diff --git a/README.md b/README.md
index 602df33cecfc8ec37fd791e3257221e66f120cb3..7215591a4f31f1946029442de291eb9ccf9beea1 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@ By participating, you are expected to uphold our [Code of Conduct](https://gitla
* If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-pylib/),
the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
However, you can also create an issue for it.
-* You can also contact us at **info (AT) caosdb.de** and join the
+* You can also contact us at **info (AT) caosdb.org** and join the
CaosDB community on
[#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
diff --git a/README_SETUP.md b/README_SETUP.md
index 48928d6c3f2c878a8d8b268b36ed2cdeba7f8014..01eea85188078ae6f2fe226e89e5c227497b4bd0 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -109,6 +109,8 @@ Now would be a good time to continue with the [tutorials](tutorials/index).
- Run a specific test function: e.g. `tox -- unittests/test_schema.py::test_config_files`
## Documentation ##
+We use sphinx to create the documentation. Docstrings in the code should comply
+with the Googly style (see link below).
Build documentation in `build/` with `make doc`.
@@ -118,5 +120,11 @@ Build documentation in `build/` with `make doc`.
- `sphinx-autoapi`
- `recommonmark`
+### How to contribute ###
+
+- [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
+- [Google Style Python Docstrings 2nd reference](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
+- [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)
+
### Troubleshooting ###
If the client is to be executed directly from the `/src` folder, an initial `.\setup.py install --user` must be called.
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index ca6aad829a3e0607292cf69b8b1d4b7f7758993e..0000000000000000000000000000000000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,3 +0,0 @@
-[pytest]
-testpaths=unittests
-addopts=-x -vv --cov=caosdb
diff --git a/setup.py b/setup.py
index 35d6d69a83338a0dc543b4b6438b56c1372b7237..fca246ed7004a25e7eedc594a4e7eceb68ee295a 100755
--- a/setup.py
+++ b/setup.py
@@ -174,7 +174,7 @@ def setup_package():
python_requires='>=3.8',
package_dir={'': 'src'},
install_requires=['lxml>=4.6.3',
- "requests[socks]>=2.28.1",
+ "requests[socks]>=2.26",
"python-dateutil>=2.8.2",
'PyYAML>=5.4.1',
'future',
diff --git a/src/caosdb/__init__.py b/src/caosdb/__init__.py
index 7e06885fe495c1e8c4ccc99b7d0c0f8ff8c34b5b..45303cc275042b4eb83ab37f2fd67ce077fa0561 100644
--- a/src/caosdb/__init__.py
+++ b/src/caosdb/__init__.py
@@ -41,11 +41,12 @@ from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
from caosdb.common.state import State, Transition
# Import of the basic API classes:
from caosdb.common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
- SUGGESTED, Container, DropOffBox, Entity,
+ SUGGESTED, Container, Entity,
File, Info, Message, Permissions, Property,
Query, QueryTemplate, Record, RecordType,
delete, execute_query, get_global_acl,
- get_known_permissions, raise_errors)
+ get_known_permissions, raise_errors,
+ Directory, Link)
from caosdb.configuration import _read_config_files, configure, get_config
from caosdb.connection.connection import configure_connection, get_connection
from caosdb.exceptions import *
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index 05f661c9b6ef2c89027e2a56fe22e6a9d1e59dff..40e49f5a6c6646d6218874a60e29666c4054d3af 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -51,7 +51,7 @@ from lxml import etree
from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, INTEGER, TEXT,
is_list_datatype, is_reference)
from caosdb.common.state import State
-from caosdb.common.utils import uuid, xml2str, experimental
+from caosdb.common.utils import uuid, xml2str
from caosdb.common.timezone import TimeZone
from caosdb.common.versioning import Version
from caosdb.configuration import get_config
@@ -115,6 +115,7 @@ class Entity(object):
self.parents = _Parents()
self.path = None
self.file = None
+ self.link_target = None
self.unit = None
self.acl = None
self.permissions = None
@@ -301,6 +302,30 @@ class Entity(object):
def path(self, new_path):
self.__path = new_path
+ @property
+ def link_target(self):
+ if self.__link_target is not None or self._wrapped_entity is None:
+ return self.__link_target
+
+ return self._wrapped_entity.link_target
+
+ @link_target.setter
+ def link_target(self, new_link_target):
+ self.__link_target = new_link_target
+
+ @property
+ def thumbnail(self):
+ warn(DeprecationWarning(
+ "The thumbnail feature has been removed from the CaosDB server "
+ "API"))
+ return None
+
+ @thumbnail.setter
+ def thumbnail(self, new_thumbnail):
+ warn(DeprecationWarning(
+ "The thumbnail feature has been removed from the CaosDB server "
+ "API"))
+
@property
def file(self):
if self.__file is not None or self._wrapped_entity is None:
@@ -314,14 +339,16 @@ class Entity(object):
@property
def pickup(self):
- if self.__pickup is not None or self._wrapped_entity is None:
- return self.__pickup
-
- return self._wrapped_entity.pickup
+ warn(DeprecationWarning(
+ "The drop-off/pickup feature has been removed from the CaosDB "
+ "server API"))
+ return None
@pickup.setter
def pickup(self, new_pickup):
- self.__pickup = new_pickup
+ warn(DeprecationWarning(
+ "The drop-off/pickup feature has been removed from the CaosDB "
+ "server API"))
def grant(self, realm=None, username=None, role=None,
permission=None, priority=False, revoke_denial=True):
@@ -1048,6 +1075,9 @@ class Entity(object):
if self.file is not None and local_serialization:
xml.set("file", self.file)
+ if self.link_target is not None:
+ xml.set("linktarget", str(self.link_target))
+
if self.checksum is not None:
xml.set("checksum", self.checksum)
@@ -1102,6 +1132,7 @@ class Entity(object):
entity.description = elem.get("description")
entity.path = elem.get("path")
entity._checksum = elem.get("checksum")
+ entity.link_target = elem.get("linktarget")
entity._size = elem.get("size")
entity.datatype = elem.get("datatype") # @ReservedAssignment
entity.unit = elem.get("unit")
@@ -1365,7 +1396,7 @@ def _parse_value(datatype, value):
# This is for a special case, where the xml parser could not differentiate
# between single values and lists with one element. As
- if hasattr(value, "__len__") and len(value) == 1:
+ if hasattr(value, "__len__") and len(value) == 1 and not isinstance(value, str):
return _parse_value(datatype, value[0])
# deal with references
@@ -1419,23 +1450,12 @@ class QueryTemplate():
self.description = description
self.query = query
self._cuid = None
- self.value = None
- self.datatype = None
self.messages = _Messages()
- self.properties = None
- self.parents = None
- self.path = None
- self.file = None
- self._checksum = None
- self._size = None
- self._upload = None
- self.unit = None
self.acl = None
self.permissions = None
self.is_valid = lambda: False
self.is_deleted = lambda: False
self.version = None
- self.state = None
def retrieve(self, raise_exception_on_error=True, unique=True, sync=True,
flags=None):
@@ -1691,9 +1711,7 @@ class Property(Entity):
class Message(object):
- # @ReservedAssignment
-
- def __init__(self, type, code=None, description=None, body=None): # @ReservedAssignment
+ def __init__(self, type, code=None, description=None, body=None):
self.type = type
self.code = code
self.description = description
@@ -1804,8 +1822,39 @@ class Record(Entity):
return Entity.to_xml(self, xml, add_properties=ALL)
-@experimental("The Directory class is experimental. It should not be used \
- until the server's file storage API has been refactored.")
+class Link(Entity):
+ """This class represents CaosDB's link entities."""
+
+ def __init__(self, name=None, id=None, description=None, path=None,
+ target=None):
+ Record.__init__(self, id=id, name=name, description=description)
+ self.role = "Link"
+ self.datatype = None
+ self.link_target = target
+
+ # location in the fileserver
+ self.path = path
+
+ def to_xml(self, xml=None, add_properties=ALL, local_serialization=False):
+ """Convert this Link to an xml element.
+
+ @return: xml element
+ """
+
+ if xml is None:
+ xml = etree.Element("Link")
+
+ return Entity.to_xml(self, xml=xml, add_properties=add_properties,
+ local_serialization=local_serialization)
+
+ def add_property(self, property=None, id=None, name=None, description=None, datatype=None,
+ value=None, unit=None, importance=FIX, inheritance=FIX):
+
+ return super().add_property(
+ property=property, id=id, name=name, description=description, datatype=datatype,
+ value=value, unit=unit, importance=importance, inheritance=inheritance)
+
+
class Directory(Record):
"""This class represents CaosDB's directory entities."""
@@ -1822,7 +1871,7 @@ class Directory(Record):
self.import_file = import_file or recursive_import
def to_xml(self, xml=None, add_properties=ALL, local_serialization=False):
- """Convert this file to an xml element.
+ """Convert this Directory to an xml element.
@return: xml element
"""
@@ -1845,14 +1894,9 @@ class File(Record):
"""This class represents CaosDB's file entities.
- For inserting a new file to the server, `path` gives the new location, and
- (exactly?) one of `file` and `pickup` should (must?) be given to specify the
- source of the file.
-
- Symlinking from the "extroot" file system is not supported by this API yet,
- it can be done manually using the `InsertFilesInDir` flag. For sample code,
- look at `test_files.py` in the Python integration tests of the
- `load_files.py` script in the advanced user tools.
+ For inserting a new file to the server or updating an existent one.
+ `path` gives the new location. `file` specifies the (local) file which is
+ to be uploaded. It is mandatory for insertions, but optionally for updates.
Parameters
----------
@@ -1870,14 +1914,16 @@ class File(Record):
A local path or python file object. The file designated by this
argument will be uploaded to the server via HTTP.
pickup : str
- A file/folder in the DropOffBox (the server will move that file into
- its "caosroot" file system). (DEPRECATED, use import feature)
+ Deprecated.
+ thumbnail : str
+ Deprecated.
import_file : bool
Import the file (don't upload it, its already there). Default: `False`
"""
def __init__(self, name=None, id=None, description=None,
- path=None, file=None, pickup=None, import_file=False):
+ path=None, file=None, pickup=None,
+ thumbnail=None, import_file=False):
Record.__init__(self, id=id, name=name, description=description)
self.role = "File"
self.datatype = None
@@ -1888,9 +1934,18 @@ class File(Record):
# local file path or pointer to local file
self.file = file
- self.pickup = pickup
self.import_file = import_file
+ if thumbnail is not None:
+ warn(DeprecationWarning(
+ "The thumbnail feature has been removed from the CaosDB "
+ "server API"))
+
+ if pickup is not None:
+ warn(DeprecationWarning(
+ "The drop-off/pickup feature has been removed from the CaosDB "
+ "server API"))
+
def to_xml(self, xml=None, add_properties=ALL, local_serialization=False):
"""Convert this file to an xml element.
@@ -1942,21 +1997,21 @@ class File(Record):
return checksum.hexdigest().lower()
@staticmethod
- def sha512(file):
- return File._get_checksum_single_file(file)
+ def _get_checksum(file):
+ if hasattr(file, "name"):
+ file_name = file.name
+ else:
+ file_name = file
- @staticmethod
- def _get_checksum_single_file(single_file):
- _file = open(single_file, 'rb')
- data = _file.read(1000)
checksum = sha512()
-
- while data:
- checksum.update(data)
+ with open(file_name, 'rb') as _file:
data = _file.read(1000)
- _file.close()
- return checksum.hexdigest()
+ while data:
+ checksum.update(data)
+ data = _file.read(1000)
+
+ return checksum.hexdigest().lower()
def add_property(self, property=None, id=None, name=None, description=None, datatype=None,
value=None, unit=None, importance=FIX, inheritance=FIX):
@@ -2499,30 +2554,13 @@ def _basic_sync(e_local, e_remote):
"this client did't know about it yet.".format(
e_remote.role, e_local.role))
- e_local.id = e_remote.id
- e_local.name = e_remote.name
- e_local.description = e_remote.description
- e_local.path = e_remote.path
- e_local._checksum = e_remote._checksum
- e_local._size = e_remote._size
- e_local.datatype = e_remote.datatype
- e_local.unit = e_remote.unit
- e_local.value = e_remote.value
- e_local.properties = e_remote.properties
- e_local.parents = e_remote.parents
- e_local.messages = e_remote.messages
- e_local.acl = e_remote.acl
- e_local.permissions = e_remote.permissions
- e_local.is_valid = e_remote.is_valid
- e_local.is_deleted = e_remote.is_deleted
- e_local.version = e_remote.version
- e_local.state = e_remote.state
-
- if hasattr(e_remote, "query"):
- e_local.query = e_remote.query
-
- if hasattr(e_remote, "affiliation"):
- e_local.affiliation = e_remote.affiliation
+ for attr in ["path", "link_target", "_checksum", "_size", "datatype",
+ "unit", "value", "properties", "parents", "messages", "acl",
+ "permissions", "is_valid", "is_deleted", "version", "state",
+ "query", "affiliation", "id", "name", "description"]:
+
+ if hasattr(e_remote, attr):
+ setattr(e_local, attr, getattr(e_remote, attr))
return e_local
@@ -3006,6 +3044,7 @@ class Container(list):
for local_entity in self:
if (sync_dict[local_entity] is None
+ and hasattr(local_entity, "path")
and local_entity.path is not None):
sync_remote_entities = []
@@ -3425,8 +3464,6 @@ class Container(list):
if hasattr(entity, '_upload') and entity._upload is not None:
entity_xml.set("upload", entity._upload)
- elif hasattr(entity, 'pickup') and entity.pickup is not None:
- entity_xml.set("pickup", entity.pickup)
elif hasattr(entity, 'import_file') and entity.import_file is True:
entity_xml.set("import", "true")
@@ -3575,8 +3612,6 @@ class Container(list):
if hasattr(entity, '_upload') and entity._upload is not None:
entity_xml.set("upload", entity._upload)
- elif hasattr(entity, 'pickup') and entity.pickup is not None:
- entity_xml.set("pickup", entity.pickup)
elif hasattr(entity, 'recursive_import') and entity.recursive_import is True:
entity_xml.set("recursive_import", "true")
elif hasattr(entity, 'import_file') and entity.import_file is True:
@@ -4292,39 +4327,6 @@ def execute_query(q, unique=False, raise_exception_on_error=True, cache=True, fl
cache=cache)
-class DropOffBox(list):
-
- path = None
-
- def sync(self):
- c = get_connection()
- _log_request("GET: Info")
- http_response = c.retrieve(["Info"])
- body = http_response.read()
- _log_response(body)
-
- xml = etree.fromstring(body)
-
- for child in xml:
- if child.tag.lower() == "stats":
- infoelem = child
-
- break
-
- for child in infoelem:
- if child.tag.lower() == "dropoffbox":
- dropoffboxelem = child
-
- break
- del self[:]
- self.path = dropoffboxelem.get('path')
-
- for f in dropoffboxelem:
- self.append(f.get('path'))
-
- return self
-
-
class UserInfo():
def __init__(self, xml):
@@ -4451,6 +4453,7 @@ def _parse_single_xml_element(elem):
'property': Property,
'file': File,
'directory': Directory,
+ 'link': Link,
'parent': Parent,
'entity': Entity}
diff --git a/tox.ini b/tox.ini
index 50c22d5716769ef2ec818f6c8fb94491ea372434..3b3371a9424cf6692a7c3c05f9c911ffdd34b957 100644
--- a/tox.ini
+++ b/tox.ini
@@ -12,3 +12,8 @@ commands=py.test --cov=caosdb -vv {posargs}
[flake8]
max-line-length=100
+
+[pytest]
+testpaths = unittests
+xfail_strict = True
+addopts = -x -vv --cov=caosdb
diff --git a/unittests/test_datatype.py b/unittests/test_datatype.py
index 9b3c6267fb018e2cd3085dea568d7396c4549ac8..5e42117581f6e1d21cac9e9a30ed95a0b658d52a 100644
--- a/unittests/test_datatype.py
+++ b/unittests/test_datatype.py
@@ -87,3 +87,9 @@ def test_parsing_of_references():
entity = db.Record(name="bla")
assert id(_parse_value(dtype, entity)) == id(entity)
+
+
+def test_parsing_of_single_list_item_str_len_one():
+ db.Record().add_property("blub", datatype=db.LIST(db.TEXT), value=["a"])
+ db.Record().add_property("blub", datatype=db.LIST(db.INTEGER), value=[1])
+ db.Record().add_property("blub", datatype=db.LIST("bla"), value=["a"])
diff --git a/unittests/test_file.py b/unittests/test_file.py
index 3c80af7f362a7cdabe0a9ebc89cd2986d04fe242..9abe3dcc41663b38083a284fd0e1a84be00b3c6a 100644
--- a/unittests/test_file.py
+++ b/unittests/test_file.py
@@ -24,14 +24,10 @@
"""Tests for the File class."""
from caosdb import File, Record, configure_connection
from caosdb.connection.mockup import MockUpServerConnection
-# pylint: disable=missing-docstring
-from nose.tools import assert_equal as eq
-from nose.tools import assert_is_not_none as there
-from nose.tools import assert_true as tru
def setup_module():
- there(File)
+ assert File is not None
configure_connection(url="unittests", username="testuser",
password_method="plain",
password="testpassword", timeout=200,
@@ -39,12 +35,12 @@ def setup_module():
def hat(obj, attr):
- tru(hasattr(obj, attr))
+ assert hasattr(obj, attr)
def test_is_record():
file_ = File()
- tru(isinstance(file_, Record))
+ assert isinstance(file_, Record)
def test_instance_variable():
@@ -57,4 +53,39 @@ def test_instance_variable():
def test_role():
file_ = File()
- eq(file_.role, "File")
+ assert file_.role == "File"
+
+
+def test_ticket_237():
+ """This is an ancient test which has been moved here from the integration
+ test suite. It checks the basic functionality of the _wrap(function)"""
+
+ f1 = File(
+ name="name1",
+ path="path1",
+ file="file1")
+ assert f1.name == "name1"
+ assert f1.path == "path1"
+ assert f1.file == "file1"
+
+ f2 = File(name="name2")
+ assert f2.name == "name2"
+ assert f2.path is None
+ assert f2.file is None
+
+ f2._wrap(f1)
+
+ assert f2.name == "name2"
+ assert f2.path == "path1"
+ assert f2.file == "file1"
+
+ f2.path = "path2"
+ f2.file = "file2"
+
+ assert f2.name == "name2"
+ assert f2.path == "path2"
+ assert f2.file == "file2"
+
+ assert f1.name == "name1"
+ assert f1.path == "path1"
+ assert f1.file == "file1"