Merge branch 'dev' into f-tsv-importer

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 ###
 

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:

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

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,

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):
         """

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."""

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):