diff --git a/README.md b/README.md
index 0e79121608b641514b7a928e43b64f8ae159a064..851405f567dc0adea442152c483eef17c285c95e 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+<!--THIS FILE HAS BEEN GENERATED BY A SCRIPT. PLEASE DON'T CHANGE IT MANUALLY.-->
+
# Welcome
This is the **CaosDB Python Client Library** repository and a part of the
diff --git a/examples/server_side_script.py b/examples/server_side_script.py
new file mode 100755
index 0000000000000000000000000000000000000000..71bd9c05b4e86133cc356e1c15359701642a9486
--- /dev/null
+++ b/examples/server_side_script.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# 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
+#
+"""server_side_script.py.
+
+An example which implements a minimal server-side script.
+
+1) This script expects to find a *.txt file in the .upload_files dir which is
+printed to stdout.
+
+2) It executes a "Count stars" query and prints the result to stdout.
+
+3) It will return with code 0 if everything is ok, or with any code that is
+specified with the commandline option --exit
+"""
+
+import sys
+from os import listdir
+from caosdb import configure_connection, execute_query
+
+
+# parse --auth-token option and configure connection
+CODE = 0
+QUERY = "COUNT stars"
+for arg in sys.argv:
+ if arg.startswith("--auth-token="):
+ auth_token = arg[13:]
+ configure_connection(auth_token=auth_token)
+ if arg.startswith("--exit="):
+ CODE = int(arg[7:])
+ if arg.startswith("--query="):
+ QUERY = arg[8:]
+
+
+############################################################
+# 1 # find and print *.txt file ############################
+############################################################
+
+try:
+ for fname in listdir(".upload_files"):
+ if fname.endswith(".txt"):
+ with open(".upload_files/{}".format(fname)) as f:
+ print(f.read())
+except FileNotFoundError:
+ pass
+
+
+############################################################
+# 2 # query "COUNT stars" ##################################
+############################################################
+
+RESULT = execute_query(QUERY)
+print(RESULT)
+
+############################################################
+# 3 ########################################################
+############################################################
+
+sys.exit(CODE)
diff --git a/pytest.ini b/pytest.ini
index abdd410e5f9e9835a3233b22687ad49cc1109235..ca6aad829a3e0607292cf69b8b1d4b7f7758993e 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,3 +1,3 @@
[pytest]
-testpaths = unittests
-addopts = -vv --cov=caosdb
+testpaths=unittests
+addopts=-x -vv --cov=caosdb
diff --git a/setup.cfg b/setup.cfg
index 74c5620b86c6fd5ee96abea95dab4010c9fb87a3..c46089e4d24843d7d4cc4f83dad6ec1351e4cc3f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,2 +1,4 @@
+[aliases]
+test=pytest
[pycodestyle]
ignore=E501,E121,E123,E126,E226,E24,E704,W503,W504
diff --git a/setup.py b/setup.py
index 6adefd59183ba8f9ddbee3fd097858977e053119..28384d3450f99f82c575b2142c396b2aa9e8ad6e 100755
--- a/setup.py
+++ b/setup.py
@@ -32,8 +32,9 @@ setup(name='PyCaosDB',
author_email='timm.fitschen@ds.mpg.de',
packages=find_packages('src'),
package_dir={'': 'src'},
- install_requires=['lxml>=3.6.4', 'coverage>=4.4.2',
+ install_requires=['lxml>=3.6.4',
'PyYaml>=3.12', 'future'],
extras_require={'keyring': ['keyring>=13.0.0']},
- tests_require=["pytest"],
+ setup_requires=["pytest-runner>=2.0,<3dev"],
+ tests_require=["pytest", "pytest-cov", "coverage>=4.4.2"],
)
diff --git a/src/caosdb/__init__.py b/src/caosdb/__init__.py
index 91b429e602245a8cea6b5c939260e754a6de5f53..cc5b3f9be545021c8a884d2fc52080c725047a8d 100644
--- a/src/caosdb/__init__.py
+++ b/src/caosdb/__init__.py
@@ -42,5 +42,7 @@ from caosdb.common.models import (delete, execute_query, raise_errors,
get_global_acl, get_known_permissions)
# Import of convenience methods:
import caosdb.apiutils
+
+# read configuration these files
configure(expanduser('~/.pycaosdb.ini'))
configure(join(getcwd(), "pycaosdb.ini"))
diff --git a/src/caosdb/common/administration.py b/src/caosdb/common/administration.py
index ee57a370db58c3f1b604014a08b8de457724005f..98687e3c25286121decb499e233aa0743eff47a8 100644
--- a/src/caosdb/common/administration.py
+++ b/src/caosdb/common/administration.py
@@ -31,6 +31,71 @@ from caosdb.connection.connection import get_connection
from caosdb.common.utils import xml2str
+def set_server_property(key, value):
+ """set_server_property.
+
+ Set a server property.
+
+ Parameters
+ ----------
+ key : str
+ The name of the server property.
+ value : str
+ The value of the server property.
+
+
+ Returns
+ -------
+ None
+ """
+ con = get_connection()
+
+ con._form_data_request(method="POST", path="_server_properties",
+ params={key: value}).read()
+
+
+def get_server_properties():
+ """get_server_properties.
+
+ Get all server properties as a dict.
+
+ Returns
+ -------
+ dict
+ The server properties.
+ """
+ con = get_connection()
+ body = con._http_request(method="GET", path="_server_properties").response
+ xml = etree.parse(body)
+ props = dict()
+ for elem in xml.getroot():
+ props[elem.tag] = elem.text
+ return props
+
+
+def get_server_property(key):
+ """get_server_property.
+
+ Get a server property.
+
+ Parameters
+ ----------
+ key : str
+ The name of the server property
+
+ Returns
+ -------
+ value : str
+ The string value of the server property.
+
+ Raises
+ ------
+ KeyError
+ If the server property is no defined.
+ """
+ return get_server_properties()[key]
+
+
def _retrieve_user(name, realm=None, **kwargs):
con = get_connection()
try:
@@ -154,6 +219,7 @@ def _delete_role(name, **kwargs):
def _set_roles(username, roles, realm=None, **kwargs):
xml = etree.Element("Roles")
+ print(roles)
for r in roles:
xml.append(etree.Element("Role", name=r))
@@ -189,8 +255,9 @@ def _get_roles(username, realm=None, **kwargs):
e.msg = "User does not exist."
raise
ret = set()
- for r in etree.fromstring(body)[0]:
- ret.add(r.get("name"))
+ for r in etree.fromstring(body).xpath('/Response/Roles')[0]:
+ if r.tag == "Role":
+ ret.add(r.get("name"))
return ret
@@ -251,11 +318,12 @@ class PermissionRule():
xml = etree.fromstring(body)
ret = set()
for c in xml:
- ret.add(PermissionRule._parse_element(c))
+ if c.tag in ["Grant", "Deny"]:
+ ret.add(PermissionRule._parse_element(c))
return ret
def __str__(self):
- return self._action + "(" + self._permission + ")" + \
+ return str(self._action) + "(" + str(self._permission) + ")" + \
("P" if self._priority is True else "")
def __repr__(self):
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index e07f97134035b79b66f1bfb9c33ee3b6d33ac97d..71c5c2b633222f3050944aecf212ea82979fda5a 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -1822,11 +1822,13 @@ class Container(list):
insertion, update, and deletion which are a applied to all entities
in the container or the whole container respectively.
"""
+
_debug = staticmethod(
lambda: (
get_config().getint(
"Container",
- "debug") if get_config().get(
+ "debug") if get_config().has_section("Container") and
+ get_config().get(
"Container",
"debug") is not None else 0))
diff --git a/src/caosdb/configuration.py b/src/caosdb/configuration.py
index 9f6b558abd7bd5e291eaa8bd89ca41ebe0c73bf8..3933845c448da8d6164447aeec76b3aa2c65a929 100644
--- a/src/caosdb/configuration.py
+++ b/src/caosdb/configuration.py
@@ -21,9 +21,6 @@
#
# ** end header
#
-
-"""Created on 20.09.2016."""
-
try:
# python2
from ConfigParser import ConfigParser
@@ -31,29 +28,10 @@ except ImportError:
# python3
from configparser import ConfigParser
-_DEFAULTS = {"Connection":
- {"url": None,
- "timeout": "200",
- "username": None,
- "password_method": "plain",
- "debug": "0",
- "cacert": None},
- "Container":
- {"debug": "0"}}
-
def _reset_config():
global _pycaosdbconf
- pycaosdbconf = None
- _pycaosdbconf = ConfigParser(allow_no_value=True)
- _init_defaults(_pycaosdbconf)
-
-
-def _init_defaults(confpar):
- for sec in _DEFAULTS.keys():
- confpar.add_section(sec)
- for opt in _DEFAULTS[sec].keys():
- confpar.set(sec, opt, _DEFAULTS[sec][opt])
+ _pycaosdbconf = ConfigParser(allow_no_value=False)
def configure(inifile):
diff --git a/src/caosdb/connection/connection.py b/src/caosdb/connection/connection.py
index d7a98b6f27dd036fa85b97d1a46b90f38b3bb563..0d4e310767bb57a009230c57a4a2e45429923985 100644
--- a/src/caosdb/connection/connection.py
+++ b/src/caosdb/connection/connection.py
@@ -72,6 +72,14 @@ class _WrappedHTTPResponse(CaosDBHTTPResponse):
class _DefaultCaosDBServerConnection(CaosDBServerConnection):
+ """_DefaultCaosDBServerConnection.
+
+ Methods
+ -------
+ configure
+ request
+ """
+
def __init__(self):
self._useragent = ("PyCaosDB - "
"DefaultCaosDBServerConnection")
@@ -79,6 +87,28 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
self._base_path = None
def request(self, method, path, headers=None, body=None, **kwargs):
+ """request.
+
+ Send a HTTP request to the server.
+
+ Parameters
+ ----------
+ method : str
+ The HTTP request method.
+ path : str
+ An URI path segment (without the 'scheme://host:port/' parts),
+ including query and frament segments.
+ headers : dict of str -> str, optional
+ HTTP request headers. (Defautl: None)
+ body : str or bytes or readable, opional
+ The body of the HTTP request. Bytes should be a utf-8 encoded
+ string.
+ **kwargs :
+ Any keyword arguments will be ignored.
+
+ Returns
+ -------
+ """
if headers is None:
headers = {}
try:
@@ -91,6 +121,27 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
return _WrappedHTTPResponse(self._http_con.getresponse())
def configure(self, **config):
+ """configure.
+
+ Configure the http connection.
+
+ Parameters
+ ----------
+ cacert : str
+ Path to the CA certificate which will be used to identify the
+ server.
+ url : str
+ The url of the CaosDB Server, e.g.
+ `https://example.com:443/rootpath`, including a possible root path.
+ **config :
+ Any further keyword arguments are being ignored.
+
+ Raises
+ ------
+ ConnectionException
+ If no url has been specified, or if the CA certificate cannot be
+ loaded.
+ """
context = ssl.SSLContext(ssl.PROTOCOL_TLSv1)
context.verify_mode = ssl.CERT_REQUIRED
if hasattr(context, "check_hostname"):
@@ -146,10 +197,36 @@ def _make_conf(*conf):
_DEFAULT_CONF = {"password_method": "plain", "implementation":
- _DefaultCaosDBServerConnection}
+ _DefaultCaosDBServerConnection, "timeout": 210}
def _get_authenticator(**config):
+ """_get_authenticator.
+
+ Import and configure the password_method.
+
+ Parameters
+ ----------
+ password_method : str
+ The simple name of a submodule of caosdb.connection.authentication.
+ Currently, there are three valid values for this parameter: 'plain',
+ 'pass', and 'keyring'.
+ **config :
+ Any other keyword arguments are passed the configre method of the
+ password_method.
+
+ Returns
+ -------
+ AbstractAuthenticator
+ An object which implements the password_method and which already
+ configured.
+
+ Raises
+ ------
+ ConnectionException
+ If the password_method string cannot be resolved to a CaosAuthenticator
+ class.
+ """
auth_module = ("caosdb.connection.authentication." +
config["password_method"])
_LOGGER.debug("import auth_module %s", auth_module)
@@ -161,29 +238,37 @@ def _get_authenticator(**config):
return auth_provider
except ImportError:
- raise RuntimeError("Password method \"{}\" not implemented. "
- "Valid methods: plain, pass, or keyring."
- .format(config["password_method"]))
+ raise ConfigurationException("Password method \"{}\" not implemented. "
+ "Valid methods: plain, pass, or keyring."
+ .format(config["password_method"]))
def configure_connection(**kwargs):
- """Configures the caosdb connection.
-
- All paramters are optional. The default configuration is taken from the
- `Connection` section of the configuration which can be retrieved by
- `get_config`
-
- Returns the Connection object.
-
- Typical arguments are:
- url The URL of the CaosDB server. E.g. https://dumiatis01:8433/playground
- username The username
- password Two options:
- 1) The plain text password
- 2) A function which returns the password.
- timeout A connection timeout in seconds.
- implementation A class which implements CaosDBServerConnection. (Default:
+ """Configures the caosdb connection and return the Connection object.
+
+ The effective configuration is governed by the default values (see
+ 'Parameters'), the global configuration (see `caosdb.get_config()`) and the
+ parameters which are passed to this function, with ascending priority.
+
+ The parameters which are listed here, are possibly not sufficient for a
+ working configuration of the connection. Check the `configure` method of
+ the implementation class and the password_method for more details.
+
+ Parameters
+ ----------
+ implementation : CaosDBServerConnection
+ The class which implements the connection. (Default:
_DefaultCaosDBServerConnection)
+ password_method : str
+ The name of a submodule of caosdb.connection.authentication which
+ implements the AbstractAuthenticator interface. (Default: 'plain')
+ timeout : int
+ A connection timeout in seconds. (Default: 210)
+
+ Returns
+ -------
+ _Connection
+ The singleton instance of the _Connection class.
"""
global_conf = (dict(get_config().items("Connection")) if
get_config().has_section("Connection") else dict())
@@ -242,7 +327,8 @@ def _handle_response_status(http_response):
class _Connection(object): # pylint: disable=useless-object-inheritance
"""This connection class provides the interface to the database connection
- allowing for retrieval, insertion, update, etc. of entries.
+ allowing for retrieval, insertion, update, etc. of entities, files, users,
+ roles and much more.
It wrapps an instance of CaosDBServerConnection which actually does the
work (how, depends on the instance).
diff --git a/src/caosdb/connection/mockup.py b/src/caosdb/connection/mockup.py
index abde5d03da4d553b523c3ecc63ff7552696cc865..6d1bb1f389823c2824bbaa3f3b1b41462e284692 100644
--- a/src/caosdb/connection/mockup.py
+++ b/src/caosdb/connection/mockup.py
@@ -47,7 +47,7 @@ class MockUpResponse(CaosDBHTTPResponse):
def __init__(self, status, headers, body):
self._status = status
self.headers = headers
- self.body = StringIO(body)
+ self.response = StringIO(body)
@property
def status(self):
@@ -56,7 +56,7 @@ class MockUpResponse(CaosDBHTTPResponse):
def read(self, size=-1):
"""Return the body of the response."""
- return self.body.read(size)
+ return self.response.read(size)
def getheader(self, name, default=None):
"""Get the contents of the header `name`, or `default` if there is no
diff --git a/src/caosdb/exceptions.py b/src/caosdb/exceptions.py
index a5d6e99662c38e6f74e2e974a68ce8152997e271..45c4570b4227031a35a486b86ea65535ff105852 100644
--- a/src/caosdb/exceptions.py
+++ b/src/caosdb/exceptions.py
@@ -70,9 +70,10 @@ class ClientErrorException(CaosDBException):
class ServerErrorException(CaosDBException):
def __init__(self, body):
xml = etree.fromstring(body)
- msg = xml[0].get("description")
- if xml[0].text is not None:
- msg = msg + "\n\n" + xml[0].text
+ error = xml.xpath('/Response/Error')[0]
+ msg = error.get("description")
+ if error.text is not None:
+ msg = msg + "\n\n" + error.text
CaosDBException.__init__(self, msg)
diff --git a/unittests/test_administraction.py b/unittests/test_administraction.py
new file mode 100644
index 0000000000000000000000000000000000000000..dc05be2ac7c19ae066b9c8829677626796cea5fa
--- /dev/null
+++ b/unittests/test_administraction.py
@@ -0,0 +1,69 @@
+# -*- encoding: utf-8 -*-
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# 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
+#
+"""Tests for the administration class."""
+# pylint: disable=missing-docstring
+from __future__ import unicode_literals
+from pytest import raises
+from caosdb import administration, configure_connection, get_connection
+from caosdb.connection.mockup import MockUpServerConnection, MockUpResponse
+
+
+def setup():
+ configure_connection(url="unittests", username="testuser",
+ password="testpassword", timeout=200,
+ implementation=MockUpServerConnection)
+
+
+def test_get_server_properties_success():
+ properties = "<Properties><TEST_PROP>TEST_VAL</TEST_PROP></Properties>"
+ get_connection()._delegate_connection.resources.append(
+ lambda **kwargs: MockUpResponse(200, {}, properties))
+ props = administration.get_server_properties()
+ assert isinstance(props, dict)
+
+
+def test_get_server_property_success():
+ properties = "<Properties><TEST_PROP>TEST_VAL</TEST_PROP></Properties>"
+ get_connection()._delegate_connection.resources.append(
+ lambda **kwargs: MockUpResponse(200, {}, properties))
+ assert "TEST_VAL" == administration.get_server_property("TEST_PROP")
+
+
+def test_get_server_property_key_error():
+ properties = "<Properties><TEST_PROP>TEST_VAL</TEST_PROP></Properties>"
+ get_connection()._delegate_connection.resources.append(
+ lambda **kwargs: MockUpResponse(200, {}, properties))
+ with raises(KeyError) as e:
+ assert administration.get_server_property("BLA")
+
+
+def test_set_server_property():
+ def check_form(**kwargs):
+ assert kwargs["path"] == "_server_properties"
+ assert kwargs["method"] == "POST"
+ assert kwargs["body"] == "TEST_PROP=TEST_VAL".encode()
+ assert kwargs["headers"]["Content-Type"] == "application/x-www-form-urlencoded"
+ return MockUpResponse(200, {}, "<Properties><TEST_PROP>TEST_VAL</TEST_PROP></Properties>")
+ get_connection()._delegate_connection.resources.append(check_form)
+ administration.set_server_property("TEST_PROP", "TEST_VAL")
diff --git a/unittests/test_connection.py b/unittests/test_connection.py
index 06838d1c15b70787be159b4ad2d7f1bb70abe6c8..26e3388dfa4dd7d360b8a373d631f5a362990f66 100644
--- a/unittests/test_connection.py
+++ b/unittests/test_connection.py
@@ -92,6 +92,8 @@ def test_make_uri_path():
def test_configure_connection():
+ if not get_config().has_section("Connection"):
+ get_config().add_section("Connection")
get_config().set("Connection", "url", "https://host.de")
get_config().set("Connection", "username", "test_username")
get_config().set("Connection", "password", "test_password")