diff --git a/.gitignore b/.gitignore
index a87719155a81c2d1398130f803674726ec831865..b1d651a7852d96ddb67170e80c1522f24573112b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ __pycache__
*.egg-info
.docker/cert
src/caosadvancedtools/version.py
+version.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e4c3fda811f838a6f83090e271f5ac5bddda9fa7..22aa4590e690ad2be9a8bc564c7c29f5069e9872 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- New class to collect possible problems with the data model
- New class for checking and importing tables
+- Function to get a file path to a shared resource directory
+- Function to setup logging appropriate for server side scripts with webui
+ output
### Changed ###
diff --git a/integrationtests/crawl.py b/integrationtests/crawl.py
index aaab4bb313dabc900170d48f40b30eb7bd361a8e..e439510fd7308888e9071476905f486c82769dc5 100755
--- a/integrationtests/crawl.py
+++ b/integrationtests/crawl.py
@@ -25,6 +25,7 @@
import argparse
import logging
+import sys
from argparse import RawTextHelpFormatter
import caosdb as db
@@ -65,6 +66,7 @@ def access(path):
if __name__ == "__main__":
logger = logging.getLogger("caosadvancedtools")
+ logger.addHandler(logging.StreamHandler(sys.stdout))
conlogger = logging.getLogger("connection")
conlogger.setLevel(level=logging.ERROR)
logger.setLevel(level=logging.DEBUG)
@@ -83,7 +85,7 @@ if __name__ == "__main__":
logger.info("Query done...")
config = db.configuration.get_config()
c = FileCrawler(files=files, use_cache=True,
- interactive=False, hideKnown=True,
+ interactive=False, hideKnown=False,
cfood_types=[ProjectCFood,
ExperimentCFood, AnalysisCFood,
PublicationCFood, SimulationCFood,
diff --git a/integrationtests/test.sh b/integrationtests/test.sh
index 9712e0e7db654c1d7a508e740b936800363e4b8e..e6baabf8feefa216648840ffb96517c2a7b1f8e3 100755
--- a/integrationtests/test.sh
+++ b/integrationtests/test.sh
@@ -16,10 +16,10 @@ pushd extroot
egrep -liRZ 'A description of another example' . | xargs -0 -l sed -i -e 's/A description of another example/A description of this example/g'
popd
echo "run crawler"
-./crawl.py / > $OUT
+./crawl.py / &> $OUT
# check whether there was something UNAUTHORIZED
set -e
-grep "UNAUTHORIZED UPDATE" $OUT
+grep "There where unauthorized changes" $OUT
# get the id of the run which is the last field of the output string
RUN_ID=$(grep "run id:" $OUT | awk '{ print $NF }')
echo $RUN_ID
@@ -27,7 +27,7 @@ echo "run crawler again"
echo "./crawl.py -a $RUN_ID /"
./crawl.py -a $RUN_ID / > $OUT
set +e
-if grep "UNAUTHORIZED UPDATE" $OUT
+if grep "There where unauthorized changes" $OUT
then
exit 1
fi
diff --git a/src/caosadvancedtools/__init__.py b/src/caosadvancedtools/__init__.py
index f96b7578f308ba2d3ee381f7a32216f1a8e02e35..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/src/caosadvancedtools/__init__.py
+++ b/src/caosadvancedtools/__init__.py
@@ -1,6 +0,0 @@
-import logging
-import sys
-
-logger = logging.getLogger("caosadvancedtools")
-logger.setLevel(level=logging.INFO)
-logger.addHandler(logging.StreamHandler(sys.stdout))
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 057273e75d092e7f3437b3f55765382f4ab2bdec..3ec1b6ed7ef5263db8349419225ca3ebf20f52fa 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -53,7 +53,7 @@ RECORDS = {}
RECORDTYPES = {}
FILES = {}
-logger = logging.getLogger("caosadvanedtools")
+logger = logging.getLogger(__name__)
def get_entity(name):
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index 50da7a2356fa41978a43a8357323f47a873e80ae..7e69ed33541d9e04b31b7298631edc671a5f896e 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -57,7 +57,7 @@ from .guard import RETRIEVE, ProhibitedException
from .guard import global_guard as guard
from .suppressKnown import SuppressKnown
-logger = logging.getLogger("caosadvancedtools")
+logger = logging.getLogger(__name__)
def separated(text):
@@ -97,7 +97,15 @@ class Crawler(object):
self.abort_on_exception = abort_on_exception
self.update_cache = UpdateCache()
self.filterKnown = SuppressKnown()
- logger.addFilter(self.filterKnown)
+ advancedtoolslogger = logging.getLogger("caosadvancedtools")
+
+ # TODO this seems to be a bad idea. What if the handler was not added
+ # yet? What if there is another stream handler, which shall not be
+ # filtered?
+
+ for hdl in advancedtoolslogger.handlers:
+ if hdl.__class__.__name__ == "StreamHandler":
+ hdl.addFilter(self.filterKnown)
if hideKnown is False:
for cat in ["matches", "inconsistency"]:
diff --git a/src/caosadvancedtools/serverside/helper.py b/src/caosadvancedtools/serverside/helper.py
index a09e6cfe867211e27fde8675d83d6b21bd14d456..67c8256a94391ce6dbc77a63812833d61f475e66 100644
--- a/src/caosadvancedtools/serverside/helper.py
+++ b/src/caosadvancedtools/serverside/helper.py
@@ -23,6 +23,8 @@ from __future__ import absolute_import
import argparse
import datetime
import json
+import logging
+import os
import sys
import caosdb as db
@@ -44,6 +46,7 @@ def wrap_bootstrap_alert(text, kind):
alert : str
A HTML str of a Bootstrap DIV.alert
"""
+
return ('<div class="alert alert-{kind} alert-dismissible" '
'role="alert">{text}</div>').format(kind=kind, text=text)
@@ -232,6 +235,7 @@ def get_data(filename, default=None):
def get_timestamp():
"""Return a ISO 8601 compliante timestamp (second precision)"""
+
return datetime.datetime.utcnow().isoformat(timespec='seconds')
@@ -276,3 +280,35 @@ def parse_arguments(args):
p = get_argument_parser()
return p.parse_args(args)
+
+
+def get_shared_filename(filename):
+ """
+ prefix a filename with a path to a shared resource directory
+
+
+ Parameters
+ ----------
+ filename : str
+ Filename to be prefixed; e.g. `log.txt`.
+
+ Returns
+ -------
+ tuple
+ (filename, filepath), where `filename` is the name that can be shared
+ with users, such that they can retrieve the file from the shared
+ directory. `filepath` is the path that can be used in a script to
+ actually store the file; e.g. with open(filepath, 'w') as fi...
+ """
+
+ if "SHARED_DIR" not in os.environ:
+ raise RuntimeError(
+ "The environment variable 'SHARED_DIR' should be "
+ "set. Cannot identifiy the directory for the shared resource")
+
+ directory = os.environ["SHARED_DIR"]
+ randname = os.path.basename(os.path.abspath(directory))
+ filepath = os.path.abspath(os.path.join(directory, filename))
+ filename = os.path.join(randname, filename)
+
+ return filename, filepath
diff --git a/src/caosadvancedtools/serverside/logging.py b/src/caosadvancedtools/serverside/logging.py
new file mode 100644
index 0000000000000000000000000000000000000000..33f5bae1a91b4bd49db32248125561fdb2bd69e5
--- /dev/null
+++ b/src/caosadvancedtools/serverside/logging.py
@@ -0,0 +1,64 @@
+# encoding: utf-8
+#
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@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 __future__ import absolute_import
+
+import logging
+import os
+import sys
+import tempfile
+from datetime import datetime
+
+from ..webui_formatter import WebUI_Formatter
+from .helper import get_shared_filename
+
+
+def configure_server_side_logging(loggername="caosadvancedtools"):
+ """
+ Set logging up to save one plain debugging log file, one plain info log
+ file (for users) and a stdout stream with messages wrapped in html elements
+
+ returns the path to the file with debugging output
+ """
+ logger = logging.getLogger(loggername)
+ logger.setLevel(level=logging.DEBUG)
+
+ filename, filepath = get_shared_filename("log.txt")
+
+ # this is a log file with INFO level for the user
+ user_file_handler = logging.FileHandler(filename=filepath)
+ user_file_handler.setLevel(logging.INFO)
+ logger.addHandler(user_file_handler)
+
+ # The output shall be printed in the webui. Thus wrap it in html elements.
+ formatter = WebUI_Formatter(full_file="/Shared/{}".format(filename))
+ web_handler = logging.StreamHandler(stream=sys.stdout)
+ web_handler.setFormatter(formatter)
+ web_handler.setLevel(logging.INFO)
+ logger.addHandler(web_handler)
+
+ # one log file with debug level output
+ debug_file = os.path.join(tempfile.gettempdir(),
+ "{}_{}.log".format(__name__,
+ datetime.now().isoformat()))
+ debug_handler = logging.FileHandler(filename=debug_file)
+ debug_handler.setLevel(logging.DEBUG)
+ logger.addHandler(debug_handler)
+
+ return debug_file
diff --git a/src/caosadvancedtools/suppressKnown.py b/src/caosadvancedtools/suppressKnown.py
index 61b016052a89db3d157f5f6e8d0562f88ee22131..c15f0e06fa7d126937497aeb877dd5d2991b6ff7 100644
--- a/src/caosadvancedtools/suppressKnown.py
+++ b/src/caosadvancedtools/suppressKnown.py
@@ -71,6 +71,16 @@ class SuppressKnown(logging.Filter):
return sha256((txt+str(identifier)).encode("utf-8")).hexdigest()
def filter(self, record):
+ """
+ Return whether the record shall be logged.
+
+
+ If either identifier of category is missing 1 is returned (logging
+ enabled). If the record has both attributes, it is checked whether the
+ combination was shown before (was_tagged). If so 0 is returned.
+ Otherwise the combination is saved and 1 is returned
+ """
+
if not hasattr(record, "identifier"):
return 1
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index 468cdba3bbe23ec7507aa394ddf0cfe7e0be0e1a..eeb91d6dcff364abd34b6407c0daa736c5813979 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -36,10 +36,10 @@ from xlrd import XLRDError
from .datainconsistency import DataInconsistencyError
from .suppressKnown import SuppressKnown
-logger = logging.getLogger("caosadvancedtools")
+logger = logging.getLogger(__name__)
-def name_converter(name):
+def assure_name_format(name):
"""
checks whether a string can be interpreted as 'LastName, FirstName'
"""
@@ -74,7 +74,6 @@ class TSVImporter(object):
class XLSImporter(object):
-
def __init__(self, converters, obligatory_columns=None, unique_keys=None):
"""
converters: dict with column names as keys and converter functions as
@@ -86,6 +85,9 @@ class XLSImporter(object):
necessary.
obligatory_columns: list of column names, optional
each listed column must not have missing values
+ unique_columns : list of column names that in
+ combination must be unique; i.e. each row has a
+ unique combination of values in those columns.
"""
self.sup = SuppressKnown()
self.required_columns = list(converters.keys())
@@ -97,7 +99,7 @@ class XLSImporter(object):
"""
converts an xls file into a Pandas DataFrame.
- The converters of the XLS_Importer object are used.
+ The converters of the XLSImporter object are used.
Raises: DataInconsistencyError
"""
@@ -126,6 +128,15 @@ class XLSImporter(object):
'category': "inconsistency"})
raise DataInconsistencyError(*e.args)
+ try:
+ df = xls_file.parse(converters=self.converters)
+ except Exception as e:
+ logger.warning(
+ "Cannot parse {}.".format(filename),
+ extra={'identifier': str(filename),
+ 'category': "inconsistency"})
+ raise DataInconsistencyError(*e.args)
+
self.check_columns(df, filename=filename)
df = self.check_missing(df, filename=filename)
@@ -167,8 +178,10 @@ class XLSImporter(object):
for unique_columns in self.unique_keys:
subtable = df[list(unique_columns)]
+
for index, row in subtable.iterrows():
element = tuple(row)
+
if element in uniques:
errmsg = (
"The {}. row contains the values '{}'.\nThis value "
diff --git a/src/caosadvancedtools/utils.py b/src/caosadvancedtools/utils.py
index b897d76ad53de8fa38ddc457e9c532fd3c274e58..4e85c9dffedbf1076f8406777ed51d6c7313dda5 100644
--- a/src/caosadvancedtools/utils.py
+++ b/src/caosadvancedtools/utils.py
@@ -29,7 +29,7 @@ import caosdb as db
def set_log_level(level):
- logger = logging.getLogger("caosadvancedtools")
+ logger = logging.getLogger(__name__)
logger.setLevel(level=logging.DEBUG)
diff --git a/unittests/test_table_importer.py b/unittests/test_table_importer.py
index b848a3ce796a126fb55e03efd2afba3c6c53f603..b662493b32a38ffa0c416b44ac914bbf540ae34c 100644
--- a/unittests/test_table_importer.py
+++ b/unittests/test_table_importer.py
@@ -23,7 +23,7 @@ from tempfile import NamedTemporaryFile
import numpy as np
import pandas as pd
from caosadvancedtools.datainconsistency import DataInconsistencyError
-from caosadvancedtools.table_importer import (XLSImporter, name_converter,
+from caosadvancedtools.table_importer import (XLSImporter, assure_name_format,
yes_no_converter)
@@ -40,9 +40,10 @@ class ConverterTest(unittest.TestCase):
self.assertRaises(ValueError, yes_no_converter, "True")
self.assertRaises(ValueError, yes_no_converter, "true")
- def test_name_converter(self):
- self.assertEqual(name_converter("Müstermann, Max"), "Müstermann, Max")
- self.assertRaises(ValueError, name_converter, "Max Mustermann")
+ def test_assure_name_format(self):
+ self.assertEqual(assure_name_format("Müstermann, Max"),
+ "Müstermann, Max")
+ self.assertRaises(ValueError, assure_name_format, "Max Mustermann")
class XLSImporterTest(unittest.TestCase):