From 5282684639aa3625ecf1a878410790aaa38625a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <henrik@trineo.org>
Date: Mon, 8 Nov 2021 17:39:30 +0100
Subject: [PATCH] MAINT: handle value errors also for tsv and csv
---
src/caosadvancedtools/table_importer.py | 24 ++++++++++++++++++++----
1 file changed, 20 insertions(+), 4 deletions(-)
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index f7f7efb4..7b4414b7 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -406,8 +406,16 @@ class XLSImporter(TableImporter):
class CSVImporter(TableImporter):
def read_file(self, filename, sep=",", **kwargs):
- df = pd.read_csv(filename, sep=sep, converters=self.converters,
- **kwargs)
+ try:
+ df = pd.read_csv(filename, sep=sep, converters=self.converters,
+ **kwargs)
+ except ValueError as ve:
+ logger.warning(
+ "Cannot parse {}.".format(filename),
+ extra={'identifier': str(filename),
+ 'category': "inconsistency"})
+ raise DataInconsistencyError(*ve.args)
+
self.check_dataframe(df, filename)
return df
@@ -415,8 +423,16 @@ class CSVImporter(TableImporter):
class TSVImporter(TableImporter):
def read_file(self, filename, **kwargs):
- df = pd.read_csv(filename, sep="\t", converters=self.converters,
- **kwargs)
+ try:
+ df = pd.read_csv(filename, sep="\t", converters=self.converters,
+ **kwargs)
+ except ValueError as ve:
+ logger.warning(
+ "Cannot parse {}.".format(filename),
+ extra={'identifier': str(filename),
+ 'category': "inconsistency"})
+ raise DataInconsistencyError(*ve.args)
+
self.check_dataframe(df, filename)
return df
--
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