From 81ccbd950939cd2ddeb1807e64d2039a359a5677 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 13 Apr 2023 10:21:53 +0200
Subject: [PATCH] MAINT: change wording of TableImporter argument and allow
converters and datatypes for nonexisting columns
---
CHANGELOG.md | 5 ++-
src/caosadvancedtools/table_importer.py | 51 ++++++++++++++++---------
unittests/test_table_importer.py | 22 ++++-------
3 files changed, 43 insertions(+), 35 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ebd85635..52b2ce4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,10 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased] ##
### Added ###
-- TableImporter now accepts a `allow_missing_values_in` argument which allows to have obligatory
- columns with missing values
+- TableImporter now accepts a `existing_columns` argument which demands that certain columns exist
+ although they may have missing values
### Changed ###
+- The converters and datatype arguments of TableImporter now may have keys for nonexisting columns
### Deprecated ###
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index 1931c047..4324bc8b 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -210,7 +210,7 @@ class TableImporter():
"""
def __init__(self, converters, obligatory_columns=None, unique_keys=None,
- datatypes=None, allow_missing_values_in=None):
+ datatypes=None, existing_columns=None):
"""
Parameters
----------
@@ -232,28 +232,31 @@ class TableImporter():
checked whether they have the provided datatype. This dict also defines what columns are
required to exist throught the existing keys.
- allow_missing_values_in : list, optional
- List of (obligatory) column names which may have missing (NULL) values
-
+ existing_columns : list, optional
+ List of column names that must exist but may have missing (NULL) values
"""
if converters is None:
converters = {}
+ self.converters = converters
- if allow_missing_values_in is None:
- allow_missing_values_in = []
+ if obligatory_columns is None:
+ obligatory_columns = []
+ self.obligatory_columns = obligatory_columns
+
+ if unique_keys is None:
+ unique_keys = []
+ self.unique_keys = unique_keys
if datatypes is None:
datatypes = {}
+ self.datatypes = datatypes
+
+ if existing_columns is None:
+ existing_columns = []
+ self.existing_columns = existing_columns
self.sup = SuppressKnown()
- self.allow_missing_values_in = allow_missing_values_in
- self.obligatory_columns = ([]
- if obligatory_columns is None
- else obligatory_columns)
- self.unique_keys = [] if unique_keys is None else unique_keys
- self.converters = converters
- self.datatypes = datatypes
def read_file(self, filename, **kwargs):
raise NotImplementedError()
@@ -269,7 +272,7 @@ class TableImporter():
"""
- for col in self.obligatory_columns+list(self.converters.keys())+list(self.datatypes.keys()):
+ for col in self.obligatory_columns+self.existing_columns:
if col not in df.columns:
errmsg = "Column '{}' missing in ".format(col)
errmsg += ("\n{}.\n".format(filename) if filename
@@ -329,6 +332,8 @@ class TableImporter():
"""
for key, datatype in self.datatypes.items():
+ if key not in df.columns:
+ continue
# Check for castable numeric types first: We unconditionally cast int to the default
# float, because CaosDB does not have different sizes anyway.
col_dtype = df.dtypes[key]
@@ -369,8 +374,7 @@ class TableImporter():
for index, row in df.iterrows():
# if none of the relevant information is given, skip
- if np.array([pd.isnull(row.loc[key]) for key in self.obligatory_columns
- if key not in self.allow_missing_values_in]).all():
+ if np.array([pd.isnull(row.loc[key]) for key in self.obligatory_columns]).all():
df = df.drop(index)
@@ -454,7 +458,10 @@ class XLSImporter(TableImporter):
"All but the first are being ignored.".format(filename))
try:
- df = xls_file.parse(converters=self.converters, **kwargs)
+ tmpdf = xls_file.parse(**kwargs)
+ applicable_converters = {k: v for k, v in self.converters.items()
+ if k in tmpdf.columns}
+ df = xls_file.parse(converters=applicable_converters, **kwargs)
except Exception as e:
logger.warning(
"Cannot parse {}.\n{}".format(filename, e),
@@ -470,7 +477,11 @@ class XLSImporter(TableImporter):
class CSVImporter(TableImporter):
def read_file(self, filename, sep=",", **kwargs):
try:
- df = pd.read_csv(filename, sep=sep, converters=self.converters,
+ tmpdf = pd.read_csv(filename, sep=sep, converters=self.converters,
+ **kwargs)
+ applicable_converters = {k: v for k, v in self.converters.items()
+ if k in tmpdf.columns}
+ df = pd.read_csv(filename, sep=sep, converters=applicable_converters,
**kwargs)
except ValueError as ve:
logger.warning(
@@ -487,6 +498,10 @@ class CSVImporter(TableImporter):
class TSVImporter(TableImporter):
def read_file(self, filename, **kwargs):
try:
+ tmpdf = pd.read_csv(filename, sep="\t", converters=self.converters,
+ **kwargs)
+ applicable_converters = {k: v for k, v in self.converters.items()
+ if k in tmpdf.columns}
df = pd.read_csv(filename, sep="\t", converters=self.converters,
**kwargs)
except ValueError as ve:
diff --git a/unittests/test_table_importer.py b/unittests/test_table_importer.py
index 40404358..a2d4b7c2 100644
--- a/unittests/test_table_importer.py
+++ b/unittests/test_table_importer.py
@@ -144,21 +144,21 @@ class ConverterTest(unittest.TestCase):
class TableImporterTest(unittest.TestCase):
def setUp(self):
self.importer_kwargs = dict(
- converters={'c': float, 'd': yes_no_converter},
- datatypes={'a': str, 'b': int},
+ converters={'c': float, 'd': yes_no_converter, 'x': float}, # x does not exist
+ datatypes={'a': str, 'b': int, 'x': int}, # x does not exist
obligatory_columns=['a', 'b'], unique_keys=[('a', 'b')],
- allow_missing_values_in=['e'],
+ existing_columns=['e'],
)
self.valid_df = pd.DataFrame(
[['a', 1, 2.0, 'yes', np.nan]], columns=['a', 'b', 'c', 'd', 'e'])
def test_missing_col(self):
- # check missing from converters
- df = pd.DataFrame(columns=['a', 'b', 'c'])
+ # check missing from obligatory
+ df = pd.DataFrame(columns=['a', 'e'])
importer = TableImporter(**self.importer_kwargs)
self.assertRaises(ValueError, importer.check_columns, df)
- # check missing from datatypes
- df = pd.DataFrame(columns=['a', 'd', 'c'])
+ # check missing from existing
+ df = pd.DataFrame(columns=['a', 'b'])
importer = TableImporter(**self.importer_kwargs)
self.assertRaises(ValueError, importer.check_columns, df)
# check valid
@@ -186,14 +186,6 @@ class TableImporterTest(unittest.TestCase):
columns=['a', 'b', 'c', 'd'])
self.assertRaises(DataInconsistencyError, importer.check_datatype, df)
- def test_allow_missing(self):
- importer = TableImporter(**self.importer_kwargs)
- importer.check_missing(self.valid_df)
- df = pd.DataFrame([['b', np.nan, 3.0, 'no'], ['b', 5, 3.0, 'no']],
- columns=['a', 'b', 'c', 'd'])
- df_new = importer.check_unique(df)
- self.assertEqual(df_new.shape[0], 2)
-
def test_unique(self):
importer = TableImporter(**self.importer_kwargs)
importer.check_missing(self.valid_df)
--
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