diff --git a/CHANGELOG.md b/CHANGELOG.md
index e00c0a51e95dfc24373ccc08817206d279322f16..0ca5f692e8c9ca1a89d2b48a23ba4ad017711234 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Introduce a cfood that can create a Record structure based on the contents of a hdf5 file
h5py is now an optional dependency
- table importer implementations for csv and tsv
+- string-in-list check for table imports
### Changed ###
diff --git a/integrationtests/model.yml b/integrationtests/model.yml
index ab302f089de8ddc1782c075ad8ee26ea1259fee2..e1753a9f84d6eff7a9a59c5d17ca4f9f9da7c4c6 100644
--- a/integrationtests/model.yml
+++ b/integrationtests/model.yml
@@ -9,6 +9,7 @@ Experiment:
# TODO empty recommended_properties is a problem
#recommended_properties:
responsible:
+ datatype: LIST<Person>
Project:
SoftwareVersion:
recommended_properties:
@@ -30,8 +31,6 @@ Person:
email:
datatype: TEXT
description: 'Email of a Person.'
-responsible:
- datatype: REFERENCE
revisionOf:
datatype: REFERENCE
results:
diff --git a/src/caosadvancedtools/cfoods/h5.py b/src/caosadvancedtools/cfoods/h5.py
index 9defe77115db7687d3a6c5f27bf7f3d268e605fc..6c68edd3668fec957126aa3234a830aab98fcd25 100644
--- a/src/caosadvancedtools/cfoods/h5.py
+++ b/src/caosadvancedtools/cfoods/h5.py
@@ -6,7 +6,7 @@
# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
# Copyright (C) 2021 Alexander Kreft
-# Copyright (C) 2021 Laboratory for Fluid Physics and Biocomplexity,
+# Copyright (C) 2021 Laboratory for Fluid Physics and Biocomplexity,
# Max-Planck-Insitute für Dynamik und Selbstorganisation <www.lfpn.ds.mpg.de>
#
# This program is free software: you can redistribute it and/or modify
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index 1eda090757336506436621f9f430cf852a8a2348..e56a492fa3e9199a312d374a622770e7836f42cb 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/src/caosadvancedtools/models/parser.py
@@ -252,9 +252,8 @@ class Parser(object):
# is it a property
and "datatype" in definition
# but not simply an RT of the model
- and not (definition["datatype"] in self.model
- or _get_listdatatype(
- definition["datatype"]) in self.model)):
+ and not (_get_listdatatype(definition["datatype"]) == name and
+ _get_listdatatype(definition["datatype"]) in self.model)):
# and create the new property
self.model[name] = db.Property(name=name,
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index 6b86b1098fd58c784ba5a190174aced3c4323281..cb61e8389de69a2d0d0527ad01cb8b9991b19ece 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -88,7 +88,10 @@ def date_converter(val, fmt="%Y-%m-%d"):
converts it using format string
"""
- return datetime_converter(val, fmt=fmt).date()
+ if val is None:
+ return None
+ else:
+ return datetime_converter(val, fmt=fmt).date()
def incomplete_date_converter(val, fmts={"%Y-%m-%d": "%Y-%m-%d",
@@ -145,6 +148,43 @@ def win_path_converter(val):
return path.as_posix()
+def string_in_list(val, options, ignore_case=True):
+ """Return the given value if it is contained in options, raise an
+ error otherwise.
+
+ Parameters
+ ----------
+ val : str
+ String value to be checked.
+ options : list<str>
+ List of possible values that val may obtain
+ ignore_case : bool, optional
+ Specify whether the comparison of val and the possible options
+ should ignor capitalization. Default is True.
+
+ Returns
+ -------
+ val : str
+ The original value if it is contained in options
+
+ Raises
+ ------
+ ValueError
+ If val is not contained in options.
+ """
+ if ignore_case:
+ val = val.lower()
+ options = [o.lower() for o in options]
+
+ if val not in options:
+ raise ValueError(
+ "Field value is '{}', but it should be one of the following "
+ "values: {}.".format(val, ", ".join(
+ ["'{}'".format(o) for o in options])))
+
+ return val
+
+
class TableImporter(object):
def __init__(self, converters, obligatory_columns=None, unique_keys=None):
"""
diff --git a/unittests/test_parser.py b/unittests/test_parser.py
index 44b01a3ab2af741497e68cb7a3b912f433d6fe35..161e2873a9c01f9ce415818116b9e4cf9aeadb5c 100644
--- a/unittests/test_parser.py
+++ b/unittests/test_parser.py
@@ -274,6 +274,22 @@ A:
parse_model_from_string(yaml)
self.assertIn("line 3", yde.exception.args[0])
+ def test_reference_property(self):
+ """Test correct creation of reference property using an RT."""
+ modeldef = """A:
+ recommended_properties:
+ ref:
+ datatype: LIST<A>
+"""
+ model = parse_model_from_string(modeldef)
+ self.assertEqual(len(model), 2)
+ for key in model.keys():
+ if key == "A":
+ self.assertTrue(isinstance(model[key], db.RecordType))
+ elif key == "ref":
+ self.assertTrue(isinstance(model[key], db.Property))
+ self.assertEqual(model[key].datatype, "LIST<A>")
+
class ExternTest(unittest.TestCase):
"""TODO Testing the "extern" keyword in the YAML."""
diff --git a/unittests/test_table_importer.py b/unittests/test_table_importer.py
index b36f8bf9eeda9166fb8ab0d0f1b43d5d1c5276a4..b574c867881141928ac59c2b002fb7f185dac7bb 100644
--- a/unittests/test_table_importer.py
+++ b/unittests/test_table_importer.py
@@ -36,6 +36,7 @@ from caosadvancedtools.table_importer import (XLSImporter, assure_name_format,
incomplete_date_converter,
win_path_converter,
win_path_list_converter,
+ string_in_list,
yes_no_converter)
@@ -52,6 +53,16 @@ class ConverterTest(unittest.TestCase):
self.assertRaises(ValueError, yes_no_converter, "True")
self.assertRaises(ValueError, yes_no_converter, "true")
+ def test_string_in_list(self):
+ self.assertEqual("false", string_in_list("false",
+ ["FALSE", "TRUE"]))
+ self.assertEqual("FALSE", string_in_list("FALSE",
+ ["FALSE", "TRUE"], False))
+ self.assertRaises(ValueError, string_in_list, "FALSE", [])
+ self.assertRaises(ValueError, string_in_list, "FALSE", ["fals"])
+ self.assertRaises(ValueError, string_in_list,
+ "FALSE", ["false"], False)
+
def test_assure_name_format(self):
self.assertEqual(assure_name_format("Müstermann, Max"),
"Müstermann, Max")
@@ -65,7 +76,7 @@ class ConverterTest(unittest.TestCase):
["/this/computer"])
self.assertEqual(win_path_list_converter(
r"\this\computer,\this\computer"),
- ["/this/computer", "/this/computer"])
+ ["/this/computer", "/this/computer"])
@pytest.mark.xfail(reason="To be fixed, see Issue #34")
def test_datetime(self):