junifer 0.0.5.dev219__py3-none-any.whl → 0.0.5.dev242__py3-none-any.whl

junifer/utils/helpers.py

@@ -3,13 +3,14 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import collections.abc
 import subprocess
-from typing import List
+from typing import Dict, List
 
 from .logging import logger, raise_error
 
 
-__all__ = ["run_ext_cmd"]
+__all__ = ["run_ext_cmd", "deep_update"]
 
 
 def run_ext_cmd(name: str, cmd: List[str]) -> None:
@@ -54,3 +55,30 @@ def run_ext_cmd(name: str, cmd: List[str]) -> None:
             ),
             klass=RuntimeError,
         )
+
+
+def deep_update(d: Dict, u: Dict) -> Dict:
+    """Deep update `d` with `u`.
+
+    From: "https://stackoverflow.com/questions/3232943/update-value-of-a-nested
+    -dictionary-of-varying-depth"
+
+    Parameters
+    ----------
+    d : dict
+        The dictionary to deep-update.
+    u : dict
+        The dictionary to deep-update `d` with.
+
+    Returns
+    -------
+    dict
+        The updated dictionary.
+
+    """
+    for k, v in u.items():
+        if isinstance(v, collections.abc.Mapping):
+            d[k] = deep_update(d.get(k, {}), v)
+        else:
+            d[k] = v
+    return d

junifer/utils/logging.py

@@ -13,6 +13,7 @@ else:  # pragma: no cover
     from looseversion import LooseVersion
 
 import logging
+import warnings
 from pathlib import Path
 from subprocess import PIPE, Popen, TimeoutExpired
 from typing import Dict, NoReturn, Optional, Type, Union
@@ -44,6 +45,23 @@ _logging_types = {
 }
 
 
+# Copied over from stdlib and tweaked to our use-case.
+def _showwarning(message, category, filename, lineno, file=None, line=None):
+    s = warnings.formatwarning(message, category, filename, lineno, line)
+    logger.warning(str(s))
+
+
+# Overwrite warnings display to integrate with logging
+
+
+def capture_warnings():
+    """Capture warnings and log them."""
+    warnings.showwarning = _showwarning
+
+
+capture_warnings()
+
+
 class WrapStdOut(logging.StreamHandler):
     """Dynamically wrap to sys.stdout.
 
@@ -325,5 +343,4 @@ def warn_with_log(
         The warning subclass (default RuntimeWarning).
 
     """
-    logger.warning(msg)
     warn(msg, category=category, stacklevel=2)

junifer/utils/tests/test_logging.py

@@ -145,8 +145,16 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Warn3 message" in line for line in lines)
         assert any("Error3 message" in line for line in lines)
 
+    # This should raise a warning (test that it was raised)
     with pytest.warns(RuntimeWarning, match=r"Warn raised"):
         warn_with_log("Warn raised")
+
+    # This should log the warning (workaround for pytest messing with logging)
+    from junifer.utils.logging import capture_warnings
+
+    capture_warnings()
+
+    warn_with_log("Warn raised 2")
     with pytest.raises(ValueError, match=r"Error raised"):
         raise_error("Error raised")
     with open(tmp_path / "test4.log") as f:

{junifer-0.0.5.dev219.dist-info → junifer-0.0.5.dev242.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev219
+Version: 0.0.5.dev242
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.5.dev219.dist-info → junifer-0.0.5.dev242.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=-T9XmiCCL0j3YLx-0Pph15sPfL5FlcBDscajjJ-V4sU,604
-junifer/_version.py,sha256=hiqR-OJM-QzJpyrvyRQTuWbgsunJYguuZMuX2R3hfCc,428
+junifer/_version.py,sha256=5ar8KTPD2riEkS9RKe7tYuw4gZesZ5Gonw6vdJ43Z_8,428
 junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
 junifer/api/__init__.py,sha256=lwyIF0hPc7fICuSoddJfay0LPqlTRxHJ_xbtizgFYZA,312
 junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
@@ -90,14 +90,14 @@ junifer/data/tests/test_data_utils.py,sha256=_DaiC8K79gs9HFHxr-udNeE2YTM6JA0-1i-
 junifer/data/tests/test_masks.py,sha256=pL42xTzrvy0qLCqpG5p5CdCCqjJ9n5nz7BCUofydfag,15723
 junifer/data/tests/test_parcellations.py,sha256=ZEU1VHIK0AyxpclcJhG_0rQU0phaBU_dHP7Erfi3mN8,38222
 junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
-junifer/datagrabber/__init__.py,sha256=uR31UhuNwNZ0i9m3oo8RZtHUyMbnG2sd1i9aLa6aG_o,967
-junifer/datagrabber/base.py,sha256=qVEeWtnnl95owug9gBCmhfG6km3402o0k5VH4QsPt8A,6335
+junifer/datagrabber/__init__.py,sha256=kYvlrRS6f64fwntAuyk_fL2c_vyw9m9mZpMWpm_cxEM,1058
+junifer/datagrabber/base.py,sha256=fFPIt6p3SdZ6vzReGQxK2qJnQzh8HTwBe87A2WYArVI,6538
 junifer/datagrabber/datalad_base.py,sha256=6B7XMIMFlBw3uixDnfoaH4gBU9EzJIO5gwmc0iHniRo,11044
 junifer/datagrabber/dmcc13_benchmark.py,sha256=se9F6QVw9WX22MNld33OQv_BtdW-yPvXXu6kYykxLNw,12225
-junifer/datagrabber/multiple.py,sha256=p_rq99kKtHNr1sAl0GJ4RJ5Ss-uUKMsJVHrdWGi1XB8,4959
-junifer/datagrabber/pattern.py,sha256=pGiYlczva76JRxtsCY7Xuok5wPCGcXWHNZMCXNGUJ_k,16013
+junifer/datagrabber/multiple.py,sha256=IjBcFN-KegIad9bwopsfAQ9b_WRRUHmCbKRX2gmus0Q,6487
+junifer/datagrabber/pattern.py,sha256=iSubnHOJjYck1Zhk_JAYRZjRPKYmfoO81tG1zowd3B4,17039
 junifer/datagrabber/pattern_datalad.py,sha256=QPWXIToYHDU4mvm9lz_hy8BjdqqoCXiGiJKCcATrT-w,4568
-junifer/datagrabber/utils.py,sha256=XoS2B8Gg0YTR7HaJR9GpPFr0drZOn8p1HO7al735mO0,9975
+junifer/datagrabber/pattern_validation_mixin.py,sha256=SSnTdUA7elaTh9HF7syvW-lTBS1VgdSkyOJiw5mT2Vw,13469
 junifer/datagrabber/aomic/__init__.py,sha256=lRezU9dyIEoL4tJYglMX01P-F5_hrnZrJxuaQxF_z2w,358
 junifer/datagrabber/aomic/id1000.py,sha256=wJpZiSZrsfil5w-506bOtKMWm3FllnbB8-cMvGDPiLM,7219
 junifer/datagrabber/aomic/piop1.py,sha256=AcjIueSUmhepuIfmbMEpocV7grUbJ2xKXG94O1dq2FA,9637
@@ -107,15 +107,15 @@ junifer/datagrabber/aomic/tests/test_piop1.py,sha256=J9ei2HLzdJPciysWjRo33cbZsqP
 junifer/datagrabber/aomic/tests/test_piop2.py,sha256=Bk23KvRse4clMTuC88YntSfJnJyTunafC79Y1OJwJI0,4166
 junifer/datagrabber/hcp1200/__init__.py,sha256=yKINewhzkPRcqVpBd6DG02jrs3qLsUbUsi93YJZOUIk,231
 junifer/datagrabber/hcp1200/datalad_hcp1200.py,sha256=hngQYLv4b8tC9Ep2X5A5R_L2sFM3ZJ8dmWTr_OlRLAA,2463
-junifer/datagrabber/hcp1200/hcp1200.py,sha256=xgIU-WZXrEvI7we2RX3sqKowKz1NxtdjtHM6g5RcPzQ,6115
+junifer/datagrabber/hcp1200/hcp1200.py,sha256=AfVPd44CdyMcrUTOfps2PSpTQrXde68QeZaLGkXUTn4,6116
 junifer/datagrabber/hcp1200/tests/test_hcp1200.py,sha256=KJ-Jq01l0a6TaboG898qjBdPTHG1E3PZtHCjJ7n-1X0,10765
 junifer/datagrabber/tests/test_base.py,sha256=fZdVhNhvfht9lpTHrAUf5E6mAfNNUP7OTQ5KLaBQ1gI,3506
-junifer/datagrabber/tests/test_datagrabber_utils.py,sha256=x1nqFiHI9xHBQFwXji0DPUG8crVoEzw6zmi3pKdhJQk,6513
 junifer/datagrabber/tests/test_datalad_base.py,sha256=71erxpAECuy8iLtkmq_SRqfP4sKQf4uEb3O8CThBHT0,16285
 junifer/datagrabber/tests/test_dmcc13_benchmark.py,sha256=DcqkDXXBoabHFVbxekGR2NZyGeugGlxpOwXIwy38Ofg,9109
-junifer/datagrabber/tests/test_multiple.py,sha256=Mx3xfDrQiWG2W5MW24P5L2XiSeALpJ2-jFlzWkKtu9w,5659
+junifer/datagrabber/tests/test_multiple.py,sha256=gdekgSHyRx_EtcMNQpJsGEyo56xSxH5-XSQRQ5P2zt4,8288
 junifer/datagrabber/tests/test_pattern.py,sha256=H55jYRPfT3rMsoIQOAnWJgw3nGrkU7m2xFa3-ed6NQE,9527
 junifer/datagrabber/tests/test_pattern_datalad.py,sha256=5lA4hkYNaIAVy3GjcVqBXj1d-3qd8-14Pv0z6QGqgtI,6483
+junifer/datagrabber/tests/test_pattern_validation_mixin.py,sha256=4diiRduuqMxOZpfWBoe-O9AhDPYb7DLQU8-JaWAfTrg,7494
 junifer/datareader/__init__.py,sha256=9TXyHpy5o-yfs-q8QHGfjUCcWdORp7qv_jrokAOPBP8,293
 junifer/datareader/default.py,sha256=peNQTYHx9x3ZqGjm2Uj5yCLlsJ6X86r0f2XiUgnpw1M,6745
 junifer/datareader/tests/test_default_reader.py,sha256=9dPZSkba1YQjFsA0XwdUbx5sq8DVIEZoy_WfMAcvRus,5220
@@ -259,17 +259,17 @@ junifer/testing/tests/test_spmauditory_datagrabber.py,sha256=1G1emk-Ze59HiNLaYsy
 junifer/testing/tests/test_testing_registry.py,sha256=oerticBaPRaRZm3yANzInLac0Mqph3Y0aZPQFayu7xA,827
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
 junifer/tests/test_stats.py,sha256=3vPMgYYpWxk8ECDFOMm3-dFBlh4XxjL83SwRBSBAHok,4155
-junifer/utils/__init__.py,sha256=V1-1FKPhACiS2nUr8TTgQFq7irEnp2an5YdIU3Zz7RY,439
+junifer/utils/__init__.py,sha256=F_I7WXtZMrBGGNLN09LvzBRwWKopL2k1z0UgCZvpwj0,471
 junifer/utils/fs.py,sha256=M3CKBLh4gPS6s9giyopgb1hHMXzLb6k3cung2wHVBjs,492
-junifer/utils/helpers.py,sha256=uEdZ3wCgvbWwp1v0DdxIbaV8qORmNSoJIaWmb9haKh0,1366
-junifer/utils/logging.py,sha256=T9gzk7l1O-dmRiZJHggVDkQGzup_P2_FV3xsaoq0BmI,9369
+junifer/utils/helpers.py,sha256=D17zdq1y92fOc-5nwnhaXfgbk8o5yHocLSct9E05YUk,1996
+junifer/utils/logging.py,sha256=ardaiJkDfZMYvak5UIL5Etxg5Ii7inmVQSBdFLdgtb8,9781
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
-junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.5.dev219.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.5.dev219.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.5.dev219.dist-info/METADATA,sha256=uQSJvuIHH7tXjaAc5fDkW0tZXQ9uGg_cWx_naZkuDf0,8280
-junifer-0.0.5.dev219.dist-info/WHEEL,sha256=-oYQCr74JF3a37z2nRlQays_SX2MqOANoqVjBBAP2yE,91
-junifer-0.0.5.dev219.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.5.dev219.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.5.dev219.dist-info/RECORD,,
+junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
+junifer-0.0.5.dev242.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.5.dev242.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.5.dev242.dist-info/METADATA,sha256=xrjlsQCL9WQaZXNlEaFdd13Wn30Ff1NogZdJDtgMpGM,8280
+junifer-0.0.5.dev242.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+junifer-0.0.5.dev242.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.5.dev242.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.5.dev242.dist-info/RECORD,,

{junifer-0.0.5.dev219.dist-info → junifer-0.0.5.dev242.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.0.3)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

junifer/datagrabber/utils.py

@@ -1,317 +0,0 @@
-"""Provide utility functions for the datagrabber sub-package."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from typing import Dict, List
-
-from ..utils import logger, raise_error
-
-
-__all__ = ["validate_types", "validate_replacements", "validate_patterns"]
-
-
-# Define schema for pattern-based datagrabber's patterns
-PATTERNS_SCHEMA = {
-    "T1w": {
-        "mandatory": ["pattern", "space"],
-        "optional": {
-            "mask": {"mandatory": ["pattern", "space"], "optional": []},
-        },
-    },
-    "T2w": {
-        "mandatory": ["pattern", "space"],
-        "optional": {
-            "mask": {"mandatory": ["pattern", "space"], "optional": []},
-        },
-    },
-    "BOLD": {
-        "mandatory": ["pattern", "space"],
-        "optional": {
-            "mask": {"mandatory": ["pattern", "space"], "optional": []},
-            "confounds": {
-                "mandatory": ["pattern", "format"],
-                "optional": ["mappings"],
-            },
-        },
-    },
-    "Warp": {
-        "mandatory": ["pattern", "src", "dst"],
-        "optional": {},
-    },
-    "VBM_GM": {
-        "mandatory": ["pattern", "space"],
-        "optional": {},
-    },
-    "VBM_WM": {
-        "mandatory": ["pattern", "space"],
-        "optional": {},
-    },
-    "VBM_CSF": {
-        "mandatory": ["pattern", "space"],
-        "optional": {},
-    },
-    "DWI": {
-        "mandatory": ["pattern"],
-        "optional": {},
-    },
-    "FreeSurfer": {
-        "mandatory": ["pattern"],
-        "optional": {
-            "aseg": {"mandatory": ["pattern"], "optional": []},
-            "norm": {"mandatory": ["pattern"], "optional": []},
-            "lh_white": {"mandatory": ["pattern"], "optional": []},
-            "rh_white": {"mandatory": ["pattern"], "optional": []},
-            "lh_pial": {"mandatory": ["pattern"], "optional": []},
-            "rh_pial": {"mandatory": ["pattern"], "optional": []},
-        },
-    },
-}
-
-
-def validate_types(types: List[str]) -> None:
-    """Validate the types.
-
-    Parameters
-    ----------
-    types : list of str
-        The object to validate.
-
-    Raises
-    ------
-    TypeError
-        If ``types`` is not a list or if the values are not string.
-
-    """
-    if not isinstance(types, list):
-        raise_error(msg="`types` must be a list", klass=TypeError)
-    if any(not isinstance(x, str) for x in types):
-        raise_error(msg="`types` must be a list of strings", klass=TypeError)
-
-
-def validate_replacements(
-    replacements: List[str], patterns: Dict[str, Dict[str, str]]
-) -> None:
-    """Validate the replacements.
-
-    Parameters
-    ----------
-    replacements : list of str
-        The object to validate.
-    patterns : dict
-        The patterns to validate against.
-
-    Raises
-    ------
-    TypeError
-        If ``replacements`` is not a list or if the values are not string.
-    ValueError
-        If a value in ``replacements`` is not part of a data type pattern or
-        if no data type patterns contain all values in ``replacements``.
-
-    """
-    if not isinstance(replacements, list):
-        raise_error(msg="`replacements` must be a list.", klass=TypeError)
-
-    if any(not isinstance(x, str) for x in replacements):
-        raise_error(
-            msg="`replacements` must be a list of strings.", klass=TypeError
-        )
-
-    for x in replacements:
-        if all(
-            x not in y
-            for y in [
-                data_type_val["pattern"] for data_type_val in patterns.values()
-            ]
-        ):
-            raise_error(msg=f"Replacement: {x} is not part of any pattern.")
-
-    # Check that at least one pattern has all the replacements
-    at_least_one = False
-    for data_type_val in patterns.values():
-        if all(x in data_type_val["pattern"] for x in replacements):
-            at_least_one = True
-    if at_least_one is False:
-        raise_error(msg="At least one pattern must contain all replacements.")
-
-
-def _validate_mandatory_keys(
-    keys: List[str], schema: List[str], data_type: str
-) -> None:
-    """Validate mandatory keys.
-
-    Parameters
-    ----------
-    keys : list of str
-        The keys to validate.
-    schema : list of str
-        The schema to validate against.
-    data_type : str
-        The data type being validated.
-
-    Raises
-    ------
-    KeyError
-        If any mandatory key is missing for a data type.
-
-    """
-    for key in schema:
-        if key not in keys:
-            raise_error(
-                msg=f"Mandatory key: `{key}` missing for {data_type}",
-                klass=KeyError,
-            )
-        else:
-            logger.debug(f"Mandatory key: `{key}` found for {data_type}")
-
-
-def _identify_stray_keys(
-    keys: List[str], schema: List[str], data_type: str
-) -> None:
-    """Identify stray keys.
-
-    Parameters
-    ----------
-    keys : list of str
-        The keys to check.
-    schema : list of str
-        The schema to check against.
-    data_type : str
-        The data type being checked.
-
-    Raises
-    ------
-    RuntimeError
-        If an unknown key is found for a data type.
-
-    """
-    for key in keys:
-        if key not in schema:
-            raise_error(
-                msg=(
-                    f"Key: {key} not accepted for {data_type} "
-                    "pattern, remove it to proceed"
-                ),
-                klass=RuntimeError,
-            )
-
-
-def validate_patterns(
-    types: List[str], patterns: Dict[str, Dict[str, str]]
-) -> None:
-    """Validate the patterns.
-
-    Parameters
-    ----------
-    types : list of str
-        The types list.
-    patterns : dict
-        The object to validate.
-
-    Raises
-    ------
-    TypeError
-        If ``patterns`` is not a dictionary.
-    ValueError
-        If length of ``types`` and ``patterns`` are different or
-        if ``patterns`` is missing entries from ``types`` or
-        if unknown data type is found in ``patterns`` or
-        if data type pattern key contains '*' as value.
-
-    """
-    # Validate the types
-    validate_types(types)
-    if not isinstance(patterns, dict):
-        raise_error(msg="`patterns` must be a dict.", klass=TypeError)
-    # Unequal length of objects
-    if len(types) > len(patterns):
-        raise_error(
-            msg="Length of `types` more than that of `patterns`.",
-            klass=ValueError,
-        )
-    # Missing type in patterns
-    if any(x not in patterns for x in types):
-        raise_error(
-            msg="`patterns` must contain all `types`", klass=ValueError
-        )
-    # Check against schema
-    for data_type_key, data_type_val in patterns.items():
-        # Check if valid data type is provided
-        if data_type_key not in PATTERNS_SCHEMA:
-            raise_error(
-                f"Unknown data type: {data_type_key}, "
-                f"should be one of: {list(PATTERNS_SCHEMA.keys())}"
-            )
-        # Check mandatory keys for data type
-        _validate_mandatory_keys(
-            keys=list(data_type_val),
-            schema=PATTERNS_SCHEMA[data_type_key]["mandatory"],
-            data_type=data_type_key,
-        )
-        # Check optional keys for data type
-        for optional_key, optional_val in PATTERNS_SCHEMA[data_type_key][
-            "optional"
-        ].items():
-            if optional_key not in data_type_val:
-                logger.debug(
-                    f"Optional key: `{optional_key}` missing for "
-                    f"{data_type_key}"
-                )
-            else:
-                logger.debug(
-                    f"Optional key: `{optional_key}` found for "
-                    f"{data_type_key}"
-                )
-                # Set nested type name for easier access
-                nested_data_type = f"{data_type_key}.{optional_key}"
-                nested_mandatory_keys_schema = PATTERNS_SCHEMA[data_type_key][
-                    "optional"
-                ][optional_key]["mandatory"]
-                nested_optional_keys_schema = PATTERNS_SCHEMA[data_type_key][
-                    "optional"
-                ][optional_key]["optional"]
-                # Check mandatory keys for nested type
-                _validate_mandatory_keys(
-                    keys=list(optional_val["mandatory"]),
-                    schema=nested_mandatory_keys_schema,
-                    data_type=nested_data_type,
-                )
-                # Check optional keys for nested type
-                for nested_optional_key in nested_optional_keys_schema:
-                    if nested_optional_key not in optional_val["optional"]:
-                        logger.debug(
-                            f"Optional key: `{nested_optional_key}` missing "
-                            f"for {nested_data_type}"
-                        )
-                    else:
-                        logger.debug(
-                            f"Optional key: `{nested_optional_key}` found for "
-                            f"{nested_data_type}"
-                        )
-                # Check stray key for nested data type
-                _identify_stray_keys(
-                    keys=optional_val["mandatory"] + optional_val["optional"],
-                    schema=nested_mandatory_keys_schema
-                    + nested_optional_keys_schema,
-                    data_type=nested_data_type,
-                )
-        # Check stray key for data type
-        _identify_stray_keys(
-            keys=list(data_type_val.keys()),
-            schema=(
-                PATTERNS_SCHEMA[data_type_key]["mandatory"]
-                + list(PATTERNS_SCHEMA[data_type_key]["optional"].keys())
-            ),
-            data_type=data_type_key,
-        )
-        # Wildcard check in patterns
-        if "}*" in data_type_val["pattern"]:
-            raise_error(
-                msg=(
-                    f"`{data_type_key}.pattern` must not contain `*` "
-                    "following a replacement"
-                ),
-                klass=ValueError,
-            )