From 35f652812aac593944010145dc4dfb5c4caaa7da Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Fri, 10 Feb 2023 20:32:24 -0600
Subject: [PATCH 01/15] Add function to get all dataset's meta-data keys

---
 bids/layout/layout.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 3462570fd..d29e8add1 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -659,6 +659,17 @@ def get_entities(self, scope: str = None, sort: bool = False, long_form: bool =
         """
         return query_entities(self.dataset, scope, sort, long_form=long_form)
 
+    def _get_metadata_keys(self):
+        """Return a list of all metadata keys found in the dataset."""
+        
+        all_metadata_objects = self.dataset.select(self.schema.MetadataArtifact).objects()
+
+        keys = set()
+        for obj in all_metadata_objects:
+            keys.update(obj['contents'].keys())
+
+        return keys
+
     def get_dataset_description(self, scope='self', all_=False) -> Union[List[Dict], Dict]:
         """Return contents of dataset_description.json.
 

From 4565f9c08440bd96ff4ece68041196a3484193df Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Fri, 10 Feb 2023 20:36:43 -0600
Subject: [PATCH 02/15] Add metadata option to get_entities

---
 bids/layout/layout.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index d29e8add1..44b63a1e6 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -631,7 +631,7 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
     def entities(self):
         return self.get_entities()
 
-    def get_entities(self, scope: str = None, sort: bool = False, long_form: bool = True) -> dict:
+    def get_entities(self, scope: str = None, sort: bool = False, long_form: bool = True, metadata: bool = False) -> dict:
         """Returns a unique set of entities found within the dataset as a dict.
         Each key of the resulting dict contains a list of values (with at least one element).
 
@@ -657,7 +657,14 @@ def get_entities(self, scope: str = None, sort: bool = False, long_form: bool =
         dict
             a unique set of entities found within the dataset as a dict
         """
-        return query_entities(self.dataset, scope, sort, long_form=long_form)
+
+        entities = query_entities(self.dataset, scope, sort, long_form=long_form)
+
+        metadata = {}
+        if metadata is True:
+            metadata = self._get_metadata_keys()
+            
+        return {**entities, **metadata}
 
     def _get_metadata_keys(self):
         """Return a list of all metadata keys found in the dataset."""

From c1c24a4da930d271f4d3666564c7a01334538803 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 13 Feb 2023 15:23:39 -0600
Subject: [PATCH 03/15] Add metadata to get_entities, and __repr__

---
 bids/layout/layout.py | 43 +++++++++++++++++++++++++++----------------
 1 file changed, 27 insertions(+), 16 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 44b63a1e6..10c64d4a8 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -1,6 +1,7 @@
 import difflib
 import enum
 import os.path
+import typing
 from collections import defaultdict
 from functools import partial
 from pathlib import Path
@@ -10,6 +11,7 @@
 from .models import BIDSFile
 from .utils import BIDSMetadata
 from .writing import build_path, write_to_file
+from ..external import inflect
 from ..exceptions import (
     BIDSEntityError,
     BIDSValidationError,
@@ -341,11 +343,15 @@ def __getattr__(self, key):
             pass
         if key.startswith('get_'):
             orig_ent_name = key.replace('get_', '')
-            ent_name = self.schema.fuzzy_match_entity(orig_ent_name).name
-            if ent_name not in self.get_entities():
-                raise BIDSEntityError(
-                    "'get_{}' can't be called because '{}' isn't a "
-                    "recognized entity name.".format(orig_ent_name, orig_ent_name))
+            entities = self.get_entities(metadata=True)
+            if ent_name not in entities:
+                sing = inflect.engine().singular_noun(ent_name)
+                if sing in entities:
+                    ent_name = sing
+                else:
+                    raise BIDSEntityError(
+                        "'get_{}' can't be called because '{}' isn't a "
+                        "recognized entity name.".format(orig_ent_name, orig_ent_name))
             return partial(self.get, return_type='id', target=ent_name)
         # Spit out default message if we get this far
         raise AttributeError("%s object has no attribute named %r" %
@@ -631,7 +637,8 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
     def entities(self):
         return self.get_entities()
 
-    def get_entities(self, scope: str = None, sort: bool = False, long_form: bool = True, metadata: bool = False) -> dict:
+    def get_entities(self, scope: str = None, sort: bool = False, 
+        long_form: bool = True, metadata: bool = True) -> dict:
         """Returns a unique set of entities found within the dataset as a dict.
         Each key of the resulting dict contains a list of values (with at least one element).
 
@@ -658,24 +665,28 @@ def get_entities(self, scope: str = None, sort: bool = False, long_form: bool =
             a unique set of entities found within the dataset as a dict
         """
 
-        entities = query_entities(self.dataset, scope, sort, long_form=long_form)
+        entities = query_entities(self.dataset, scope, long_form=long_form)
 
-        metadata = {}
         if metadata is True:
-            metadata = self._get_metadata_keys()
-            
-        return {**entities, **metadata}
+            results = {**entities, **self._get_unique_metadata()}
+
+        if sort:
+            results = {k: sorted(v) for k, v in sorted(results.items())}
+
+        return results
 
-    def _get_metadata_keys(self):
-        """Return a list of all metadata keys found in the dataset."""
+    def _get_unique_metadata(self):
+        """Return a list of all unique metadata key and values found in the dataset."""
         
         all_metadata_objects = self.dataset.select(self.schema.MetadataArtifact).objects()
 
-        keys = set()
+        metadata = defaultdict(set)
         for obj in all_metadata_objects:
-            keys.update(obj['contents'].keys())
+            for k, v in obj['contents'].items():
+                if isinstance(v, typing.Hashable):
+                    metadata[k].add(v)
 
-        return keys
+        return metadata
 
     def get_dataset_description(self, scope='self', all_=False) -> Union[List[Dict], Dict]:
         """Return contents of dataset_description.json.

From 57205e3b98271b9e450422d98febb98626d09944 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 11:54:40 -0600
Subject: [PATCH 04/15] Implement invalid filters rules

---
 bids/layout/layout.py | 30 ++++++++++++++++++++++++------
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 10c64d4a8..0dd3d04dc 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -342,7 +342,7 @@ def __getattr__(self, key):
         except KeyError:
             pass
         if key.startswith('get_'):
-            orig_ent_name = key.replace('get_', '')
+            ent_name = key.replace('get_', '')
             entities = self.get_entities(metadata=True)
             if ent_name not in entities:
                 sing = inflect.engine().singular_noun(ent_name)
@@ -351,7 +351,7 @@ def __getattr__(self, key):
                 else:
                     raise BIDSEntityError(
                         "'get_{}' can't be called because '{}' isn't a "
-                        "recognized entity name.".format(orig_ent_name, orig_ent_name))
+                        "recognized entity name.".format(ent_name, ent_name))
             return partial(self.get, return_type='id', target=ent_name)
         # Spit out default message if we get this far
         raise AttributeError("%s object has no attribute named %r" %
@@ -550,8 +550,8 @@ def count_matches(f):
 
     def get(self, return_type: str = 'object', target: str = None, scope: str = None,
             extension: Union[str, List[str]] = None, suffix: Union[str, List[str]] = None,
-            regex_search=None,
-            **entities) -> Union[List[str], List[object]]:
+            regex_search=None, invalid_filters: str = 'error', 
+            **filters) -> Union[List[str], List[object]]:
         """Retrieve files and/or metadata from the current Layout.
 
         Parameters
@@ -606,12 +606,30 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
         if regex_search is None:
             regex_search = self._regex_search
 
+        self_entities = self.get_entities()
+
+        if invalid_filters != 'allow':
+            bad_filters = set(filters.keys()) - set(self_entities.keys())
+            if bad_filters:
+                if invalid_filters == 'drop':
+                    for bad_filt in bad_filters:
+                        filters.pop(bad_filt)
+                elif invalid_filters == 'error':
+                    first_bad = list(bad_filters)[0]
+                    msg = "'{}' is not a recognized entity. ".format(first_bad)
+                    ents = list(self_entities.keys())
+                    suggestions = difflib.get_close_matches(first_bad, ents)
+                    if suggestions:
+                        msg += "Did you mean {}? ".format(suggestions)
+                    raise ValueError(msg + "If you're sure you want to impose "
+                                        "this constraint, set "
+                                        "invalid_filters='allow'.")
+
         # Provide some suggestions if target is specified and invalid.
         if return_type in ("dir", "id"):
             if target is None:
                 raise TargetError(f'If return_type is "id" or "dir", a valid target '
                                   'entity must also be specified.')
-            self_entities = self.get_entities()
             if target not in self_entities:
                 potential = list(self_entities.keys())
                 suggestions = difflib.get_close_matches(target, potential)
@@ -622,7 +640,7 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
                 raise TargetError(f"Unknown target '{target}'. {message}")  
 
         folder = self.dataset
-        result = query(folder, return_type, target, scope, extension, suffix, regex_search, **entities)
+        result = query(folder, return_type, target, scope, extension, suffix, regex_search, **filters)
         if return_type == 'file':
             result = natural_sort(result)
         if return_type == "object":

From 82a4c44fea2b3e24d8026fcc48e921b75f43a041 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 15:18:30 -0600
Subject: [PATCH 05/15] Add relative paths to BIDSFile

---
 bids/layout/layout.py            | 12 ++++++------
 bids/layout/models.py            | 10 +++++++---
 bids/layout/tests/test_layout.py |  2 +-
 3 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 0dd3d04dc..f6a4f6fc4 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -298,6 +298,7 @@ def __init__(
         self.validationReport = None
 
         self._regex_search = regex_search
+        self._absolute_paths = absolute_paths
 
         if validate:
             self.validationReport = self.validate()
@@ -320,11 +321,6 @@ def __init__(
                 "indexer no longer has any effect and will be removed",
                 DeprecationWarning
             )
-        if absolute_paths is not None:
-            warnings.warn(
-                "absolute_paths no longer has any effect and will be removed",
-                DeprecationWarning
-            )
         if kwargs:
             warnings.warn(f"Unknown keyword arguments: {kwargs}")
         if config is not None:
@@ -640,13 +636,17 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
                 raise TargetError(f"Unknown target '{target}'. {message}")  
 
         folder = self.dataset
+
+        if not self._absolute_paths:
+            filters['absolute_path'] = False
+
         result = query(folder, return_type, target, scope, extension, suffix, regex_search, **filters)
         if return_type == 'file':
             result = natural_sort(result)
         if return_type == "object":
             if result:
                 result = natural_sort(
-                    [BIDSFile(res) for res in result],
+                    [BIDSFile(res, absolute_path=self._absolute_paths) for res in result],
                     "path"
                 )
         return result
diff --git a/bids/layout/models.py b/bids/layout/models.py
index bfd3067ba..48f3fc82f 100644
--- a/bids/layout/models.py
+++ b/bids/layout/models.py
@@ -37,10 +37,11 @@ def from_filename(cls, filename):
                 break
         return cls(path)
 
-    def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None):
+    def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None, absolute_paths=True):
         self._path = None
         self._artifact = None
         self._schema = schema
+        self._absolute_path = absolute_paths
         if isinstance(file_ref, (str, os.PathLike)):
             self._path = Path(file_ref)
         elif isinstance(file_ref, Artifact):
@@ -51,7 +52,10 @@ def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None):
     def path(self):
         """ Convenience property for accessing path as a string."""
         try:
-            return self._artifact.get_absolute_path()
+            if self._absolute_path:
+                return self._artifact.get_absolute_path()
+            else:
+                return self._artifact.get_relative_path()
         except AttributeError:
             return str(self._path)
 
@@ -80,7 +84,7 @@ def __fspath__(self):
     @property
     def relpath(self):
         """ No longer have access to the BIDSLayout root directory """
-        raise NotImplementedError
+        raise self._artifact.get_relative_path()
 
     def get_associations(self, kind=None, include_parents=False):
         """Get associated files, optionally limiting by association kind.
diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index 5f094cf1f..4708bb064 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -360,7 +360,7 @@ def test_query_derivatives(layout_ds005_derivs):
                                      extension='.tsv')
     result = [f.path for f in result]
     assert len(result) == 49
-    assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result
+    assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result # Fails due to absolute path
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      scope='raw', extension='.tsv')
     assert len(result) == 48

From 9faa52c3d5195d201cd1bc545f2e8760487a3774 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 15:24:00 -0600
Subject: [PATCH 06/15] Fix absolute paths

---
 bids/layout/layout.py | 5 ++---
 bids/layout/models.py | 6 ++++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index f6a4f6fc4..7f9a8635c 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -637,10 +637,9 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
 
         folder = self.dataset
 
-        if not self._absolute_paths:
-            filters['absolute_path'] = False
+        result = query(folder, return_type, target, scope, extension, suffix, regex_search, 
+            absolute_paths=self._absolute_paths, **filters)
 
-        result = query(folder, return_type, target, scope, extension, suffix, regex_search, **filters)
         if return_type == 'file':
             result = natural_sort(result)
         if return_type == "object":
diff --git a/bids/layout/models.py b/bids/layout/models.py
index 48f3fc82f..934d793f2 100644
--- a/bids/layout/models.py
+++ b/bids/layout/models.py
@@ -37,11 +37,13 @@ def from_filename(cls, filename):
                 break
         return cls(path)
 
-    def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None, absolute_paths=True):
+    def __init__(self, file_ref: Union[str, os.PathLike, Artifact], schema = None, 
+            absolute_path=True):
+
         self._path = None
         self._artifact = None
         self._schema = schema
-        self._absolute_path = absolute_paths
+        self._absolute_path = absolute_path
         if isinstance(file_ref, (str, os.PathLike)):
             self._path = Path(file_ref)
         elif isinstance(file_ref, Artifact):

From 2c9b5dc0709fe1ae0ff218c76285c707982ca109 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 15:55:09 -0600
Subject: [PATCH 07/15] Add xfails

---
 bids/layout/layout.py            |  2 +-
 bids/layout/models.py            |  2 +-
 bids/layout/tests/test_layout.py | 20 +++++++++++++-------
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 7f9a8635c..653bdd541 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -267,7 +267,7 @@ def __init__(
         database_path: Optional[str]=None,
         reset_database: Optional[bool]=None,
         indexer: Optional[Callable]=None,
-        absolute_paths: Optional[bool]=None,
+        absolute_paths: Optional[bool]=True,
         ignore: Optional[List[str]]=None,
         force_index: Optional[List[str]]=None,
         **kwargs,
diff --git a/bids/layout/models.py b/bids/layout/models.py
index 934d793f2..10e215571 100644
--- a/bids/layout/models.py
+++ b/bids/layout/models.py
@@ -86,7 +86,7 @@ def __fspath__(self):
     @property
     def relpath(self):
         """ No longer have access to the BIDSLayout root directory """
-        raise self._artifact.get_relative_path()
+        return self._artifact.get_relative_path()
 
     def get_associations(self, kind=None, include_parents=False):
         """Get associated files, optionally limiting by association kind.
diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index 4708bb064..b74b56097 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -108,6 +108,7 @@ def test_get_file(layout_ds005_derivs):
 
 
 class TestDerivativeAsRoot:
+    @pytest.mark.xfail(reason="derivative as root not yet supported")
     def test_dataset_without_datasettype_parsed_as_raw(self):
         dataset_path = Path("ds005_derivs", "format_errs", "no_dataset_type")
         unvalidated = BIDSLayout(
@@ -121,17 +122,20 @@ def test_dataset_without_datasettype_parsed_as_raw(self):
         validated = BIDSLayout(Path(get_test_data_path()) / dataset_path)
         assert len(validated.get()) == 1
 
+    @pytest.mark.xfail(reason="derivative as root not yet supported")
     def test_dataset_missing_generatedby_fails_validation(self):
         dataset_path = Path("ds005_derivs", "format_errs", "no_pipeline_description")
         with pytest.raises(BIDSDerivativesValidationError):
             BIDSLayout(Path(get_test_data_path()) / dataset_path)
 
+    @pytest.mark.xfail(reason="derivative as root not yet supported")
     def test_correctly_formatted_derivative_loads_as_derivative(self):
         dataset_path = Path("ds005_derivs", "dummy")
         layout = BIDSLayout(Path(get_test_data_path()) / dataset_path)
         assert len(layout.get()) == 4
         assert len(layout.get(desc="preproc")) == 3
 
+    @pytest.mark.xfail(reason="derivative as root not yet supported")
     @pytest.mark.parametrize(
         "dataset_path",
         [
@@ -240,7 +244,7 @@ def test_get_with_bad_target(layout_7t_trt):
     msg = str(exc.value)
     assert 'subject' in msg and 'reconstruction' not in msg
 
-
+@pytest.mark.xfail(reason="datatype not yet implemented")
 def test_get_bvals_bvecs(layout_ds005):
     dwifile = layout_ds005.get(subject="01", datatype="dwi")[0]
     result = layout_ds005.get_bval(dwifile.path)
@@ -325,7 +329,7 @@ def test_get_return_sorted(layout_7t_trt):
     paths = layout_7t_trt.get(target='subject', return_type='file')
     assert natural_sort(paths) == paths
 
-
+@pytest.mark.xfail(reason="selecting adding of derivatives is not suported")
 def test_layout_with_derivs(layout_ds005_derivs):
     assert layout_ds005_derivs.root == join(get_test_data_path(), 'ds005')
     assert isinstance(layout_ds005_derivs.files, dict)
@@ -338,7 +342,7 @@ def test_layout_with_derivs(layout_ds005_derivs):
     entities = deriv.query_entities(long_form=True)
     assert 'subject' in entities
 
-
+@pytest.mark.xfail(reason="out of tree derivatives are not supported")
 def test_layout_with_multi_derivs(layout_ds005_multi_derivs):
     assert layout_ds005_multi_derivs.root == join(get_test_data_path(), 'ds005')
     assert isinstance(layout_ds005_multi_derivs.files, dict)
@@ -358,18 +362,18 @@ def test_layout_with_multi_derivs(layout_ds005_multi_derivs):
 def test_query_derivatives(layout_ds005_derivs):
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      extension='.tsv')
-    result = [f.path for f in result]
+    result = [f.relpath for f in result]
     assert len(result) == 49
     assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result # Fails due to absolute path
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      scope='raw', extension='.tsv')
     assert len(result) == 48
-    result = [f.path for f in result]
+    result = [f.relpath for f in result]
     assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' not in result
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      desc='extra', extension='.tsv')
     assert len(result) == 1
-    result = [f.path for f in result]
+    result = [f.relpath for f in result]
     assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result
 
 
@@ -396,6 +400,7 @@ def test_get_tr(layout_7t_trt):
 
 
 # XXX 0.14: Add dot to extension (difficult to parametrize with module-scoped fixture)
+@pytest.mark.xfail(reason="scope and config not implemented")
 def test_parse_file_entities_from_layout(layout_synthetic):
     layout = layout_synthetic
     filename = '/sub-03_ses-07_run-4_desc-bleargh_sekret.nii.gz'
@@ -429,7 +434,8 @@ def test_path_arguments():
     assert layout.get(scope='derivatives/events')
     assert not layout.get(scope='nonexistent')
 
-
+    
+@pytest.mark.xfail(reason="adding derivatives is not supported")
 def test_get_dataset_description(layout_ds005_derivs):
     dd = layout_ds005_derivs.get_dataset_description()
     assert isinstance(dd, dict)

From 0876d494ccb7d92ddc56728e34e6b81892c804bd Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 16:25:04 -0600
Subject: [PATCH 08/15] get_procs doesn't exist, because long-name is used

---
 bids/layout/tests/test_layout.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index b74b56097..2696c5d36 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -188,9 +188,9 @@ def test_get_metadata4(layout_ds005):
 
 def test_get_metadata_meg(layout_ds117):
     funcs = ['get_subjects', 'get_sessions', 'get_tasks', 'get_runs',
-             'get_acquisitions', 'get_procs']
+             'get_acquisitions', 'get_processing']
     assert all([hasattr(layout_ds117, f) for f in funcs])
-    procs = layout_ds117.get_procs()
+    procs = layout_ds117.get_processing()
     assert procs == ['sss']
     target = 'sub-02/ses-meg/meg/sub-02_ses-meg_task-facerecognition_run-01_meg.fif'
     target = target.split('/')
@@ -233,16 +233,17 @@ def test_get_metadata_error(layout_7t_trt):
     with pytest.raises(KeyError) as err:
         result['Missing']
 
-
+# Changed this test to not expect 'reconstruction' and 'proc'
+# which AFAIK ae not in 7t_trt
 def test_get_with_bad_target(layout_7t_trt):
     with pytest.raises(TargetError) as exc:
         layout_7t_trt.get(target='unicorn', return_type='id')
     msg = str(exc.value)
-    assert 'subject' in msg and 'reconstruction' in msg and 'proc' in msg
+    assert 'subject' in msg and 'session' in msg and 'acquisition' in msg
     with pytest.raises(TargetError) as exc:
         layout_7t_trt.get(target='subject')
     msg = str(exc.value)
-    assert 'subject' in msg and 'reconstruction' not in msg
+    assert 'subject' in msg and 'session' not in msg
 
 @pytest.mark.xfail(reason="datatype not yet implemented")
 def test_get_bvals_bvecs(layout_ds005):

From 307aa8cbb0c344d3d6de57d262c43fbb927ad264 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 16:34:09 -0600
Subject: [PATCH 09/15] Add comment about Enum

---
 bids/layout/tests/test_layout.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index 2696c5d36..8c597949a 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -241,7 +241,7 @@ def test_get_with_bad_target(layout_7t_trt):
     msg = str(exc.value)
     assert 'subject' in msg and 'session' in msg and 'acquisition' in msg
     with pytest.raises(TargetError) as exc:
-        layout_7t_trt.get(target='subject')
+        layout_7t_trt.get(target='sub')
     msg = str(exc.value)
     assert 'subject' in msg and 'session' not in msg
 
@@ -313,7 +313,11 @@ def test_get_val_enum_any(layout_7t_trt):
                                    suffix='bold', acquisition="*")
     assert len(bold_files) == 2
 
-
+# The following test should have argubly been a failure in pybids
+# but it was not. Session does not exist in dataset, yet since Query
+# Enum is set to optional the query passes even with 'ignore_filters'
+# set to False. 
+@pytest.mark.xfail(reason="Optional entity using Enum not supported.")
 def test_get_val_enum_any_optional(layout_7t_trt, layout_ds005):
     # layout with sessions
     bold_files = layout_7t_trt.get(suffix='bold', run=1, subject='01')

From 490ed73e3914207c1d457cdc94dcab1ae9d8b15b Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Mon, 27 Feb 2023 17:26:11 -0600
Subject: [PATCH 10/15] Mark all xfails

---
 bids/layout/layout.py            | 56 +++++++++++++++++++-------------
 bids/layout/tests/conftest.py    |  4 +--
 bids/layout/tests/test_layout.py | 46 ++++++++++++++------------
 3 files changed, 61 insertions(+), 45 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 653bdd541..b00bf4a7f 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -599,42 +599,52 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
         list of :obj:`bids.layout.BIDSFile` or str
             A list of BIDSFiles (default) or strings (see return_type).
         """
+        
+        # error check on users accidentally passing in filters
+        if isinstance(filters.get('filters'), dict):
+            raise RuntimeError('You passed in filters as a dictionary named '
+                               'filters; please pass the keys in as named '
+                               'keywords to the `get()` call. For example: '
+                               '`layout.get(**filters)`.')
+
         if regex_search is None:
             regex_search = self._regex_search
 
         self_entities = self.get_entities()
 
-        if invalid_filters != 'allow':
-            bad_filters = set(filters.keys()) - set(self_entities.keys())
-            if bad_filters:
-                if invalid_filters == 'drop':
-                    for bad_filt in bad_filters:
-                        filters.pop(bad_filt)
-                elif invalid_filters == 'error':
-                    first_bad = list(bad_filters)[0]
-                    msg = "'{}' is not a recognized entity. ".format(first_bad)
-                    ents = list(self_entities.keys())
-                    suggestions = difflib.get_close_matches(first_bad, ents)
-                    if suggestions:
-                        msg += "Did you mean {}? ".format(suggestions)
-                    raise ValueError(msg + "If you're sure you want to impose "
-                                        "this constraint, set "
-                                        "invalid_filters='allow'.")
+        def _suggest(target):
+            """Suggest a valid value for an entity."""
+            potential = list(self_entities.keys())
+            suggestions = difflib.get_close_matches(target, potential)
+            if suggestions:
+                message = "Did you mean one of: {}?".format(suggestions)
+            else:
+                message = "Valid options are: {}".format(potential)
+            return message
 
         # Provide some suggestions if target is specified and invalid.
         if return_type in ("dir", "id"):
             if target is None:
                 raise TargetError(f'If return_type is "id" or "dir", a valid target '
                                   'entity must also be specified.')
+            
             if target not in self_entities:
-                potential = list(self_entities.keys())
-                suggestions = difflib.get_close_matches(target, potential)
-                if suggestions:
-                    message = "Did you mean one of: {}?".format(suggestions)
-                else:
-                    message = "Valid targets are: {}".format(potential)
-                raise TargetError(f"Unknown target '{target}'. {message}")  
+                raise TargetError(f"Unknown target '{target}'. {_suggest(target)}")  
 
+        if invalid_filters != 'allow':
+            bad_filters = set(filters.keys()) - set(self_entities.keys())
+            if bad_filters:
+                if invalid_filters == 'drop':
+                    for bad_filt in bad_filters:
+                        filters.pop(bad_filt)
+                elif invalid_filters == 'error':
+                    first_bad = list(bad_filters)[0]
+                    message = _suggest(first_bad)
+                    raise ValueError(f"Unknown entity. {message}",
+                                     "If you're sure you want to impose ",
+                                     "this constraint, set ",
+                                     "invalid_filters='allow'.")
+                                     
         folder = self.dataset
 
         result = query(folder, return_type, target, scope, extension, suffix, regex_search, 
diff --git a/bids/layout/tests/conftest.py b/bids/layout/tests/conftest.py
index e03d33490..19abb42bb 100644
--- a/bids/layout/tests/conftest.py
+++ b/bids/layout/tests/conftest.py
@@ -18,11 +18,11 @@ def layout_7t_trt_relpath():
     data_dir = join(get_test_data_path(), '7t_trt')
     return BIDSLayout(data_dir, absolute_paths=False)
 
-
+# AD: Manually ignoring derivatives for now
 @pytest.fixture(scope="module")
 def layout_ds005():
     data_dir = join(get_test_data_path(), 'ds005')
-    return BIDSLayout(data_dir)
+    return BIDSLayout(data_dir, ignore=['derivatives', 'models'])
 
 
 @pytest.fixture(scope="module")
diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index 8c597949a..7ccc170ac 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -241,7 +241,7 @@ def test_get_with_bad_target(layout_7t_trt):
     msg = str(exc.value)
     assert 'subject' in msg and 'session' in msg and 'acquisition' in msg
     with pytest.raises(TargetError) as exc:
-        layout_7t_trt.get(target='sub')
+        layout_7t_trt.get(target='sub', return_type='id')
     msg = str(exc.value)
     assert 'subject' in msg and 'session' not in msg
 
@@ -363,13 +363,14 @@ def test_layout_with_multi_derivs(layout_ds005_multi_derivs):
     preproc = layout_ds005_multi_derivs.get(desc='preproc')
     assert len(preproc) == 3
 
-
+@pytest.mark.xfail(reason="Fails because derivatives are indexed by ancpbids as a normal file," 
+    "so path is relatively to main root, not to the derivative root")
 def test_query_derivatives(layout_ds005_derivs):
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      extension='.tsv')
     result = [f.relpath for f in result]
     assert len(result) == 49
-    assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result # Fails due to absolute path
+    assert 'sub-01_task-mixedgamblestask_run-01_desc-extra_events.tsv' in result
     result = layout_ds005_derivs.get(suffix='events', return_type='object',
                                      scope='raw', extension='.tsv')
     assert len(result) == 48
@@ -387,7 +388,9 @@ def test_derivative_getters():
     full_layout = BIDSLayout(synth_path)
     assert set(full_layout.get_spaces()) == {'MNI152NLin2009cAsym', 'T1w'}
 
-
+## The following fails because ancpids does not index meta-data correctly
+## when an entity is missing. E.g. when a run has no run entity, it should
+## match to a more general sidecar, but it does not.
 def test_get_tr(layout_7t_trt):
     # Bad subject, should fail
     with pytest.raises(NoMatchError) as exc:
@@ -451,7 +454,7 @@ def test_get_dataset_description(layout_ds005_derivs):
     names = {'Mixed-gambles task'}
     assert set([d['Name'] for d in dd]) == names
 
-
+@pytest.mark.xfail(reason="handling wrong dtypes not implemented")
 def test_get_with_wrong_dtypes(layout_7t_trt):
     ''' Test automatic dtype sanitization. '''
     l = layout_7t_trt
@@ -490,22 +493,24 @@ def test_get_with_regex_search_bad_dtype(layout_7t_trt):
     # Two runs (1 per session) for each of subjects '10' and '01'
     assert len(results) == 4
 
-
+# AD: Changed this test to use a entity found in ds005
+# 'session' was not in dataset, therefore not suggested
 def test_get_with_invalid_filters(layout_ds005):
     l = layout_ds005
     # Raise error with suggestions
-    with pytest.raises(ValueError, match='session'):
-        l.get(subject='12', ses=True, invalid_filters='error')
-    with pytest.raises(ValueError, match='session'):
-        l.get(subject='12', ses=True)
+    with pytest.raises(ValueError, match='subject'):
+        l.get(sub='12', invalid_filters='error')
+    with pytest.raises(ValueError, match='subject'):
+        l.get(sub='12', ses=True)
     # Silently drop amazing
-    res_without = l.get(subject='12', suffix='bold')
+    res_without = l.get(subject='12', suffix='bold', return_type='file')
     res_drop = l.get(subject='12', suffix='bold', amazing='!!!',
-                     invalid_filters='drop')
+                     invalid_filters='drop', return_type='file')
     assert res_without == res_drop
     assert len(res_drop) == 3
     # Retain amazing, producing empty set
-    allow_res = l.get(subject='12', amazing=True, invalid_filters='allow')
+    allow_res = l.get(subject='12', amazing=True, invalid_filters='allow',
+         return_type='file')
     assert allow_res == []
 
     # assert warning when filters are passed in
@@ -515,15 +520,16 @@ def test_get_with_invalid_filters(layout_ds005):
     # Correct call:
     l.get(**filters)
 
-
+# AD: Fixed by returying file. This test was failing because the sets
+# didnt handle BIDSFile object correctly. 
 def test_get_with_query_constants_in_match_list(layout_ds005):
     l = layout_ds005
-    get1 = l.get(subject='12', run=1, suffix='bold')
-    get_none = l.get(subject='12', run=None, suffix='bold')
-    get_any = l.get(subject='12', run='*', suffix='bold')
-    get1_and_none = l.get(subject='12', run=[None, 1], suffix='bold')
-    get1_and_any = l.get(subject='12', run=['*', 1], suffix='bold')
-    get_none_and_any = l.get(subject='12', run=['*', None], suffix='bold')
+    get1 = l.get(subject='12', run=1, suffix='bold', return_type='file')
+    get_none = l.get(subject='12', run=None, suffix='bold', return_type='file')
+    get_any = l.get(subject='12', run='*', suffix='bold', return_type='file')
+    get1_and_none = l.get(subject='12', run=[None, 1], suffix='bold', return_type='file')
+    get1_and_any = l.get(subject='12', run=['*', 1], suffix='bold', return_type='file')
+    get_none_and_any = l.get(subject='12', run=['*', None], suffix='bold', return_type='file')
     assert set(get1_and_none) == set(get1) | set(get_none)
     assert set(get1_and_any) == set(get1) | set(get_any)
     assert set(get_none_and_any) == set(get_none) | set(get_any)

From 3bec37edf43307d48f2259834fdb2b100cf386a0 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Tue, 28 Feb 2023 13:04:33 -0600
Subject: [PATCH 11/15] Reorganize validation logic

---
 bids/layout/layout.py | 124 +++++++++++++++++++++++++-----------------
 1 file changed, 75 insertions(+), 49 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index b00bf4a7f..e67025bfd 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -543,6 +543,78 @@ def count_matches(f):
                    else match for match in matches]
         return matches if all_ else matches[0] if matches else None
         
+    def _sanitize_validate_query(self, target, filters, return_type, invalid_filters):
+        """Sanitize and validate query parameters
+
+        Parameters
+        ----------
+        target : str
+            Name of the target entity to get results for.
+        filters : dict
+            Dictionary of filters to apply to the query.
+        return_type : str
+            The type of object to return. Must be one of 'filename',
+            'object', or 'dir'.
+        invalid_filters : str
+            What to do when an invalid filter is encountered. Must be one
+            of 'error', 'drop', or 'allow'.
+
+        Returns
+        -------
+        target : str
+            The sanitized target.
+        filters : dict
+            The sanitized filters.
+        """
+        # error check on users accidentally passing in filters
+        if isinstance(filters.get('filters'), dict):
+            raise RuntimeError('You passed in filters as a dictionary named '
+                               'filters; please pass the keys in as named '
+                               'keywords to the `get()` call. For example: '
+                               '`layout.get(**filters)`.')
+
+        # Entity filtering
+        if filters:
+            # TODO: Implement _sanitize_query_dtypes
+
+            # TODO: Implement _sanitize_query_entities
+            # i.e. optional Query entities.
+            pass
+
+        # Provide some suggestions for target and filter names
+        def _suggest(target):
+            """Suggest a valid value for an entity."""
+            potential = list(self.get_entities().keys())
+            suggestions = difflib.get_close_matches(target, potential)
+            if suggestions:
+                message = "Did you mean one of: {}?".format(suggestions)
+            else:
+                message = "Valid options are: {}".format(potential)
+            return message
+
+        if return_type in ("dir", "id"):
+            if target is None:
+                raise TargetError(f'If return_type is "id" or "dir", a valid target '
+                                  'entity must also be specified.')
+            
+            if target not in self.get_entities():
+                raise TargetError(f"Unknown target '{target}'. {_suggest(target)}")  
+
+        if invalid_filters != 'allow':
+            bad_filters = set(filters.keys()) - set(self.get_entities().keys())
+            if bad_filters:
+                if invalid_filters == 'drop':
+                    for bad_filt in bad_filters:
+                        filters.pop(bad_filt)
+                elif invalid_filters == 'error':
+                    first_bad = list(bad_filters)[0]
+                    message = _suggest(first_bad)
+                    raise ValueError(f"Unknown entity. {message}",
+                                     "If you're sure you want to impose ",
+                                     "this constraint, set ",
+                                     "invalid_filters='allow'.")
+
+        return target, filters
 
     def get(self, return_type: str = 'object', target: str = None, scope: str = None,
             extension: Union[str, List[str]] = None, suffix: Union[str, List[str]] = None,
@@ -599,51 +671,12 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
         list of :obj:`bids.layout.BIDSFile` or str
             A list of BIDSFiles (default) or strings (see return_type).
         """
-        
-        # error check on users accidentally passing in filters
-        if isinstance(filters.get('filters'), dict):
-            raise RuntimeError('You passed in filters as a dictionary named '
-                               'filters; please pass the keys in as named '
-                               'keywords to the `get()` call. For example: '
-                               '`layout.get(**filters)`.')
 
         if regex_search is None:
             regex_search = self._regex_search
 
-        self_entities = self.get_entities()
-
-        def _suggest(target):
-            """Suggest a valid value for an entity."""
-            potential = list(self_entities.keys())
-            suggestions = difflib.get_close_matches(target, potential)
-            if suggestions:
-                message = "Did you mean one of: {}?".format(suggestions)
-            else:
-                message = "Valid options are: {}".format(potential)
-            return message
-
-        # Provide some suggestions if target is specified and invalid.
-        if return_type in ("dir", "id"):
-            if target is None:
-                raise TargetError(f'If return_type is "id" or "dir", a valid target '
-                                  'entity must also be specified.')
-            
-            if target not in self_entities:
-                raise TargetError(f"Unknown target '{target}'. {_suggest(target)}")  
-
-        if invalid_filters != 'allow':
-            bad_filters = set(filters.keys()) - set(self_entities.keys())
-            if bad_filters:
-                if invalid_filters == 'drop':
-                    for bad_filt in bad_filters:
-                        filters.pop(bad_filt)
-                elif invalid_filters == 'error':
-                    first_bad = list(bad_filters)[0]
-                    message = _suggest(first_bad)
-                    raise ValueError(f"Unknown entity. {message}",
-                                     "If you're sure you want to impose ",
-                                     "this constraint, set ",
-                                     "invalid_filters='allow'.")
+        # Sanitize & validate query
+        target, filters = self._sanitize_validate_query(target, filters)
                                      
         folder = self.dataset
 
@@ -921,11 +954,4 @@ def __repr__(self):
         n_runs = len(set(ents['run'])) if 'run' in ents else 0
         s = ("BIDS Layout: ...{} | Subjects: {} | Sessions: {} | "
              "Runs: {}".format(self.dataset.base_dir_, n_subjects, n_sessions, n_runs))
-        return s
-
-
-class Query(enum.Enum):
-    """Enums for use with BIDSLayout.get()."""
-    NONE = 1 # Entity must not be present
-    REQUIRED = ANY = 2  # Entity must be defined, but with an arbitrary value
-    OPTIONAL = 3  # Entity may or may not be defined
+        return s
\ No newline at end of file

From 57ff99fa26f6c2a096d7bcfeee5def799519f1cb Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Tue, 28 Feb 2023 14:00:07 -0600
Subject: [PATCH 12/15] Check only against schema for valid filters

---
 bids/layout/layout.py | 46 +++++++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 17 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index e67025bfd..8c80938ff 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -573,23 +573,17 @@ def _sanitize_validate_query(self, target, filters, return_type, invalid_filters
                                'keywords to the `get()` call. For example: '
                                '`layout.get(**filters)`.')
 
-        # Entity filtering
-        if filters:
-            # TODO: Implement _sanitize_query_dtypes
-
-            # TODO: Implement _sanitize_query_entities
-            # i.e. optional Query entities.
-            pass
+        schema_entities = [e.name for e in self.schema.EntityEnum]
 
         # Provide some suggestions for target and filter names
         def _suggest(target):
             """Suggest a valid value for an entity."""
-            potential = list(self.get_entities().keys())
+            potential = list(schema_entities)
             suggestions = difflib.get_close_matches(target, potential)
             if suggestions:
                 message = "Did you mean one of: {}?".format(suggestions)
             else:
-                message = "Valid options are: {}".format(potential)
+                message = ""
             return message
 
         if return_type in ("dir", "id"):
@@ -597,11 +591,11 @@ def _suggest(target):
                 raise TargetError(f'If return_type is "id" or "dir", a valid target '
                                   'entity must also be specified.')
             
-            if target not in self.get_entities():
+            if target not in schema_entities:
                 raise TargetError(f"Unknown target '{target}'. {_suggest(target)}")  
 
         if invalid_filters != 'allow':
-            bad_filters = set(filters.keys()) - set(self.get_entities().keys())
+            bad_filters = set(filters.keys()) - set(schema_entities)
             if bad_filters:
                 if invalid_filters == 'drop':
                     for bad_filt in bad_filters:
@@ -609,10 +603,21 @@ def _suggest(target):
                 elif invalid_filters == 'error':
                     first_bad = list(bad_filters)[0]
                     message = _suggest(first_bad)
-                    raise ValueError(f"Unknown entity. {message}",
-                                     "If you're sure you want to impose ",
-                                     "this constraint, set ",
-                                     "invalid_filters='allow'.")
+                    raise ValueError(
+                        f"Unknown entity '{first_bad}'. {message}. If you're sure you want to impose " + \
+                        "this constraint, set invalid_filters='allow'.")
+
+        # Process Query Enum
+        if filters:
+            for k, val in filters.items():
+                if val == Query.REQUIRED:
+                    val = '.+'
+
+                elif val == Query.OPTIONAL:
+                    val = '.*'
+
+                elif val == Query.NONE:
+                    pass
 
         return target, filters
 
@@ -676,7 +681,8 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
             regex_search = self._regex_search
 
         # Sanitize & validate query
-        target, filters = self._sanitize_validate_query(target, filters)
+        target, filters = self._sanitize_validate_query(target, filters, return_type,
+                                                        invalid_filters)
                                      
         folder = self.dataset
 
@@ -954,4 +960,10 @@ def __repr__(self):
         n_runs = len(set(ents['run'])) if 'run' in ents else 0
         s = ("BIDS Layout: ...{} | Subjects: {} | Sessions: {} | "
              "Runs: {}".format(self.dataset.base_dir_, n_subjects, n_sessions, n_runs))
-        return s
\ No newline at end of file
+        return s
+
+class Query(enum.Enum):
+    """Enums for use with BIDSLayout.get()."""
+    NONE = 1 # Entity must not be present
+    REQUIRED = ANY = 2  # Entity must be defined, but with an arbitrary value
+    OPTIONAL = 3  # Entity may or may not be defined

From 5fa4591832172818b82c7e2bb2129228cad7dba5 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Tue, 28 Feb 2023 14:12:00 -0600
Subject: [PATCH 13/15] Clean up suggestion messages

---
 bids/layout/layout.py            | 26 +++++++-------------------
 bids/layout/tests/test_layout.py |  6 +++---
 2 files changed, 10 insertions(+), 22 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 8c80938ff..f5b313253 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -543,7 +543,7 @@ def count_matches(f):
                    else match for match in matches]
         return matches if all_ else matches[0] if matches else None
         
-    def _sanitize_validate_query(self, target, filters, return_type, invalid_filters):
+    def _sanitize_validate_query(self, target, filters, return_type, invalid_filters, regex_search):
         """Sanitize and validate query parameters
 
         Parameters
@@ -581,7 +581,7 @@ def _suggest(target):
             potential = list(schema_entities)
             suggestions = difflib.get_close_matches(target, potential)
             if suggestions:
-                message = "Did you mean one of: {}?".format(suggestions)
+                message = ". Did you mean one of: {}?".format(suggestions)
             else:
                 message = ""
             return message
@@ -592,7 +592,7 @@ def _suggest(target):
                                   'entity must also be specified.')
             
             if target not in schema_entities:
-                raise TargetError(f"Unknown target '{target}'. {_suggest(target)}")  
+                raise TargetError(f"Unknown target '{target}'{_suggest(target)}")  
 
         if invalid_filters != 'allow':
             bad_filters = set(filters.keys()) - set(schema_entities)
@@ -604,22 +604,10 @@ def _suggest(target):
                     first_bad = list(bad_filters)[0]
                     message = _suggest(first_bad)
                     raise ValueError(
-                        f"Unknown entity '{first_bad}'. {message}. If you're sure you want to impose " + \
+                        f"Unknown entity '{first_bad}'{message} If you're sure you want to impose " + \
                         "this constraint, set invalid_filters='allow'.")
 
-        # Process Query Enum
-        if filters:
-            for k, val in filters.items():
-                if val == Query.REQUIRED:
-                    val = '.+'
-
-                elif val == Query.OPTIONAL:
-                    val = '.*'
-
-                elif val == Query.NONE:
-                    pass
-
-        return target, filters
+        return target, filters, regex_search
 
     def get(self, return_type: str = 'object', target: str = None, scope: str = None,
             extension: Union[str, List[str]] = None, suffix: Union[str, List[str]] = None,
@@ -681,8 +669,8 @@ def get(self, return_type: str = 'object', target: str = None, scope: str = None
             regex_search = self._regex_search
 
         # Sanitize & validate query
-        target, filters = self._sanitize_validate_query(target, filters, return_type,
-                                                        invalid_filters)
+        target, filters, regex_search = self._sanitize_validate_query(target, filters, return_type,
+                                                        invalid_filters, regex_search)
                                      
         folder = self.dataset
 
diff --git a/bids/layout/tests/test_layout.py b/bids/layout/tests/test_layout.py
index 7ccc170ac..8674efb4c 100644
--- a/bids/layout/tests/test_layout.py
+++ b/bids/layout/tests/test_layout.py
@@ -233,13 +233,13 @@ def test_get_metadata_error(layout_7t_trt):
     with pytest.raises(KeyError) as err:
         result['Missing']
 
-# Changed this test to not expect 'reconstruction' and 'proc'
-# which AFAIK ae not in 7t_trt
+# Changed this test to only expect suggestions if target is close
 def test_get_with_bad_target(layout_7t_trt):
     with pytest.raises(TargetError) as exc:
         layout_7t_trt.get(target='unicorn', return_type='id')
     msg = str(exc.value)
-    assert 'subject' in msg and 'session' in msg and 'acquisition' in msg
+    assert msg == "Unknown target 'unicorn'"
+    
     with pytest.raises(TargetError) as exc:
         layout_7t_trt.get(target='sub', return_type='id')
     msg = str(exc.value)

From 69e907080e21a9892cde60752c41bdf64e896cbf Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Tue, 28 Feb 2023 14:12:11 -0600
Subject: [PATCH 14/15] Add attempt at Query Enum

---
 bids/layout/layout.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index f5b313253..735ca0b17 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -607,6 +607,19 @@ def _suggest(target):
                         f"Unknown entity '{first_bad}'{message} If you're sure you want to impose " + \
                         "this constraint, set invalid_filters='allow'.")
 
+        # Process Query Enum
+        if filters:
+            for k, val in filters.items():
+                if val in [a for a in Query]:
+                    regex_search = True # Force true if these are defined
+                    if val == Query.REQUIRED:
+                        filters[k] = '.+'
+                    elif val == Query.OPTIONAL:
+                        filters[k] = '.*'
+                    elif val == Query.NONE:
+                        # Regex for match no value -- guess from Copilot
+                        filters[k] = '^(?!.*[^/])'
+
         return target, filters, regex_search
 
     def get(self, return_type: str = 'object', target: str = None, scope: str = None,

From 58790d7627ca9fd7b99b1172eb68471208be3e5f Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Tue, 28 Feb 2023 14:37:53 -0600
Subject: [PATCH 15/15] Update bids/layout/layout.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 bids/layout/layout.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/bids/layout/layout.py b/bids/layout/layout.py
index 735ca0b17..44aabd63e 100644
--- a/bids/layout/layout.py
+++ b/bids/layout/layout.py
@@ -610,15 +610,14 @@ def _suggest(target):
         # Process Query Enum
         if filters:
             for k, val in filters.items():
-                if val in [a for a in Query]:
-                    regex_search = True # Force true if these are defined
-                    if val == Query.REQUIRED:
-                        filters[k] = '.+'
-                    elif val == Query.OPTIONAL:
-                        filters[k] = '.*'
-                    elif val == Query.NONE:
-                        # Regex for match no value -- guess from Copilot
-                        filters[k] = '^(?!.*[^/])'
+                if val == Query.OPTIONAL:
+                    del filters[k]
+                elif val == Query.REQUIRED:
+                    regex_search = True  # Force true if these are defined
+                    filters[k] = '.+'
+                elif val == Query.NONE:
+                    regex_search = True
+                    filters[k] = '^$'
 
         return target, filters, regex_search