From 246b0a9522774a63144587020ac4b2a4dbf05363 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Tue, 14 Jul 2020 15:04:35 +0200
Subject: [PATCH] FIX: use filter in table_importer
---
src/caosadvancedtools/suppressKnown.py | 2 +-
src/caosadvancedtools/table_importer.py | 26 ++++++++++++-------------
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/src/caosadvancedtools/suppressKnown.py b/src/caosadvancedtools/suppressKnown.py
index 127ed04e..61b01605 100644
--- a/src/caosadvancedtools/suppressKnown.py
+++ b/src/caosadvancedtools/suppressKnown.py
@@ -22,7 +22,7 @@ class SuppressKnown(logging.Filter):
when they are known.
"""
- def __init__(self, db_file=None, logger=None):
+ def __init__(self, db_file=None):
if db_file:
self.db_file = db_file
else:
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index c859f675..5f84e855 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -22,7 +22,7 @@ import logging
import numpy as np
import pandas as pd
-from caosadvancedtools.suppressable import Suppressable
+from caosadvancedtools.suppressKnown import SuppressKnown
logger = logging.getLogger("caosadvancedtools")
@@ -61,7 +61,7 @@ class XLS_Importer(object):
obligatory_columns: list of column names, optional
each listed column must not have missing values
"""
- self.sup = Suppressable(logger=logger)
+ self.sup = SuppressKnown()
self.required_columns = list(converters.keys())
self.obligatory_columns = obligatory_columns
self.unique_columns = unique_columns
@@ -89,9 +89,9 @@ class XLS_Importer(object):
def check_columns(self, df, filename=None):
for col in self.required_columns:
if col not in df.columns:
- errmssg = "Column '{}' missing in ".format(col)
- errmssg += "{}.".format(filename) if filename else "the file."
- raise ValueError(errmssg)
+ errmsg = "Column '{}' missing in ".format(col)
+ errmsg += "{}.".format(filename) if filename else "the file."
+ raise ValueError(errmsg)
def check_unique(self, df, filename=None):
df = df.copy()
@@ -101,15 +101,15 @@ class XLS_Importer(object):
element = tuple(row.loc[key] for key in self.unique_columns)
if element in uniques:
- errmssg = (
+ errmsg = (
"The {}. row contains the values '{}'.\nThis value "
"combination should be unique, but was used in a previous "
"row in\n").format(index+1, element)
- errmssg += "{}.".format(filename) if filename else "the file."
- errmssg += "\nThis row will be ignored!"
+ errmsg += "{}.".format(filename) if filename else "the file."
+ errmsg += "\nThis row will be ignored!"
- self.sup.warning(errmssg, identifier=filename,
- category="inconsistency")
+ logger.warning(errmsg, extra={'identifier':filename,
+ 'category':"inconsistency"})
df = df.drop(index)
else:
uniques.append(element)
@@ -134,13 +134,13 @@ class XLS_Importer(object):
for key in self.obligatory_columns:
if pd.isnull(row.loc[key]):
- errmssg = (
+ errmsg = (
"Required information is missing ({}) in {}. row"
" (without header) of "
"file:\n{}".format(key, index+1, filename))
- self.sup.warning(errmssg, identifier=filename,
- category="inconsistency")
+ logger.warning(errmsg, extra={'identifier':filename,
+ 'category':"inconsistency"})
df = df.drop(index)
continue
--
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