Initial Commit

AGPLv3 Veröffentlichung gemäß Dienstanweisung vom 15. August 2018.

.gitignore

+# dot files
+.*
+!/.gitignore
+
+# compiled python and dist stuff
+*.egg
+__pycache__/
+*.pyc
+*.egg-info/
+dist/
+build/

README.md

+# Welcome
+
+This is the **CaosDB Python Client Library** repository and a part of the
+CaosDB project.
+
+# Setup
+
+Please read the [README_SETUP.md](README_SETUP.md) for instructions on how to
+setup this code.
+
+
+# Further Reading
+
+Please refer to the [official gitlab repository of the CaosDB
+project](https://gitlab.gwdg.de/bmp-caosdb/caosdb) for more information.
+
+# License
+
+Copyright (C) 2018 Research Group Biomedical Physics, Max Planck Institute for
+Dynamics and Self-Organization Göttingen.
+
+All files in this repository are licensed under a [GNU Affero General Public
+License](LICENCE.md) (version 3 or later).
+

README_SETUP.md

+# Installation
+pip install . --user
+pip install tox --user
+
+# Run Unit Tests
+tox
+
+# Code Formatting
+
+autopep8 -i -r ./

pytest.ini

+[pytest]
+testpaths = unittests
\ No newline at end of file

setup.cfg

+[nosetests]
+verbosity=2
+detailed-errors=1
+with-coverage=1
+cover-package=caosdb
+cover-inclusive=1
+cover-branches=1
+cover-erase=1
+#with-doctest=1
+
+[pycodestyle]
+ignore=E501,E121,E123,E126,E226,E24,E704,W503,W504

setup.py

+#!/bin/python
+# -*- 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
+#
+"""Install and (nose-)test caosdb."""
+from setuptools import setup, find_packages
+
+setup(name='PyCaosDB',
+      version='0.1.0',
+      description='Python Interface for CaosDB',
+      author='Timm Fitschen',
+      author_email='timm.fitschen@ds.mpg.de',
+      packages=find_packages('src'),
+      package_dir={'': 'src'},
+      install_requires=['lxml>=3.6.4', 'coverage>=4.4.2',
+                        'PyYaml>=3.12', 'future'],
+      extras_require={'keyring': ['keyring>=13.0.0']},
+      tests_require=["nose>=1.0"],
+      )

src/caosdb/__init__.py

+# -*- 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
+#
+
+# Import of the connection function (which is used to connect to the DB):
+from os.path import expanduser, join
+from os import getcwd
+from caosdb.configuration import configure, get_config
+
+from caosdb.common import administration
+from caosdb.connection.connection import configure_connection, get_connection
+# Import of the basic  API classes:
+from caosdb.common.models import (QueryTemplate, Permissions, ACL, File, Record,
+                                  RecordType, Property, Message, Container,
+                                  DropOffBox, Entity, Query, Info, LIST,
+                                  DOUBLE, REFERENCE, TEXT, DATETIME, INTEGER,
+                                  FILE, BOOLEAN, TIMESPAN, OBLIGATORY,
+                                  SUGGESTED, RECOMMENDED, FIX, ALL, NONE)
+# Import of exceptions
+from caosdb.exceptions import *
+from caosdb.common.models import (delete, execute_query, raise_errors,
+                                  get_global_acl, get_known_permissions)
+# Import of convenience methods:
+import caosdb.apiutils
+configure(expanduser('~/.pycaosdb.ini'))
+configure(join(getcwd(), "pycaosdb.ini"))

src/caosdb/common/administration.py

+# -*- 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
+#
+
+"""missing docstring."""
+
+from lxml import etree
+from caosdb.exceptions import (ClientErrorException, AuthorizationException,
+                               EntityDoesNotExistError)
+from caosdb.connection.connection import get_connection
+from caosdb.common.utils import xml2str
+
+
+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:
+        e.msg = "You are not permitted to retrieve this user."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "User does not exist."
+        raise
+
+
+def _delete_user(name, **kwargs):
+    con = get_connection()
+    try:
+        return con._http_request(method="DELETE", path="User/" + name, **kwargs).read()
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to delete this user."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "User does not exist."
+        raise
+
+
+def _update_user(name, realm=None, password=None, status=None,
+                 email=None, entity=None, **kwargs):
+    con = get_connection()
+    params = {}
+    if password is not None:
+        params["password"] = password
+    if status is not None:
+        params["status"] = status
+    if email is not None:
+        params["email"] = email
+    if entity is not 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:
+        e.msg = "User does not exist."
+        raise
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to update this user."
+        raise
+    except ClientErrorException as e:
+        if e.status == 409:
+            e.msg = "Entity does not exist."
+        raise
+
+
+def _insert_user(name, password=None, status=None, email=None, entity=None, **kwargs):
+    con = get_connection()
+    params = {"username": name}
+    if password is not None:
+        params["password"] = password
+    if status is not None:
+        params["status"] = status
+    if email is not None:
+        params["email"] = email
+    if entity is not None:
+        params["entity"] = entity
+    try:
+        return con.post_form_data(entity_uri_segment="User", params=params, **kwargs).read()
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to insert a new user."
+        raise e
+    except ClientErrorException as e:
+        if e.status == 409:
+            e.msg = "User name is yet in use."
+        raise e
+
+
+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:
+        e.msg = "You are not permitted to insert a new role."
+        raise
+    except ClientErrorException as e:
+        if e.status == 409:
+            e.msg = "Role name is already in use. Choose a different name."
+        raise
+
+
+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:
+        e.msg = "You are not permitted to update this role."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "Role does not exist."
+        raise
+
+
+def _retrieve_role(name, **kwargs):
+    con = get_connection()
+    try:
+        return con._http_request(method="GET", path="Role/" + name, **kwargs).read()
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to retrieve this role."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "Role does not exist."
+        raise
+
+
+def _delete_role(name, **kwargs):
+    con = get_connection()
+    try:
+        return con._http_request(method="DELETE", path="Role/" + name, **kwargs).read()
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to delete this role."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "Role does not exist."
+        raise
+
+
+def _set_roles(username, roles, realm=None, **kwargs):
+    xml = etree.Element("Roles")
+    for r in roles:
+        xml.append(etree.Element("Role", name=r))
+
+    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:
+        e.msg = "You are not permitted to set this user's roles."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "User does not exist."
+        raise
+    except ClientErrorException as e:
+        if e.status == 409:
+            e.msg = "Role does not exist."
+        raise
+    ret = set()
+    for r in etree.fromstring(body)[0]:
+        if r.tag == "Role":
+            ret.add(r.get("name"))
+    return ret
+
+
+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:
+        e.msg = "You are not permitted to retrieve this user's roles."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "User does not exist."
+        raise
+    ret = set()
+    for r in etree.fromstring(body)[0]:
+        ret.add(r.get("name"))
+    return ret
+
+
+def _set_permissions(role, permission_rules, **kwargs):
+    xml = etree.Element("PermissionRules")
+    for p in permission_rules:
+        xml.append(p._to_xml())
+
+    body = xml2str(xml)
+    con = get_connection()
+    try:
+        return con._http_request(method="PUT", path="PermissionRules/" + role, body=body, **kwargs).read()
+    except AuthorizationException as e:
+        e.msg = "You are not permitted to set this role's permissions."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "Role does not exist."
+        raise
+
+
+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:
+        e.msg = "You are not permitted to retrieve this role's permissions."
+        raise
+    except EntityDoesNotExistError as e:
+        e.msg = "Role does not exist."
+        raise
+
+
+class PermissionRule():
+
+    @staticmethod
+    def _parse_boolean(bstr):
+        return str(bstr) in ["True", "true", "TRUE", "yes"]
+
+    def __init__(self, action, permission, priority=False):
+        self._action = action
+        self._permission = permission
+        self._priority = PermissionRule._parse_boolean(priority)
+
+    def _to_xml(self):
+        xml = etree.Element(self._action)
+        xml.set("permission", self._permission)
+        if self._priority is True:
+            xml.set("priority", "true")
+        return xml
+
+    @staticmethod
+    def _parse_element(elem):
+        return PermissionRule(elem.tag, elem.get(
+            "permission"), elem.get("priority"))
+
+    @staticmethod
+    def _parse_body(body):
+        xml = etree.fromstring(body)
+        ret = set()
+        for c in xml:
+            ret.add(PermissionRule._parse_element(c))
+        return ret
+
+    def __str__(self):
+        return self._action + "(" + self._permission + ")" + \
+            ("P" if self._priority is True else "")
+
+    def __repr__(self):
+        return str(self)
+
+    def __hash__(self):
+        return hash(str(self).lower())
+
+    def __eq__(self, other):
+        return str(other).lower() == str(self).lower()

src/caosdb/common/utils.py

+# -*- 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
+#
+
+"""mising docstring."""
+from lxml import etree
+from multiprocessing import Lock
+from uuid import uuid4
+from sys import hexversion
+_uuid_lock = Lock()
+
+
+def xml2str(xml):
+    return etree.tostring(xml, pretty_print=True, encoding='unicode')
+
+
+def uuid():
+    exc = None
+    ret = None
+    try:
+        _uuid_lock.acquire()
+        ret = uuid4()
+    except Exception as e:
+        exc = e
+    finally:
+        _uuid_lock.release()
+        if exc:
+            raise exc
+    return ret
+
+
+def is_int(obj):
+    try:
+        int(obj)
+        return True
+    except ValueError:
+        return False