class _Messages(dict):
<<< del msgs["HelloWorld",2]
<<< assert msgs.get("HelloWorld",2) == None
- <<< # this Message has no code and no description (make easy things easy...)
+ # this Message has no code and no description (make easy things easy...)
+ <<<
<<< msgs["HelloWorld"] = "Hello!"
<<< assert msgs["HelloWorld"] == "Hello!"
@@ -2237,15 +2245,19 @@ def _basic_sync(e_local, e_remote):
def _deletion_sync(e_local, e_remote):
if e_local is None or e_remote is None:
- return None
+ return
+
try:
- e_remote.get_messages()[('info', 10)]
- _basic_sync(e_local, e_remote)
- e_local.is_valid = lambda: False
- e_local.is_deleted = lambda: True
- e_local.id = None
+ e_remote.get_messages()["info", 10] # try and get the deletion info
except KeyError:
+ # deletion info wasn't there
e_local.messages = e_remote.messages
+ return
+
+ _basic_sync(e_local, e_remote)
+ e_local.is_valid = lambda: False
+ e_local.is_deleted = lambda: True
+ e_local.id = None
class Container(list):
@@ -2286,11 +2298,11 @@ class Container(list):
"""
if entity in self:
- super(Container, self).remove(entity)
+ super().remove(entity)
else:
for ee in self:
if entity == ee.id:
- super(Container, self).remove(ee)
+ super().remove(ee)
return ee
raise ValueError(
@@ -2408,13 +2420,13 @@ class Container(list):
"""
if isinstance(entity, Entity):
- super(Container, self).append(entity)
+ super().append(entity)
elif isinstance(entity, int):
- super(Container, self).append(Entity(id=entity))
+ super().append(Entity(id=entity))
elif hasattr(entity, "encode"):
- super(Container, self).append(Entity(name=entity))
+ super().append(Entity(name=entity))
elif isinstance(entity, QueryTemplate):
- super(Container, self).append(entity)
+ super().append(entity)
else:
raise TypeError(
"Entity was neither an id nor a name nor an entity." +
@@ -2430,8 +2442,8 @@ class Container(list):
@return xml element
"""
tmpid = 0
- ''' users might already have specified some tmpids. -> look for smallest.'''
+ # users might already have specified some tmpids. -> look for smallest.
for e in self:
tmpid = min(tmpid, Container._get_smallest_tmpid(e))
tmpid -= 1
@@ -2650,8 +2662,7 @@ class Container(list):
# list of remote entities which already have a local equivalent
used_remote_entities = []
- ''' match by cuid '''
-
+ # match by cuid
for local_entity in self:
sync_dict[local_entity] = None
@@ -2677,10 +2688,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by id '''
+ raise MismatchingEntitiesError(msg)
+ # match by id
for local_entity in self:
if sync_dict[local_entity] is None and local_entity.id is not None:
sync_remote_entities = []
@@ -2702,10 +2712,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by path '''
+ raise MismatchingEntitiesError(msg)
+ # match by path
for local_entity in self:
if (sync_dict[local_entity] is None
and local_entity.path is not None):
@@ -2732,10 +2741,9 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
-
- ''' match by name '''
+ raise MismatchingEntitiesError(msg)
+ # match by name
for local_entity in self:
if (sync_dict[local_entity] is None
and local_entity.name is not None):
@@ -2762,7 +2770,7 @@ class Container(list):
local_entity.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
+ raise MismatchingEntitiesError(msg)
# add remaining entities to this remote_container
sync_remote_entities = []
@@ -2781,7 +2789,7 @@ class Container(list):
remote_container.add_message(Message("Error", None, msg))
if raise_exception_on_error:
- raise AmbiguityException(msg)
+ raise MismatchingEntitiesError(msg)
return sync_dict
@@ -2799,8 +2807,10 @@ class Container(list):
if len(self) == 0:
if raise_exception_on_error:
- raise TransactionError(
- self, "There are no entities to be deleted. This container is empty.")
+ te = TransactionError(
+ msg="There are no entities to be deleted. This container is empty.",
+ container=self)
+ raise te
return self
self.clear_server_messages()
@@ -2824,15 +2834,17 @@ class Container(list):
description="This entity has no identifier. It cannot be deleted."))
if raise_exception_on_error:
- raise EntityError(
+ ee = EntityError(
"This entity has no identifier. It cannot be deleted.", entity)
- else:
- entity.is_valid = lambda: False
+ raise TransactionError(ee)
+ entity.is_valid = lambda: False
if len(id_str) == 0:
if raise_exception_on_error:
- raise TransactionError(
- self, "There are no entities to be deleted.")
+ te = TransactionError(
+ msg="There are no entities to be deleted.",
+ container=self)
+ raise te
return self
entity_url_segments = [_ENTITY_URI_SEGMENT, "&".join(id_str)]
@@ -2892,10 +2904,11 @@ class Container(list):
description="This entity has no identifier. It cannot be retrieved."))
if raise_exception_on_error:
- raise EntityError(
- "This entity has no identifier. It cannot be retrieved.", entity)
- else:
- entity.is_valid = lambda: False
+ ee = EntityError(
+ "This entity has no identifier. It cannot be retrieved.",
+ entity)
+ raise TransactionError(ee)
+ entity.is_valid = lambda: False
else:
entities_str.append(str(query))
@@ -2936,12 +2949,12 @@ class Container(list):
"&".join(entities))], query_dict=flags)
return Container._response_to_entities(http_response)
- except URITooLongException as uri_e:
+ except HTTPURITooLongError as uri_e:
try:
# split up
uri1, uri2 = Container._split_uri_string(entities)
- except ValueError:
- raise uri_e
+ except ValueError as val_e:
+ raise uri_e from val_e
c1 = self._retrieve(entities=uri1, flags=flags)
c2 = self._retrieve(entities=uri2, flags=flags)
c1.extend(c2)
@@ -2984,9 +2997,10 @@ class Container(list):
"""Update these entites."""
if len(self) < 1:
- raise TransactionError(
- container=self,
- msg="There are no entities to be updated. This container is empty.")
+ te = TransactionError(
+ msg="There are no entities to be updated. This container is empty.",
+ container=self)
+ raise te
self.clear_server_messages()
insert_xml = etree.Element("Update")
@@ -3003,8 +3017,10 @@ class Container(list):
for entity in self:
if (entity.id is None or entity.id < 0):
- raise TransactionError(
- self, "You tried to update an entity without a valid id.")
+ ee = EntityError(
+ "You tried to update an entity without a valid id.",
+ entity)
+ raise TransactionError(ee)
self._linearize()
@@ -3174,9 +3190,10 @@ class Container(list):
insert_xml.append(entity_xml)
if len(self) > 0 and len(insert_xml) < 1:
- raise TransactionError(
- container=self,
- msg="There are no entities to be inserted. This container contains existent entities only.")
+ te = TransactionError(
+ msg="There are no entities to be inserted. This container contains existent entities only.",
+ container=self)
+ raise te
_log_request("POST: " + _ENTITY_URI_SEGMENT +
('' if flags is None else "?" + str(flags)), insert_xml)
@@ -3637,6 +3654,23 @@ class ACL():
class Query():
+ """Query
+
+ Attributes
+ ----------
+ q : str
+ The query string.
+ flags : dict of str
+ A dictionary of flags to be send with the query request.
+ messages : _Messages()
+ A container of messages included in the last query response.
+ cached : bool
+ indicates whether the server used the query cache for the execution of
+ this query.
+ results : int or Container
+ The number of results (when this was a count query) or the container
+ with the resulting entities.
+ """
def putFlag(self, key, value=None):
self.flags[key] = value
@@ -3652,28 +3686,60 @@ class Query():
def __init__(self, q):
self.flags = dict()
self.messages = _Messages()
+ self.cached = None
if isinstance(q, etree._Element):
self.q = q.get("string")
self.results = int(q.get("results"))
+ if q.get("cached") is None:
+ self.cached = False
+ else:
+ self.cached = q.get("cached").lower() == "true"
+
for m in q:
if m.tag.lower() == 'warning' or m.tag.lower() == 'error':
self.messages.append(_parse_single_xml_element(m))
else:
self.q = q
- def execute(self, unique=False, raise_exception_on_error=True,
- **kwargs):
+ def execute(self, unique=False, raise_exception_on_error=True, cache=True):
+ """Execute a query (via a server-requests) and return the results.
+
+ Parameters
+ ----------
+
+ unique : bool
+ Whether the query is expected to have only one entity as result.
+ Defaults to False.
+ raise_exception_on_error : bool
+ Whether an exception should be raises when there are errors in the
+ resulting entities. Defaults to True.
+ cache : bool
+ Whether to use the query cache (equivalent to adding a "cache"
+ flag) to the Query object. Defaults to True.
+
+ Returns
+ -------
+ results : Container or integer
+ Returns an integer when it was a `COUNT` query. Otherwise, returns a
+ Container with the resulting entities.
+ """
connection = get_connection()
- query_dict = dict(self.flags)
+
+ flags = self.flags
+ if cache is False:
+ flags["cache"] = "false"
+ query_dict = dict(flags)
query_dict["query"] = str(self.q)
+
_log_request("GET Entity?" + str(query_dict), None)
http_response = connection.retrieve(
entity_uri_segments=["Entity"],
- query_dict=query_dict, **kwargs)
+ query_dict=query_dict)
cresp = Container._response_to_entities(http_response)
self.results = cresp.query.results
+ self.cached = cresp.query.cached
if self.q.lower().startswith('count') and len(cresp) == 0:
# this was a count query
@@ -3685,10 +3751,12 @@ class Query():
if unique:
if len(cresp) > 1 and raise_exception_on_error:
- raise AmbiguityException("This query wasn't unique")
- elif len(cresp) == 0 and raise_exception_on_error:
- raise EntityDoesNotExistError("No such entity found.")
- elif len(cresp) == 1:
+ raise QueryNotUniqueError(
+ "Query '{}' wasn't unique.".format(self.q))
+ if len(cresp) == 0 and raise_exception_on_error:
+ raise EmptyUniqueQueryError(
+ "Query '{}' found no results.".format(self.q))
+ if len(cresp) == 1:
r = cresp[0]
r.messages.extend(cresp.messages)
@@ -3698,8 +3766,32 @@ class Query():
return cresp
-def execute_query(q, unique=False, raise_exception_on_error=True, flags=None,
- **kwargs):
+def execute_query(q, unique=False, raise_exception_on_error=True, cache=True, flags=None):
+ """Execute a query (via a server-requests) and return the results.
+
+ Parameters
+ ----------
+
+ q : str
+ The query string.
+ unique : bool
+ Whether the query is expected to have only one entity as result.
+ Defaults to False.
+ raise_exception_on_error : bool
+ Whether an exception should be raises when there are errors in the
+ resulting entities. Defaults to True.
+ cache : bool
+ Whether to use the query cache (equivalent to adding a "cache" flag).
+ Defaults to True.
+ flags : dict of str
+ Flags to be added to the request.
+
+ Returns
+ -------
+ results : Container or integer
+ Returns an integer when it was a `COUNT` query. Otherwise, returns a
+ Container with the resulting entities.
+ """
query = Query(q)
if flags is not None:
@@ -3707,7 +3799,7 @@ def execute_query(q, unique=False, raise_exception_on_error=True, flags=None,
return query.execute(unique=unique,
raise_exception_on_error=raise_exception_on_error,
- **kwargs)
+ cache=cache)
class DropOffBox(list):
@@ -3761,7 +3853,7 @@ class Info():
c = get_connection()
try:
http_response = c.retrieve(["Info"])
- except ConnectionException as conn_e:
+ except CaosDBConnectionError as conn_e:
print(conn_e)
return
@@ -3883,6 +3975,8 @@ def _parse_single_xml_element(elem):
elif elem.tag.lower() == "value":
if len(elem) == 1 and elem[0].tag.lower() == "emptystring":
return ""
+ elif len(elem) == 1 and elem[0].tag.lower() in classmap:
+ return _parse_single_xml_element(elem[0])
elif elem.text is None or elem.text.strip() == "":
return None
@@ -3908,124 +4002,119 @@ def _parse_single_xml_element(elem):
"code"), description=elem.get("description"), body=elem.text)
-def raise_errors(arg0):
- if isinstance(arg0, (Entity, QueryTemplate)):
- entity_error = EntityError(
- entity=arg0, error=Message('Error', 0, 'EntityMultiError'))
- found114 = False
- found116 = False
+def _evaluate_and_add_error(parent_error, ent):
+ """Evaluate the error message(s) attached to entity and add a
+ corresponding exception to parent_error.
- for e in arg0.get_errors():
- try:
- if e.code is not None:
- if int(e.code) == 101: # arg0 does not exist
- raise EntityDoesNotExistError(error=e, entity=arg0)
- elif int(e.code) == 110: # entity has no data type
- raise EntityHasNoDatatypeError(error=e, entity=arg0)
- elif int(e.code) == 403: # Transaction not permitted
- raise AuthorizationException(error=e, entity=arg0)
- elif int(e.code) == 114: # unqualified properties
- found114 = True
- unqualified_properties_error = UnqualifiedPropertiesError(
- error=e, entity=arg0)
-
- for p in arg0.get_properties():
- try:
- raise_errors(p)
- except EntityError as pe:
- unqualified_properties_error.add_error(pe)
- raise unqualified_properties_error
- elif int(e.code) == 116: # unqualified parents
- found116 = True
- unqualified_parents_error = UnqualifiedParentsError(
- error=e, entity=arg0)
-
- for p in arg0.get_parents():
- try:
- raise_errors(p)
- except EntityError as pe:
- unqualified_parents_error.add_error(pe)
- raise unqualified_parents_error
- elif int(e.code) == 152: # name was not unique
- raise UniqueNamesError(error=e, entity=arg0)
- raise EntityError(error=e, entity=arg0)
- except EntityError as ee:
- entity_error.add_error(ee)
+ Parameters:
+ -----------
+ parent_error : TrancactionError
+ Parent error to which the new exception will be attached. This
+ exception will be a direct child.
+ ent : Entity
+ Entity that caused the TransactionError. An exception is
+ created depending on its error message(s).
- if not found114:
- for p in arg0.get_properties():
- try:
- raise_errors(p)
- except EntityError as pe:
- entity_error.add_error(pe)
+ Returns:
+ --------
+ TransactionError :
+ Parent error with new exception(s) attached to it.
+ """
+ if isinstance(ent, (Entity, QueryTemplate)):
+ # Check all error messages
+ found114 = False
+ found116 = False
+ for err in ent.get_errors():
+ # Evaluate specific EntityErrors depending on the error
+ # code
+ if err.code is not None:
+ if int(err.code) == 101: # ent doesn't exist
+ new_exc = EntityDoesNotExistError(entity=ent,
+ error=err)
+ elif int(err.code) == 110: # ent has no data type
+ new_exc = EntityHasNoDatatypeError(entity=ent,
+ error=err)
+ elif int(err.code) == 403: # no permission
+ new_exc = AuthorizationError(entity=ent,
+ error=err)
+ elif int(err.code) == 152: # name wasn't unique
+ new_exc = UniqueNamesError(entity=ent, error=err)
+ elif int(err.code) == 114: # unqualified properties
+ found114 = True
+ new_exc = UnqualifiedPropertiesError(entity=ent,
+ error=err)
+ for prop in ent.get_properties():
+ new_exc = _evaluate_and_add_error(new_exc,
+ prop)
+ elif int(err.code) == 116: # unqualified parents
+ found116 = True
+ new_exc = UnqualifiedParentsError(entity=ent,
+ error=err)
+ for par in ent.get_parents():
+ new_exc = _evaluate_and_add_error(new_exc,
+ par)
+ else: # General EntityError for other codes
+ new_exc = EntityError(entity=ent, error=err)
+ else: # No error code causes a general EntityError, too
+ new_exc = EntityError(entity=ent, error=err)
+ parent_error.add_error(new_exc)
+ # Check for possible errors in parents and properties that
+ # weren't detected up to here
+ if not found114:
+ dummy_err = EntityError(entity=ent)
+ for prop in ent.get_properties():
+ dummy_err = _evaluate_and_add_error(dummy_err, prop)
+ if dummy_err.errors:
+ parent_error.add_error(dummy_err)
if not found116:
- for p in arg0.get_parents():
- try:
- raise_errors(p)
- except EntityError as pe:
- entity_error.add_error(pe)
-
- if len(entity_error.get_errors()) == 1:
- r = entity_error.get_errors().pop()
- raise r
- elif len(entity_error.get_errors()) > 1:
- r = entity_error._convert()
- raise r
- elif isinstance(arg0, Container):
- transaction_error = TransactionError(
- container=arg0, msg="This transaction terminated with Errors.")
- doRaise = False
- found12 = False
-
- if arg0.get_errors() is not None:
- for er in arg0.get_errors():
- if er.code is not None:
- if int(er.code) == 12: # atomicity violation
- found12 = True
- atomic_error = TransactionError(
- container=arg0, error=er, msg=er.description)
-
- for e in arg0:
- try:
- raise_errors(e)
- except EntityError as ee:
- atomic_error.add_error(ee)
-
- if len(atomic_error.get_errors()) > 0:
- transaction_error.add_error(
- atomic_error._convert())
- doRaise = True
- else:
- transaction_error.add_error(atomic_error)
- doRaise = True
- else:
- te = TransactionError(
- container=arg0, error=er, msg=er.description)
- transaction_error.add_error(te)
- doRaise = True
-
- if len(transaction_error.get_errors()) == 1:
- transaction_error = transaction_error.get_errors().pop()
-
- if not found12:
- for e in arg0:
- try:
- raise_errors(e)
- except EntityError as ee:
- transaction_error.add_error(ee)
- doRaise = True
-
- if len(transaction_error.get_errors()) == 1:
- t = transaction_error.get_errors().pop()
- raise t
- elif len(transaction_error.get_errors()) > 1:
- t = transaction_error._convert()
- raise t
- elif doRaise:
- raise transaction_error
+ dummy_err = EntityError(entity=ent)
+ for par in ent.get_parents():
+ dummy_err = _evaluate_and_add_error(dummy_err, par)
+ if dummy_err.errors:
+ parent_error.add_error(dummy_err)
+
+ elif isinstance(ent, Container):
+ parent_error.container = ent
+ if ent.get_errors() is not None:
+ parent_error.code = ent.get_errors()[0].code
+ # In the highly unusual case of more than one error
+ # message, attach all of them.
+ parent_error.msg = '\n'.join(
+ [x.description for x in ent.get_errors()])
+ # Go through all container elements and add them:
+ for elt in ent:
+ parent_error = _evaluate_and_add_error(parent_error, elt)
+
else:
- raise TypeError("Parameter arg0 is to be an Entity or a Container")
+ raise TypeError("Parameter ent is to be an Entity or a Container")
+
+ return parent_error
+
+
+def raise_errors(arg0):
+ """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
+ arg0.
+
+ Parameters:
+ -----------
+ arg0 : Entity, QueryTemplate, or Container
+ CaosDB object whose messages are evaluated according to their
+ error codes
+
+ """
+ transaction_error = _evaluate_and_add_error(TransactionError(),
+ arg0)
+ # Raise if any error was found
+ if len(transaction_error.all_errors) > 0:
+ raise transaction_error
+ # Cover the special case of an empty container with error
+ # message(s) (e.g. query syntax error)
+ if (transaction_error.container is not None and
+ transaction_error.container.has_errors()):
+ raise transaction_error
def delete(ids, raise_exception_on_error=True):
diff --git a/src/caosdb/connection/authentication/auth_token.py b/src/caosdb/connection/authentication/auth_token.py
index fbce78fb86d78e06d97ef00dd162c1ed57f7560d..688123867f68153d3631bb8559baa235f6f02da5 100644
--- a/src/caosdb/connection/authentication/auth_token.py
+++ b/src/caosdb/connection/authentication/auth_token.py
@@ -30,7 +30,7 @@ An Authentictor which only uses only a pre-supplied authentication token.
from __future__ import absolute_import, unicode_literals, print_function
from .interface import AbstractAuthenticator, CaosDBServerConnection
from caosdb.connection.utils import auth_token_to_cookie
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
def get_authentication_provider():
@@ -68,11 +68,11 @@ class AuthTokenAuthenticator(AbstractAuthenticator):
self._login()
def _login(self):
- raise LoginFailedException("The authentication token is expired or you "
- "have been logged out otherwise. The "
- "auth_token authenticator cannot log in "
- "again. You must provide a new "
- "authentication token.")
+ raise LoginFailedError("The authentication token is expired or you "
+ "have been logged out otherwise. The "
+ "auth_token authenticator cannot log in "
+ "again. You must provide a new "
+ "authentication token.")
def logout(self):
self._logout()
diff --git a/src/caosdb/connection/authentication/interface.py b/src/caosdb/connection/authentication/interface.py
index d9a9b4306b1dbdedbc67dfda81a3ca3d7b4aeb41..a364aeb564ee929d995b2f8098bd21e30e9733ab 100644
--- a/src/caosdb/connection/authentication/interface.py
+++ b/src/caosdb/connection/authentication/interface.py
@@ -31,7 +31,7 @@ import logging
from caosdb.connection.utils import urlencode
from caosdb.connection.interface import CaosDBServerConnection
from caosdb.connection.utils import parse_auth_token, auth_token_to_cookie
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
# meta class compatible with Python 2 *and* 3:
ABC = ABCMeta('ABC', (object, ), {'__slots__': ()})
@@ -197,9 +197,9 @@ class CredentialsAuthenticator(AbstractAuthenticator):
# we need a username for this:
if username is None:
- raise LoginFailedException("No username was given.")
+ raise LoginFailedError("No username was given.")
if password is None:
- raise LoginFailedException("No password was given")
+ raise LoginFailedError("No password was given")
headers = {}
headers["Content-Type"] = "application/x-www-form-urlencoded"
@@ -210,7 +210,7 @@ class CredentialsAuthenticator(AbstractAuthenticator):
response.read() # clear socket
if response.status != 200:
- raise LoginFailedException("LOGIN WAS NOT SUCCESSFUL")
+ raise LoginFailedError("LOGIN WAS NOT SUCCESSFUL")
self.on_response(response)
return response
diff --git a/src/caosdb/connection/authentication/keyring.py b/src/caosdb/connection/authentication/keyring.py
index 1dc986174acbe23191305632afda91cda0c718d2..d8be7ddf030577545230c9111fdad542b6d6e7e2 100644
--- a/src/caosdb/connection/authentication/keyring.py
+++ b/src/caosdb/connection/authentication/keyring.py
@@ -30,7 +30,7 @@ retrieve the password.
import sys
import imp
from getpass import getpass
-from caosdb.exceptions import ConfigurationException
+from caosdb.exceptions import ConfigurationError
from .external_credentials_provider import ExternalCredentialsProvider
from .interface import CredentialsAuthenticator
@@ -67,10 +67,10 @@ def _get_external_keyring():
def _call_keyring(**config):
if "username" not in config:
- raise ConfigurationException("Your configuration did not provide a "
- "`username` which is needed by the "
- "`KeyringCaller` to retrieve the "
- "password in question.")
+ raise ConfigurationError("Your configuration did not provide a "
+ "`username` which is needed by the "
+ "`KeyringCaller` to retrieve the "
+ "password in question.")
url = config.get("url")
username = config.get("username")
app = "caosdb — {}".format(url)
diff --git a/src/caosdb/connection/authentication/pass.py b/src/caosdb/connection/authentication/pass.py
index 9399fc4f4a76407ad94618785adcfbb945d4c788..853cdf0ed92039e7b5fc9beda8bb76cc0f3cc030 100644
--- a/src/caosdb/connection/authentication/pass.py
+++ b/src/caosdb/connection/authentication/pass.py
@@ -28,7 +28,7 @@ password.
"""
from subprocess import check_output, CalledProcessError
-from caosdb.exceptions import ConfigurationException
+from caosdb.exceptions import ConfigurationError
from .interface import CredentialsAuthenticator
from .external_credentials_provider import ExternalCredentialsProvider
@@ -50,10 +50,10 @@ def get_authentication_provider():
def _call_pass(**config):
if "password_identifier" not in config:
- raise ConfigurationException("Your configuration did not provide a "
- "`password_identifier` which is needed "
- "by the `PassCaller` to retrieve the "
- "password in question.")
+ raise ConfigurationError("Your configuration did not provide a "
+ "`password_identifier` which is needed "
+ "by the `PassCaller` to retrieve the "
+ "password in question.")
try:
return check_output(
diff --git a/src/caosdb/connection/authentication/unauthenticated.py b/src/caosdb/connection/authentication/unauthenticated.py
index 53a2756eb59259a0be012e41f2ea213735568838..65febae8fd8f02f3ee0d339fafb36af512fc7be7 100644
--- a/src/caosdb/connection/authentication/unauthenticated.py
+++ b/src/caosdb/connection/authentication/unauthenticated.py
@@ -30,7 +30,7 @@ cookies.
"""
from __future__ import absolute_import, unicode_literals, print_function
from .interface import AbstractAuthenticator, CaosDBServerConnection
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
def get_authentication_provider():
@@ -70,11 +70,11 @@ class Unauthenticated(AbstractAuthenticator):
self._login()
def _login(self):
- raise LoginFailedException("This caosdb client is configured to stay "
- "unauthenticated. Change your "
- "`password_method` and provide an "
- "`auth_token` or credentials if you want "
- "to authenticate this client.")
+ raise LoginFailedError("This caosdb client is configured to stay "
+ "unauthenticated. Change your "
+ "`password_method` and provide an "
+ "`auth_token` or credentials if you want "
+ "to authenticate this client.")
def logout(self):
self._logout()
diff --git a/src/caosdb/connection/connection.py b/src/caosdb/connection/connection.py
index 703897d62a40a820a6ff578869a862f6c7c4c019..fc699ab5db1db36bc1ee63034b6828eec4d16bc1 100644
--- a/src/caosdb/connection/connection.py
+++ b/src/caosdb/connection/connection.py
@@ -33,11 +33,14 @@ from errno import EPIPE as BrokenPipe
from socket import error as SocketError
from caosdb.configuration import get_config
-from caosdb.exceptions import (AuthorizationException, CaosDBException,
- ClientErrorException, ConfigurationException,
- ConnectionException, EntityDoesNotExistError,
- LoginFailedException, ServerErrorException,
- URITooLongException)
+from caosdb.exceptions import (CaosDBException, HTTPClientError,
+ ConfigurationError,
+ CaosDBConnectionError,
+ HTTPForbiddenError,
+ LoginFailedError,
+ HTTPResourceNotFoundError,
+ HTTPServerError,
+ HTTPURITooLongError)
from caosdb.version import version
from pkg_resources import resource_filename
@@ -61,6 +64,10 @@ class _WrappedHTTPResponse(CaosDBHTTPResponse):
def __init__(self, response):
self.response = response
+ @property
+ def reason(self):
+ return self.response.reason
+
@property
def status(self):
return self.response.status
@@ -88,7 +95,8 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
"""
def __init__(self):
- self._useragent = ("caosdb-pylib/{version} - {implementation}".format(version=version, implementation=type(self).__name__))
+ self._useragent = ("caosdb-pylib/{version} - {implementation}".format(
+ version=version, implementation=type(self).__name__))
self._http_con = None
self._base_path = None
@@ -132,7 +140,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
self._http_con.request(method=method, url=self._base_path + path,
headers=headers, body=body)
except SocketError as socket_err:
- raise ConnectionException(
+ raise CaosDBConnectionError(
"Connection failed. Network or server down? " + str(socket_err)
)
@@ -156,7 +164,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
Raises
------
- ConnectionException
+ CaosDBConnectionError
If no url has been specified, or if the CA certificate cannot be
loaded.
"""
@@ -193,9 +201,9 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
try:
context.load_verify_locations(config["cacert"])
except Exception as exc:
- raise ConnectionException("Could not load the cacert in"
- "`{}`: {}".format(config["cacert"],
- exc))
+ raise CaosDBConnectionError("Could not load the cacert in"
+ "`{}`: {}".format(config["cacert"],
+ exc))
context.load_default_certs()
@@ -204,7 +212,7 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
host = parsed_url.netloc
self._base_path = parsed_url.path
else:
- raise ConnectionException(
+ raise CaosDBConnectionError(
"No connection url specified. Please "
"do so via caosdb.configure_connection(...) or in a config "
"file.")
@@ -276,7 +284,7 @@ def _get_authenticator(**config):
Raises
------
- ConnectionException
+ ConfigurationError
If the password_method string cannot be resolved to a CaosAuthenticator
class.
"""
@@ -292,10 +300,10 @@ def _get_authenticator(**config):
return auth_provider
except ImportError:
- raise ConfigurationException("Password method \"{}\" not implemented. "
- "Try `plain`, `pass`, `keyring`, or "
- "`auth_token`."
- .format(config["password_method"]))
+ raise ConfigurationError("Password method \"{}\" not implemented. "
+ "Try `plain`, `pass`, `keyring`, or "
+ "`auth_token`."
+ .format(config["password_method"]))
def configure_connection(**kwargs):
@@ -398,29 +406,24 @@ def _handle_response_status(http_response):
# emtpy response buffer
body = http_response.read()
+ if status == 404:
+ raise HTTPResourceNotFoundError("This resource has not been found.")
+ elif status > 499:
+ raise HTTPServerError(body=body)
+
+ reason = http_response.reason
+ standard_message = ("Request failed. The response returned with status "
+ "{} - {}.".format(status, reason))
if status == 401:
- raise LoginFailedException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise LoginFailedError(standard_message)
elif status == 403:
- raise AuthorizationException(
- "Request failed. The response returned with status "
- "{}.".format(status))
- elif status == 404:
- raise EntityDoesNotExistError("This entity does not exist.")
+ raise HTTPForbiddenError(standard_message)
elif status in (413, 414):
- raise URITooLongException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise HTTPURITooLongError(standard_message)
elif 399 < status < 500:
- raise ClientErrorException(msg=("Request failed. The response returned "
- "with status {}.").format(status), status=status, body=body)
- elif status > 499:
- raise ServerErrorException(body=body)
+ raise HTTPClientError(msg=standard_message, status=status, body=body)
else:
- raise CaosDBException(
- "Request failed. The response returned with status "
- "{}.".format(status))
+ raise CaosDBException(standard_message)
class _Connection(object): # pylint: disable=useless-object-inheritance
@@ -454,7 +457,7 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
self.is_configured = True
if "implementation" not in config:
- raise ConfigurationException(
+ raise ConfigurationError(
"Missing CaosDBServerConnection implementation. You did not "
"specify an `implementation` for the connection.")
try:
@@ -465,20 +468,20 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
raise TypeError("The `implementation` callable did not return "
"an instance of CaosDBServerConnection.")
except TypeError as type_err:
- raise ConfigurationException(
+ raise ConfigurationError(
"Bad CaosDBServerConnection implementation. The "
"implementation must be a callable object which returns an "
"instance of `CaosDBServerConnection` (e.g. a constructor "
- "or a factory).", type_err)
+ "or a factory).\n{}".format(type_err.args[0]))
self._delegate_connection.configure(**config)
if "auth_token" in config:
# deprecated, needed for older scripts
config["password_method"] = "auth_token"
if "password_method" not in config:
- raise ConfigurationException("Missing password_method. You did "
- "not specify a `password_method` for"
- "the connection.")
+ raise ConfigurationError("Missing password_method. You did "
+ "not specify a `password_method` for"
+ "the connection.")
self._authenticator = _get_authenticator(
connection=self._delegate_connection, **config)
@@ -554,8 +557,8 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
uri_segments.extend(path.split("/"))
return self.retrieve(entity_uri_segments=uri_segments)
- except EntityDoesNotExistError:
- raise EntityDoesNotExistError("This file does not exist.")
+ except HTTPResourceNotFoundError:
+ raise HTTPResourceNotFoundError("This file does not exist.")
def _login(self):
self._authenticator.login()
@@ -576,7 +579,7 @@ class _Connection(object): # pylint: disable=useless-object-inheritance
headers=headers, body=body,
reconnect=False,
**kwargs)
- except LoginFailedException:
+ except LoginFailedError:
if kwargs.get("reconnect", True) is True:
self._login()
diff --git a/src/caosdb/exceptions.py b/src/caosdb/exceptions.py
index c406ad9624f353a400a375314f5ce9bbbb8fe804..f02a4630356726f99d8439fd821b6dd327ab22c7 100644
--- a/src/caosdb/exceptions.py
+++ b/src/caosdb/exceptions.py
@@ -5,6 +5,8 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Florian Spreckelsen <f.spreckelsen@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -21,6 +23,10 @@
#
# ** end header
#
+"""The exceptions module defines exceptions for HTTP Errors (4xx and 5xx and
+HTTP response codes) and for transaction errors (i.e. missing permissions,
+dependencies, non-passing consistency checks etc.).
+"""
from lxml import etree
@@ -28,13 +34,13 @@ from lxml import etree
class CaosDBException(Exception):
"""Base class of all CaosDB exceptions."""
- def __init__(self, msg=None, *args):
- Exception.__init__(self, msg, *args)
+ def __init__(self, msg):
+ Exception.__init__(self, msg)
self.msg = msg
-class ConfigurationException(CaosDBException):
- """ConfigurationException.
+class ConfigurationError(CaosDBException):
+ """ConfigurationError.
Indicates a misconfiguration.
@@ -43,7 +49,6 @@ class ConfigurationException(CaosDBException):
msg : str
A descriptin of the misconfiguration. The constructor adds
a few lines with explainingg where to find the configuration.
- *args
Attributes
----------
@@ -51,13 +56,11 @@ class ConfigurationException(CaosDBException):
A description of the misconfiguration.
"""
- def __init__(self, msg, *args):
- super(ConfigurationException, self).__init__(msg +
- ConfigurationException._INFO,
- *args)
+ def __init__(self, msg):
+ super().__init__(msg + ConfigurationError._INFO)
_INFO = ("\n\nPlease check your ~/.pycaosdb.ini and your $PWD/"
- ".pycaosdb.ini. Do at least one of them exist and are they correct?")
+ ".pycaosdb.ini. Does at least one of them exist and are they correct?")
class ServerConfigurationException(CaosDBException):
@@ -67,14 +70,18 @@ class ServerConfigurationException(CaosDBException):
"""
-class ClientErrorException(CaosDBException):
+class HTTPClientError(CaosDBException):
+ """HTTPClientError represents 4xx HTTP client errors."""
+
def __init__(self, msg, status, body):
self.status = status
self.body = body
CaosDBException.__init__(self, msg)
-class ServerErrorException(CaosDBException):
+class HTTPServerError(CaosDBException):
+ """HTTPServerError represents 5xx HTTP server errors."""
+
def __init__(self, body):
xml = etree.fromstring(body)
error = xml.xpath('/Response/Error')[0]
@@ -85,107 +92,126 @@ class ServerErrorException(CaosDBException):
CaosDBException.__init__(self, msg)
-class ConnectionException(CaosDBException):
+class CaosDBConnectionError(CaosDBException):
"""Connection is not configured or the network is down."""
def __init__(self, msg=None):
CaosDBException.__init__(self, msg)
-class URITooLongException(CaosDBException):
+class HTTPURITooLongError(HTTPClientError):
"""The URI of the last request was too long."""
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg)
+ HTTPClientError.__init__(self, msg=msg, status=414, body=None)
+
+class LoginFailedError(CaosDBException):
+ """Login failed.
-class AmbiguityException(CaosDBException):
- """A retrieval of an entity that was supposed to be uniquely identifiable
- returned two or more entities."""
+ Probably, your username/password pair is wrong.
+ """
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg)
+ CaosDBException.__init__(self, msg=msg)
-class LoginFailedException(CaosDBException):
- """Login failed.
+class HTTPForbiddenError(HTTPClientError):
+ """You're lacking the required permissions. Corresponds to HTTP status
+ 403.
- Probably, your username/password pair is wrong.
"""
def __init__(self, msg=None):
- CaosDBException.__init__(self, msg=msg)
+ HTTPClientError.__init__(self, msg=msg, status=403, body=None)
-class TransactionError(CaosDBException):
+class HTTPResourceNotFoundError(HTTPClientError):
+ """The requested resource doesn't exist; corresponds to HTTP status
+ 404.
- def _calc_bases(self):
- types = dict()
- # collect each class once
+ """
- for err in self.errors:
- types[id(type(err))] = type(err)
- # delete redundant super classes
+ def __init__(self, msg=None):
+ HTTPClientError.__init__(self, msg=msg, status=404, body=None)
- if len(types.values()) > 1:
- # remove TransactionError
- try:
- del types[id(TransactionError)]
- except KeyError:
- pass
- if len(types.values()) > 1:
- # remove EntityError
- try:
- del types[id(EntityError)]
- except KeyError:
- pass
+class MismatchingEntitiesError(CaosDBException):
+ """Mismatching entities were found during container sync."""
- ret = ()
- for t in types.values():
- ret += (t,)
+# ######################### Bad query errors ###########################
- if ret == ():
- ret = (type(self),)
- return ret
+class BadQueryError(CaosDBException):
+ """Base class for query errors that are not transaction errors."""
- def __init__(self, container=None, error=None, msg=None):
- self.container = container
- self.errors = []
- self.msg = msg if msg is not None else str(error)
- self.error = error
- def print_errs(self):
- print(self)
+class QueryNotUniqueError(BadQueryError):
+ """A unique query or retrieve found more than one entity."""
+
+
+class EmptyUniqueQueryError(BadQueryError):
+ """A unique query or retrieve dound no result."""
+
- for err in self.errors:
- err.print_errs()
+# ######################### Transaction errors #########################
- def _convert(self):
- t = self._calc_bases()
- try:
- newtype = type('TransactionError', t, {})
- except BaseException:
- self.print_errs()
- raise
- newinstance = newtype(container=self.container, error=self.msg)
- newinstance.errors = self.errors
- newinstance.get_entities = self.get_entities
- return newinstance
+class TransactionError(CaosDBException):
+ """An error of this type is raised whenever any transaction fails with
+ one or more entities between client and CaosDB server. More
+ detailed errors are collected as direct and indirect children in
+ the 'errors' list (direct children) and the 'all_errors' set (set
+ of all direct and indirect children).
- def get_container(self):
- '''
- @return: The container that raised this TransactionError during the last
- transaction.
- '''
+ """
- return self.container
+ def __init__(self, error=None,
+ msg="An error occured during the transaction.",
+ container=None):
+ CaosDBException.__init__(self, msg=msg)
+ self.errors = []
+ self.all_errors = set()
+ self.entities = []
+ self.all_entities = set()
+ self.container = container
+ # special case of faulty container
+ if container is not None and container.get_errors() is not None:
+ self.code = container.get_errors()[0].code
+ else:
+ self.code = None
+ if error is not None:
+ self.add_error(error)
+
+ def has_error(self, error_t, direct_children_only=False):
+ """Check whether this transaction error contains an error of type
+ error_t. If direct_children_only is True, only direct children
+ are checked.
+
+ Parameters:
+ -----------
+ error_t : EntityError
+ error type to be checked
+ direct_children_only: bool, optional
+ If True, only direct children, i.e., all errors in
+ self.errors are checked. Else all direct and indirect
+ children, i.e., all errors in self.all_errors are
+ used. Default is false.
+
+ Returns:
+ --------
+ has_error : bool
+ True if at least one of the children is of type error_t,
+ False otherwise.
+
+ """
+
+ test_set = self.errors if direct_children_only else self.all_errors
+ return any([isinstance(err, error_t) for err in test_set])
def add_error(self, error):
- """Add an error to this TransactionError.
+ """Add an error as a direct child to this TransactionError.
@param error: An EntityError or a list of EntityErrors.
@@ -196,35 +222,31 @@ class TransactionError(CaosDBException):
"""
if hasattr(error, "__iter__"):
- for e in error:
- self.add_error(e)
+ for err in error:
+ self.add_error(err)
return self
- elif isinstance(error, TransactionError):
+ elif isinstance(error, EntityError):
self.errors.append(error)
+ self.entities.append(error.entity)
+
+ self.all_errors.add(error)
+ self.all_errors.update(error.all_errors)
+ self.all_entities.add(error.entity)
+ self.all_entities.update(error.all_entities)
return self
else:
raise TypeError(
- "Argument is to be an TransactionError or a list of TransactionErrors.")
-
- def get_errors(self):
- '''
- @return: A list of all EntityError objects.
- '''
-
- if hasattr(self, 'errors'):
- return self.errors
-
- return None
+ "Argument is to be an EntityError or a list of EntityErrors.")
def _repr_reasons(self, indent):
- if self.get_errors() is not None and len(self.get_errors()) > 0:
+ if self.errors is not None and len(self.errors) > 0:
ret = "\n" + indent + " +--| REASONS |--"
- for c in self.get_errors():
+ for err in self.errors:
ret += '\n' + indent + ' | -> ' + \
- c.__str__(indent=indent + ' |')
+ err.__str__(indent=indent + ' |')
ret += "\n" + indent + " +----------------"
return ret
@@ -232,8 +254,11 @@ class TransactionError(CaosDBException):
return ''
def _repr_head(self, indent):
- return str(type(self).__name__) + ((': ' + self.msg)
- if hasattr(self, 'msg') and self.msg is not None else '')
+ return indent + str(type(self).__name__) + (
+ (': ' + self.msg)
+ if hasattr(self, 'msg') and self.msg is not None
+ else ''
+ )
def __str__(self, indent=''):
ret = self._repr_head(indent=indent)
@@ -244,58 +269,21 @@ class TransactionError(CaosDBException):
def __repr__(self):
return self.__str__()
- def get_entities(self):
- '''
- @return: A list of all Entity objects with errors.
- '''
- ret = []
-
- if hasattr(self, 'get_entity') and self.get_entity() is not None:
- ret.append(self.get_entity())
-
- for error in self.errors:
- if hasattr(error, 'get_entity'):
- if error.get_entity() not in ret:
- ret.append(error.get_entity())
-# if hasattr(error, 'get_entities'):
-# for e in error.get_entities():
-# if e not in ret:
-# ret.append(e)
- return ret
-
- def get_error(self):
- return self.error
-
class EntityError(TransactionError):
+ """This is the most basic entity error. It is constructed using an
+ entity that caused the error and the error message attached by the
+ server.
- @staticmethod
- def _sort_t(t):
- if len(t) > 1:
- ret = ()
- '''remove EntityError'''
-
- for i in range(len(t)):
- if t[i] != EntityError:
- ret += (t[i],)
- t = ret
-
- return t
-
- def _convert(self):
- t = self._calc_bases()
- # TODO is it really a good idea to create dynamically types here?
- newtype = type('EntityMultiError', t+(Exception,), {})
- newinstance = newtype(error=self.error, entity=self.entity)
- setattr(newinstance, 'msg', self.msg)
- setattr(newinstance, 'errors', self.errors)
- setattr(newinstance, 'container', self.container)
-
- return newinstance
+ """
- def __init__(self, error=None, container=None, entity=None):
- TransactionError.__init__(self, container=container)
+ def __init__(self, error=None, entity=None):
+ TransactionError.__init__(self)
self.error = error
+ if hasattr(error, "code"):
+ self.code = error.code
+ else:
+ self.code = None
self.entity = entity
if error is not None and hasattr(error, "encode"):
@@ -307,34 +295,17 @@ class EntityError(TransactionError):
else:
self.msg = str(error)
- def get_entity(self):
- '''
- @return: The entity that caused this error.
- '''
-
- if hasattr(self, 'entity'):
- return self.entity
-
- return None
-
@property
def description(self):
+ """The description of the error."""
return self.error.description if self.error is not None else None
- def get_code(self):
- return self.error.code if self.error is not None else None
-
- def get_error(self):
- '''
- @return: Error Message object of this Error.
- '''
-
- return self.error
-
def _repr_head(self, indent):
if hasattr(self, 'entity') and self.entity is not None:
- return str(type(self.entity).__name__).upper() + " (" + str(self.entity.id) + (("," + "'" + str(self.entity.name) + "'")
- if self.entity.name is not None else '') + ") CAUSED " + TransactionError._repr_head(self, indent)
+ return (str(type(self.entity).__name__).upper() + " (id: " +
+ str(self.entity.id) + ((", name: " + "'" + str(self.entity.name) + "'") if
+ self.entity.name is not None else '') + ") CAUSED " +
+ TransactionError._repr_head(self, indent))
else:
return TransactionError._repr_head(self, indent)
@@ -344,15 +315,19 @@ class UniqueNamesError(EntityError):
class UnqualifiedParentsError(EntityError):
- """This entity has unqualified parents (call 'get_errors()' for a list of
- errors of the parent entities or 'get_entities()' for a list of parent
- entities with errors)."""
+ """This entity has unqualified parents (see 'errors' attribute for a
+ list of errors of the parent entities or 'entities' attribute for
+ a list of parent entities with errors).
+
+ """
class UnqualifiedPropertiesError(EntityError):
- """This entity has unqualified properties (call 'get_errors()' for a list
- of errors of the properties or 'get_entities()' for a list of properties
- with errors)."""
+ """This entity has unqualified properties (see 'errors' attribute for
+ a list of errors of the properties or 'entities' attribute for a
+ list of properties with errors).
+
+ """
class EntityDoesNotExistError(EntityError):
@@ -364,11 +339,17 @@ class EntityHasNoDatatypeError(EntityError):
class ConsistencyError(EntityError):
- pass
+ """The transaction violates database consistency."""
-class AuthorizationException(EntityError):
+class AuthorizationError(EntityError):
"""You are not allowed to do what ever you tried to do.
- Maybe you need more privileges or a user account at all.
+ Maybe you need more privileges or a user account.
+ """
+
+
+class AmbiguousEntityError(EntityError):
+ """A retrieval of the entity was not possible because there is more
+ than one possible candidate.
"""
diff --git a/src/caosdb/utils/caosdb_admin.py b/src/caosdb/utils/caosdb_admin.py
index ab8cec654f2fd0eb2b77df0c969295b1f084171c..392d8bea2ce3d9a868c32854800ca6cb78f021ba 100755
--- a/src/caosdb/utils/caosdb_admin.py
+++ b/src/caosdb/utils/caosdb_admin.py
@@ -33,7 +33,7 @@ from argparse import ArgumentParser, RawDescriptionHelpFormatter
import caosdb as db
from caosdb import administration as admin
-from caosdb.exceptions import ClientErrorException
+from caosdb.exceptions import HTTPClientError
__all__ = []
__version__ = 0.3
@@ -123,7 +123,7 @@ def do_create_user(args):
try:
admin._insert_user(name=args.user_name,
email=args.user_email, password=password)
- except ClientErrorException as e:
+ except HTTPClientError as e:
print(e.msg)
@@ -141,20 +141,20 @@ def do_set_user_password(args):
def do_add_user_roles(args):
- roles = admin._get_roles(user=args.user_name, realm=None)
+ roles = admin._get_roles(username=args.user_name, realm=None)
for r in args.user_roles:
roles.add(r)
- admin._set_roles(user=args.user_name, roles=roles)
+ admin._set_roles(username=args.user_name, roles=roles)
def do_remove_user_roles(args):
- roles = admin._get_roles(user=args.user_name, realm=None)
+ roles = admin._get_roles(username=args.user_name, realm=None)
for r in args.user_roles:
if r in roles:
roles.remove(r)
- admin._set_roles(user=args.user_name, roles=roles)
+ admin._set_roles(username=args.user_name, roles=roles)
def do_set_user_entity(args):
@@ -178,7 +178,7 @@ def do_delete_user(args):
def do_retrieve_user_roles(args):
- print(admin._get_roles(user=args.user_name))
+ print(admin._get_roles(username=args.user_name))
def do_retrieve_role_permissions(args):
diff --git a/src/doc/administration.rst b/src/doc/administration.rst
new file mode 100644
index 0000000000000000000000000000000000000000..91b85344a018618284349b4e8dd34fe6b365b94d
--- /dev/null
+++ b/src/doc/administration.rst
@@ -0,0 +1,14 @@
+Administration
+==============
+
+The Python script ``caosdb_admin.py`` should be used for administrative tasks.
+Call ``python3 caosdb_admin.py --help`` to see how to use it.
+
+The most common task is to create a new user (in the CaosDB realm) and set a
+password for the user (note that a user typically needs to be activated)::
+
+ python3 caosdb_admin.py create_user anna
+ python3 caosdb_admin.py set_user_password anna
+ python3 caosdb_admin.py add_user_roles anna administration
+ python3 caosdb_admin.py activate_user anna
+
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 9e2924ae726e13aacd2f955ae1904b39ad73cbc3..f276f325273b71d4b697bc57990259e842b2dbc3 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -182,10 +182,16 @@ epub_exclude_files = ['search.html']
# -- Extension configuration -------------------------------------------------
-# -- Options for intersphinx extension ---------------------------------------
+# -- Options for intersphinx -------------------------------------------------
+
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/", None),
+ "caosdb-mysqlbackend": ("https://caosdb.gitlab.io/caosdb-mysqlbackend/",
+ None),
+ "caosdb-server": ("https://caosdb.gitlab.io/caosdb-server/", None),
+}
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
# TODO Which options do we want?
autodoc_default_options = {
diff --git a/src/doc/index.rst b/src/doc/index.rst
index e8cc93aa398de36c30833bc97ca79ce20564daa6..76a2f88f6d31dd9b5f17995b6d54ccc63eb33631 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -10,7 +10,8 @@ Welcome to PyCaosDB's documentation!
Getting started <README_SETUP>
tutorials/index
Concepts <concepts>
- Configuration <configuration>
+ Configuration <configuration>
+ Administration <administration>
API documentation<_apidoc/modules>
This is the documentation for the Python client library for CaosDB, ``PyCaosDB``.
diff --git a/src/doc/tutorials/Data-Insertion.rst b/src/doc/tutorials/Data-Insertion.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2ead1cc259c807ee12f2459f7e452558eb1b63a2
--- /dev/null
+++ b/src/doc/tutorials/Data-Insertion.rst
@@ -0,0 +1,163 @@
+Data Insertion
+==============
+
+Data Models
+~~~~~~~~~~~
+
+Data is stored and structured in CaosDB using a concept of RecordTypes,
+Properties, Records etc. If you do not know what these are, please look
+at the chapter :any:`caosdb-server:Data Model` .
+
+In order to insert some actual data, we need to create a data model
+using RecordTypes and Properties (You may skip this if you use a CaosDB
+instance that already has the required types). So, let’s create a simple
+Property called “a†of datatype double. This is very easy in pylib:
+
+.. code:: python
+
+ a = db.Property(name="a", datatype=db.DOUBLE)
+
+There are a few basic datatypes: db.INTEGER, db.TEXT. See `data
+type <Specification/Datatype>`__ for a full list.
+
+We can create our own small data model for e.g. a simulation by adding
+two more Properties and a RecordType:
+
+.. code:: python
+
+ b = db.Property(name="b", datatype=db.DOUBLE)
+ epsilon = db.Property(name="epsilon", datatype=db.DOUBLE)
+ recordtype = db.RecordType(name="BarkleySimulation")
+ recordtype.add_property(a)
+ recordtype.add_property(b)
+ recordtype.add_property(epsilon)
+ container = db.Container()
+ container.extend([a, b, epsilon, recordtype])
+ container.insert()
+
+Insert Actual Data
+~~~~~~~~~~~~~~~~~~
+
+Suppose the RecordType “Experiment†and the Property “date†exist in the
+database. You can then create single data Records by using the
+corresponding python class:
+
+.. code:: python
+
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="date", value="2020-01-07")
+ rec.insert()
+
+Here, the record has a parent: The RecordType “Experimentâ€. And a
+Property: date.
+
+Note, that if you want to use a property that is not a primitive
+datatype like db.INTEGER and so on, you need to use the ID of the Entity
+that you are referencing.
+
+.. code:: python
+
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="report", value=235507)
+ rec.add_property(name="Analysis", value=230007)
+ rec.insert()
+
+Of course, the IDs 235507 and 230007 need to exist in CaosDB. The first
+example shows how to use a db.REFERENCE Property (report) and the second
+shows that you can use any RecordType as Property to reference a Record
+that has such a parent.
+
+Most Records do not have name however it can absolutely make sense. In
+that case use the name argument when creating it. Another useful feature
+is the fact that properties can have units:
+
+.. code:: python
+
+ rec = db.Record("DeviceNo-AB110")
+ rec.add_parent(name="SlicingMachine")
+ rec.add_property(name="weight", value="1749", unit="kg")
+ rec.insert()
+
+If you are in some kind of analysis you can do this in batch mode with a
+container. E.g. if you have a python list ``analysis_results``:
+
+.. code:: python
+
+ cont = db.Container()
+ for date, result in analysis_results:
+ rec = db.Record()
+ rec.add_parent(name="Experiment")
+ rec.add_property(name="date", value=date)
+ rec.add_property(name="result", value=result)
+ cont.append(rec)
+
+ cont.insert()
+
+Useful is also, that you can insert directly tabular data.
+
+.. code:: python
+
+ from caosadvancedtools.table_converter import from_tsv
+
+ recs = from_tsv("test.csv", "Experiment")
+ print(recs)
+ recs.insert()
+
+With this example file
+`test.csv <uploads/4f2c8756a26a3984c0af09d206d583e5/test.csv>`__.
+
+Inheritance of Properties
+-------------------------
+
+Given, you want to insert a new RecordType “Fridge temperatur
+experiment†as a child of the existing RecordType “Experimentâ€. The
+latter may have an obligatory Property “date†(since every experiment is
+conducted at some time). It is a natural way of thinking, that every sub
+type of “Experiment†also has this obligatory Property—in terms of
+object oriented programing the “Fridge temperatur experiment†*inherits*
+that Property.
+
+::
+
+ rt = h.RecordType(name="Fridge temperatur experiment",
+ description="RecordType which inherits all obligatory properties from Experiment"
+ ).add_parent(name="Experiment", inheritance="obligatory").insert()
+
+ print(rt.get_property(name="date").importance) ### rt now has a "date"-property -> this line prints "obligatory"
+
+The parameter *``inheritance=(obligatory|recommended|fix|all|none)``* of
+``add_parent`` tells the server to assign obligatory:: properties of the
+parent to the child automatically, recommended:: properties of the
+parent to the child automatically, fix:: properties of the parent to the
+child automatically, all:: properties of the parent to the child
+automatically, none:: of the properties of the parent to child
+automatically,
+
+File Update
+-----------
+
+Updating an existing file by uploading a new version.
+
+1. Retrieve the file record of interest, e.g. by ID:
+
+.. code:: python
+
+ import caosdb as db
+
+ file_upd = db.File(id=174).retrieve()
+
+2. Set the new local file path. The remote file path is stored in the
+ file object as ``file_upd.path`` while the local path can be found in
+ ``file_upd.file``.
+
+.. code:: python
+
+ file_upd.file = "./supplements.pdf"
+
+3. Update the file:
+
+.. code:: python
+
+ file_upd.update()
diff --git a/src/doc/tutorials/data-model-interface.md b/src/doc/tutorials/data-model-interface.md
new file mode 100644
index 0000000000000000000000000000000000000000..f6967c57a0a3de6e7c6fd3d2b64d3f59620526de
--- /dev/null
+++ b/src/doc/tutorials/data-model-interface.md
@@ -0,0 +1,36 @@
+# Data Models
+
+
+
+You also want to change the datamodel? Also call
+```bash
+pip3 install --user --no-deps .
+```
+in
+```bash
+CaosDB/data_models
+```
+
+Change to the appropriate directory
+```bash
+cd CaosDB/data_models
+```
+There are "data models" defined in
+```bash
+caosdb_models
+```
+having an ending like "_model.py"
+A set of data models is also considered to be a model
+You can create an UML representation of a model or a set of models by calling
+```bash
+./model_interface.py -u model_name [model_name2]
+```
+If you have troubles look at
+```bash
+./model_interface.py -h
+```
+You can change existing models (but be careful! I hope you know what you are doing) or add new ones by changing the appropriate files or adding a new XXXX_model.py
+Once you are done, you can sync your changes with the server
+```bash
+./model_interface.py -s model_name [model_name2]
+```
diff --git a/src/doc/tutorials/errors.rst b/src/doc/tutorials/errors.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ba386dc31baad1021f01d53b2b12a2623d8278ad
--- /dev/null
+++ b/src/doc/tutorials/errors.rst
@@ -0,0 +1,53 @@
+
+Error Handling
+--------------
+
+HeartDBException
+~~~~~~~~~~~~~~~~
+
+TransactionError
+~~~~~~~~~~~~~~~~
+
+Every transaction (calling ``insert``, ``update``, ``retrieve``, or
+``delete`` on a container or an entity) may finish with errors. They
+indicate, for instance, that an entity does not exist or that you need
+to specify a data type for your property and much more. If and only if
+one or more errors occur during a transaction a ``TransactionError``
+will be raised by the transaction method. The ``TransactionError`` class
+is a container for all errors which occur during a transaction. It can
+help you to find the crucial problems with your transaction by two
+important methods: \* ``get_errors()`` which returns a list of instances
+of ``EntityError``. \* ``get_entities()`` which returns a list of
+entities in the transaction container which are erroneous.
+
+Additionally, ``print(transaction_error`` prints a tree-like
+representation of all errors regarding the transaction in question.
+
+EntityError
+~~~~~~~~~~~
+
+An ``EntityError`` represents a single error that has been returned by
+the server. You might call \* ``get_entity()`` which returns the entity
+which caused the error. \* ``get_description()`` which returns a
+description of the error. \* ``get_code()`` which returns the error code
+(if specified) or 0 (if not).
+
+In fact, the ``EntityError`` class is a subclass of
+``TransactionError``. So, it inherits the ``get_entities()``. Unless
+overridden by subclasses of ``EntityError``, it return a list with only
+one item—the entity which caused this error. Similarly, unless
+overridden by subclasses, the ``get_errors()`` method returns a list
+with only one item—``[self]``.
+
+Special Errors
+~~~~~~~~~~~~~~
+
+Subclasses of ``EntityError`` for special purposes: \*
+``EntityDoesNotExistError`` \* ``EntityHasNoDataTypeError`` \*
+``UniqueNamesError`` \* ``UnqualifiedParentsError`` - overrides
+``get_entities()``: returns all parent entities with errors. - overrides
+``get_errors()``: returns a list of EntityErrors which have been caused
+by parent entities. \* ``UnqualifiedPropertiesError`` - overrides
+``get_entities()``: returns all properties with errors. - overrides
+``get_errors()``: returns a list of EntityErrors which have been caused
+by properties.
diff --git a/src/doc/tutorials/first_steps.rst b/src/doc/tutorials/first_steps.rst
index 3da05b05c4d4025f6d81490550fd1482ae147fb4..3eb804776960ba93acb9baf78824f0cf8a06e1f7 100644
--- a/src/doc/tutorials/first_steps.rst
+++ b/src/doc/tutorials/first_steps.rst
@@ -113,6 +113,8 @@ You can download files (if the LinkAhead server has access to them)
The file will be saved under target_path.
If the files are large data files, it is often a better idea to only retrieve the path of the file and access them via a local mount.
+
+
Summary
-------
diff --git a/src/doc/tutorials/index.rst b/src/doc/tutorials/index.rst
index 311f7080045e8925dd26eb03c2da3b12b1dba6e4..3889edb8f47e973cc7ae25c9134d75cfeab95f65 100644
--- a/src/doc/tutorials/index.rst
+++ b/src/doc/tutorials/index.rst
@@ -12,4 +12,7 @@ advanced usage of the Python client.
first_steps
basic_analysis
+ Data-Insertion
+ errors
+ data-model-interface
diff --git a/unittests/test_authentication_auth_token.py b/unittests/test_authentication_auth_token.py
index 1eaf091863e23205c9ffca5373e51b654a5a42e4..15e54121fc0d7b5c2be645cdb88bc20804a10980 100644
--- a/unittests/test_authentication_auth_token.py
+++ b/unittests/test_authentication_auth_token.py
@@ -32,7 +32,7 @@ from unittest.mock import Mock
from caosdb.connection.authentication import auth_token as at
from caosdb.connection.mockup import MockUpServerConnection, MockUpResponse
from caosdb.connection.utils import parse_auth_token
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
from caosdb import configure_connection
@@ -73,7 +73,7 @@ def test_login_raises():
c = configure_connection(url="https://example.com",
password_method="auth_token",
auth_token="[auth_token]")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
c._login()
diff --git a/unittests/test_authentication_unauthenticated.py b/unittests/test_authentication_unauthenticated.py
index 9ea864a9999c5e3a74fa22fd3f6942c4e5806256..52146b08ed4e1026660eebacedf348aeb2ff2721 100644
--- a/unittests/test_authentication_unauthenticated.py
+++ b/unittests/test_authentication_unauthenticated.py
@@ -32,7 +32,7 @@ from unittest.mock import Mock
from caosdb.connection.authentication import unauthenticated
from caosdb.connection.mockup import MockUpServerConnection, MockUpResponse
from caosdb.connection.utils import parse_auth_token
-from caosdb.exceptions import LoginFailedException
+from caosdb.exceptions import LoginFailedError
from caosdb import configure_connection
from .test_authentication_auth_token import response_with_auth_token
@@ -67,5 +67,5 @@ def test_configure_connection():
def test_login_raises():
c = configure_connection(url="https://example.com",
password_method="unauthenticated")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
c._login()
diff --git a/unittests/test_connection.py b/unittests/test_connection.py
index 1dfd1fce730d4d4ba627eb4c27830b0c5156fb29..16370f00b7d5e3389582befaac1762b1d2992fcf 100644
--- a/unittests/test_connection.py
+++ b/unittests/test_connection.py
@@ -37,7 +37,7 @@ from caosdb.connection.connection import (CaosDBServerConnection,
from caosdb.connection.mockup import (MockUpResponse, MockUpServerConnection,
_request_log_message)
from caosdb.connection.utils import make_uri_path, quote, urlencode
-from caosdb.exceptions import ConfigurationException, LoginFailedException
+from caosdb.exceptions import ConfigurationError, LoginFailedError
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
@@ -234,7 +234,7 @@ def test_test_request_with_two_responses():
def test_missing_implementation():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure()
assert exc_info.value.args[0].startswith(
"Missing CaosDBServerConnection implementation.")
@@ -242,27 +242,26 @@ def test_missing_implementation():
def test_bad_implementation_not_callable():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=None)
assert exc_info.value.args[0].startswith(
"Bad CaosDBServerConnection implementation.")
- assert exc_info.value.args[1].args[0] == "'NoneType' object is not callable"
+ assert "'NoneType' object is not callable" in exc_info.value.args[0]
def test_bad_implementation_wrong_class():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=dict)
assert exc_info.value.args[0].startswith(
"Bad CaosDBServerConnection implementation.")
- assert exc_info.value.args[1].args[0] == (
- "The `implementation` callable did not return an instance of "
- "CaosDBServerConnection.")
+ assert ("The `implementation` callable did not return an instance of "
+ "CaosDBServerConnection.") in exc_info.value.args[0]
def test_missing_auth_method():
connection = configure_connection()
- with raises(ConfigurationException) as exc_info:
+ with raises(ConfigurationError) as exc_info:
connection.configure(implementation=MockUpServerConnection)
assert exc_info.value.args[0].startswith("Missing password_method.")
@@ -272,11 +271,12 @@ def test_missing_password():
connection.configure(implementation=setup_two_resources,
password_method="plain")
connection._authenticator.auth_token = "[test-auth-token]"
- assert connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=%5Btest-auth-token%5D;"
+ assert connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=%5Btest-auth-token%5D;"
connection.configure(implementation=setup_two_resources,
password_method="plain")
- with raises(LoginFailedException):
+ with raises(LoginFailedError):
connection.delete(["401"])
@@ -284,11 +284,13 @@ def test_auth_token_connection():
connection = configure_connection(auth_token="blablabla",
password_method="auth_token",
implementation=setup_two_resources)
- connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=blablabla;"
+ connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=blablabla;"
connection._logout()
- with raises(LoginFailedException) as cm:
- connection.retrieve(["some"]).headers["Cookie"] == "SessionToken=blablabla;"
+ with raises(LoginFailedError) as cm:
+ connection.retrieve(
+ ["some"]).headers["Cookie"] == "SessionToken=blablabla;"
assert cm.value.args[0] == ("The authentication token is expired or you "
"have been logged out otherwise. The "
"auth_token authenticator cannot log in "
diff --git a/unittests/test_connection_utils.py b/unittests/test_connection_utils.py
index c21b453e3a7588f30d86be8d2ed39bb4d7a1d31e..3890ae05cfe38b78a5ba0829753420246bdb560d 100644
--- a/unittests/test_connection_utils.py
+++ b/unittests/test_connection_utils.py
@@ -28,7 +28,7 @@ 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 caosdb.exceptions import ConfigurationException, LoginFailedException
+from caosdb.exceptions import ConfigurationError, LoginFailedError
from caosdb.connection.utils import parse_auth_token, auth_token_to_cookie
from caosdb.connection.connection import (
configure_connection, CaosDBServerConnection,
@@ -45,8 +45,10 @@ def setup_module():
def test_parse_auth_token():
- assert parse_auth_token("SessionToken=%5Bblablabla%5D; expires=bla; ...") == "[blablabla]"
+ assert parse_auth_token(
+ "SessionToken=%5Bblablabla%5D; expires=bla; ...") == "[blablabla]"
def test_auth_token_to_cookie():
- assert auth_token_to_cookie("[blablabla]") == "SessionToken=%5Bblablabla%5D;"
+ assert auth_token_to_cookie(
+ "[blablabla]") == "SessionToken=%5Bblablabla%5D;"
diff --git a/unittests/test_error_handling.py b/unittests/test_error_handling.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f974e7db826d093e335b250953658b08db062cd
--- /dev/null
+++ b/unittests/test_error_handling.py
@@ -0,0 +1,317 @@
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2020 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+"""Test the new (as of June 2020) error handling. All errors should
+be TransactionErrors at first which may have one or more level of
+children.
+
+"""
+import caosdb as db
+from caosdb.common.models import raise_errors
+from caosdb.exceptions import (AuthorizationError,
+ EntityDoesNotExistError, EntityError,
+ EntityHasNoDatatypeError,
+ TransactionError, UniqueNamesError,
+ UnqualifiedParentsError,
+ UnqualifiedPropertiesError)
+
+from pytest import raises
+
+
+# #################### Single Error Tests ####################
+
+
+def _add_error_message_to_entity(entity, code, description="Error message"):
+ """Attach error message with code and description to entity"""
+ message = db.Message(type="Error", code=code,
+ description=description)
+ entity.add_message(message)
+
+ return entity
+
+
+def test_has_no_datatype_error():
+ """Code 110; property without datatype"""
+ code = 110
+ prop = _add_error_message_to_entity(db.Property(name="TestProp"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(prop)
+ # There should be exactly one child
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ # check type and entity of only child
+ assert isinstance(err, EntityHasNoDatatypeError)
+ assert err.entity.name == prop.name
+
+
+def test_entity_does_not_exist_error():
+ """Code 101; entity does not exist"""
+ code = 101
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ # There should be exactly one child
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ # check type and entity of only child
+ assert isinstance(err, EntityDoesNotExistError)
+ assert err.entity.name == ent.name
+
+
+def test_entity_error():
+ """Code 0; most basic."""
+ code = 0
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, EntityError)
+ assert err.entity.name == ent.name
+
+
+def test_unique_names_error():
+ """Code 152; name is not unique"""
+ code = 152
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, UniqueNamesError)
+ assert err.entity.name == ent.name
+
+
+def test_authorization_exception():
+ """Code 403; transaction not allowed"""
+ code = 403
+ ent = _add_error_message_to_entity(db.Entity(name="TestEnt"),
+ code)
+ with raises(TransactionError) as e:
+ raise_errors(ent)
+ assert len(e.value.errors) == 1
+ err = e.value.errors[0]
+ assert isinstance(err, AuthorizationError)
+ assert err.entity.name == ent.name
+
+
+def test_empty_container_with_error():
+ """Has to raise an error, even though container is empty."""
+ code = 0
+ cont = _add_error_message_to_entity(db.Container(), code)
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ # No entity errors
+ assert len(e.value.errors) == 0
+ assert e.value.container == cont
+ assert int(e.value.code) == code
+
+
+def test_faulty_container_with_healthy_entities():
+ """Raises a TransactionError without any EntityErrors since only the
+ container, but none of its entities has an error.
+
+ """
+ code = 0
+ cont = _add_error_message_to_entity(db.Container(), code)
+ cont.append(db.Entity("TestHealthyEnt1"))
+ cont.append(db.Entity("TestHealthyEnt2"))
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ # No entity errors
+ assert len(e.value.errors) == 0
+ assert len(e.value.entities) == 0
+ assert e.value.container == cont
+ assert int(e.value.code) == code
+
+
+# #################### Children with children ####################
+
+
+def test_unqualified_parents_error():
+ """Code 116; parent does not exist"""
+ code = 116
+ entity_does_not_exist_code = 101
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"),
+ entity_does_not_exist_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ code)
+ rec.add_parent(parent)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ te = e.value
+ # One direct child, two errors in total
+ assert len(te.errors) == 1
+ assert len(te.all_errors) == 2
+ # UnqualifiedParentsError in Record ...
+ assert isinstance(te.errors[0], UnqualifiedParentsError)
+ assert te.errors[0].entity.name == rec.name
+ # ... caused by non-existing parent
+ assert isinstance(te.errors[0].errors[0], EntityDoesNotExistError)
+ assert te.errors[0].errors[0].entity.name == parent.name
+
+
+def test_unqualified_properties_error():
+ """Code 114; properties do not exist or have wrong data types or
+ values.
+
+ """
+ code = 114
+ entity_code = 0
+ no_entity_code = 101
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ code)
+ rec.add_property(prop1).add_property(prop2)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ te = e.value
+ assert len(te.errors) == 1
+ upe = te.errors[0]
+ assert upe.entity.name == rec.name
+ assert len(upe.errors) == 2
+ for error_t in [UnqualifiedPropertiesError, EntityError,
+ EntityDoesNotExistError]:
+ assert any([isinstance(x, error_t) for x in te.all_errors])
+ assert upe.code == code
+
+
+# #################### Multiple errors ####################
+
+def test_parent_and_properties_errors():
+ """Record with UnqualifiedParentsError and UnqualifiedPropertiesError,
+ and corresponding parent and properties with their errors as
+ above. Test whether all levels are in order.
+
+ """
+ prop_code = 114
+ parent_code = 116
+ entity_code = 0
+ no_entity_code = 101
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"), no_entity_code)
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ rec = _add_error_message_to_entity(db.Record(name="TestRecord"),
+ prop_code)
+ rec = _add_error_message_to_entity(rec, parent_code)
+ rec.add_parent(parent)
+ rec.add_property(prop1).add_property(prop2)
+ with raises(TransactionError) as e:
+ raise_errors(rec)
+ # Now there should be two direct children; both have to be
+ # displayed correctly.
+ te = e.value
+ # exactly two children:
+ assert len(te.errors) == 2
+ # both have to have the right codes and entities
+ found_parent = False
+ found_prop = False
+ for err in te.errors:
+ if err.code == parent_code:
+ found_parent = True
+ assert err.errors[0].entity.name == parent.name
+ assert prop1.name not in [x.name for x in
+ err.all_entities]
+ assert prop2.name not in [x.name for x in
+ err.all_entities]
+ elif err.code == prop_code:
+ found_prop = True
+ assert parent.name not in [x.name for x in
+ err.all_entities]
+ for sub_err in err.errors:
+ if sub_err.code == entity_code:
+ assert sub_err.entity.name == prop1.name
+ elif sub_err.code == no_entity_code:
+ assert sub_err.entity.name == prop2.name
+ assert found_parent
+ assert found_prop
+
+
+def test_container_with_faulty_elements():
+ """Code 12; container with valid and invalid entities. All faulty
+ entities have to be reflected correctly in the errors list of the
+ TransactionError raised by the container.
+
+ """
+ container_code = 12
+ prop_code = 114
+ parent_code = 116
+ name_code = 152
+ auth_code = 403
+ entity_code = 0
+ no_entity_code = 101
+ # Broken parents and properties
+ parent = _add_error_message_to_entity(
+ db.RecordType(name="TestParent"), no_entity_code)
+ prop1 = _add_error_message_to_entity(db.Property(
+ name="TestProp1"), entity_code)
+ prop2 = _add_error_message_to_entity(db.Property(
+ name="TestProp2"), no_entity_code)
+ cont = _add_error_message_to_entity(db.Container(),
+ container_code)
+ # healthy record and property
+ good_rec = db.Record(name="TestRecord1")
+ good_prop = db.Property(name="TestProp3")
+ cont.extend([good_rec, good_prop])
+ # broken records with single and multiole errors
+ rec_name = _add_error_message_to_entity(db.Record(name="TestRecord2"),
+ code=name_code)
+ rec_auth = _add_error_message_to_entity(db.Record(name="TestRecord3"),
+ code=auth_code)
+ rec_par_prop = _add_error_message_to_entity(
+ db.Record(name="TestRecord"), prop_code)
+ rec_par_prop = _add_error_message_to_entity(rec_par_prop, parent_code)
+ rec_par_prop.add_parent(parent)
+ rec_par_prop.add_property(prop1).add_property(prop2)
+ cont.extend([rec_name, rec_auth, rec_par_prop])
+ with raises(TransactionError) as e:
+ raise_errors(cont)
+ te = e.value
+ assert te.container == cont
+ assert te.code == container_code
+ # no healthy entity caused an error
+ for good in [good_rec, good_prop]:
+ assert good not in te.all_entities
+ # all records that caused problems
+ assert {rec_name, rec_auth, rec_par_prop}.issubset(te.all_entities)
+ # the container error contains the errors caused by the records
+ for err in te.errors:
+ if err.entity.name == rec_name.name:
+ assert isinstance(err, UniqueNamesError)
+ elif err.entity.name == rec_auth.name:
+ assert isinstance(err, AuthorizationError)
+ elif err.entity.name == rec_par_prop.name:
+ # record raises both of them
+ assert (isinstance(err, UnqualifiedParentsError) or
+ isinstance(err, UnqualifiedPropertiesError))
diff --git a/unittests/test_property.py b/unittests/test_property.py
index 8b2deeb4b06cfbf3d42881201307a1e2122124e3..752ee01f0eafef14dbffd1e62c99d1c816c45d05 100644
--- a/unittests/test_property.py
+++ b/unittests/test_property.py
@@ -84,3 +84,8 @@ def test_get_property_with_entity():
p = Property(id=1234)
r.add_property(id=1234, value="bla")
assert r.get_property(p).value == "bla"
+
+
+def test_selected_reference_list():
+ assert len(testrecord.get_property("Conductor").value) == 1
+ assert isinstance(testrecord.get_property("Conductor").value[0], Entity)
diff --git a/unittests/test_query.py b/unittests/test_query.py
new file mode 100644
index 0000000000000000000000000000000000000000..f4b3ee9762d9d76b65ace9a5b9b3f4039c0c6919
--- /dev/null
+++ b/unittests/test_query.py
@@ -0,0 +1,45 @@
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2021 Timm Fitschen <f.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+from lxml import etree
+import caosdb as db
+
+
+def test_query_parsing():
+ s = '<Query string="FIND bla" results="0" cached="true"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "FIND bla"
+ assert q.results == 0
+ assert q.cached is True
+
+ s = '<Query string="COUNT bla" results="1" cached="false"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "COUNT bla"
+ assert q.results == 1
+ assert q.cached is False
+
+ s = '<Query string="COUNT blub" results="4"/>'
+ q = db.Query(etree.fromstring(s))
+ assert q.q == "COUNT blub"
+ assert q.results == 4
+ assert q.cached is False
diff --git a/unittests/test_record.xml b/unittests/test_record.xml
index e961bdc6b88eb8e62b92696b52d7ad6a2dbf8089..018c747c11027a2c3996c65d1deab1d18514e17b 100644
--- a/unittests/test_record.xml
+++ b/unittests/test_record.xml
@@ -328,4 +328,10 @@
<Value>45531</Value>
<Value>45532</Value>
</Property>
+ <Property datatype="LIST<Person>" description="DESCRIBE ME!" id="1634561234" importance="FIX" name="Conductor">
+ <Value>
+ <Record id="23456543">
+ </Record>
+ </Value>
+ </Property>
</Record>
diff --git a/unittests/test_utils.py b/unittests/test_utils.py
index f308445ed1a06331a54ebf67411dc154836557ca..42d18ba06eb7516bb318de54cb537f548cfe9081 100644
--- a/unittests/test_utils.py
+++ b/unittests/test_utils.py
@@ -24,7 +24,6 @@
"""Tests for caosdb.common.utils."""
from __future__ import unicode_literals
from lxml.etree import Element
-from nose.tools import assert_equals as eq
from caosdb.common.utils import xml2str
@@ -32,4 +31,4 @@ def test_xml2str():
name = 'Björn'
element = Element(name)
serialized = xml2str(element)
- eq(serialized, "<Björn/>\n")
+ assert serialized == "<Björn/>\n"