diff --git a/CHANGELOG.md b/CHANGELOG.md
index f24f8f299b0af2cf04688194e0766fd2c6b5d8fa..c4a81f1cef3b2dfac5a36f1fa566369340047745 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added ###
+* Parsing from YAML now allows to give an existing model to which the YAML data model shall be
+ added.
+
### Changed ###
* A bit better error handling in the yaml model parser.
diff --git a/src/caosadvancedtools/models/data_model.py b/src/caosadvancedtools/models/data_model.py
index df2f3ad2244c24049830cb3c2f06d1def5b22e0c..beff7e9d847c6a0854d4e38d7cee900d8a376eab 100644
--- a/src/caosadvancedtools/models/data_model.py
+++ b/src/caosadvancedtools/models/data_model.py
@@ -60,7 +60,8 @@ class DataModel(dict):
different purpose (e.g. someone else's experiment).
DataModel inherits from dict. The keys are always the names of the
- entities. Thus you cannot have unnamed entities in your model.
+ entities. Thus you cannot have unnamed or ambiguously named entities in your
+ model.
Example:
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index 60021a8048af3c2f8d26409f3a278fbe8762f989..b354c42bc555a73e97f69889d4a64b6b50b56c83 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/src/caosadvancedtools/models/parser.py
@@ -1,8 +1,8 @@
# This file is a part of the CaosDB Project.
#
-# Copyright (C) 2022 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
-# Copyright (C) 2022 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2023 Daniel Hornung <d.hornung@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -42,7 +42,7 @@ import re
import sys
import yaml
-from typing import List
+from typing import List, Optional
from warnings import warn
import jsonschema
@@ -140,15 +140,29 @@ class JsonSchemaDefinitionError(RuntimeError):
super().__init__(msg)
-def parse_model_from_yaml(filename, existing_model=None):
- """Shortcut if the Parser object is not needed."""
+def parse_model_from_yaml(filename, existing_model: Optional[dict] = None):
+ """Shortcut if the Parser object is not needed.
+
+Parameters
+----------
+
+existing_model : dict, optional
+ An existing model to which the created model shall be added.
+ """
parser = Parser()
return parser.parse_model_from_yaml(filename, existing_model=existing_model)
-def parse_model_from_string(string, existing_model=None):
- """Shortcut if the Parser object is not needed."""
+def parse_model_from_string(string, existing_model: Optional[dict] = None):
+ """Shortcut if the Parser object is not needed.
+
+Parameters
+----------
+
+existing_model : dict, optional
+ An existing model to which the created model shall be added.
+ """
parser = Parser()
return parser.parse_model_from_string(string, existing_model=existing_model)
@@ -158,28 +172,37 @@ def parse_model_from_json_schema(
filename: str,
top_level_recordtype: bool = True,
types_for_missing_array_items: dict = {},
- ignore_unspecified_array_items: bool = False
+ ignore_unspecified_array_items: bool = False,
+ existing_model: Optional[dict] = None
):
"""Return a datamodel parsed from a json schema definition.
Parameters
----------
+
filename : str
The path of the json schema file that is to be parsed
+
top_level_recordtype : bool, optional
Whether there is a record type defined at the top level of the
schema. Default is true.
+
types_for_missing_array_items : dict, optional
dictionary containing fall-back types for json entries with `type:
array` but without `items` specification. Default is an empty dict.
+
ignore_unspecified_array_items : bool, optional
Whether to ignore `type: array` entries the type of which is not
specified by their `items` property or given in
`types_for_missing_array_items`. An error is raised if they are not
ignored. Default is False.
+ existing_model : dict, optional
+ An existing model to which the created model shall be added.
+
Returns
-------
+
out : Datamodel
The datamodel generated from the input schema which then can be used for
synchronizing with CaosDB.
@@ -207,7 +230,7 @@ class Parser(object):
self.model = {}
self.treated = []
- def parse_model_from_yaml(self, filename, existing_model=None):
+ def parse_model_from_yaml(self, filename, existing_model: Optional[dict] = None):
"""Create and return a data model from the given file.
Parameters
@@ -215,6 +238,9 @@ class Parser(object):
filename : str
The path to the YAML file.
+ existing_model : dict, optional
+ An existing model to which the created model shall be added.
+
Returns
-------
out : DataModel
@@ -225,7 +251,7 @@ class Parser(object):
return self._create_model_from_dict(ymlmodel, existing_model=existing_model)
- def parse_model_from_string(self, string, existing_model=None):
+ def parse_model_from_string(self, string, existing_model: Optional[dict] = None):
"""Create and return a data model from the given YAML string.
Parameters
@@ -233,6 +259,9 @@ class Parser(object):
string : str
The YAML string.
+ existing_model : dict, optional
+ An existing model to which the created model shall be added.
+
Returns
-------
out : DataModel
@@ -242,7 +271,7 @@ class Parser(object):
return self._create_model_from_dict(ymlmodel, existing_model=existing_model)
- def _create_model_from_dict(self, ymlmodel, existing_model=None):
+ def _create_model_from_dict(self, ymlmodel, existing_model: Optional[dict] = None):
"""Create and return a data model out of the YAML dict `ymlmodel`.
Parameters
@@ -251,7 +280,7 @@ class Parser(object):
The dictionary parsed from a YAML file.
existing_model : dict, optional
- An existing model to which the ymlmodel shall be added.
+ An existing model to which the created model shall be added.
Returns
-------
@@ -356,8 +385,7 @@ class Parser(object):
if definition is None:
return
- if (self.model[name] is None
- and isinstance(definition, dict)
+ if (self.model[name] is None and isinstance(definition, dict)
# is it a property
and "datatype" in definition
# but not simply an RT of the model
diff --git a/unittests/test_yaml_model_parser.py b/unittests/test_yaml_model_parser.py
index b1177a46a90d51feb9aea0fa7c3d3d5d95cc2a7a..a26cdf034eea80df0caf64a73ba0d715f66c31db 100644
--- a/unittests/test_yaml_model_parser.py
+++ b/unittests/test_yaml_model_parser.py
@@ -1,3 +1,21 @@
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2023 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
import unittest
from datetime import date
from tempfile import NamedTemporaryFile
@@ -340,6 +358,35 @@ A:
assert "line {}".format(line) in yde.exception.args[0]
+def test_existing_model():
+ """Parsing more than one model may require to append to existing models."""
+ model_str_1 = """
+A:
+ obligatory_properties:
+ number:
+ datatype: INTEGER
+ """
+ model_str_2 = """
+B:
+ obligatory_properties:
+ A:
+ """
+ model_1 = parse_model_from_string(model_str_1)
+ model_2 = parse_model_from_string(model_str_2, existing_model=model_1)
+ for ent in ["A", "B", "number"]:
+ assert ent in model_2
+
+ model_str_redefine = """
+number:
+ datatype: DOUBLE
+ description: Hello number!
+ """
+ model_redefine = parse_model_from_string(model_str_redefine, existing_model=model_1)
+ print(model_redefine)
+ assert model_redefine["number"].description == "Hello number!"
+ assert model_redefine["number"].datatype == db.INTEGER # FIXME Shouldn't this be DOUBLE?
+
+
def test_define_role():
model = """
A: