Merge branch 'dev' into f-server-154

.docker/Dockerfile

@@ -4,7 +4,7 @@ RUN apt-get update && \
     curl \
     git \
     openjdk-11-jdk-headless \
-    python-autopep8 \
+    python3-autopep8 \
     python3-pip \
     tox \
     -y

tests/test_misc.py

@@ -34,6 +34,7 @@ import caosdb as db
 from caosdb import (Container, Info, Property, Record, RecordType,
                     execute_query)
 from pytest import raises
+from pytest import mark
 
 
 def setup():
@@ -581,3 +582,12 @@ def test_cache_performance():
         t2 = t.time() - t1
         print("Time [s]: " + str(t2))
         n += 10
+
+
+@mark.xfail(reason="Waits for MR https://gitlab.indiscale.com/caosdb/src/caosdb-pylib/-/merge_requests/15")
+def test_role_after_retrieve():
+    rt = db.RecordType("TestRT").insert()
+    entity = db.Entity(id=rt.id)
+    assert entity.role is None
+    entity.retrieve()
+    assert entity.role == rt.role

tests/test_parents.py

+# encoding: utf-8
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
+# Copyright (C) 2021 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
+# 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/>.
+#
+from pytest import raises, mark
+import caosdb as db
+
+
+def setup():
+    teardown()
+
+
+def teardown():
+    d = db.execute_query("FIND Test*")
+    if len(d) > 0:
+        d.delete()
+
+
+@mark.xfail(reason="Should raise an error or at least a warning. "
+            "caosdb-server#171")
+def test_parent_name_id_mismatch():
+    rt1 = db.RecordType(name="TestRT1").insert()
+    rt2 = db.RecordType(name="TestRT2").add_parent(id=rt1.id, name=rt1.name +
+                                                   "_wrong")
+    with raises(db.TransactionError):
+        rt2.insert()
+        print(rt2)

tests/test_server_side_scripting.py

@@ -26,20 +26,22 @@
 Integration tests for the implementation of the server-side-scripting api.
 """
 from __future__ import print_function, unicode_literals
+
+import json
 import os
+import ssl
 import tempfile
-from pytest import raises, mark
-import json
-from lxml import etree
 from http.client import HTTPSConnection
-import ssl
-from caosdb import get_connection, get_config, Info, execute_query, RecordType
-from caosdb.exceptions import (HTTPClientError,
-                               HTTPResourceNotFoundError)
+
+from caosdb import Info, RecordType
+from caosdb import administration as admin
+from caosdb import execute_query, get_config, get_connection
 from caosdb.connection.encode import MultipartParam, multipart_encode
 from caosdb.connection.utils import urlencode, urlparse
-from caosdb import administration as admin
+from caosdb.exceptions import HTTPClientError, HTTPResourceNotFoundError
 from caosdb.utils.server_side_scripting import run_server_side_script
+from lxml import etree
+from pytest import mark, raises
 
 _TEST_SCRIPTS = ["not_executable", "ok", "err", "ok_anonymous"]
 
@@ -63,6 +65,7 @@ _ORIGINAL_SERVER_SCRIPTING_BIN_DIR = ""
 def clean_database():
     admin._set_permissions("anonymous", [])
     d = execute_query("FIND ENTITY WITH ID > 99")
+
     if len(d) > 0:
         d.delete()
 
@@ -84,15 +87,17 @@ def setup_module():
     clean_database()
 
     from os import makedirs
-    from os.path import join, isdir, exists
+    from os.path import exists, isdir, join
     from shutil import copyfile, copymode
     print("bin dir (local): " + str(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL))
     print("bin dir (server): " + str(_SERVER_SIDE_SCRIPTING_BIN_DIR_SERVER))
     print("tests scripts: " + str(_TEST_SCRIPTS))
+
     if not exists(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL):
         makedirs(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL)
         _REMOVE_FILES_AFTERWARDS.append(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL)
     assert isdir(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL)
+
     for script_file in _TEST_SCRIPTS:
         target = join(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL, script_file)
         src = join(_TEST_SCRIPTS_DIR, script_file)
@@ -105,6 +110,7 @@ def teardown_module():
     from os import remove
     from os.path import exists, isdir
     from shutil import rmtree
+
     for obsolete in _REMOVE_FILES_AFTERWARDS:
         if exists(obsolete):
             if isdir(obsolete):
@@ -160,6 +166,7 @@ def test_call_err():
     assert xml.xpath("/Response/script/stderr")[0].text == "err"
 
 
+@mark.xfail(reason=("package incompatibility: pandas and numexpr"))
 def test_run_server_side_script_with_file_as_positional_param():
     RecordType("TestRT").insert()
     _REMOVE_FILES_AFTERWARDS.append("test_file.txt")
@@ -185,6 +192,7 @@ def test_run_server_side_script_with_file_as_positional_param():
     assert "./.upload_files/test_file.txt" in json_data["files"]
 
 
+@mark.xfail(reason=("package incompatibility: pandas and numexpr"))
 def test_run_server_side_script_with_additional_file():
     RecordType("TestRT").insert()
     _REMOVE_FILES_AFTERWARDS.append("test_file.txt")
@@ -208,6 +216,7 @@ def test_run_server_side_script_with_additional_file():
     assert "./.upload_files/test_file.txt" in json_data["files"]
 
 
+@mark.xfail(reason=("package incompatibility: pandas and numexpr"))
 def test_diagnostics_basic():
     RecordType("TestRT").insert()
 
@@ -246,6 +255,7 @@ def test_diagnostics_basic():
     assert xml.xpath("/Response/script/stderr")[0].text is None
 
 
+@mark.xfail(reason=("package incompatibility: pandas and numexpr"))
 def test_diagnostics_with_file_upload():
     RecordType("TestRT").insert()
     _REMOVE_FILES_AFTERWARDS.append("test_file.txt")
@@ -330,6 +340,7 @@ def request(method, headers, path, body=None):
     """
     context = ssl.SSLContext(ssl.PROTOCOL_TLSv1_2)
     context.verify_mode = ssl.CERT_REQUIRED
+
     if hasattr(context, "check_hostname"):
         context.check_hostname = True
     context.load_verify_locations(get_config().get("Connection", "cacert"))
@@ -341,6 +352,7 @@ def request(method, headers, path, body=None):
         str(fullurl.netloc), timeout=200, context=context)
     http_con.request(method=method, headers=headers, url=str(fullurl.path) +
                      path, body=body)
+
     return http_con.getresponse()
 
 
@@ -398,6 +410,7 @@ def test_anonymous_script_calling_success():
 @mark.local_server
 def test_evil_path():
     subdir = os.path.join(_SERVER_SIDE_SCRIPTING_BIN_DIR_LOCAL, "subdir")
+
     if not os.path.exists(subdir):
         os.makedirs(subdir)
         _REMOVE_FILES_AFTERWARDS.append(subdir)