Merge branch 'logging-setup' into tmp

.docker/Dockerfile

@@ -15,10 +15,10 @@ RUN apt-get update && \
      libxml2 \
 	 -y
 COPY .docker/wait-for-it.sh /wait-for-it.sh
-ADD https://gitlab.com/api/v4/projects/13656973/repository/branches/master \
+ADD https://gitlab.com/api/v4/projects/13656973/repository/branches/dev \
    pylib_version.json
 RUN git clone https://gitlab.com/caosdb/caosdb-pylib.git && \
-   cd caosdb-pylib && pip3 install .
+   cd caosdb-pylib && git checkout dev && pip3 install .
 ADD https://gitlab.com/api/v4/projects/13656965/repository/branches/master \
    model_version.json
 RUN git clone https://gitlab.com/caosdb/caosdb-models.git && \

.gitignore

 __pycache__
 .tox
+.eggs
 .coverage
 *cache.db
 *.egg-info
 .docker/cert
+src/caosadvancedtools/version.py

CHANGELOG.md

@@ -16,8 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed ###
 
+- The suppression module is now a logging filter
 - The WebUIHandler is now a python logging formatter.
-- the suppression module is now a logging filter
 - instead of `get_entity`, type-specific functions are used in
   `cfood.py` when the type of the entity in question is known.
 - Logger is used instead of `print` for errors in `crawler.py`.

src/caosadvancedtools/table_importer.py

@@ -75,7 +75,8 @@ class TSV_Importer(object):
 
 
 class XLS_Importer(object):
-    def __init__(self, converters, obligatory_columns=[], unique_columns=[]):
+
+    def __init__(self, converters, obligatory_columns=None, unique_columns=None):
         """
         converters: dict with column names as keys and converter functions as
                     values
@@ -89,8 +90,8 @@ class XLS_Importer(object):
         """
         self.sup = SuppressKnown()
         self.required_columns = list(converters.keys())
-        self.obligatory_columns = obligatory_columns
-        self.unique_columns = unique_columns
+        self.obligatory_columns = [] if obligatory_columns is None else obligatory_columns
+        self.unique_columns = [] if unique_columns is None else unique_columns
         self.converters = converters
 
     def read_xls(self, filename):
@@ -111,9 +112,8 @@ class XLS_Importer(object):
 
         if len(xls_file.sheet_names) > 1:
             # Multiple sheets is the default now. Only show in debug
-            logger.debug(
-                "Excel file {} contains multiple sheets. "
-                "All but the first are being ignored.".format(filename))
+            logger.debug("Excel file %s contains multiple sheets. "
+                         "All but the first are being ignored.", filename)
 
         try:
             df = xls_file.parse(converters=self.converters)
@@ -161,9 +161,9 @@ class XLS_Importer(object):
         df = df.copy()
         uniques = []
 
-        for index, row in df.iterrows():
-            element = tuple(row.loc[key] for key in self.unique_columns)
-
+        subtable = df[list(self.unique_columns)]
+        for index, row in subtable.iterrows():
+            element = tuple(row)
             if element in uniques:
                 errmsg = (
                     "The {}. row contains the values '{}'.\nThis value "